SitesBLAST

2gn2A Crystal structure of tetrameric biodegradative threonine deaminase (tdcb) from salmonella typhimurium in complex with cmp at 2.5a resolution (hexagonal form) (see paper)
44% identity, 73% coverage: 13:314/411 of query aligns to 9:314/326 of 2gn2A

query
sites
2gn2A

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x
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D

active site: K56 (= K60), A81 (= A85), Q207 (= Q211), V211 (≠ Y215), G213 (≠ S217), G235 (= G237), I308 (≠ V308), S309 (≠ T309)
binding cytidine-5'-monophosphate: R51 (≠ F55), T52 (= T56), G53 (≠ A57), A114 (≠ Q118), D117 (≠ G121), Y118 (≠ H122), N312 (= N312)

A4F2N8 L-threo-3-hydroxyaspartate ammonia-lyase; L-threo-3-hydroxyaspartate dehydratase; L-THA DH; EC 4.3.1.16 from Pseudomonas sp. (see paper)
39% identity, 75% coverage: 15:322/411 of query aligns to 8:317/319 of A4F2N8

query
sites
A4F2N8

D

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K53 (= K60) mutation to A: Loss of enzymatic activity.

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)
37% identity, 77% coverage: 10:324/411 of query aligns to 18:338/339 of Q7XSN8

query
sites
Q7XSN8

A

A

P

A

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K

E219 (≠ Q211) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-225.
D225 (≠ P216) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-219.

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)
37% identity, 74% coverage: 12:314/411 of query aligns to 8:318/340 of Q9GZT4

query
sites
Q9GZT4

G

S

I

F

A

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D

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x
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x
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D

D

E13 (≠ R17) binding Mg(2+)
S31 (= S35) binding ATP
S32 (≠ R36) binding ATP
I33 (≠ T37) binding ATP
K51 (≠ F55) binding ATP
T52 (= T56) binding ATP
K56 (= K60) modified: N6-(pyridoxal phosphate)lysine
P69 (≠ L71) binding Ca(2+)
T81 (≠ A82) binding Ca(2+)
N86 (= N87) binding pyridoxal 5'-phosphate
Q89 (= Q90) binding ATP
Y121 (≠ H122) binding ATP
D178 (= D179) binding Mg(2+)
G185 (= G186) binding pyridoxal 5'-phosphate
G186 (= G187) binding pyridoxal 5'-phosphate
G187 (= G188) binding pyridoxal 5'-phosphate
G188 (= G189) binding pyridoxal 5'-phosphate
M189 (≠ L190) binding pyridoxal 5'-phosphate
E210 (≠ Q211) binding Ca(2+); binding Mg(2+); binding Mn(2+)
A214 (≠ Y215) binding Ca(2+); binding Mg(2+); binding Mn(2+)
D216 (≠ S217) binding Ca(2+); binding Mg(2+); binding Mn(2+)
N247 (≠ L246) binding Ca(2+); binding Mg(2+)
K279 (= K278) binding ATP
S313 (≠ T309) binding pyridoxal 5'-phosphate
N316 (= N312) binding ATP

7nbhAAA structure of human serine racemase in complex with DSiP fragment Z26781964, XChem fragment screen (see paper)
37% identity, 74% coverage: 12:314/411 of query aligns to 5:315/320 of 7nbhAAA

query
sites
7nbhAAA

G

S

I

F

A

A

D

D

I

V

R

E

A

K

A

A

A

H

D

I

R

N

I

I

A

R

G

D

A

S

V

I

V

H

R

L

T

T

P

P

T

V

L

L

L

T

S

S

R

S

T

I

L

L

S

N

D

Q

L

L

T

T

G

G

A

R

N

N

V

L

W

F

L

F

K

K

F

C

E

E

N

L

L

F

Q

Q

F

K

T

T

A

G

A

S

Y

F

K
|
K

E

I

R

R

G

G

A

A

L

L

N

N

K

A

L

V

-

R

-

S

L

L

L

V

L

P

D

D

E

A

A

L

T

E

R

R

R

K

-

P

R

K

G

A

V

V

I

V

A

T

A

H

S

S

A
x
S

G

G

N

N

H

H

S
x
G

Q
|
Q

A

A

V

L

A

T

Y

Y

H

A

G

A

R

K

R

L

L

E

G

G

V

I

P

P

V

A

T

Y

I

I

V

V

M

V

P

P

K

Q

P

T

T

A

P

P

T

D

M

C

K
|
K

V

K

V

L

Q

A

T
x
I

E

Q

G

A

H
x
Y

G

G

A

A

T

S

V

I

V

V

L

-

H

Y

G

C

E

E

L

P

F

S

D

D

E

E

A

S

Y

R

A

E

K

N

-

V

A

A

R

K

E

R

M

V

E

T

G

E

E

E

L

T

G

E

L

G

T

I

F

M

V

V

H

H

P

P

F

N

D

Q

D

E

P

P

A

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

A

A

L

L

E

E

M

V

L

L

D

N

D

Q

A

V

P

P

N

L

I

V

D

D

T

A

L

L

V

V

P

P

I

V

G

G

L

M

I

L

S

A

G

G

M

I

A

A

A

I

A

T

A

V

K

K

A

A

V

L

K

K

P

P

D

S

I

V

A

K

V

V

V

Y

G

A

A

A

Q
x
E

A

P

E

S

L

N

Y
x
A

P

D

S
x
D

M

C

Y

Y

-

Q

A

S

H

K

I

L

E

K

G

G

R

K

E

L

M

M

P

P

S

N

-

L

-

Y

S

P

G

P

D

E

T

T

I

I

A

A

E
x
D

G
|
G

I

V

A

K

V

-

K

S

R

S

P

I

G

G

D

L

L

N

T

T

R

W

Q

P

M

I

V

I

A

R

D

D

L

L

V

V

D

D

E

D

I

I

L

F

L

T

V

V

P

T

E

E

R

D

A

E

I

I

E

K

T

C

A

A

V

T

S

Q

L

L

L

V

V

W

Q

E

I

R

E

M

K

K

T

L

V

L

A

I

E

E

G
x
P

A

T

G

A

A

G

T

V

G

G

L

V

A

A

L

V

L

L

T

S

H

-

P

-

E

Q

R

H

F

F

R

Q

G

T

-

V

-

S

-

P

-

E

-

V

R

K

N

N

V

I

G

C

L

I

V

V

V
x
L

T
x
S

G

G

N
|
N

I
x
V

D
|
D

active site: K53 (= K60), S81 (≠ A85), E207 (≠ Q211), A211 (≠ Y215), D213 (≠ S217), G236 (= G237), L309 (≠ V308), S310 (≠ T309)
binding calcium ion: E207 (≠ Q211), A211 (≠ Y215), D213 (≠ S217)
binding N-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide: S81 (≠ A85), G85 (≠ S89), Q86 (= Q90), K111 (= K115), I115 (≠ T119), Y118 (≠ H122), D235 (≠ E236), P281 (≠ G283), N313 (= N312), V314 (≠ I313), D315 (= D314)

7nbgAAA structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
37% identity, 74% coverage: 12:314/411 of query aligns to 5:315/322 of 7nbgAAA

query
sites
7nbgAAA

G

S

I

F

A

A

D

D

I

V

R

E

A

K

A

A

A

H

D

I

R

N

I

I

A

R

G

D

A

S

V

I

V

H

R

L

T

T

P

P

T

V

L

L

L

T

S

S

R

S

T

I

L

L

S

N

D

Q

L

L

T

T

G

G

A

R

N

N

V

L

W

F

L

F

K

K

F

C

E

E

N

L

L

F

Q

Q

F

K

T

T

A

G

A

S

Y
x
F

K
|
K

E

I

R

R

G

G

A

A

L

L

N

N

K

A

L

V

-

R

-

S

L

L

L

V

L

P

D

D

E

A

A

L

T

E

R

R

R

K

-

P

R

K

G

A

V

V

I

V

A

T

A

H

S

S

A
x
S

G

G

N
|
N

H

H

S
x
G

Q
|
Q

A

A

V

L

A

T

Y

Y

H

A

G

A

R

K

R

L

L

E

G

G

V

I

P

P

V

A

T

Y

I
|
I

V

V

M

V

P

P

K

Q

P

T

T

A

P

P

T

D

M

C

K
|
K

V

K

V

L

Q

A

T
x
I

E

Q

G

A

H
x
Y

G

G

A

A

T

S

V

I

V

V

L

-

H

Y

G

C

E

E

L

P

F

S

D

D

E

E

A

S

Y

R

A

E

K

N

-

V

A

A

R

K

E

R

M

V

E

T

G

E

E

E

L

T

G

E

L

G

T

I

F

M

V

V

H

H

P

P

F

N

D

Q

D

E

P

P

A

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

A

A

L

L

E

E

M

V

L

L

D

N

D

Q

A

V

P

P

N

L

I

V

D

D

T

A

L

L

V

V

P

P

I

V

G
|
G

L
x
M

I

L

S

A

G

G

M

I

A

A

A

I

A

T

A

V

K

K

A

A

V

L

K

K

P

P

D

S

I

V

A

K

V

V

V

Y

G

A

A

A

Q
x
E

A

P

E

S

L

N

Y
x
A

P

D

S
x
D

M

C

Y

Y

-

Q

A

S

H

K

I

L

E

K

G

G

R

K

E

L

M

M

P

P

S

N

-

L

-

Y

S

P

G

P

D

E

T

T

I

I

A

A

E

D

G
|
G

I
x
V

A

K

V

-

K

S

R

S

P

I

G

G

D

L

L

N

T

T

R

W

Q

P

M

I

V

I

A

R

D

D

L

L

V

V

D

D

E

D

I

I

L

F

L

T

V

V

P

T

E

E

R

D

A

E

I

I

E

K

T

C

A

A

V

T

S

Q

L

L

L

V

V

W

Q

E

I

R

E

M

K

K

T

L

V

L

A

I

E

E

G

P

A
x
T

G

A

A

G

T

V

G

G

L

V

A

A

L

V

L

L

T

S

H

-

P

-

E

Q

R

H

F

F

R

Q

G

T

-

V

-

S

-

P

-

E

-

V

R

K

N

N

V

I

G

C

L

I

V

V

V
x
L

T
x
S

G
|
G

G

G

N

N

I

V

D

D

active site: K53 (= K60), S81 (≠ A85), E207 (≠ Q211), A211 (≠ Y215), D213 (≠ S217), G236 (= G237), L309 (≠ V308), S310 (≠ T309)
binding calcium ion: E207 (≠ Q211), A211 (≠ Y215), D213 (≠ S217)
binding pyridoxal-5'-phosphate: F52 (≠ Y59), K53 (= K60), N83 (= N87), G182 (= G186), G183 (= G187), G184 (= G188), G185 (= G189), M186 (≠ L190), G236 (= G237), V237 (≠ I238), T282 (≠ A284), S310 (≠ T309), G311 (= G310)
binding ~{N}-[2-(2-methylphenyl)ethyl]ethanamide: S81 (≠ A85), G85 (≠ S89), Q86 (= Q90), I101 (= I105), K111 (= K115), I115 (≠ T119), Y118 (≠ H122)

7nbfAAA structure of human serine racemase in complex with DSiP fragment Z126932614, XChem fragment screen (see paper)
37% identity, 74% coverage: 12:314/411 of query aligns to 5:315/323 of 7nbfAAA

query
sites
7nbfAAA

G

S

I

F

A

A

D

D

I

V

R

E

A

K

A

A

A

H

D

I

R

N

I

I

A

R

G

D

A

S

V

I

V
x
H

R
x
L

T
|
T

P
|
P

T

V

L
|
L

L
x
T

S

S

R

S

T

I

L

L

S

N

D

Q

L

L

T

T

G

G

A

R

N

N

V

L

W

F

L

F

K

K

F

C

E

E

N

L

L
x
F

Q

Q

F

K

T

T

A

G

A

S

Y
x
F

K
|
K

E

I

R

R

G

G

A

A

L

L

N

N

K

A

L

V

-

R

-

S

L

L

L

V

L

P

D

D

E

A

A

L

T

E

R

R

R

K

-

P

R

K

G

A

V

V

I

V

A

T

A

H

S

S

A
x
S

G

G

N
|
N

H

H

S

G

Q

Q

A

A

V

L

A

T

Y

Y

H

A

G

A

R

K

R

L

L

E

G

G

V

I

P

P

V

A

T

Y

I

I

V

V

M

V

P

P

K

Q

P

T

T

A

P

P

T

D

M

C

K

K

V

K

V

L

Q

A

T

I

E

Q

G

A

H

Y

G

G

A

A

T

S

V

I

V

V

L

-

H

Y

G

C

E

E

L

P

F

S

D

D

E

E

A

S

Y

R

A

E

K

N

-

V

A

A

R

K

E

R

M

V

E

T

G

E

E

E

L

T

G

E

L

G

T

I

F

M

V

V

H

H

P

P

F

N

D

Q

D

E

P

P

A

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

A

A

L

L

E

E

M

V

L

L

D

N

D

Q

A

V

P

P

N

L

I

V

D

D

T

A

L

L

V

V

P

P

I

V

G
|
G

L
x
M

I

L

S

A

G

G

M

I

A

A

A

I

A

T

A

V

K

K

A

A

V

L

K

K

P

P

D

S

I

V

A

K

V

V

V

Y

G

A

A

A

Q
x
E

A

P

E

S

L

N

Y
x
A

P

D

S
x
D

M

C

Y

Y

-

Q

A

S

H

K

I

L

E

K

G

G

R

K

E

L

M

M

P

P

S

N

-

L

-

Y

S

P

G

P

D

E

T

T

I

I

A

A

E

D

G
|
G

I
x
V

A

K

V

-

K

S

R

S

P

I

G

G

D

L

L
x
N

T

T

R

W

Q

P

M

I

V

I

A

R

D

D

L

L

V

V

D

D

E

D

I

I

L

F

L

T

V

V

P

T

E

E

R

D

A

E

I

I

E

K

T

C

A

A

V

T

S

Q

L

L

L

V

V

W

Q

E

I

R

E

M

K

K

T

L

V

L

A

I

E

E

G

P

A
x
T

G

A

A

G

T

V

G

G

L

V

A

A

L

V

L

L

T

S

H

-

P

-

E

Q

R

H

F

F

R

Q

G

T

-

V

-

S

-

P

-

E

-

V

R

K

N

N

V

I

G

C

L

I

V

V

V
x
L

T
x
S

G
|
G

G

G

N

N

I

V

D

D

active site: K53 (= K60), S81 (≠ A85), E207 (≠ Q211), A211 (≠ Y215), D213 (≠ S217), G236 (= G237), L309 (≠ V308), S310 (≠ T309)
binding calcium ion: E207 (≠ Q211), A211 (≠ Y215), D213 (≠ S217)
binding magnesium ion: N244 (≠ L246)
binding pyridoxal-5'-phosphate: F52 (≠ Y59), K53 (= K60), N83 (= N87), G182 (= G186), G183 (= G187), G184 (= G188), G185 (= G189), M186 (≠ L190), G236 (= G237), V237 (≠ I238), T282 (≠ A284), S310 (≠ T309), G311 (= G310)
binding 2-[(methylsulfonyl)methyl]-1H-benzimidazole: H21 (≠ V28), L22 (≠ R29), T23 (= T30), P24 (= P31), L26 (= L33), T27 (≠ L34), F46 (≠ L53)

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)
37% identity, 74% coverage: 12:314/411 of query aligns to 5:315/323 of 7nbdAAA

query
sites
7nbdAAA

G

S

I

F

A

A

D

D

I

V

R

E

A

K

A

A

A

H

D

I

R

N

I

I

A

R

G

D

A

S

V

I

V

H

R

L

T

T

P

P

T

V

L

L

L

T

S

S

R

S

T

I

L

L

S

N

D

Q

L

L

T

T

G

G

A

R

N

N

V

L

W

F

L

F

K

K

F

C

E

E

N

L

L

F

Q

Q

F

K

T

T

A

G

A

S

Y
x
F

K
|
K

E

I

R

R

G

G

A

A

L

L

N

N

K

A

L

V

-

R

-

S

L

L

L

V

L

P

D

D

E

A

A

L

T

E

R

R

R

K

-

P

R

K

G

A

V

V

I

V

A

T

A

H

S

S

A
x
S

G

G

N
|
N

H

H

S

G

Q

Q

A

A

V

L

A

T

Y

Y

H

A

G

A

R

K

R

L

L

E

G

G

V

I

P

P

V

A

T

Y

I

I

V

V

M

V

P

P

K

Q

P

T

T

A

P

P

T

D

M

C

K

K

V

K

V

L

Q

A

T

I

E

Q

G

A

H

Y

G

G

A

A

T

S

V

I

V

V

L

-

H

Y

G

C

E

E

L

P

F

S

D

D

E

E

A

S

Y

R

A

E

K

N

-

V

A

A

R

K

E

R

M

V

E

T

G

E

E

E

L

T

G

E

L

G

T

I

F

M

V

V

H

H

P

P

F

N

D

Q

D

E

P

P

A

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

A

A

L

L

E

E

M

V

L

L

D

N

D

Q

A

V

P

P

N

L

I

V

D

D

T

A

L

L

V

V

P

P

I

V

G
|
G

L
x
M

I

L

S

A

G

G

M

I

A

A

A

I

A

T

A

V

K

K

A

A

V

L

K

K

P

P

D

S

I

V

A

K

V

V

V

Y

G

A

A

A

Q
x
E

A

P

E

S

L

N

Y
x
A

P

D

S
x
D

M

C

Y

Y

-

Q

A

S

H

K

I

L

E

K

G

G

R

K

E

L

M

M

P

P

S

N

-

L

-

Y

S

P

G

P

D

E

T

T

I

I

A

A

E

D

G
|
G

I
x
V

A

K

V

-

K

S

R

S

P

I

G

G

D

L

L
x
N

T

T

R

W

Q

P

M

I

V

I

A

R

D

D

L

L

V

V

D

D

E

D

I

I

L

F

L

T

V

V

P

T

E

E

R

D

A

E

I

I

E

K

T

C

A

A

V

T

S

Q

L

L

L

V

V
x
W

Q

E

I

R

E

M

K

K

T

L

V
x
L

A

I

E
|
E

G

P

A
x
T

G

A

A

G

T

V

G

G

L

V

A

A

L

V

L

L

T

S

H

-

P

-

E

Q

R

H

F

F

R

Q

G

T

-

V

-

S

-

P

-

E

-

V

R

K

N

N

V

I

G

C

L

I

V

V

V
x
L

T
x
S

G
|
G

G

G

N

N

I
x
V

D

D

active site: K53 (= K60), S81 (≠ A85), E207 (≠ Q211), A211 (≠ Y215), D213 (≠ S217), G236 (= G237), L309 (≠ V308), S310 (≠ T309)
binding calcium ion: E207 (≠ Q211), A211 (≠ Y215), D213 (≠ S217)
binding [4-(1H-benzimidazol-1-yl)phenyl]methanol: W272 (≠ V274), L278 (≠ V280), V314 (≠ I313)
binding magnesium ion: N244 (≠ L246)
binding pyridoxal-5'-phosphate: F52 (≠ Y59), K53 (= K60), N83 (= N87), G182 (= G186), G183 (= G187), G184 (= G188), G185 (= G189), M186 (≠ L190), G236 (= G237), V237 (≠ I238), E280 (= E282), T282 (≠ A284), S310 (≠ T309), G311 (= G310)

Sites not aligning to the query:

7nbcCCC structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen (see paper)
37% identity, 74% coverage: 12:314/411 of query aligns to 5:315/323 of 7nbcCCC

query
sites
7nbcCCC

G

S

I

F

A

A

D

D

I

V

R

E

A

K

A

A

A

H

D

I

R

N

I

I

A

R

G

D

A

S

V

I

V

H

R

L

T

T

P

P

T

V

L

L

L

T

S

S

R

S

T

I

L

L

S

N

D

Q

L

L

T

T

G

G

A

R

N

N

V

L

W

F

L

F

K

K

F

C

E

E

N

L

L

F

Q

Q

F

K

T

T

A

G

A

S

Y
x
F

K
|
K

E

I

R

R

G

G

A

A

L

L

N

N

K

A

L

V

-

R

-

S

L

L

L

V

L

P

D

D

E

A

A

L

T

E

R

R

R

K

-

P

R

K

G

A

V

V

I

V

A
x
T

A
x
H

S

S

A
x
S

G

G

N
|
N

H
|
H

S

G

Q

Q

A

A

V

L

A

T

Y

Y

H

A

G

A

R

K

R

L

L

E

G

G

V

I

P

P

V

A

T

Y

I

I

V

V

M

V

P

P

K

Q

P

T

T

A

P

P

T

D

M

C

K

K

V

K

V

L

Q

A

T

I

E

Q

G

A

H

Y

G

G

A

A

T

S

V

I

V

V

L

-

H

Y

G

C

E

E

L

P

F

S

D

D

E

E

A

S

Y

R

A

E

K

N

-

V

A

A

R

K

E

R

M

V

E

T

G

E

E

E

L

T

G

E

L

G

T

I

F

M

V
|
V

H
|
H

P
|
P

F

N

D

Q

D

E

P

P

A

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

A

A

L

L

E

E

M

V

L

L

D

N

D

Q

A

V

P

P

N

L

I

V

D

D

T

A

L

L

V

V

P

P

I

V

G
|
G

L
x
M

I

L

S

A

G

G

M

I

A

A

A

I

A

T

A

V

K

K

A

A

V

L

K

K

P

P

D

S

I

V

A

K

V

V

V

Y

G

A

A

A

Q
x
E

A

P

E

S

L

N

Y
x
A

P

D

S
x
D

M

C

Y

Y

-

Q

A

S

H

K

I

L

E

K

G

G

R

K

E

L

M

M

P

P

S

N

-

L

-

Y

S

P

G

P

D

E

T

T

I

I

A

A

E

D

G
|
G

I
x
V

A

K

V

-

K

S

R

S

P

I

G

G

D

L

L

N

T

T

R

W

Q

P

M

I

V

I

A

R

D

D

L

L

V

V

D

D

E

D

I

I

L

F

L

T

V

V

P

T

E

E

R

D

A

E

I

I

E

K

T

C

A

A

V

T

S

Q

L

L

L

V

V

W

Q

E

I

R

E

M

K

K

T

L

V

L

A

I

E

E

G

P

A
x
T

G

A

A

G

T

V

G

G

L

V

A

A

L

V

L

L

T

S

H

-

P

-

E

Q

R

H

F

F

R

Q

G

T

-

V

-

S

-

P

-

E

-

V

R

K

N

N

V

I

G

C

L

I

V

V

V
x
L

T
x
S

G
|
G

G

G

N

N

I

V

D

D

active site: K53 (= K60), S81 (≠ A85), E207 (≠ Q211), A211 (≠ Y215), D213 (≠ S217), G236 (= G237), L309 (≠ V308), S310 (≠ T309)
binding biphenyl-4-ylacetic acid: T78 (≠ A82), H79 (≠ A83), H84 (= H88), V148 (= V152), H149 (= H153), P150 (= P154)
binding calcium ion: E207 (≠ Q211), A211 (≠ Y215), D213 (≠ S217)
binding pyridoxal-5'-phosphate: F52 (≠ Y59), K53 (= K60), N83 (= N87), G182 (= G186), G183 (= G187), G184 (= G188), G185 (= G189), M186 (≠ L190), G236 (= G237), V237 (≠ I238), T282 (≠ A284), S310 (≠ T309), G311 (= G310)

7nbcAAA structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen (see paper)
37% identity, 74% coverage: 12:314/411 of query aligns to 5:315/323 of 7nbcAAA

query
sites
7nbcAAA

G

S

I

F

A

A

D

D

I

V

R

E

A

K

A

A

A

H

D

I

R

N

I

I

A

R

G

D

A

S

V

I

V

H

R

L

T

T

P

P

T

V

L

L

L

T

S

S

R

S

T

I

L

L

S

N

D

Q

L

L

T

T

G

G

A

R

N

N

V

L

W

F

L

F

K

K

F

C

E

E

N

L

L

F

Q

Q

F

K

T

T

A

G

A

S

Y
x
F

K
|
K

E

I

R

R

G

G

A

A

L

L

N

N

K

A

L

V

-

R

-

S

L

L

L

V

L

P

D

D

E

A

A

L

T

E

R

R

R

K

-

P

R

K

G

A

V

V

I

V

A

T

A

H

S

S

A
x
S

G

G

N
|
N

H

H

S

G

Q

Q

A

A

V

L

A

T

Y

Y

H

A

G

A

R

K

R

L

L

E

G

G

V

I

P

P

V

A

T

Y

I

I

V

V

M

V

P

P

K

Q

P

T

T

A

P

P

T

D

M

C

K

K

V

K

V

L

Q

A

T

I

E

Q

G

A

H

Y

G

G

A

A

T

S

V

I

V

V

L

-

H

Y

G

C

E

E

L

P

F

S

D

D

E

E

A

S

Y

R

A

E

K

N

-

V

A

A

R

K

E

R

M

V

E

T

G

E

E

E

L

T

G

E

L

G

T

I

F

M

V

V

H

H

P

P

F

N

D

Q

D

E

P

P

A

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

A

A

L

L

E

E

M

V

L

L

D

N

D

Q

A

V

P

P

N

L

I

V

D

D

T

A

L

L

V

V

P

P

I

V

G
|
G

L
x
M

I

L

S

A

G

G

M

I

A

A

A

I

A

T

A

V

K

K

A

A

V

L

K

K

P

P

D

S

I

V

A

K

V

V

V

Y

G

A

A

A

Q
x
E

A

P

E

S

L

N

Y
x
A

P

D

S
x
D

M

C

Y

Y

-

Q

A

S

H

K

I

L

E

K

G

G

R

K

E

L

M

M

P

P

S

N

-

L

-

Y

S

P

G

P

D

E

T

T

I

I

A

A

E

D

G
|
G

I
x
V

A

K

V

-

K

S

R

S

P

I

G

G

D

L

L
x
N

T

T

R

W

Q

P

M

I

V

I

A

R

D

D

L

L

V

V

D

D

E

D

I

I

L

F

L

T

V

V

P

T

E

E

R

D

A

E

I

I

E

K

T

C

A

A

V

T

S

Q

L

L

L

V

V

W

Q

E

I

R

E

M

K

K

T

L

V

L

A

I

E

E

G

P

A
x
T

G

A

A

G

T

V

G

G

L

V

A

A

L

V

L

L

T

S

H

-

P

-

E

Q

R

H

F

F

R

Q

G

T

-

V

-

S

-

P

-

E

-

V

R

K

N

N

V

I

G

C

L

I

V

V

V
x
L

T
x
S

G
|
G

G

G

N

N

I

V

D

D

active site: K53 (= K60), S81 (≠ A85), E207 (≠ Q211), A211 (≠ Y215), D213 (≠ S217), G236 (= G237), L309 (≠ V308), S310 (≠ T309)
binding calcium ion: E207 (≠ Q211), A211 (≠ Y215), D213 (≠ S217)
binding magnesium ion: N244 (≠ L246)
binding pyridoxal-5'-phosphate: F52 (≠ Y59), K53 (= K60), N83 (= N87), G182 (= G186), G183 (= G187), G184 (= G188), G185 (= G189), M186 (≠ L190), G236 (= G237), V237 (≠ I238), T282 (≠ A284), S310 (≠ T309), G311 (= G310)

Sites not aligning to the query:

binding magnesium ion: 3

6zspAAA serine racemase bound to atp and malonate. (see paper)
37% identity, 74% coverage: 12:314/411 of query aligns to 5:308/320 of 6zspAAA

query
sites
6zspAAA

G

S

I

F

A

A

D

D

I

V

R

E

A

K

A

A

A

H

D

I

R

N

I

I

A

R

G

D

A

S

V

I

V

H

R

L

T

T

P

P

T

V

L

L

L

T

S
|
S

R
x
S

T
x
I

L

L

S

N

D

Q

L

L

T

T

G

G

A

R

N

N

V

L

W

F

L

F

K

K

F

C

E

E

N

L

L

F

Q

Q

F
x
K

T
|
T

A

G

A

S

Y

F

K
|
K

E

I

R

R

G

G

A

A

L

L

N

N

K

A

L

V

L

R

L

S

L

L

D

-

E

-

A

-

T

-

R

K

R

P

R

K

G

A

V

V

I

V

A

T

A

H

S
|
S

A
x
S

G

G

N
|
N

H
|
H

S

G

Q
|
Q

A

A

V

L

A

T

Y

Y

H

A

G

A

R

K

R

L

L

E

G

G

V

I

P

P

V

A

T

Y

I

I

V

V

M

V

P

P

K

Q

P

T

T

A

P

P

T

D

M

C

K

K

V

K

V

L

Q

A

T

I

E

Q

G

A

H
x
Y

G

G

A

A

T

S

V

I

V

V

L

-

H

Y

G

C

E

E

L

P

F

S

D

D

E

E

A

S

Y
x
R

A

E

K

N

-

V

A

A

R

K

E

R

M

V

E

T

G

E

E

E

L

T

G

E

L

G

T

I

F

M

V

V

H

H

P

P

F

N

D

Q

D

E

P

P

A

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

A

A

L

L

E

E

M

V

L

L

D

N

D

Q

A

V

P

P

N

L

I

V

D

D

T

A

L

L

V

V

P

P

I

V

G

G

L

M

I

L

S

A

G

G

M

I

A

A

A

I

A

T

A

V

K

K

A

A

V

L

K

K

P

P

D

S

I

V

A

K

V

V

V

Y

G

A

A

A

Q
x
E

A

P

E

S

L

N

Y
x
A

P

D

S
x
D

M

C

Y

Y

-

Q

A

S

H

K

I

L

E

K

G

G

R

K

E

L

M

M

P

P

S

N

-

L

-

Y

S

P

G

P

D

E

T

T

I

I

A

A

E

D

G
|
G

I

V

A

K

V

-

K
x
S

R

S

P

I

G

G

D

L

L

N

T

T

R

W

Q

P

M

I

V

I

A

R

D

D

L

L

V

V

D

D

E

D

I

I

L

F

L

T

V

V

P

T

E

E

R

D

A

E

I

I

E

K

T

C

A

A

V

T

S

Q

L

L

L

V

V

W

Q
x
E

I
x
R

E

M

K
|
K

T

L

V

L

A

I

E

E

G

P

A

T

G

A

A

G

T

V

G

G

L

V

A

A

L

V

L

L

T

S

H

-

P

-

E

Q

R

H

F

F

R

Q

G

T

-

V

-

S

-

P

-

E

-

V

R

K

N

N

V

I

G

C

L

I

V

V

V
x
L

T
x
S

G

G

N
|
N

I

V

D

D

active site: K53 (= K60), S74 (≠ A85), E200 (≠ Q211), A204 (≠ Y215), D206 (≠ S217), G229 (= G237), L302 (≠ V308), S303 (≠ T309)
binding adenosine-5'-triphosphate: S28 (= S35), S29 (≠ R36), I30 (≠ T37), K48 (≠ F55), T49 (= T56), Q79 (= Q90), Y111 (≠ H122), E266 (≠ Q275), R267 (≠ I276), K269 (= K278), N306 (= N312)
binding magnesium ion: E200 (≠ Q211), A204 (≠ Y215), D206 (≠ S217)
binding malonate ion: K53 (= K60), S73 (= S84), S74 (≠ A85), N76 (= N87), H77 (= H88), R125 (≠ Y137), G229 (= G237), S232 (≠ K241)

3l6bA X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor (see paper)
37% identity, 74% coverage: 12:314/411 of query aligns to 6:311/322 of 3l6bA

query
sites
3l6bA

G

S

I

F

A

A

D

D

I

V

R

E

A

K

A

A

A

H

D

I

R

N

I

I

A

R

G

D

A

S

V

I

V

H

R

L

T

T

P

P

T

V

L

L

L

T

S

S

R

S

T

I

L

L

S

N

D

Q

L

L

T

T

G

G

A

R

N

N

V

L

W

F

L

F

K

K

F

C

E

E

N

L

L

F

Q

Q

F

K

T

T

A

G

A

S

Y
x
F

K
|
K

E

I

R

R

G

G

A

A

L

L

N

N

K

A

L

V

L

R

L

S

L

L

D

-

E

-

A

V

T

R

R

K

R

P

R

K

G

A

V

V

I

V

A

T

A

H

S
|
S

A
x
S

G

G

N
|
N

H
|
H

S

G

Q

Q

A

A

V

L

A

T

Y

Y

H

A

G

A

R

K

R

L

L

E

G

G

V

I

P

P

V

A

T

Y

I

I

V

V

M

V

P

P

K

Q

P

T

T

A

P

P

T

D

M

C

K

K

V

K

V

L

Q

A

T

I

E

Q

G

A

H

Y

G

G

A

A

T

S

V

I

V

V

L

-

H

Y

G

C

E

E

L

P

F

S

D

D

E

E

A

S

Y
x
R

A

E

K

N

-

V

A

A

R

K

E

R

M

V

E

T

G

E

E

E

L

T

G

E

L

G

T

I

F

M

V

V

H

H

P

P

F

N

D

Q

D

E

P

P

A

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

A

A

L

L

E

E

M

V

L

L

D

N

D

Q

A

V

P

P

N

L

I

V

D

D

T

A

L

L

V

V

P

P

I

V

G
|
G

L
x
M

I

L

S

A

G

G

M

I

A

A

A

I

A

T

A

V

K

K

A

A

V

L

K

K

P

P

D

S

I

V

A

K

V

V

V

Y

G

A

A

A

Q
x
E

A

P

E

S

L

N

Y
x
A

P

D

S
x
D

M

C

Y

Y

-

Q

A

S

H

K

I

L

E

K

G

G

R

K

E

L

M

M

P

P

S

N

-

L

-

Y

S

P

G

P

D

E

T

T

I

I

A

A

E

D

G
|
G

I
x
V

A

K

V

-

K

S

R

S

P

I

G

G

D

L

L

N

T

T

R

W

Q

P

M

I

V

I

A

R

D

D

L

L

V

V

D

D

E

D

I

I

L

F

L

T

V

V

P

T

E

E

R

D

A

E

I

I

E

K

T

C

A

A

V

T

S

Q

L

L

L

V

V

W

Q

E

I

R

E

M

K

K

T

L

V

L

A

I

E
|
E

G

P

A
x
T

G

A

A

G

T

V

G

G

L

V

A

A

L

V

L

L

T

S

H

-

P

-

E

Q

R

H

F

F

R

Q

G

T

-

V

-

S

-

P

-

E

-

V

R

K

N

N

V

I

G

C

L

I

V

V

V
x
L

T
x
S

G
|
G

G

G

N

N

I

V

D

D

active site: K54 (= K60), S77 (≠ A85), E203 (≠ Q211), A207 (≠ Y215), D209 (≠ S217), G232 (= G237), T278 (≠ A284), L305 (≠ V308), S306 (≠ T309)
binding malonate ion: K54 (= K60), S76 (= S84), S77 (≠ A85),