SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing 3607475 FitnessBrowser__Dino:3607475 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)

Q7XSN8 Serine racemase; D-serine dehydratase; D-serine ammonia-lyase; L-serine dehydratase; L-serine ammonia-lyase; EC 5.1.1.18; EC 4.3.1.18; EC 4.3.1.17 from Oryza sativa subsp. japonica (Rice) (see paper)
48% identity, 93% coverage: 19:319/324 of query aligns to 27:332/339 of Q7XSN8

query
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Q7XSN8

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E219 (= E211) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-225.
D225 (= D217) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-219.

7nbfAAA structure of human serine racemase in complex with DSiP fragment Z126932614, XChem fragment screen (see paper)
45% identity, 96% coverage: 12:322/324 of query aligns to 5:323/323 of 7nbfAAA

query
sites
7nbfAAA

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active site: K53 (= K60), S81 (= S85), E207 (= E211), A211 (= A215), D213 (= D217), G236 (= G239), L309 (≠ V309), S310 (≠ T310)
binding calcium ion: E207 (= E211), A211 (= A215), D213 (= D217)
binding magnesium ion: N244 (≠ L247)
binding pyridoxal-5'-phosphate: F52 (= F59), K53 (= K60), N83 (= N87), N151 (≠ Y155), V181 (≠ I185), G182 (= G186), G183 (= G187), G184 (= G188), G185 (= G189), M186 (= M190), G236 (= G239), V237 (≠ L240), E280 (= E283), T282 (≠ S285), S310 (≠ T310), G311 (= G311)
binding 2-[(methylsulfonyl)methyl]-1H-benzimidazole: H21 (= H28), L22 (≠ R29), T23 (= T30), P24 (= P31), V25 (= V32), L26 (= L33), T27 (= T34), F46 (= F53)

Sites not aligning to the query:

binding magnesium ion: 3

7nbdAAA structure of human serine racemase in complex with DSiP fragment Z235449082, XChem fragment screen (see paper)
45% identity, 96% coverage: 12:322/324 of query aligns to 5:323/323 of 7nbdAAA

query
sites
7nbdAAA

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active site: K53 (= K60), S81 (= S85), E207 (= E211), A211 (= A215), D213 (= D217), G236 (= G239), L309 (≠ V309), S310 (≠ T310)
binding calcium ion: E207 (= E211), A211 (= A215), D213 (= D217)
binding [4-(1H-benzimidazol-1-yl)phenyl]methanol: W272 (= W275), L278 (≠ V281), V314 (= V314), D315 (= D315), L316 (= L316), S319 (≠ K318)
binding magnesium ion: N244 (≠ L247)
binding pyridoxal-5'-phosphate: F52 (= F59), K53 (= K60), N83 (= N87), N151 (≠ Y155), V181 (≠ I185), G182 (= G186), G183 (= G187), G184 (= G188), G185 (= G189), M186 (= M190), G236 (= G239), V237 (≠ L240), E280 (= E283), T282 (≠ S285), S310 (≠ T310), G311 (= G311)

Sites not aligning to the query:

binding magnesium ion: 3

7nbcCCC structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen (see paper)
45% identity, 96% coverage: 12:322/324 of query aligns to 5:323/323 of 7nbcCCC

query
sites
7nbcCCC

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A

D

D

G
|
G

L
x
V

K

K

V

S

P

S

L

I

K

G

D

L

L

N

T

T

W

W

H

P

F

I

V

I

S

R

N

D

H

L

V

V

S

D

D

D

I

I

L

F

T

T

A

V

S

T

E

E

Q

D

E

E

I

I

I

K

D

C

A

A

M

T

K

Q

L

L

T

V

W

W

Q

E

R

R

M

M

K

K

I

L

V

L

M

I

E
|
E

P

P

S
x
T

C

A

A

G

V

V

P

G

L

V

A

A

T

A

I

V

L

L

K

S

N

Q

K

H

D

F

K

Q

F

T

A

V

G

S

-

P

-

E

-

V

K

K

R

N

V

I

G

C

V

I

I

V

V
x
L

T
x
S

G
|
G

G

G

N

N

V

V

D

D

L

L

-

T

D

S

K

S

L

I

P

T

W

W

I

V

active site: K53 (= K60), S81 (= S85), E207 (= E211), A211 (= A215), D213 (= D217), G236 (= G239), L309 (≠ V309), S310 (≠ T310)
binding biphenyl-4-ylacetic acid: T78 (= T82), H79 (= H83), H84 (= H88), V148 (= V152), H149 (= H153), P150 (= P154)
binding calcium ion: E207 (= E211), A211 (= A215), D213 (= D217)
binding pyridoxal-5'-phosphate: F52 (= F59), K53 (= K60), N83 (= N87), N151 (≠ Y155), V181 (≠ I185), G182 (= G186), G183 (= G187), G184 (= G188), G185 (= G189), M186 (= M190), G236 (= G239), V237 (≠ L240), E280 (= E283), T282 (≠ S285), S310 (≠ T310), G311 (= G311)

7nbcAAA structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen (see paper)
45% identity, 96% coverage: 12:322/324 of query aligns to 5:323/323 of 7nbcAAA

query
sites
7nbcAAA

T

S

Y

F

D

A

D

D

V

V

V

E

A

K

A

A

H

H

E

I

R

N

I

I

K

R

P

D

H

S

I

I

H

H

R

L

T

T

P

P

V

V

L

L

T

T

S

S

Y

I

F

L

N

N

D

Q

L

L

V

T

G

G

A

R

E

N

L

L

F

F

K

K

C

C

E

E

N

L

F

F

Q

Q

K

K

A

T

G

G

A

S

F
|
F

K
|
K

V

I

R

R

G

G

A

A

C

L

N

N

A

A

V

V

F

R

G

S

L

L

-

V

S

P

D

D

A

A

L

L

A

E

E

R

R

K

-

P

-

K

G

A

V

V

A

V

T

T

H

H

S

S

S
|
S

G

G

N
|
N

H

H

A

G

L

Q

S

A

L

L

S

T

Y

Y

A

A

G

K

R

L

R

E

G

G

I

I

P

P

C

A

N

Y

V

I

V

V

M

V

P

P

R

Q

T

T

A

A

P

P

E

D

A

C

K

K

A

L

A

A

V

I

R

Q

G

A

Y

Y

G

G

G

A

I

S

I

I

T

V

E

Y

C

C

E

E

P

P

S

S

T

D

T

E

S

S

R

R

E

E

A

N

V

V

F

A

A

K

E

R

V

V

Q

T

E

E

R

E

T

T

G

E

A

G

E

I

F

M

V

V

H

H

P

P

Y
x
N

N

Q

D

E

P

P

R

A

V

V

V

I

A

A

G

G

Q

Q

G

G

T

T

C

I

S

A

R

L

E

E

F

V

M

L

E

N

Q

Q

T

V

D

P

G

L

L

V

D

D

M

A

M

L

I

V

A

V

P

P

I
x
V

G
|
G

M
|
M

I

L

S

A

G

G

C

I

C

A

L

I

T

T

L

V

S

K

N

A

I

L

A

K

P

P

E

S

V

V

Q

K

I

V

I

Y

A

A

E
|
E

P

P

E

S

Q

N

A
|
A

D

D

D
|
D

A

C

Y

Y

R

Q

S

S

F

K

K

L

A

K

G

G

H

K

I

L

I

M

A

P

D

N

-

L

D

Y

A

P

P

P

V

E

T

T

I

I

A

A

D

D

G
|
G

L
x
V

K

K

V

S

P

S

L

I

K

G

D

L

L
x
N

T

T

W

W

H

P

F

I

V

I

S

R

N

D

H

L

V

V

S

D

D

D

I

I

L

F

T

T

A

V

S

T

E

E

Q

D

E

E

I

I

I

K

D

C

A

A

M

T

K

Q

L

L

T

V

W

W

Q

E

R

R

M

M

K

K

I

L

V

L

M

I

E
|
E

P

P

S
x
T

C

A

A

G

V

V

P

G

L

V

A

A

T

A

I

V

L

L

K

S

N

Q

K

H

D

F

K

Q

F

T

A

V

G

S

-

P

-

E

-

V

K

K

R

N

V

I

G

C

V

I

I

V

V
x
L

T
x
S

G
|
G

G

G

N

N

V

V

D

D

L

L

-

T

D

S

K

S

L

I

P

T

W

W

I

V

active site: K53 (= K60), S81 (= S85), E207 (= E211), A211 (= A215), D213 (= D217), G236 (= G239), L309 (≠ V309), S310 (≠ T310)
binding calcium ion: E207 (= E211), A211 (= A215), D213 (= D217)
binding magnesium ion: N244 (≠ L247)
binding pyridoxal-5'-phosphate: F52 (= F59), K53 (= K60), N83 (= N87), N151 (≠ Y155), V181 (≠ I185), G182 (= G186), G183 (= G187), G184 (= G188), G185 (= G189), M186 (= M190), G236 (= G239), V237 (≠ L240), E280 (= E283), T282 (≠ S285), S310 (≠ T310), G311 (= G311)

Sites not aligning to the query:

binding magnesium ion: 3

5cvcA Structure of maize serine racemase (see paper)
47% identity, 94% coverage: 14:319/324 of query aligns to 6:316/329 of 5cvcA

query
sites
5cvcA

D

D

D

S

V

I

V

R

A

E

A

A

H

Q

E

A

R

R

I

I

K

A

P

P

H

Y

I

V

H

H

R

R

T

T

P

P

V

V

L

M

T

S

S

S

S

T

Y

S

F

I

N

D

D

A

L

M

V

V

G

G

A

K

E

K

L

L

F

F

K

K

C

C

E

E

N

C

F

F

Q

Q

K

K

A

A

G

G

A

A

F
|
F

K
|
K

V

I

R

R

G

G

A

A

C

S

N

N

A

S

V

I

F

F

G

A

L

L

S

D

D

D

A

E

L

Q

A

V

E

S

R

K

G

G

V

V

A

V

T

T

H

H

S

S

S
|
S

G

G

N
|
N

H

H

A

A

L

A

S

A

L

V

S

A

Y

L

A

A

G

K

R

L

R

R

G

G

I

I

P

P

C

A

N

H

V

I

V

V

M

I

P

P

R

R

T

N

A

A

P

P

E

A

A

S

K

K

K

V

A

E

A

N

V

V

R

K

G

C

Y

Y

G

G

I

H

I

I

T

I

E

W

C

S

E

D

P

A

S

S

T

I

T

E

S

S

R

R

E

E

A

Y

V

V

F

S

A

K

E

R

V

V

Q

Q

E

E

R

E

T

T

G

G

A

A

E

V

F

L

V

I

H

H

P

P

Y

I

N

N

D

S

P

K

R

Y

V

T

V

I

A

S

G

G

Q

Q

G

G

T

T

C

V

S

S

R

L

E

E

F

L

M

L

E

E

Q

Q

T

V

D

P

G

E

L

I

D

D

M

T

M

I

I

I

A

V

P

P

I
|
I

G
x
S

G
|
G

M
x
L

I

I

S

S

G

G

C

V

C

A

L

L

T

A

L

A

S

K

N

A

I

I

A

N

P

P

E

S

V

I

Q

R

I

I

I

L

A

A

E
|
E

P

P

E

K

Q

G

A
|
A

D

D

D
|
D

A

S

Y

A

R

Q

S

S

F

K

K

A

A

A

G

G

H

K

I

I

A

T

D

L

D

P

A

S

P

T

V

N

T

T

I

I

A

A

D

D

G
|
G

L
|
L

K

R

V

A

P

F

L

L

K

G

D

D

L

L

T

T

W

W

H

P

F

V

V

V

S

R

N

D

H

L

V

V

S

D

D

D

I

V

L

I

T

V

A

V

S

D

E

D

Q

T

E

A

I

I

I

V

D

D

A

A

M

M

K

K

L

M

T

C

W

Y

Q

E

R

I

M

L

K

K

I

V

V

A

M

V

E
|
E

P

P

S
|
S

C

G

A

A

V

I

P

G

L

L

A

A

T

A

I

A

L

L

K

S

N

D

K

E

D

F

K

K

F

Q

A

S

-

S

-

A

-

W

-

H

-

E

G

S

K

S

R

K

V

I

G

G

V

I

I

I

V
|
V

T
x
S

G
|
G

G

G

N

N

V

V

D

D

L

L

D

G

K

T

L

L

active site: K52 (= K60), S77 (= S85), E203 (= E211), A207 (= A215), D209 (= D217), G231 (= G239), V306 (= V309), S307 (≠ T310)
binding magnesium ion: E203 (= E211), A207 (= A215), D209 (= D217)
binding pyridoxal-5'-phosphate: F51 (= F59), K52 (= K60), N79 (= N87), I177 (= I185), S178 (≠ G186), G179 (= G187), G180 (= G188), G181 (= G189), L182 (≠ M190), G231 (= G239), L232 (= L240), E275 (= E283), S277 (= S285), S307 (≠ T310), G308 (= G311)

6zspAAA serine racemase bound to atp and malonate. (see paper)
45% identity, 96% coverage: 12:322/324 of query aligns to 5:316/320 of 6zspAAA

query
sites
6zspAAA

T

S

Y

F

D

A

D

D

V

V

V

E

A

K

A

A

H

H

E

I

R

N

I

I

K

R

P

D

H

S

I

I

H

H

R

L

T

T

P

P

V

V

L

L

T

T

S
|
S

Y
x
I

F

L

N

N

D

Q

L

L

V

T

G

G

A

R

E

N

L

L

F

F

K

K

C

C

E

E

N

L

F

F

Q

Q

K
|
K

A
x
T

G
|
G

A

S

F

F

K
|
K

V

I

R

R

G

G

A

A

C

L

N

N

A

A

V

V

F

-

G

-

L

-

S

-

D

R

A

S

L

L

A

K

E

P

R

K

G

A

V

V

A

V

T

T

H

H

S
|
S

G
|
G

N
|
N

H
|
H

A

G

L
x
Q

S

A

L

L

S

T

Y

Y

A

A

G

K

R

L

R

E

G

G

I

I

P

P

C

A

N

Y

V

I

V

V

M

V

P

P

R

Q

T

T

A

A

P

P

E

D

A

C

K

K

A

L

A
|
A

V

I

R

Q

G
x
A

Y
|
Y

G

G

G

A

I

S

I

I

T

V

E

Y

C

C

E

E

P

P

S

S

T

D

T

E

S

S

R
|
R

E

E

A

N

V

V

F

A

A

K

E

R

V

V

Q

T

E

E

R

E

T

T

G

E

A

G

E

I

F

M

V

V

H

H

P
|
P

Y

N

N

Q

D

E

P

P

R

A

V

V

V

I

A

A

G

G

Q

Q

G

G

T

T

C

I

S

A

R

L

E

E

F

V

M

L

E

N

Q

Q

T

V

D

P

G

L

L

V

D

D

M

A

M

L

I

V

A

V

P

P

I

V

G

G

M

M

I

L

S

A

G

G

C

I

C

A

L

I

T

T

L

V

S

K

N

A

I

L

A

K

P

P

E

S

V

V

Q

K

I

V

I

Y

A

A

E
|
E

P

P

E

S

Q

N

A
|
A

D

D

D
|
D

A

C

Y

Y

R

Q

S

S

F

K

K

L

A

K

G

G

H

K

I

L

I

M

A

P

D

N

-

L

D

Y

A

P

P

P

V

E

T

T

I

I

A

A

D

D

G
|
G

L

V

K

K

V
x
S

P

S

L

I

K

G

D

L

L

N

T

T

W

W

H

P

F

I

V

I

S

R

N

D

H

L

V

V

S

D

D

D

I

I

L

F

T

T

A

V

S

T

E

E

Q

D

E

E

I

I

I

K

D

C

A

A

M

T

K

Q

L

L

T

V

W

W

Q
x
E

R
|
R

M

M

K
|
K

I

L

V

L

M

I

E

E

P

P

S

T

C

A

A

G

V

V

P

G

L

V

A

A

T

A

I

V

L

L

K

S

N

Q

K

H

D

F

K

Q

F

T

A

V

G

S

-

P

-

E

-

V

K

K

R

N

V

I

G

C

V

I

I

V

V
x
L

T
x
S

G

G

N
|
N

V

V

D

D

L

L

-

T

D

S

K

S

L

I

P

T

W

W

I

V

active site: K53 (= K60), S74 (= S85), E200 (= E211), A204 (= A215), D206 (= D217), G229 (= G239), L302 (≠ V309), S303 (≠ T310)
binding adenosine-5'-triphosphate: S28 (= S35), S29 (= S36), I30 (≠ Y37), K48 (= K55), T49 (≠ A56), G50 (= G57), Q79 (≠ L90), A107 (= A118), A110 (≠ G121), Y111 (= Y122), E266 (≠ Q276), R267 (= R277), K269 (= K279), N306 (= N313)
binding magnesium ion: E200 (= E211), A204 (= A215), D206 (= D217)
binding malonate ion: K53 (= K60), S73 (= S84), S74 (= S85), G75 (= G86), N76 (= N87), H77 (= H88), R125 (= R136), P143 (= P154), G229 (= G239), S232 (≠ V242)

7nbgAAA structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
46% identity, 94% coverage: 12:316/324 of query aligns to 5:316/322 of 7nbgAAA

query
sites
7nbgAAA

T

S

Y

F

D

A

D

D

V

V

V

E

A

K

A

A

H

H

E

I

R

N

I

I

K

R

P

D

H

S

I

I

H

H

R

L

T

T

P

P

V

V

L

L

T

T

S

S

Y

I

F

L

N

N

D

Q

L

L

V

T

G

G

A

R

E

N

L

L

F

F

K

K

C

C

E

E

N

L

F

F

Q

Q

K

K

A

T

G

G

A

S

F
|
F

K
|
K

V

I

R

R

G

G

A

A

C

L

N

N

A

A

V

V

F

R

G

S

L

L

-

V

S

P

D

D

A

A

L

L

A

E

E

R

R

K

-

P

-

K

G

A

V

V

A

V

T

T

H

H

S

S

S
|
S

G
|
G

N
|
N

H

H

A
x
G

L
x
Q

S

A

L

L

S
x
T

Y

Y

A

A

G

K

R

L

R

E

G

G

I

I

P

P

C

A

N

Y

V
x
I

V

V

M

V

P

P

R

Q

T

T

A

A

P

P

E

D

A

C

K
|
K

K

K

A

L

A
|
A

V
x
I

R

Q

G

A

Y
|
Y

G

G

G

A

I

S

I

I

T

V

E

Y

C

C

E

E

P

P

S

S

T

D

T

E

S

S

R

R

E

E

A

N

V

V

F

A

A

K

E

R

V

V

Q

T

E

E

R

E

T

T

G

E

A

G

E

I

F

M

V

V

H

H

P

P

Y
x
N

N

Q

D

E

P

P

R

A

V

V

V

I

A

A

G

G

Q

Q

G

G

T

T

C

I

S

A

R

L

E

E

F

V

M

L

E

N

Q

Q

T

V

D

P

G

L

L

V

D

D

M

A

M

L

I

V

A

V

P

P

I
x
V

G
|
G

M
|
M

I

L

S

A

G

G

C

I

C

A

L

I

T

T

L

V

S

K

N

A

I

L

A

K

P

P

E

S

V

V

Q

K

I

V

I

Y

A

A

E
|
E

P

P

E

S

Q

N

A
|
A

D

D

D
|
D

A

C

Y

Y

R

Q

S

S

F

K

K

L

A

K

G

G

H

K

I

L

I

M

A

P

D

N

-

L

D

Y

A

P

P

P

V

E

T

T

I

I

A

A

D

D

G
|
G

L
x
V

K

K

V

S

P

S

L

I

K

G

D

L

L

N

T

T

W

W

H

P

F

I

V

I

S

R

N

D

H

L

V

V

S

D

D

D

I

I

L

F

T

T

A

V

S

T

E

E

Q

D

E

E

I

I

I

K

D

C

A

A

M

T

K

Q

L

L

T

V

W

W

Q

E

R

R

M

M

K

K

I

L

V

L

M

I

E
|
E

P

P

S
x
T

C

A

A

G

V

V

P

G

L

V

A

A

T

A

I

V

L

L

K

S

N

Q

K

H

D

F

K

Q

F

T

A

V

G

S

-

P

-

E

-

V

K

K

R

N

V

I

G

C

V

I

I

V

V
x
L

T
x
S

G
|
G

G

G

N

N

V

V

D

D

L

L

active site: K53 (= K60), S81 (= S85), E207 (= E211), A211 (= A215), D213 (= D217), G236 (= G239), L309 (≠ V309), S310 (≠ T310)
binding calcium ion: E207 (= E211), A211 (= A215), D213 (= D217)
binding pyridoxal-5'-phosphate: F52 (= F59), K53 (= K60), N83 (= N87), N151 (≠ Y155), V181 (≠ I185), G182 (= G186), G183 (= G187), G184 (= G188), G185 (= G189), M186 (= M190), G236 (= G239), V237 (≠ L240), E280 (= E283), T282 (≠ S285), S310 (≠ T310), G311 (= G311)
binding ~{N}-[2-(2-methylphenyl)ethyl]ethanamide: S81 (= S85), G82 (= G86), G85 (≠ A89), Q86 (≠ L90), T89 (≠ S93), I101 (≠ V105), K111 (= K115), A114 (= A118), I115 (≠ V119), Y118 (= Y122)

7nbhAAA structure of human serine racemase in complex with DSiP fragment Z26781964, XChem fragment screen (see paper)
46% identity, 94% coverage: 12:316/324 of query aligns to 5:316/320 of 7nbhAAA

query
sites
7nbhAAA

T

S

Y

F

D

A

D

D

V

V

V

E

A

K

A

A

H

H

E

I

R

N

I

I

K

R

P

D

H

S

I

I

H

H

R

L

T

T

P

P

V

V

L

L

T

T

S

S

Y

I

F

L

N

N

D

Q

L

L

V

T

G

G

A

R

E

N

L

L

F

F

K

K

C

C

E

E

N

L

F

F

Q

Q

K

K

A

T

G

G

A

S

F

F

K
|
K

V

I

R

R

G

G

A

A

C

L

N

N

A

A

V

V

F

R

G

S

L

L

-

V

S

P

D

D

A

A

L

L

A

E

E

R

R

K

-

P

-

K

G

A

V

V

A

V

T

T

H

H

S

S

S
|
S

G
|
G

N
|
N

H

H

A
x
G

L
x
Q

S

A

L

L

S
x
T

Y

Y

A

A

G

K

R

L

R

E

G

G

I

I

P

P

C

A

N

Y

V
x
I

V

V

M

V

P

P

R

Q

T

T

A

A

P

P

E

D

A

C

K
|
K

K

K

A

L

A
|
A

V
x
I

R

Q

G

A

Y
|
Y

G

G

G

A

I

S

I

I

T

V

E

Y

C

C

E

E

P

P

S

S

T

D

T

E

S

S

R

R

E

E

A

N

V

V

F

A

A

K

E

R

V

V

Q

T

E

E

R

E

T

T

G

E

A

G

E

I

F

M

V

V

H

H

P

P

Y

N

N

Q

D

E

P

P

R

A

V

V

V

I

A

A

G

G

Q

Q

G

G

T

T

C

I

S

A

R

L

E

E

F

V

M

L

E

N

Q

Q

T

V

D

P

G

L

L

V

D

D

M

A

M

L

I

V

A

V

P

P

I

V

G

G

M

M

I

L

S

A

G

G

C

I

C

A

L

I

T

T

L

V

S

K

N

A

I

L

A

K

P

P

E

S

V

V

Q

K

I

V

I

Y

A

A

E
|
E

P

P

E

S

Q

N

A
|
A

D

D

D
|
D

A

C

Y

Y

R

Q

S

S

F

K

K

L

A

K

G

G

H

K

I

L

I

M

A

P

D

N

-

L

D

Y

A

P

P

P

V

E

T

T

I

I

A

A

D
|
D

G
|
G

L

V

K

K

V

S

P

S

L

I

K

G

D

L

L

N

T

T

W

W

H

P

F

I

V

I

S

R

N

D

H

L

V

V

S

D

D

D

I

I

L

F

T

T

A

V

S

T

E

E

Q

D

E

E

I

I

I

K

D

C

A

A

M

T

K

Q

L

L

T

V

W

W

Q

E

R

R

M

M

K

K

I

L

V

L

M

I

E

E

P
|
P

S

T

C

A

A

G

V

V

P

G

L

V

A

A

T

A

I

V

L

L

K

S

N

Q

K

H

D

F

K

Q

F

T

A

V

G

S

-

P

-

E

-

V

K

K

R

N

V

I

G

C

V

I

I

V

V
x
L

T
x
S

G

G

N
|
N

V
|
V

D
|
D

L

L

active site: K53 (= K60), S81 (= S85), E207 (= E211), A211 (= A215), D213 (= D217), G236 (= G239), L309 (≠ V309), S310 (≠ T310)
binding calcium ion: E207 (= E211), A211 (= A215), D213 (= D217)
binding N-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide: S81 (= S85), G82 (= G86), N83 (= N87), G85 (≠ A89), Q86 (≠ L90), T89 (≠ S93), I101 (≠ V105), K111 (= K115), A114 (= A118), I115 (≠ V119), Y118 (= Y122), D235 (= D238), D235 (= D238), P281 (= P284), N313 (= N313), N313 (= N313), V314 (= V314), D315 (= D315)

Sites not aligning to the query:

binding N-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide: 319, 320

3l6bA X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor (see paper)
45% identity, 96% coverage: 12:322/324 of query aligns to 6:319/322 of 3l6bA

query
sites
3l6bA

T

S

Y

F

D

A

D

D

V

V

V

E

A

K

A

A

H

H

E

I

R

N

I

I

K

R

P

D

H

S

I

I

H

H

R

L

T

T

P

P

V

V

L

L

T

T

S

S

Y

I

F

L

N

N

D

Q

L

L

V

T

G

G

A

R

E

N

L

L

F

F

K

K

C

C

E

E

N

L

F

F

Q

Q

K

K

A

T

G

G

A

S

F
|
F

K
|
K

V

I

R

R

G

G

A

A

C

L

N

N

A

A

V

V

F

R

G

S

L

L

S

-

D

-

A

V

L

R

A

K

E

P

R

K

G

A

V

V

A

V

T

T

H

H

S
|
S

G
|
G

N
|
N

H
|
H

A

G

L

Q

S

A

L

L

S

T

Y

Y

A

A

G

K

R

L

R

E

G

G

I

I

P

P

C

A

N

Y

V

I

V

V

M

V

P

P

R

Q

T

T

A

A

P

P

E

D

A

C

K

K

A

L

A

A

V

I

R

Q

G

A

Y

Y

G

G

G

A

I

S

I

I

T

V

E

Y

C

C

E

E

P

P

S

S

T

D

T

E

S

S

R
|
R

E

E

A

N

V

V

F

A

A

K

E

R

V

V

Q

T

E

E

R

E

T

T

G

E

A

G

E

I

F

M

V

V

H

H

P
|
P

Y
x
N

N

Q

D

E

P

P

R

A

V

V

V

I

A

A

G

G

Q

Q

G

G

T

T

C

I

S

A

R

L

E

E

F

V

M

L

E

N

Q

Q

T

V

D

P

G

L

L

V

D

D

M

A

M

L

I

V

A

V

P
|
P

I
x
V

G
|
G

M
|
M

I

L

S

A

G

G

C

I

C

A

L

I

T

T

L

V

S

K

N

A

I

L

A

K

P

P

E

S

V

V

Q

K

I

V

I

Y

A

A

E
|
E

P

P

E

S

Q

N

A
|
A

D

D

D
|
D

A

C

Y

Y

R

Q

S

S

F

K

K

L

A

K

G

G

H

K

I

L

I

M

A

P

D

N

-

L

D

Y

A

P

P

P

V

E

T

T

I

I

A

A

D

D

G
|
G

L
x
V

K

K

V
x
S

P

S

L

I

K

G

D

L

L

N

T

T

W

W

H

P

F

I

V

I

S

R

N

D

H

L

V

V

S

D

D

D

I

I

L

F

T

T

A

V

S

T

E

E

Q

D

E

E

I

I

I

K

D

C

A

A

M

T

K

Q

L

L

T

V

W

W

Q

E

R

R

M

M

K

K

I

L

V

L

M

I

E
|
E

P

P

S
x
T

C

A

A

G

V

V

P

G

L

V

A

A

T

A

I

V

L

L

K

S

N

Q

K

H

D

F

K

Q

F

T

A

V

G

S

-

P

-

E

-

V

K

K

R

N

V

I

G

C

V

I

I

V

V
x
L

T
x
S

G
|
G

G

G

N

N

V

V

D

D

L

L

-

T

D

S

K

S

L

I

P

T

W

W

I

V

active site: K54 (= K60), S77 (= S85), E203 (= E211), A207 (= A215), D209 (= D217), G232 (= G239), T278 (≠ S285), L305 (≠ V309), S306 (≠ T310)
binding malonate ion: K54 (= K60), S76 (= S84), S77 (= S85), G78 (= G86), N79 (= N87), H80 (= H88), R128 (= R136), P146 (= P154), G232 (= G239), S235 (≠ V242)
binding manganese (ii) ion: E203 (= E211), A207 (= A215), D209 (= D217)
binding pyridoxal-5'-phosphate: F53 (= F59), K54 (= K60), N79 (= N87), N147 (≠ Y155), P176 (= P184), V177 (≠ I185), G178 (= G186), G179 (= G187), G180 (= G188), G181 (= G189), M182 (= M190), G232 (= G239), V233 (≠ L240), E276 (= E283), T278 (≠ S285), S306 (≠ T310), G307 (= G311)

7nbgDDD structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
45% identity, 94% coverage: 12:315/324 of query aligns to 5:310/310 of 7nbgDDD

query
sites
7nbgDDD

T

S

Y

F

D

A

D

D

V

V

V

E

A

K

A

A

H

H

E

I

R

N

I

I

K

R

P

D

H

S

I

I

H

H

R

L

T

T

P

P

V

V

L

L

T

T

S

S

Y

I

F

L

N

N

D

Q

L

L

V

T

G

G

A

R

E

N

L

L

F

F

K

K

C

C

E

E

N

L

F

F

Q

Q

K

K

A

T

G

G

A

S

F
|
F

K
|
K

V

I

R

R

G

G

A

A

C

L

N

N

A

A

V

V

F

R

G

S

L

L

S

-

D

-

A

V

L

R

A

K

E

P

R

K

G

A

V

V

A

V

T

T

H

H

S

S

S
|
S

G

G

N
|
N

H

H

A
x
G

L
x
Q

S

A

L

L

S
x
T

Y

Y

A

A

G

K

R

L

R

E

G

G

I

I

P

P

C

A

N

Y

V
x
I

V

V

M

V

P

P

R

Q

T

T

A

A

P

P

E

D

A

C

K

K

A

L

A

A

V
x
I

R

Q

G

A

Y
|
Y

G

G

G

A

I

S

I

I

T

V

E

Y

C

C

E

E

P

P

S

S

T

D

T

E

S

S

R

R

E

E

A

N

V

V

F

A

A

K

E

R

V

V

Q

T

E

E

R

E

T

T

G

E

A

G

E

I

F

M

V

V

H

H

P

P

Y
x
N

N

Q

D

E

P

P

R

A

V

V

V

I

A

A

G

G

Q

Q

G

G

T

T

C

I

S

A

R

L

E

E

F

V

M

L

E

N

Q

Q

T

V

D

P

G

L

L

V

D

D

M

A

M

L

I

V

A

V

P

P

I
x
V

G
|
G

M
|
M

I

L

S

A

G

G

C

I

C

A

L

I

T

T

L

V

S

K

N

A

I

L

A

K

P

P

E

S

V

V

Q

K

I

V

I

Y

A

A

E
|
E

P

P

E

S

Q

N

A
|
A

D

D

D
|
D

A

C

Y

Y

R

Q

S

S

F

K

K

L

A

K

G

G

H

K

I

L

I

M

A

P

D

N

-

L

D

Y

A

P

P

P

V

E

T

T

I

I

A

A

D

D

G
|
G

L
x
V

K

K

V

S

P

S

L

I

K

G

D

L

L
x
N

T

T

W

W

H

P

F

I

V

I

S

R

N

D

H

L

V

V

S

D

D

D

I

I

L

F

T

T

A

V

S

T

E

E

Q

D

E

E

I

I

I

K

D

C

A

A

M

T

K

Q

L

L

T

V

W

W

Q

E

R

R

M

M

K

K

I

L

V

L

M

I

E
|
E

P

P

S
x
T

C

A

A

G

V

V

P

G

L

V

A

A

T

A

I

V

L

L

K

S

N

Q

K

H

D

F

K

Q

F

T

A

V

G

S

-

P

-

E

-

V

K

K

R

N

V

I

G

C

V

I

I

V

V
x
L

T
x
S

G
|
G

G

G

N

N

V

V

D

D

active site: K53 (= K60), S76 (= S85), E202 (= E211), A206 (= A215), D208 (= D217), G231 (= G239), L304 (≠ V309), S305 (≠ T310)
binding calcium ion: E202 (= E211), A206 (= A215), D208 (= D217)
binding magnesium ion: N239 (≠ L247)
binding ortho-xylene: S76 (= S85), G80 (≠ A89), Q81 (≠ L90), T84 (≠ S93), I96 (≠ V105), I110 (≠ V119), Y113 (= Y122)
binding pyridoxal-5'-phosphate: F52 (= F59), K53 (= K60), N78 (= N87), N146 (≠ Y155), V176 (≠ I185), G177 (= G186), G178 (= G187), G179 (= G188), G180 (= G189), M181 (= M190), G231 (= G239), V232 (≠ L240), E275 (= E283), T277 (≠ S285), S305 (≠ T310), G306 (= G311)

Sites not aligning to the query:

binding magnesium ion: 3

O59791 Serine racemase; D-serine ammonia-lyase; D-serine dehydratase; L-serine ammonia-lyase; L-serine dehydratase; EC 4.3.1.17; EC 4.3.1.18; EC 5.1.1.18 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
46% identity, 97% coverage: 6:318/324 of query aligns to 3:316/323 of O59791

query
sites
O59791

D

D

P

N

A

L

V

V

I

L

P

P

T

T

Y

Y

D

D

V

V

V

A

A

S

A

A

H

S

E

E

R

R

I

I

K

K

P

K

H

F

I

A

H

N

R

K

T

T

P

P

V

V

L

L

T

T

S

S

Y

T

F

V

N

N

D

K

L

E

V

F

G

V

A

A

E

E

L

V

F

F

K

K

C

C

E

E

N

N

F

F

Q

Q

K

K

A

M

G

G

A

A

F

F

K

K

V

F

R

R

G

G

A

A

C

L

N

N

A

A

V

L

F

S

G

Q

L

L

S

N

D

E

A

A

L

Q

A

R

E

K

R

A

G

G

V

V

A

L

T

T

H

F

S

S

S
|
S

G

G

N

N

H

H

A

A

L

Q

S

A

L

I

S

A

Y

L

A

S

A

A

G

K

R

I

R

L

G

G

I

I

P

P

C

A

N

K

V

I

M

M

P

P

R

L

T

D

A

A

P

P

E

E

A

A

K

K

K

V

A

A

V

T

R

K

G

G

Y

Y

G

G

I

Q

I

V

T

I

E

M

C

Y

E

D

P

R

S

Y

T

K

T

D

S

D

R

R

E

E

A

K

V

M

F

A

A

K

E

E

V

I

Q

S

E

E

R

R

T

E

G

G

A

L

E

T

F

I

V

I

H

P

P

P

Y

Y

N

D

D

H

P

P

R

H

V

V

V

L

A

A

G

G

Q

Q

G

G

T

T

C

A

S

A

R

K

E

E

F

L

M

F

E

E

Q

E

T

V

D

G

G

P

L

L

D

D

M

A

M

L

I

F

A

V

P

C

I

L

G

G

M

L

I

L

S

S

G

G

C

S

C

A

L

L

T

A

L

A

S

R

N

H

I

F

A

A

P

P

E

N

V

C

Q

E

I

V

I

Y

A

G

A

V

E

E

P

P

E

E

Q

A

A

G

D

N

D

D

A

G

Y

Q

R

Q

S

S

F

F

K

R

A

K

G

G

H

S

I

I

I

V

A

H

D

I

D

D

A

T

P

P

V

K

T

T

I

I

A

A

D

D

G

G

L

A

K

Q

V

T

P

Q

-

H

L

L

K

G

D

N

L

Y

T

T

W

F

H

S

F

I

V

I

S

K

N

E

H

K

V

V

S

D

D

D

I

I

L

L

T

T

A

V

S

S

E

D

Q

E

E

E

I

L

I

I

D

D

A

C

M

L

K

K

L

F

T

Y

W

A

Q

A

R

R

M

M

K

K

I

I

V

V

M

V

E

E

P

P

S

T

C

G

A

C

V

L

P

S

L

F

A

A

T

A

I

A

L

R

K

A

N

M

K

K

D

E

K

K

F

L

A

K

G

N

K

K

R

R

V

I

G

G

V

I

I

I

V

I

T

S

G

G

N

N

V

V

D

D

L

I

D

E

K

R

S82 (= S85) mutation to A: Loss of racemase activity. Reduces D-serine dehydratase activity by 99%. Slightly reduced L-serine dehydratase activity.

2zr8A Crystal structure of modified serine racemase complexed with serine (see paper)
46% identity, 96% coverage: 9:318/324 of query aligns to 2:312/319 of 2zr8A

query
sites
2zr8A

V

V

I

L

P

P

T

T

Y

Y

D

D

V

V

V

A

A

S

A

A

H

S

E

E

R

R

I

I

K

K

P

K

H

F

I

A

H

N

R

K

T

T

P

P

V

V

L

L

T

T

S

S

Y

T

F

V

N

N

D

K

L

E

V

F

G

V

A

A

E

E

L

V

F

F

K

K

C

C

E

E

N

N

F

F

Q

Q

K

K

A

M

G

G

A

A

F
|
F

K
|
K

V

F

R

R

G

G

A

A

C

L

N

N

A

A

V

L

F

S

G

Q

L

L

S

N

D

E

A

A

L

Q

A

R

E

K

R

A

G

G

V

V

A

L

T

T

H

F

S
|
S

G
|
G

N
|
N

H
|
H

A

A

L

Q

S

A

L

I

S

A

Y

L

A

S

A

A

G

K

R

I

R

L

G

G

I

I

P

P

C

A

N

K

V

I

M

M

P

P

R

L

T

D

A

A

P

P

E

E

A

A

K

K

K

V

A

A

V

T

R

K

G

G

Y

Y

G

G

I

Q

I

V

T

I

E

M

C

Y

E

D

P

R

S

Y

T

K

T

D

S

D

R
|
R

E

E

A

K

V

M

F

A

A

K

E

E

V

I

Q

S

E

E

R

R

T

E

G

G

A

L

E

T

F

I

V

I

H

P

P
|
P

Y
|
Y

N

D

D

H

P

P

R

H

V

V

V

L

A

A

G

G

Q

Q

G

G

T

T

C

A

S

A

R

K

E

E

F

L

M

F

E

E

Q

E

T

V

D

G

G

P

L

L

D

D

M

A

M

L

I

F

A

V

P

C

I
x
L

G
|
G

M
x
L

I

L

S

S

G

G

C

S

C

A

L

L

T

A

L

A

S

R

N

H

I

F

A

A

P

P

E

N

V

C

Q

E

I

V

I

Y

A

G

A

V

E
|
E

P

P

E

E

Q

A

A
x
G

D

N

D
|
D

A

G