SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing WP_011876077.1 NCBI__GCF_000016205.1:WP_011876077.1 to proteins with known functional sites using BLASTp with E ≤ 0.001.

Or try Sites on a Tree, PaperBLAST, Conserved Domains, or compare to all protein structures

Found 20 (the maximum) hits to proteins with known functional sites (download)

P66899 Diaminopropionate ammonia-lyase; DAPAL; 2,3-diaminopropionate ammonia-lyase; Alpha,beta-diaminopropionate ammonia-lyase; Diaminopropionatase; EC 4.3.1.15 from Escherichia coli (strain K12) (see paper)
39% identity, 86% coverage: 44:396/412 of query aligns to 45:396/398 of P66899

query
sites
P66899

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K77 (= K76) mutation K->H,R: No longer binds cofactor, loss of enzymatic activity.
D120 (= D121) mutation to N: No activity on D-DAP, 150-fold reduced catalytic efficiency for L-DAP; alters substrate stereospecificity.
D189 (= D190) mutation to N: 10000-fold reduced catalytic efficiency for both D- and L-DAP.
C265 (= C268) modified: Disulfide link with 291
C291 (= C294) modified: Disulfide link with 265

4d9nA Crystal structure of diaminopropionate ammonia lyase from escherichia coli in complex with d-serine (see paper)
39% identity, 86% coverage: 44:396/412 of query aligns to 44:390/391 of 4d9nA

query
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4d9nA

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active site: K76 (= K76), T370 (= T376)
binding d-serine: K76 (= K76), T118 (= T120), D119 (= D121), H122 (= H124), D188 (= D190)

4d9mA Crystal structure of diaminopropionate ammonia lyase from escherichia coli in complex with aminoacrylate-plp azomethine reaction intermediate (see paper)
39% identity, 86% coverage: 44:396/412 of query aligns to 44:377/378 of 4d9mA

query
sites
4d9mA

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active site: K76 (= K76), T357 (= T376)
binding 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid: K76 (= K76), T108 (= T120), D109 (= D121), N111 (= N123), H112 (= H124), G221 (= G235), V222 (= V236), G223 (= G237), A224 (≠ G238), G269 (= G291), L270 (= L292), T357 (= T376), E358 (= E377)

5ygrD Crystal structure of plp bound diaminopropionate ammonia lyase from salmonella typhimurium (see paper)
38% identity, 84% coverage: 44:389/412 of query aligns to 35:382/388 of 5ygrD

query
sites
5ygrD

T

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W

V

I

M

M

Q

Q

G

G

Y

Y

G

M

V

T

I

L

P

A

A

V

E

E

V

A

L

Y

A

E

Q

Q

L

L

N

A

E

E

E

T

H

N

S

S

R

-

P

P

A

L

F

P

T

T

H

H

V

L

F

I

L

L

Q

Q

G

A

G

G

V

V

G

G

G

S

L

F

A

A

A

G

G

S

V

V

A

M

S

G

Y

Y

L

F

W

V

E

E

H

K

Y

M

G

Q

A

E

E

N

R

I

P

P

T

N

F

I

I

I

V

V

E

E

P

P

Q

H

Q

Q

A

A

D

N

C

C

L

L

Y

Y

Q

Q

S

S

A

A

I

V

A

M

-

D

G

G

R

Q

A

P

S

H

K

C

A

V

T

T

G

A

S

-

V

-

D

-

S

T

I

I

M

M

A

A

G

G

L

L

A

A

C

C

G

G

E

E

A

P

S

N

P

I

L

I

A

S

W

W

K

P

I

I

L

I

E

R

Q

D

C

N

V

T

D

S

Y

C

F

F

M

I

T

S

I

A

D

D

E

C

D

L

A

A

V

A

A

K

A

G

M

M

-

R

C

I

S

S

L

A

A

A

K

P

G

R

S

P

D

G

R

T

D

D

A
x
T

P

P

L

F

V

I

V

S

G

G

E

E

S

S

G

G

A

A

A

I

G

G

Y

V

A

G

G

L

L

L

T

Y

T

E

V

L

M

M

K

N

S

N

L

H

E

Y

L

Q

A

D

H

L

A

A

T

N

G

R

L

L

G

Q

P

L

D

D

-

A

S

A

H

H

V

V

L

L

V

L

I

I

N

S

T

T

E

E

G

G

A

D

T

T

A

S

P

P

S

D

V

I

Y

Y

R

E

Q

D

L

I

V

V

binding phosphate ion: H38 (≠ W47), K67 (= K76), T113 (= T120), D114 (= D121), N116 (= N123), H117 (= H124), T327 (≠ A335)

5ygrB Crystal structure of plp bound diaminopropionate ammonia lyase from salmonella typhimurium (see paper)
37% identity, 84% coverage: 44:389/412 of query aligns to 35:359/365 of 5ygrB

query
sites
5ygrB

T

T

P

P

L

L

W

H

D

N

L

L

P

A

D

H

A

L

A

S

A

Q

R

R

L

L

G

G

V

L

A

G

Q

S

L

I

S

H

L

I

K

K

D

D

E

E

S

S

F

W

R

R

S

F

P

G

L

L

G

N

S

A

F

F

K
|
K

A

G

L

L

G

G

A

G

P

S

I

Y

A

A

L

V

M

G

R

K

L

Y

I

L

M

A

R

D

Q

K

W

L

H

Q

A

C

H

D

G

-

I

I

D

N

P

S

K

K

A

-

L

-

V

-

T

-

G

-

Q

-

Y

-

A

-

Q

E

M

K

L

I

S

K

N

D

M

C

T

V

V

F

I

V

S

T

A

A

T
|
T

D
|
D

G

G

N
|
N

H
|
H

G

G

K

R

S

G

L

V

A

A

A

W

A

A

R

E

A

Q

I

L

G

G

C

L

Y

K

C

A

V

V

I

V

V

Y

L

M

H

P

A

K

N

G

V

S

S

S

I

L

E

I

R

R

E

A

Q

E

A

N

I

I

A

R

A

H

Y

H

G

G

A

A

K

E

I

C

V

T

R

I

I

T

D

D

G

L

N

N

Y

Y

D

D

E

D

S

A

V

V

Q

R

H

L

A

A

A

H

Q

R

L

M

A

A

A

Q

E

T

N

K

G

G

W

W

H

V

V

L

S

Q

D

D

T

T

S

A

Y

W

E

T

G

G

Y

Y

E

E

T

E

I

I

P

P

R

T

D

W

V

I

M

M

Q

Q

G

G

Y

Y

G

M

V

T

I

L

P

A

A

V

E

E

V

A

L

Y

A

E

Q

Q

L

L

N

A

E

E

E

N

H

S

S

P

R

L

P

P

A

-

F

-

T

T

H

H

V

L

F

I

L

L

Q

Q

G

A

G

G

V

V

G

G

G

S

L

F

A

A

A

G

G

S

V

V

A

M

S

G

Y

Y

L

F

W

V

E

E

H

K

Y

M

G

Q

A

E

E

N

R

I

P

P

T

N

F

I

I

I

V

V

E

E

P

P

Q

H

Q

Q

A

A

D

N

C

C

L

L

Y

Y

Q

Q

S

S

A

A

I

V

A

M

G

-

R

-

A

-

S

-

K

-

A

-

T

-

G

-

S

-

V

-

D

-

S

-

I

I

M

M

A

A

G

G

L

L

A

A

C

C

G

G

E

E

A

P

S

N

P

I

L

I

A

S

W

W

K

P

I

I

L

I

E

R

Q

D

C

N

V

T

D

S

Y

C

F

F

M

I

T

S

I

A

D

D

E

C

D

L

A

A

V

A

A

K

A

G

M

M

-

R

C

I

S

S

L

A

A

A

K

P

G

R

S

P

D

G

R

T

D

D

A

T

P

P

L

F

V

I

V

S

G

G

E

E

S

S

G

G

A

A

A

I

G

G

Y

V

A

G

G

L

L

L

T

Y

T

E

V

L

M

M

K

N

S

N

L

M

E

H

L

Y

A

Q

H

D

A

L

T

A

G

R

L

L

G

Q

P

L

D

D

-

A

S

A

H

H

V

V

L

L

V

L

I

I

N

S

T

T

E

E

G

G

A

D

T

T

A

S

P

P

S

D

V

I

Y

Y

R

E

Q

D

L

I

V

V

binding phosphate ion: K67 (= K76), T102 (= T120), D103 (= D121), N105 (= N123), H106 (= H124)

4d9kA Crystal structure of escherichia coli diaminopropionate ammonia lyase in apo form (see paper)
35% identity, 86% coverage: 44:396/412 of query aligns to 45:364/366 of 4d9kA

query
sites
4d9kA

T

T

P

P

L

L

W

C

D

A

L

L

P

D

D

D

A

L

A

A

A

N

R

L

L

F

G

G

V

V

A

K

Q

K

L

I

S

L

L

V

K

K

D

D

E

E

S

S

F

K

R

R

S

F

P

G

L

L

G

N

S

A

F

F

K
|
K

A

M

L

L

G

G

A

G

P

A

I

Y

A

A

L

I

M

A

R

Q

L

L

I

L

M

C

R

E

Q

K

W

Y

H

H

A

-

H

-

G

-

I

L

D

D

P

I

K

E

A

T

L

L

V

S

T

F

G

E

Q

H

Y

L

A

K

Q

N

M

A

L

G

S

E

N

K

M

M

T

T

V

F

I

A

S

T

A

T

T

T

D

D

G

G

N

N

H

H

G

G

K

R

S

G

L

V

A

A

A

W

A

A

R

Q

A

Q

I

L

G

G

C

Q

Y

N

C

A

V

V

I

I

V

Y

L

M

H

P

A

K

N

G

V

S

S

A

I

Q

E

E

R

R

E

V

Q

D

A

A

I

I

A

L

A

N

Y

L

G

G

A

A

K

E

I

C

V

I

R

V

I

T

D

D

G

M

N

N

Y

Y

D

D

E

D

S

T

V

V

Q

R

H

L

A

T

A

M

Q

Q

L

H

A

A

A

Q

E

Q

N

H

G

G

W

W

H

E

V

V

S

Q

D

D

T

T

S

A

Y

W

E

E

G

G

Y

Y

E

T

T

K

I

I

P

P

R

T

D

W

V

I

M

M

Q

Q

G

G

Y

Y

G

A

V

T

I

L

P

A

A

D

E

E

V

A

L

V

A

E

Q

Q

L

M

N

R

E

E

E

M

H

G

S

V

R

T

P

P

A

-

F

-

T

T

H

H

V

V

F

L

L

L

Q

Q

G
x
A

G
|
G

V
|
V

G

G

G
x
A

L
x
M

A

A

A

G

G

G

V

V

A

L

S

G

Y

Y

L

L

W

V

E

D

H

V

Y

Y

G

S

A

P

E

Q

R

N

P

L

T

H

F

S

I

I

V

I

V

V

E

E

P

P

Q

D

Q

K

A

P

D

N

C

-

L

-

Y

-

Q

-

S

-

A

-

I

-

A

-

G

-

R

-

A

-

S

-

K

-

A

-

T

-

G

-

S

-

V

-

D

-

S

-

I

-

M

-

A

-

G

-

L

-

A

-

C

-

G

-

E

-

A

-

S

-

P

P

L

L

A

G

W

W

K

E

I

I

L

L

E

R

Q

N

C

C

V

A

D

T

Y

Q

F

F

M

I

T

S

I

C

D

Q

D

D

E

S

D

V

A

A

V

A

A

L

A

G

M

M

C

R

S

V

L

L

A

G

K

N

G

P

S

Y

D

G

R

N

D

D

A

P

P

R

L

I

V

I

V

S

G

G

E

E

S

S

G

G

A

A

A

V

G

G

Y

L

A

G

G

V

L

L

T

A

V

V

M

H

-

Y

-

H

-

P

K

Q

S

R

L

Q

E

S

L

L

A

M

H

E

A

K

T

L

G

A

L

L

G

N

P

K

D

D

S

A

H

V

V

V

L

L

V

V

I

I

N

S

T
|
T

E

E

G

G

A

D

T

T

A

D

P

V

S

K

V

H

Y

Y

R

R

Q

E

L

V

V

V

G

W

E

E

S

G

A

K

E

H

A

A

V

V

active site: K77 (= K76), T344 (= T376)
binding phosphate ion: A230 (≠ G234), G231 (= G235), V232 (= V236), A234 (≠ G238), M235 (≠ L239)

8y1jA Structure of the pyridoxal 5'-phosphate-dependent (plp) threonine deaminase ilva1 from pseudomonas aeruginosa pao1 (see paper)
29% identity, 86% coverage: 43:398/412 of query aligns to 19:331/502 of 8y1jA

query
sites
8y1jA

D

E

T

T

P

P

L

L

W

Q

D

P

L

A

P

R

D

Q

A

L

A

S

A

E

R

R

L

L

G

G

V

-

A

N

Q

Q

L

V

S

L

L

L

K

K

D

R

E

E

S

D

F

L

R

Q

S

-

P

P

L

V

G

F

S

S

F

F

K
|
K

A

I

L

R

G

G

A

A

P

Y

I

N

A

K

L

V

M

A

R

Q

L

L

I

-

M

T

R

E

Q

E

W

E

H

K

A

A

H

R

G

G

I

-

D

-

P

-

K

-

A

-

L

-

V

-

T

-

G

-

Q

-

Y

-

A

-

Q

-

M

-

L

-

S

-

N

-

M

-

T

-

V

V

I

I

S

A

A

A

T
x
S

D

A

G

G

N

N

H
|
H

G

A

K

Q

S

G

L

L

A

A

A

L

A

A

R

K

A

R

I

Q

G

G

C

I

Y

R

C

A

V

V

I

I

V

V

L

M

H

P

A

K

N

T

V

T

S

P

I

E

E

I

R

K

E

V

Q

Q

A

A

I

V

A

R

A

A

Y

H

G

G

A

A

K

K

I

A

V

V

R

L

I

H

D

G

G

D

N

A

Y

F

D

P

E

E

S

A

V

L

Q

A

H

H

A

A

A

L

Q

K

L

L

A

V

A

D

E

E

N

K

G

G

W

Y

H

T

V

F

V

V

S

H

D

-

T

-

S

P

Y

Y

E

D

G

D

Y

P

E

D

T

T

I

I

P

-

R

-

D

-

V

-

M

-

Q

A

G

G

Y

Q

G

G

V

T

I

V

P

A

A

M

E

E

V

I

L

L

A

R

Q

Q

L

-

N

-

E

-

H

-

S

-

R

Q

P

P

A

G

-

R

F

L

T

D

H

A

V

I

F

F

L

V

Q

P

G

V

G

G

V

G

G

G

L

L

A

V

A

A

G

G

V

I

A

A

S

A

Y

Y

L

V

W

-

E

-

H

K

Y

Y

G

L

A

R

E

P

R

E

P

I

T

K

F

V

I

I

V

G

V

V

E

E

P

P

Q

D

Q

E

A

S

D

N

C

C

L

L

Y

-

Q

Q

S

A

A

A

I

M

A

A

G

A

R

G

A

E

S

R

K

V

A

V

T

L

G

G

S

Q

V

V

D

G

S

L

I

F

M

A

A

D

G

G

L

V

A

A

C

V

G

A

E

Q

A

I

S

G

P

Q

L

H

A

T

W

F

K

D

I

I

L

C

E

K

Q

D

C

H

V

V

D

D

Y

E

F

V

M

I

T

T

I

V

D

S

D

T

E

D

D

E

A

-

V

-

A

-

M

I

C

C

S

A

L

A

A

I

K

K

G

D

S

I

D

Y

R

D

D

D

A

T

P

R

L

S

V

I

V

T

G

E

E

P

S

A

G

G

A

A

A

L

G

A

Y

V

A

A

G

G

L

-

T

-

V

I

M

K

K

K

S

Y

L

V

E

E

L

R

A

E

H

R

A

A

T

E

G

G

L

-

G

-

P

-

D

-

S

-

H

Q

V

T

L

L

V

V

I

A

N

I

T

D

E

S

G

G

A

A

T

N

A

V

P

N

-

F

-

D

-

R

-

L

-

R

-

H

S

V

V

A

Y

E

R

R

Q

A

L

E

V

L

G

G

E

E

S

R

A

R

E

E

A

A

V

I

I

I

A

A

binding 2-ketobutyric acid: K50 (= K76), S74 (≠ T120), H78 (= H124)

Sites not aligning to the query:

binding 2-ketobutyric acid: 336, 337, 338, 340, 341, 358, 448, 449

3l6bA X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor (see paper)
28% identity, 63% coverage: 60:319/412 of query aligns to 39:259/322 of 3l6bA

query
sites
3l6bA

Q

N

L

L

S

F

L

F

K

K

D

C

E

E

S

L

F

F

R

Q

S

K

P

-

L

T

G

G

S

S

F
|
F

K
|
K

A

I

L

R

G

G

A

A

P

L

I

N

A

A

L

V

M

R

R

S

L

L

I

V

M

R

R

K

Q

-

W

-

H

-

A

-

H

-

G

-

I

-

D

-

P

P

K

K

A

A

L

V

V

V

T

T

G

-

Q

-

Y

-

A

-

Q

-

M

-

L

-

S

-

N

-

M

-

T

-

V

-

I

-

S

-

A

H

T
x
S

D
x
S

G

G

N
|
N

H
|
H

G

G

K

Q

S

A

L

L

A

T

A

Y

A

A

R

K

A

L

I

E

G

G

C

I

Y

P

C

A

V

Y

I

I

V

V

L

V

H

P

A

Q

N

T

V

A

S

P

I

D

E

C

R

K

E

K

Q

L

A

A

I

I

A

Q

A

A

Y

Y

G

G

A

A

K

S

I

I

V

V

R

Y

I

C

D

E

G

P

N

S

Y

-

D

D

E

E

S

S

V
x
R

Q

E

H

N

A

V

A

A

Q

K

L

R

A

V

A

T

E

E

N

E

G

T

W

E

H

G

V

I

V

M

S

V

D

H

T

P

S

N

Y

Q

E

E

G

P

Y

A

E

-

T

-

I

-

P

-

R

-

D

-

V

V

M

I

Q

A

G

G

Y

Q

G

G

V

T

I

I

P

A

A

L

E

E

V

V

L

L

A

N

Q

Q

L

V

N

-

E

-

H

-

S

-

R

-

P

P

A

L

F

V

T

D

H

A

V

L

F

V

L

V

Q

P

G

V

G
|
G

V
x
G

G
|
G

L
x
M

A

L

A

A

G

G

V

I

A

A

S

I

Y

T

L

V

W

-

E

-

H

-

Y

-

G

K

A

A

E

L

R

K

P

P

T

S

F

V

I

K

V

V

-

Y

-

A

V

A

E
|
E

P

P

Q

S

Q

N

A
|
A

D

D

C
x
D

L

C

Y

Y

Q

Q

S

S

A

K

I

L

A

K

G

G

R

K

A

L

S

M

K

P

A

N

T

L

G

Y

S

P

V

P

D

E

S

T

I

I

M

A

A

D

G
|
G

L
x
V

A

K

C

-

G

S

E

S

A

I

S

G

P

L

L

N

A

T

W

W

K

P

I

I

L

I

E

R

Q

D

C

L

V

V

D

D

Y

D

F

I

M

F

T

T

I

V

D

T

D

E

E

D

D

E

active site: K54 (= K76), S77 (≠ D121), E203 (= E262), A207 (= A266), D209 (≠ C268), G232 (= G291)
binding malonate ion: K54 (= K76), S76 (≠ T120), S77 (≠ D121), N79 (= N123), H80 (= H124), R128 (≠ V173), G232 (= G291)
binding manganese (ii) ion: E203 (= E262), A207 (= A266), D209 (≠ C268)
binding pyridoxal-5'-phosphate: F53 (= F75), K54 (= K76), N79 (= N123), G178 (= G235), G179 (≠ V236), G180 (= G237), G181 (= G238), M182 (≠ L239), V233 (≠ L292)

Sites not aligning to the query:

active site: 278, 305, 306
binding pyridoxal-5'-phosphate: 276, 278, 306, 307

7nbgDDD structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
28% identity, 63% coverage: 60:319/412 of query aligns to 38:258/310 of 7nbgDDD

query
sites
7nbgDDD

Q

N

L

L

S

F

L

F

K

K

D

C

E

E

S

L

F

F

R

Q

S

K

P

-

L

T

G

G

S

S

F
|
F

K
|
K

A

I

L

R

G

G

A

A

P

L

I

N

A

A

L

V

M

R

R

S

L

L

I

V

M

R

R

K

Q

-

W

-

H

-

A

-

H

-

G

-

I

-

D

-

P

P

K

K

A

A

L

V

V

V

T

T

G

-

Q

-

Y

-

A

-

Q

-

M

-

L

-

S

-

N

-

M

-

T

-

V

-

I

-

S

-

A

H

T

S

D
x
S

G

G

N
|
N

H

H

G

G

K
x
Q

S

A

L

L

A

T

A

Y

A

A

R

K

A

L

I

E

G

G

C

I

Y

P

C

A

V

Y

I
|
I

V

V

L

V

H

P

A

Q

N

T

V

A

S

P

I

D

E

C

R

K

E

K

Q

L

A

A

I

I

A

Q

A

A

Y
|
Y

G

G

A

A

K

S

I

I

V

V

R

Y

I

C

D

E

G

P

N

S

Y

-

D

D

E

E

S

S

V

R

Q

E

H

N

A

V

A

A

Q

K

L

R

A

V

A

T

E

E

N

E

G

T

W

E

H

G

V

I

V

M

S

V

D

H

T

P

S

N

Y

Q

E

E

G

P

Y

A

E

-

T

-

I

-

P

-

R

-

D

-

V

V

M

I

Q

A

G

G

Y

Q

G

G

V

T

I

I

P

A

A

L

E

E

V

V

L

L

A

N

Q

Q

L

V

N

-

E

-

H

-

S

-

R

-

P

P

A

L

F

V

T

D

H

A

V

L

F

V

L

V

Q

P

G

V

G
|
G

V
x
G

G
|
G

L
x
M

A

L

A

A

G

G

V

I

A

A

S

I

Y

T

L

V

W

-

E

-

H

-

Y

-

G

K

A

A

E

L

R

K

P

P

T

S

F

V

I

K

V

V

-

Y

-

A

V

A

E
|
E

P

P

Q

S

Q

N

A
|
A

D

D

C
x
D

L

C

Y

Y

Q

Q

S

S

A

K

I

L

A

K

G

G

R

K

A

L

S

M

K

P

A

N

T

L

G

Y

S

P

V

P

D

E

S

T

I

I

M

A

A

D

G
|
G

L
x
V

A

K

C

-

G

S

E

S

A

I

S

G

P

L

L
x
N

A

T

W

W

K

P

I

I

L

I

E

R

Q

D

C

L

V

V

D

D

Y

D

F

I

M

F

T

T

I

V

D

T

D

E

E

D

D

E

active site: K53 (= K76), S76 (≠ D121), E202 (= E262), A206 (= A266), D208 (≠ C268), G231 (= G291)
binding calcium ion: E202 (= E262), A206 (= A266), D208 (≠ C268)
binding magnesium ion: N239 (≠ L300)
binding ortho-xylene: S76 (≠ D121), Q81 (≠ K126), I96 (= I141), Y113 (= Y158)
binding pyridoxal-5'-phosphate: F52 (= F75), K53 (= K76), N78 (= N123), G177 (= G235), G178 (≠ V236), G179 (= G237), G180 (= G238), M181 (≠ L239), G231 (= G291), V232 (≠ L292)

Sites not aligning to the query:

active site: 304, 305
binding magnesium ion: 3
binding pyridoxal-5'-phosphate: 275, 277, 305, 306

7nbhAAA structure of human serine racemase in complex with DSiP fragment Z26781964, XChem fragment screen (see paper)
28% identity, 63% coverage: 60:319/412 of query aligns to 38:263/320 of 7nbhAAA

query
sites
7nbhAAA

Q

N

L

L

S

F

L

F

K

K

D

C

E

E

S

L

F

F

R

Q

S

K

P

-

L

T

G

G

S

S

F

F

K
|
K

A

I

L

R

G

G

A

A

P

L

I

N

A

A

L

V

M

R

R

S

L

L

I

V

M

P

R

D

Q

A

W

L

H

E

A

R

H

K

G

-

I

-

D

-

P

P

K

K

A

A

L

V

V

V

T

T

G

-

Q

-

Y

-

A

-

Q

-

M

-

L

-

S

-

N

-

M

-

T

-

V

-

I

-

S

-

A

H

T

S

D
x
S

G

G

N

N

H

H

G
|
G

K
x
Q

S

A

L

L

A

T

A

Y

A

A

R

K

A

L

I

E

G

G

C

I

Y

P

C

A

V

Y

I

I

V

V

L

V

H

P

A

Q

N

T

V

A

S

P

I

D

E

C

R
x
K

E

K

Q

L

A

A

I
|
I

A

Q

A

A

Y
|
Y

G

G

A

A

K

S

I

I

V

V

R

Y

I

C

D

E

G

P

N

S

Y

-

D

D

E

E

S

S

V

R

Q

E

H

N

A

V

A

A

Q

K

L

R

A

V

A

T

E

E

N

E

G

T

W

E

H

G

V

I

V

M

S

V

D

H

T

P

S

N

Y

Q

E

E

G

P

Y

A

E

-

T

-

I

-

P

-

R

-

D

-

V

V

M

I

Q

A

G

G

Y

Q

G

G

V

T

I

I

P

A

A

L

E

E

V

V

L

L

A

N

Q

Q

L

V

N

-

E

-

H

-

S

-

R

-

P

P

A

L

F

V

T

D

H

A

V

L

F

V

L

V

Q

P

G

V

G

G

V

G

G

G

L

M

A

L

A

A

G

G

V

I

A

A

S

I

Y

T

L

V

W

-

E

-

H

-

Y

-

G

K

A

A

E

L

R

K

P

P

T

S

F

V

I

K

V

V

-

Y

-

A

V

A

E
|
E

P

P

Q

S

Q

N

A
|
A

D

D

C
x
D

L

C

Y

Y

Q

Q

S

S

A

K

I

L

A

K

G

G

R

K

A

L

S

M

K

P

A

N

T

L

G

Y

S

P

V

P

D

E

S

T

I

I

M

A

A
x
D

G
|
G

L

V

A

K

C

-

G

S

E

S

A

I

S

G

P

L

L

N

A

T

W

W

K

P

I

I

L

I

E

R

Q

D

C

L

V

V

D

D

Y

D

F

I

M

F

T

T

I

V

D

T

D

E

E

D

D

E

active site: K53 (= K76), S81 (≠ D121), E207 (= E262), A211 (= A266), D213 (≠ C268), G236 (= G291)
binding calcium ion: E207 (= E262), A211 (= A266), D213 (≠ C268)
binding N-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide: S81 (≠ D121), G85 (= G125), Q86 (≠ K126), K111 (≠ R151), I115 (= I155), Y118 (= Y158), D235 (≠ A290)

Sites not aligning to the query:

active site: 309, 310
binding N-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide: 281, 313, 314, 315

7nbgAAA structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
28% identity, 63% coverage: 60:319/412 of query aligns to 38:263/322 of 7nbgAAA

query
sites
7nbgAAA

Q

N

L

L

S

F

L

F

K

K

D

C

E

E

S

L

F

F

R

Q

S

K

P

-

L

T

G

G

S

S

F
|
F

K
|
K

A

I

L

R

G

G

A

A

P

L

I

N

A

A

L

V

M

R

R

S

L

L

I

V

M

P

R

D

Q

A

W

L

H

E

A

R

H

K

G

-

I

-

D

-

P

P

K

K

A

A

L

V

V

V

T

T

G

-

Q

-

Y

-

A

-

Q

-

M

-

L

-

S

-

N

-

M

-

T

-

V

-

I

-

S

-

A

H

T

S

D
x
S

G

G

N
|
N

H

H

G
|
G

K
x
Q

S

A

L

L

A

T

A

Y

A

A

R

K

A

L

I

E

G

G

C

I

Y

P

C

A

V

Y

I
|
I

V

V

L

V

H

P

A

Q

N

T

V

A

S

P

I

D

E

C

R
x
K

E

K

Q

L

A

A

I
|
I

A

Q

A

A

Y
|
Y

G

G

A

A

K

S

I

I

V

V

R

Y

I

C

D

E

G

P

N

S

Y

-

D

D

E

E

S

S

V

R

Q

E

H

N

A

V

A

A

Q

K

L

R

A

V

A

T

E

E

N

E

G

T

W

E

H

G

V

I

V

M

S

V

D

H

T

P

S

N

Y

Q

E

E

G

P

Y

A

E

-

T

-

I

-

P

-

R

-

D

-

V

V

M

I

Q

A

G

G

Y

Q

G

G

V

T

I

I

P

A

A

L

E

E

V

V

L

L

A

N

Q

Q

L

V

N

-

E

-

H

-

S

-

R

-

P

P

A

L

F

V

T

D

H

A

V

L

F

V

L

V

Q

P

G

V

G
|
G

V
x
G

G
|
G

L
x
M

A

L

A

A

G

G

V

I

A

A

S

I

Y

T

L

V

W

-

E

-

H

-

Y

-

G

K

A

A

E

L

R

K

P

P

T

S

F

V

I

K

V

V

-

Y

-

A

V

A

E
|
E

P

P

Q

S

Q

N

A
|
A

D

D

C
x
D

L

C

Y

Y

Q

Q

S

S

A

K

I

L

A

K

G

G

R

K

A

L

S

M

K

P

A

N

T

L

G

Y

S

P

V

P

D

E

S

T

I

I

M

A

A

D

G
|
G

L
x
V

A

K

C

-

G

S

E

S

A

I

S

G

P

L

L

N

A

T

W

W

K

P

I

I

L

I

E

R

Q

D

C

L

V

V

D

D

Y

D

F

I

M

F

T

T

I

V

D

T

D

E

E

D

D

E

active site: K53 (= K76), S81 (≠ D121), E207 (= E262), A211 (= A266), D213 (≠ C268), G236 (= G291)
binding calcium ion: E207 (= E262), A211 (= A266), D213 (≠ C268)
binding pyridoxal-5'-phosphate: F52 (= F75), K53 (= K76), N83 (= N123), G182 (= G235), G183 (≠ V236), G184 (= G237), G185 (= G238), M186 (≠ L239), G236 (= G291), V237 (≠ L292)
binding ~{N}-[2-(2-methylphenyl)ethyl]ethanamide: S81 (≠ D121), G85 (= G125), Q86 (≠ K126), I101 (= I141), K111 (≠ R151), I115 (= I155), Y118 (= Y158)

Sites not aligning to the query:

active site: 309, 310
binding pyridoxal-5'-phosphate: 282, 310, 311

7nbfAAA structure of human serine racemase in complex with DSiP fragment Z126932614, XChem fragment screen (see paper)
28% identity, 63% coverage: 60:319/412 of query aligns to 38:263/323 of 7nbfAAA

query
sites
7nbfAAA

Q

N

L

L

S

F

L

F

K

K

D

C

E

E

S

L

F
|
F

R

Q

S

K

P

-

L

T

G

G

S

S

F
|
F

K
|
K

A

I

L

R

G

G

A

A

P

L

I

N

A

A

L

V

M

R

R

S

L

L

I

V

M

P

R

D

Q

A

W

L

H

E

A

R

H

K

G

-

I

-

D

-

P

P

K

K

A

A

L

V

V

V

T

T

G

-

Q

-

Y

-

A

-

Q

-

M

-

L

-

S

-

N

-

M

-

T

-

V

-

I

-

S

-

A

H

T

S

D
x
S

G

G

N
|
N

H

H

G

G

K

Q

S

A

L

L

A

T

A

Y

A

A

R

K

A

L

I

E

G

G

C

I

Y

P

C

A

V

Y

I

I

V

V

L

V

H

P

A

Q

N

T

V

A

S

P

I

D

E

C

R

K

E

K

Q

L

A

A

I

I

A

Q

A

A

Y

Y

G

G

A

A

K

S

I

I

V

V

R

Y

I

C

D

E

G

P

N

S

Y

-

D

D

E

E

S

S

V

R

Q

E

H

N

A

V

A

A

Q

K

L

R

A

V

A

T

E

E

N

E

G

T

W

E

H

G

V

I

V

M

S

V

D

H

T

P

S

N

Y

Q

E

E

G

P

Y

A

E

-

T

-

I

-

P

-

R

-

D

-

V

V

M

I

Q

A

G

G

Y

Q

G

G

V

T

I

I

P

A

A

L

E

E

V

V

L

L

A

N

Q

Q

L

V

N

-

E

-

H

-

S

-

R

-

P

P

A

L

F

V

T

D

H

A

V

L

F

V

L

V

Q

P

G

V

G
|
G

V
x
G

G
|
G

L
x
M

A

L

A

A

G

G

V

I

A

A

S

I

Y

T

L

V

W

-

E

-

H

-

Y

-

G

K

A

A

E

L

R

K

P

P

T

S

F

V

I

K

V

V

-

Y

-

A

V

A

E
|
E

P

P

Q

S

Q

N

A
|
A

D

D

C
x
D

L

C

Y

Y

Q

Q

S

S

A

K

I

L

A

K

G

G

R

K

A

L

S

M

K

P

A

N

T

L

G

Y

S

P

V

P

D

E

S

T

I

I

M

A

A

D

G
|
G

L
x
V

A

K

C

-

G

S

E

S

A

I

S

G

P

L

L
x
N

A

T

W

W

K

P

I

I

L

I

E

R

Q

D

C

L

V

V

D

D

Y

D

F

I

M

F

T

T

I

V

D

T

D

E

E

D

D

E

active site: K53 (= K76), S81 (≠ D121), E207 (= E262), A211 (= A266), D213 (≠ C268), G236 (= G291)
binding calcium ion: E207 (= E262), A211 (= A266), D213 (≠ C268)
binding magnesium ion: N244 (≠ L300)
binding pyridoxal-5'-phosphate: F52 (= F75), K53 (= K76), N83 (= N123), G182 (= G235), G183 (≠ V236), G184 (= G237), G185 (= G238), M186 (≠ L239), G236 (= G291), V237 (≠ L292)
binding 2-[(methylsulfonyl)methyl]-1H-benzimidazole: F46 (= F68)

Sites not aligning to the query:

active site: 309, 310
binding magnesium ion: 3
binding pyridoxal-5'-phosphate: 282, 310, 311
binding 2-[(methylsulfonyl)methyl]-1H-benzimidazole: 21, 22, 23, 24, 26, 27

7nbdAAA structure of human serine racemase in complex with DSiP fragment Z235449082, XChem fragment screen (see paper)
28% identity, 63% coverage: 60:319/412 of query aligns to 38:263/323 of 7nbdAAA

query
sites
7nbdAAA

Q

N

L

L

S

F

L

F

K

K

D

C

E

E

S

L

F

F

R

Q

S

K

P

-

L

T

G

G

S

S

F
|
F

K
|
K

A

I

L

R

G

G

A

A

P

L

I

N

A

A

L

V

M

R

R

S

L

L

I

V

M

P

R

D

Q

A

W

L

H

E

A

R

H

K

G

-

I

-

D

-

P

P

K

K

A

A

L

V

V

V

T

T

G

-

Q

-

Y

-

A

-

Q

-

M

-

L

-

S

-

N

-

M

-

T

-

V

-

I

-

S

-

A

H

T

S

D
x
S

G

G

N
|
N

H

H

G

G

K

Q

S

A

L

L

A

T

A

Y

A

A

R

K

A

L

I

E

G

G

C

I

Y

P

C

A

V

Y

I

I

V

V

L

V

H

P

A

Q

N

T

V

A

S

P

I

D

E

C

R

K

E

K

Q

L

A

A

I

I

A

Q

A

A

Y

Y

G

G

A

A

K

S

I

I

V

V

R

Y

I

C

D

E

G

P

N

S

Y

-

D

D

E

E

S

S

V

R

Q

E

H

N

A

V

A

A

Q

K

L

R

A

V

A

T

E

E

N

E

G

T

W

E

H

G

V

I

V

M

S

V

D

H

T

P

S

N

Y

Q

E

E

G

P

Y

A

E

-

T

-

I

-

P

-

R

-

D

-

V

V

M

I

Q

A

G

G

Y

Q

G

G

V

T

I

I

P

A

A

L

E

E

V

V

L

L

A

N

Q

Q

L

V

N

-

E

-

H

-

S

-

R

-

P

P

A

L

F

V

T

D

H

A

V

L

F

V

L

V

Q

P

G

V

G
|
G

V
x
G

G
|
G

L
x
M

A

L

A

A

G

G

V

I

A

A

S

I

Y

T

L

V

W

-

E

-

H

-

Y

-

G

K

A

A

E

L

R

K

P

P

T

S

F

V

I

K

V

V

-

Y

-

A

V

A

E
|
E

P

P

Q

S

Q

N

A
|
A

D

D

C
x
D

L

C

Y

Y

Q

Q

S

S

A

K

I

L

A

K

G

G

R

K

A

L

S

M

K

P

A

N

T

L

G

Y

S

P

V

P

D

E

S

T

I

I

M

A

A

D

G
|
G

L
x
V

A

K

C

-

G

S

E

S

A

I

S

G

P

L

L
x
N

A

T

W

W

K

P

I

I

L

I

E

R

Q

D

C

L

V

V

D

D

Y

D

F

I

M

F

T

T

I

V

D

T

D

E

E

D

D

E

active site: K53 (= K76), S81 (≠ D121), E207 (= E262), A211 (= A266), D213 (≠ C268), G236 (= G291)
binding calcium ion: E207 (= E262), A211 (= A266), D213 (≠ C268)
binding magnesium ion: N244 (≠ L300)
binding pyridoxal-5'-phosphate: F52 (= F75), K53 (= K76), N83 (= N123), G182 (= G235), G183 (≠ V236), G184 (= G237), G185 (= G238), M186 (≠ L239), G236 (= G291), V237 (≠ L292)

Sites not aligning to the query:

active site: 309, 310
binding [4-(1H-benzimidazol-1-yl)phenyl]methanol: 272, 278, 314, 316
binding magnesium ion: 3
binding pyridoxal-5'-phosphate: 280, 282, 310, 311

7nbcCCC structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen (see paper)
28% identity, 63% coverage: 60:319/412 of query aligns to 38:263/323 of 7nbcCCC

query
sites
7nbcCCC

Q

N

L

L

S

F

L

F

K

K

D

C

E

E

S

L

F

F

R

Q

S

K

P

-

L

T

G

G

S

S

F
|
F

K
|
K

A

I

L

R

G

G

A

A

P

L

I

N

A

A

L

V

M

R

R

S

L

L

I

V

M

P

R

D

Q

A

W

L

H

E

A

R

H

K

G

-

I

-

D

-

P

P

K

K

A

A

L

V

V

V

T
|
T

G

-

Q

-

Y

-

A

-

Q

-

M

-

L

-

S

-

N

-

M

-

T

-

V

-

I

-

S

-

A
x
H

T

S

D
x
S

G

G

N
|
N

H
|
H

G

G

K

Q

S

A

L

L

A

T

A

Y

A

A

R

K

A

L

I

E

G

G

C

I

Y

P

C

A

V

Y

I

I

V

V

L

V

H

P

A

Q

N

T

V

A

S

P

I

D

E

C

R

K

E

K

Q

L

A

A

I

I

A

Q

A

A

Y

Y

G

G

A

A

K

S

I

I

V

V

R

Y

I

C

D

E

G

P

N

S

Y

-

D

D

E

E

S

S

V

R

Q

E

H

N

A

V

A

A

Q

K

L

R

A

V

A

T

E

E

N

E

G

T

W

E

H

G

V

I

V

M

S
x
V

D
x
H

T
x
P

S

N

Y

Q

E

E

G

P

Y

A

E

-

T

-

I

-

P

-

R

-

D

-

V

V

M

I

Q

A

G

G

Y

Q

G

G

V

T

I

I

P

A

A

L

E

E

V

V

L

L

A

N

Q

Q

L

V

N

-

E

-

H

-

S

-

R

-

P

P

A

L

F

V

T

D

H

A

V

L

F

V

L

V

Q

P

G

V

G
|
G

V
x
G

G
|
G

L
x
M

A

L

A

A

G

G

V

I

A

A

S

I

Y

T

L

V

W

-

E

-

H

-

Y

-

G

K

A

A

E

L

R

K

P

P

T

S

F

V

I

K

V

V

-

Y

-

A

V

A

E
|
E

P

P

Q

S

Q

N

A
|
A

D

D

C
x
D

L

C

Y

Y

Q

Q

S

S

A

K

I

L

A

K

G

G

R

K

A

L

S

M

K

P

A

N

T

L

G

Y

S

P

V

P

D

E

S

T

I

I

M

A

A

D

G
|
G

L
x
V

A

K

C

-

G

S

E

S

A

I

S

G

P

L

L

N

A

T

W

W

K

P

I

I

L

I

E

R

Q

D

C

L

V

V

D

D

Y

D

F

I

M

F

T

T

I

V

D

T

D

E

E

D

D

E

active site: K53 (= K76), S81 (≠ D121), E207 (= E262), A211 (= A266), D213 (≠ C268), G236 (= G291)
binding biphenyl-4-ylacetic acid: T78 (= T104), H79 (≠ A119), H84 (= H124), V148 (≠ S189), H149 (≠ D190), P150 (≠ T191)
binding calcium ion: E207 (= E262), A211 (= A266), D213 (≠ C268)
binding pyridoxal-5'-phosphate: F52 (= F75), K53 (= K76), N83 (= N123), G182 (= G235), G183 (≠ V236), G184 (= G237), G185 (= G238), M186 (≠ L239), G236 (= G291), V237 (≠ L292)

Sites not aligning to the query:

active site: 309, 310
binding pyridoxal-5'-phosphate: 282, 310, 311

7nbcAAA structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen (see paper)
28% identity, 63% coverage: 60:319/412 of query aligns to 38:263/323 of 7nbcAAA

query
sites
7nbcAAA

Q

N

L

L

S

F

L

F

K

K

D

C

E

E

S

L

F

F

R

Q

S

K

P

-

L

T

G

G

S

S

F
|
F

K
|
K

A

I

L

R

G

G

A

A

P

L

I

N

A

A

L

V

M

R

R

S

L

L

I

V

M

P

R

D

Q

A

W

L

H

E

A

R

H

K

G

-

I

-

D

-

P

P

K

K

A

A

L

V

V

V

T

T

G

-

Q

-

Y

-

A

-

Q

-

M

-

L

-

S

-

N

-

M

-

T

-

V

-

I

-

S

-

A

H

T

S

D
x
S

G

G

N
|
N

H

H

G

G

K

Q

S

A

L

L

A

T

A

Y

A

A

R

K

A

L

I

E

G

G

C

I

Y

P

C

A

V

Y

I

I

V

V

L

V

H

P

A

Q

N

T

V

A

S

P

I

D

E

C

R

K

E

K

Q

L

A

A

I

I

A

Q

A

A

Y

Y

G

G

A

A

K

S

I

I

V

V

R

Y

I

C

D

E

G

P

N

S

Y

-

D

D

E

E

S

S

V

R

Q

E

H

N

A

V

A

A

Q

K

L

R

A

V

A

T

E

E

N

E

G

T

W

E

H

G

V

I

V

M

S

V

D

H

T

P

S

N

Y

Q

E

E

G

P

Y

A

E

-

T

-

I

-

P

-

R

-

D

-

V

V

M

I

Q

A

G

G

Y

Q

G

G

V

T

I

I

P

A

A

L

E

E

V

V

L

L

A

N

Q

Q

L

V

N

-

E

-

H

-

S

-

R

-

P

P

A

L

F

V

T

D

H

A

V

L

F

V

L

V

Q

P

G

V

G
|
G

V
x
G

G
|
G

L
x
M

A

L

A

A

G

G

V

I

A

A

S

I

Y

T

L

V

W

-

E

-

H

-

Y

-

G

K

A

A

E

L

R

K

P

P

T

S

F

V

I

K

V

V

-

Y

-

A

V

A

E
|
E

P

P

Q

S

Q

N

A
|
A

D

D

C
x
D

L

C

Y

Y

Q

Q

S

S

A

K

I

L

A

K

G

G

R

K

A

L

S

M

K

P

A

N

T

L

G

Y

S

P

V

P

D

E

S

T

I

I

M

A

A

D

G
|
G

L
x
V

A

K

C

-

G

S

E

S

A

I

S

G

P

L

L
x
N

A

T

W

W

K

P

I

I

L

I

E

R

Q

D

C

L

V

V

D

D

Y

D

F

I

M

F

T

T

I

V

D

T

D

E

E

D

D

E

active site: K53 (= K76), S81 (≠ D121), E207 (= E262), A211 (= A266), D213 (≠ C268), G236 (= G291)
binding calcium ion: E207 (= E262), A211 (= A266), D213 (≠ C268)
binding magnesium ion: N244 (≠ L300)
binding pyridoxal-5'-phosphate: F52 (= F75), K53 (= K76), N83 (= N123), G182 (= G235), G183 (≠ V236), G184 (= G237), G185 (= G238), M186 (≠ L239), G236 (= G291), V237 (≠ L292)

Sites not aligning to the query:

active site: 309, 310
binding magnesium ion: 3
binding pyridoxal-5'-phosphate: 282, 310, 311

Q9GZT4 Serine racemase; D-serine ammonia-lyase; D-serine dehydratase; L-serine ammonia-lyase; L-serine dehydratase; EC 5.1.1.18; EC 4.3.1.18; EC 4.3.1.17 from Homo sapiens (Human) (see 4 papers)
28% identity, 63% coverage: 60:319/412 of query aligns to 41:266/340 of Q9GZT4

query
sites
Q9GZT4

Q

N

L

L

S

F

L

F

K

K

D

C

E

E

S

L

F

F

R

Q

S
x
K

P

-

L
x
T

G

G

S

S

F

F

K
|
K

A

I

L

R

G

G

A

A

P

L

I

N

A

A

L

V

M

R

R

S

L

L

I

V

M
x
P

R

D

Q

A

W

L

H

E

A

R

H

K

G

-

I

-

D

-

P

P

K

K

A

A

L

V

V

V

T
|
T

G

H

Q

-

Y

-

A

-

Q

-

M

-

L

-

S

-

N

-

M

-

T

-

V

-

I

-

S

-

A

-

T

S

D

S

G

G

N
|
N

H

H

G

G

K
x
Q

S

A

L

L

A

T

A

Y

A

A

R

K

A

L

I

E

G

G

C

I

Y

P

C

A

V

Y

I

I

V

V

L

V

H

P

A

Q

N

T

V

A

S

P

I

D

E

C

R

K

E

K

Q

L

A

A

I

I

A

Q

A

A

Y
|
Y

G

G

A

A

K

S

I

I

V

V

R

Y

I

C

D

E

G

P

N

S

Y

-

D

D

E

E

S

S

V

R

Q

E

H

N

A

V

A

A

Q

K

L

R

A

V

A

T

E

E

N

E

G

T

W

E

H

G

V

I

V

M

S

V

D

H

T

P

S

N

Y

Q

E

E

G

P

Y

A

E

-

T

-

I

-

P

-

R

-

D

-

V

V

M

I

Q

A

G

G

Y

Q

G

G

V

T

I

I

P

A

A

L

E

E

V

V

L

L

A

N

Q

Q

L

V

N

-

E

-

H

-

S

-

R

-

P

P

A

L

F

V

T
x
D

H

A

V

L

F

V

L

V

Q

P

G

V

G
|
G

V
x
G

G
|
G

L
x
M

A

L

A

A

G

G

V

I

A

A

S

I

Y

T

L

V

W

-

E

-

H

-

Y

-

G

K

A

A

E

L

R

K

P

P

T

S

F

V

I

K

V

V

-

Y

-

A

V

A

E
|
E

P

P

Q

S

Q

N

A
|
A

D

D

C
x
D

L

C

Y

Y

Q

Q

S

S

A

K

I

L

A

K

G

G

R

K

A

L

S

M

K

P

A

N

T

L

G

Y

S

P

V

P

D

E

S

T

I

I

M

A

A

D

G

G

L

V

A

K

C

-

G

S

E

S

A

I

S

G

P

L

L
x
N

A

T

W

W

K

P

I

I

L

I

E

R

Q

D

C

L

V

V

D

D

Y

D

F

I

M

F

T

T

I

V

D

T

D

E

E

D

D

E

K51 (≠ S70) binding ATP
T52 (≠ L72) binding ATP
K56 (= K76) modified: N6-(pyridoxal phosphate)lysine
P69 (≠ M89) binding Ca(2+)
T81 (= T104) binding Ca(2+)
N86 (= N123) binding pyridoxal 5'-phosphate
Q89 (≠ K126) binding ATP
Y121 (= Y158) binding ATP
D178 (≠ T228) binding Mg(2+)
G185 (= G235) binding pyridoxal 5'-phosphate
G186 (≠ V236) binding pyridoxal 5'-phosphate
G187 (= G237) binding pyridoxal 5'-phosphate
G188 (= G238) binding pyridoxal 5'-phosphate
M189 (≠ L239) binding pyridoxal 5'-phosphate
E210 (= E262) binding Ca(2+); binding Mg(2+); binding Mn(2+)
A214 (= A266) binding Ca(2+); binding Mg(2+); binding Mn(2+)
D216 (≠ C268) binding Ca(2+); binding Mg(2+); binding Mn(2+)
N247 (≠ L300) binding Ca(2+); binding Mg(2+)

Sites not aligning to the query:

13 binding Mg(2+)
31 binding ATP
32 binding ATP
33 binding ATP
279 binding ATP
313 binding pyridoxal 5'-phosphate
316 binding ATP

6zspAAA serine racemase bound to atp and malonate. (see paper)
28% identity, 63% coverage: 60:319/412 of query aligns to 38:256/320 of 6zspAAA

query
sites
6zspAAA

Q

N

L

L

S

F

L

F

K

K

D

C

E

E

S

L

F

F

R

Q

S
x
K

P

-

L
x
T

G

G

S

S

F

F

K
|
K

A

I

L

R

G

G

A

A

P

L

I

N

A

A

L

V

M

R

R

S

L

L

I

-

M

-

R

-

Q

-

W

-

H

-

A

-

H

-

G

-

I

-

D

K

P

P

K

K

A

A

L

V

V

V

T

T

G

-

Q

-

Y

-

A

-

Q

-

M

-

L

-

S

-

N

-

M

-

T

-

V

-

I

-

S

-

A

H

T
x
S

D
x
S

G

G

N
|
N

H
|
H

G

G

K
x
Q

S

A

L

L

A

T

A

Y

A

A

R

K

A

L

I

E

G

G

C

I

Y

P

C

A

V

Y

I

I

V

V

L

V

H

P

A

Q

N

T

V

A

S

P

I

D

E

C

R

K

E

K

Q

L

A

A

I

I

A

Q

A

A

Y
|
Y

G

G

A

A

K

S

I

I

V

V

R

Y

I

C

D

E

G

P

N

S

Y

-

D

D

E

E

S

S

V
x
R

Q

E

H

N

A

V

A

A

Q

K

L

R

A

V

A

T

E

E

N

E

G

T

W

E

H

G

V

I

V

M

S

V

D

H

T

P

S

N

Y

Q

E

E

G

P

Y

A

E

-

T

-

I

-

P

-

R

-

D

-

V

V

M

I

Q

A

G

G

Y

Q

G

G

V

T

I

I

P

A

A

L

E

E

V

V

L

L

A

N

Q

Q

L

V

N

-

E

-

H

-

S

-

R

-

P

P

A

L

F

V

T

D

H

A

V

L

F

V

L

V

Q

P

G

V

G

G

V

G

G

G

L

M

A

L

A

A

G

G

V

I

A

A

S

I

Y

T

L

V

W

-

E

-

H

-

Y

-

G

K

A

A

E

L

R

K

P

P

T

S

F

V

I

K

V

V

-

Y

-

A

V

A

E
|
E

P

P

Q

S

Q

N

A
|
A

D

D

C
x
D

L

C

Y

Y

Q

Q

S

S

A

K

I

L

A

K

G

G

R

K

A

L

S

M

K

P

A

N

T

L

G

Y

S

P

V

P

D

E

S

T

I

I

M

A

A

D

G
|
G

L

V

A

K

C

-

G
x
S

E

S

A

I

S

G

P

L

L

N

A

T

W

W

K

P

I

I

L

I

E

R

Q

D

C

L

V

V

D

D

Y

D

F

I

M

F

T

T

I

V

D

T

D

E

E

D

D

E

active site: K53 (= K76), S74 (≠ D121), E200 (= E262), A204 (= A266), D206 (≠ C268), G229 (= G291)
binding adenosine-5'-triphosphate: K48 (≠ S70), T49 (≠ L72), Q79 (≠ K126), Y111 (= Y158)
binding magnesium ion: E200 (= E262), A204 (= A266), D206 (≠ C268)
binding malonate ion: K53 (= K76), S73 (≠ T120), S74 (≠ D121), N76 (= N123), H77 (= H124), R125 (≠ V173), G229 (= G291), S232 (≠ G295)

Sites not aligning to the query:

active site: 302, 303
binding adenosine-5'-triphosphate: 28, 29, 30, 266, 267, 269, 306

5i6dB Mycobacterium tuberculosis cysm in complex with the urea-scaffold inhibitor 5 [3-(3-(p-tolyl)ureido) benzoic acid] (see paper)
29% identity, 59% coverage: 44:288/412 of query aligns to 21:228/287 of 5i6dB

query
sites
5i6dB

T

S

P

P

L

R

W

W

D

D

L

G

P

P

D

H

A

V

A

-

R

R

L

L

G

W

V

A

A

-

Q

-

L

-

S

K

L

L

K

E

D

D

E

-

S

-

F

-

R

R

S

N

P

P

L

T

G

G

S

S

F

I

K
|
K

A

D

L

R

G

P

A

A

P

-

I

-

A

-

L

-

M

V

R

R

L

M

I

I

M

-

R

E

Q

Q

W

A

H

E

A

A

H

D

G

G

I

L

D

-

P

-

K

-

A

-

L

-

V

-

T

-

G

-

Q

-

Y

-

A

-

Q

-

M

L

L

R

S

P

N

G

M

A

T

T

V

I

I

L

S

E

A

P

T
|
T

D
x
S

G

G

N
|
N

H
x
T

G

G

K

I

S

S

L

L

A

A

A

M

A

A

R

R

A

L

I

K

G

G

C

Y

Y

R

C

L

V

I

I

C

V

V

L

M

H

P

A

E

N

N

V

T

S

S

I

V

E

E

R

R

E

R

Q

Q

A

L

I

L

A

E

A

L

Y

Y

G

G

A

A

K

Q

I

I

V

I

-

F

-

S

R

A

I

A

D

E

G

G

N

G

Y

S

D

N

E

T

S

A

V

V

Q

A

H

T

A

A

A

K

Q

E

L

L

A

A

E

T

N

N

-

P

G

S

W

W

H

V

V

M

V

L

S

Y

D
x
Q

T
x
Y

S

G

Y

N

E

-

G

-

Y

-

E

-

T

-

I

-

P

P

R

A

D

N

V

T

M

D

Q

S

G

H

Y

Y

G

C

V

G

I

T

P

G

A

P

E

E

V

L

L

L

A

A

Q

D

L

L

N

-

E

-

H

-

S

-

R

-

P

P

A

E

F

I

T

T

H

H

V

F

F

V

L

A

Q

G

G

L

G
|
G

V
x
T

G
x
T

G

G

L
x
T

A

L

A

M

G

G

V

T

A

G

S

R

Y

F

L

L

W

R

E

E

H

H

Y

V

G

A

A

N

E

V

R

K

P

-

T

-

F

I

I

V

V

A

E
|
E

P
|
P

Q

R

Q

F

A

V

D

P

C

E

L

L

Y

Y

Q

D

S

P

A

E

I

I

A

L

G

-

R

T

A

A

S

R

K

Y

A

S

T

V

G

G

S

A

V

V

D

D

S

A

I

V

active site: K45 (= K76)
binding 3-{[(4-methylphenyl)carbamoyl]amino}benzoic acid: K45 (= K76), T72 (= T120), S73 (≠ D121), N75 (= N123), T76 (≠ H124), Q145 (≠ D190), Y146 (≠ T191), G178 (= G235), T179 (≠ V236), E203 (= E262), P204 (= P263)
binding pyridoxal-5'-phosphate: K45 (= K76), N75 (= N123), G178 (= G235), T179 (≠ V236), T180 (≠ G237), T182 (≠ L239)

Sites not aligning to the query:

active site: 245
binding 3-{[(4-methylphenyl)carbamoyl]amino}benzoic acid: 245
binding pyridoxal-5'-phosphate: 245, 274, 275

5i7hB Mycobacterium tuberculosis cysm in complex with the urea-scaffold inhibitor 6 [3-(3-(4-bromophenyl)ureido)benzoic acid] (see paper)
31% identity, 42% coverage: 115:288/412 of query aligns to 71:232/291 of 5i7hB

query
sites
5i7hB

T

T

V

I

I

L

S

E

A

P

T
|
T

D
x
S

G

G

N
|
N

H
x
T

G

G

K

I

S

S

L

L

A

A

A

M

A

A

R

R

A

L

I

K

G

G

C

Y

Y

R

C

L

V

I

I

C

V

V

L

M

H

P

A

E

N

N

V

T

S

S

I

V

E

E

R

R

E

R

Q

Q

A

L

I

L

A

E

A

L

Y

Y

G

G

A

A

K

Q

I

I

V

I

-

F

-

S

R

A

I

A

D

E

G

G

N

G

Y

S

D

N

E

T

S

A

V

V

Q

A

H

T

A

A

A

K

Q

E

L

L

A

A

E

T

N

N

-

P

G

S

W

W

H

V

V

M

V

L

S

Y

D
x
Q

T
x
Y

S

G

Y

N

E

-

G

-

Y

-

E

-

T

-

I

-

P

P

R

A

D

N

V

T

M

D

Q

S

G

H

Y

Y

G

C

V

G

I

T

P

G

A

P

E

E

V

L

L

L

A

A

Q

D

L

L

N

-

E

-

H

-

S

-

R

-

P

P

A

E

F

I

T

T

H

H

V

F

F

V

L

A

Q

G

G

L

G
|
G

V
x
T

G
x
T

G

G

L
x
T

A

L

A

M

G

G

V

T

A

G

S

R

Y

F

L

L

W

R

E

E

H

H

Y

V

G

A

A

N

E

V

R

K

P

-

T

-

F

I

I

V

V

A

V
x
A

E
|
E

P
|
P

Q

R

Q

F

A

V

D

P

C

E

L

L

Y

Y

Q

D

S

P

A

E

I

I

A

L

G

-

R

T

A

A

S

R

K

Y

A

S

T

V

G

G

S

A

V

V

D

D

S

A

I

V

binding 3-{[(4-bromophenyl)carbamoyl]amino}benzoic acid: T76 (= T120), S77 (≠ D121), N79 (= N123), T80 (≠ H124), Q149 (≠ D190), Y150 (≠ T191), G182 (= G235), T183 (≠ V236), A206 (≠ V261), E207 (= E262), P208 (= P263)
binding pyridoxal-5'-phosphate: N79 (= N123), G182 (= G235), T183 (≠ V236), T184 (≠ G237), T186 (≠ L239)

Sites not aligning to the query:

active site: 49, 249
binding 3-{[(4-bromophenyl)carbamoyl]amino}benzoic acid: 49, 249
binding pyridoxal-5'-phosphate: 49, 249, 278, 279

5i6dA Mycobacterium tuberculosis cysm in complex with the urea-scaffold inhibitor 5 [3-(3-(p-tolyl)ureido) benzoic acid] (see paper)
30% identity, 42% coverage: 115:288/412 of query aligns to 71:225/285 of 5i6dA

query
sites
5i6dA

T

T

V

I

I

L

S

E

A

P

T
|
T

D
x
S

G

G

N
|
N

H
x
T

G

G

K

I

S

S

L

L

A

A

A

M

A

A

R

R

A

L

I

K

G

G

C

Y

Y

R

C

L

V

I

I

C

V

V

L

M

H

P

A

E

N

N

V

T

S

S

I

V

E

E

R

R

E

R

Q

Q

A

L

I

L

A

E

A

L

Y

Y

G

G

A

A

K

Q

I

I

V

I

R

-

I

-

D

-

G

-

N

-

Y

F

D

S

E

T

S

A

V

V

Q

A

H

T

A

A

A

K

Q

E

L

L

A

A

E

T

N

N

-

P

G

S

W

W

H

V

V

M

V

L

S

Y

D
x
Q

T
x
Y

S

G

Y

N

E

-

G

-

Y

-

E

-

T

-

I

-

P

P

R

A

D

N

V

T

M

D

Q

S

G

H

Y

Y

G

C

V

G

I

T

P

G

A

P

E

E

V

L

L

L

A

A

Q

D

L

L

N

-

E

-

H

-

S

-

R

-

P

P

A

E

F

I

T

T

H

H

V

F

F

V

L

A

Q

G

G

L

G
|
G

V
x
T

G
x
T

G

G

L
x
T

A

L

A

M

G

G

V

T

A

G

S

R

Y

F

L

L

W

R

E

E

H

H

Y

V

G

A

A

N

E

V

R

K

P

-

T

-

F

I

I

V

V

A

V
x
A

E
|
E

P
|
P

Q

R

Q

F

A

V

D

P

C

E

L

L

Y

Y

Q

D

S

P

A

E

I

I

A

L

G

T

R

-

A

A

S

R

K

Y

A

S

T

V

G

G

S

A

V

V

D

D

S

A

I

V

binding 3-{[(4-methylphenyl)carbamoyl]amino}benzoic acid: T76 (= T120), S77 (≠ D121), N79 (= N123), T80 (≠ H124), Q142 (≠ D190), Y143 (≠ T191), G175 (= G235), A199 (≠ V261), E200 (= E262), P201 (= P263)
binding pyridoxal-5'-phosphate: N79 (= N123), G175 (= G235), T176 (≠ V236), T177 (≠ G237), T179 (≠ L239)

Sites not aligning to the query:

active site: 49, 242
binding 3-{[(4-methylphenyl)carbamoyl]amino}benzoic acid: 49, 242
binding pyridoxal-5'-phosphate: 49, 242, 271, 272

Query Sequence

>WP_011876077.1 NCBI__GCF_000016205.1:WP_011876077.1
MLIANPRSCRASYPEELRGILNIKSAHESGAWLSSWDQISRSDTPLWDLPDAAARLGVAQ
LSLKDESFRSPLGSFKALGAPIALMRLIMRQWHAHGIDPKALVTGQYAQMLSNMTVISAT
DGNHGKSLAAAARAIGCYCVIVLHANVSIEREQAIAAYGAKIVRIDGNYDESVQHAAQLA
AENGWHVVSDTSYEGYETIPRDVMQGYGVIPAEVLAQLNEEHSRPAFTHVFLQGGVGGLA
AGVASYLWEHYGAERPTFIVVEPQQADCLYQSAIAGRASKATGSVDSIMAGLACGEASPL
AWKILEQCVDYFMTIDDEDAVAAMCSLAKGSDRDAPLVVGESGAAGYAGLTTVMKSLELA
HATGLGPDSHVLVINTEGATAPSVYRQLVGESAEAVIARQDAWKQRVVQSAT

Or try a new SitesBLAST search

SitesBLAST's Database

SitesBLAST's database includes (1) SwissProt entries with experimentally-supported functional features; and (2) protein structures with bound ligands, from the BioLip database.

by Morgan Price, Arkin group
Lawrence Berkeley National Laboratory