SitesBLAST

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)
38% identity, 98% coverage: 2:321/325 of query aligns to 20:338/339 of Q7XSN8

query
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Q7XSN8

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E219 (= E205) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-225.
D225 (= D211) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-219.

2zr8A Crystal structure of modified serine racemase complexed with serine (see paper)
39% identity, 97% coverage: 6:321/325 of query aligns to 9:319/319 of 2zr8A

query
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2zr8A

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active site: K53 (= K50), S78 (= S75), E204 (= E205), G208 (≠ F209), D210 (= D211), G232 (≠ A234), I303 (= I305), S304 (= S306)
binding magnesium ion: E204 (= E205), G208 (≠ F209), D210 (= D211)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F49), K53 (= K50), S77 (= S74), S78 (= S75), N80 (= N77), H81 (= H78), P147 (= P144), G179 (= G180), G180 (= G181), G181 (= G182), G182 (= G183), G232 (≠ A234), E277 (= E279), T279 (≠ G281), S304 (= S306)
binding serine: S78 (= S75), R129 (= R126), D231 (= D233), G232 (≠ A234), A233 (≠ I235), Q234 (≠ V236), T235 (= T237)

2zpuA Crystal structure of modified serine racemase from s.Pombe. (see paper)
39% identity, 97% coverage: 6:321/325 of query aligns to 9:319/319 of 2zpuA

query
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2zpuA

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active site: K53 (= K50), S78 (= S75), E204 (= E205), G208 (≠ F209), D210 (= D211), G232 (≠ A234), I303 (= I305), S304 (= S306)
binding magnesium ion: E204 (= E205), G208 (≠ F209), D210 (= D211)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F49), K53 (= K50), S77 (= S74), S78 (= S75), N80 (= N77), H81 (= H78), P147 (= P144), G179 (= G180), G180 (= G181), G181 (= G182), G182 (= G183), G232 (≠ A234), E277 (= E279), T279 (≠ G281), S304 (= S306)

O59791 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 Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see 2 papers)
39% identity, 97% coverage: 6:321/325 of query aligns to 13:323/323 of O59791

query
sites
O59791

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M

D

A

C

M

L

A

K

Q

F

A

Y

F

A

S

A

R

R

L

M

K

K

L

I

V

V

A

V

E

E

P

P

G

T

G

G

A

C

V

L

A

S

L

F

A

A

L

R

Y

A

H

M

G

K

D

E

Q

K

L

L

D

K

G

N

D

K

A

R

V

I

I

G

C

I

T

I

I

I

S
|
S

G

G

N

N

V

V

D

D

R

I

A

E

V

R

F

Y

L

A

R

H

A

F

L

L

E

S

Q

Q

K57 (= K50) active site, Proton acceptor; modified: Lysino-D-alanine (Lys); alternate; modified: N6-(pyridoxal phosphate)lysine; alternate
S82 (= S75) active site, Proton acceptor; mutation to A: Loss of racemase activity. Reduces D-serine dehydratase activity by 99%. Slightly reduced L-serine dehydratase activity.
N84 (= N77) binding pyridoxal 5'-phosphate
G183 (= G180) binding pyridoxal 5'-phosphate
G184 (= G181) binding pyridoxal 5'-phosphate
G185 (= G182) binding pyridoxal 5'-phosphate
G186 (= G183) binding pyridoxal 5'-phosphate
L187 (= L184) binding pyridoxal 5'-phosphate
E208 (= E205) binding Mg(2+)
G212 (≠ F209) binding Mg(2+)
D214 (= D211) binding Mg(2+)
S308 (= S306) binding pyridoxal 5'-phosphate

1wtcA Crystal structure of s.Pombe serine racemase complex with amppcp (see paper)
39% identity, 97% coverage: 6:321/325 of query aligns to 8:318/318 of 1wtcA

query
sites
1wtcA

I

V

E

A

A

S

A

A

A

S

G

E

R

R

L

I

K

K

G

K

H

F

A

A

R
x
N

V

K

T

T

P

P

L

V

L

L

S

T

S

S

P

S

F

T

L

V

D

N

D

K

I

E

A

F

G

V

R

A

R

E

V

V

L

F

V

F

K

K

A

C

E

E

C

N

L

F

Q

Q

H
x
K

T
x
M

G

G

S

A

F
|
F

K
|
K

Y

F

R

R

G

G

A

A

R

L

S

N

A

A

V

L

S

S

A

Q

L

L

P

N

E

E

D

A

K

Q

R

R

K

K

N

A

G

G

V

V

I

L

A

T

Y

F

S

S

S
|
S

G

G

N
|
N

H

H

A

A

Q

Q

G

A

V

I

A

A

L

L

A

S

A

A

R

K

Q

I

F

L

G

G

V

I

A

P

A

A

V

K

I

I

V

I

M

M

P

P

S

L

D

D

A

A

P

P

K

E

M

A

K

K

I

V

D
x
A

N
x
A

T

T

R

K

A

G

L
x
Y

G

G

A

G

E

Q

V

V

V

I

L

M

Y

Y

D

D

R

R

A

Y

N

K

E

D

D

D

R

R

D

E

A

K

I

M

G

A

T

K

K

E

L

I

S

S

E

E

E

R

R

E

G

G

L

L

T

T

L

I

I

I

R

P

P

P

F

Y

D

D

E

H

P

P

E

H

V

V

I

L

A

A

G

G

Q

Q

G

G

T

T

C

A

G

A

L

K

E

E

I

L

A

F

A

E

Q

E

A

V

A

G

E

P

L

L

G

D

V

A

T

-

E

-

A

-

D

-

V

L

I

F

V

V

C

C

C

L

G
|
G

L

L

T

L

S

S

G

G

I

S

A

A

L

L

A

A

L

A

E

R

A

H

R

F

A

A

P

P

G

N

M

C

R

E

V

V

R

Y

P

G

A

V

E
|
E

P

P

E

E

G

A

F
x
G

D

N

D
|
D

V

G

T

Q

R

Q

S

S

L

F

A

R

S

K

G

G

R

S

I

I

E

V

H

H

N

-

A

I

S

D

S

T

A

P

N

K

G

T

L

I

C

A

D

D

A
x
G

I

A

V

Q

T

T

P

Q

Q

H

P

L

G

G

N

N

L

Y

T

T

F

F

P

S

I

I

M

I

N

K

R

E

L

K

C

V

G

D

P

D

G

I

I

L

V

T

V

V

T

S

D

D

D

E

E

E

A

L

Q

I

M

D

A

C

M

L

A

K

Q

F

A

Y

F

A

S

A

R

R

L

M

K

K

L

I

V

V

A

V

E
|
E

P

P

G
x
T

G

G

A

C

V

L

A

S

L

F

A

A

L

R

Y

A

H

M

G

K

D

E

Q

K

L

L

D

K

G

N

D

K

A

R

V

I

I

G

C

I

T

I

I
|
I

S
|
S

G

G

N

N

V

V

D

D

R

I

A

E

V

R

F

Y

L

A

R

H

A

F

L

L

E

S

Q

Q

active site: K52 (= K50), S77 (= S75), E203 (= E205), G207 (≠ F209), D209 (= D211), G231 (≠ A234), I302 (= I305), S303 (= S306)
binding phosphomethylphosphonic acid adenylate ester: N20 (≠ R18), K47 (≠ H45), M48 (≠ T46), A109 (≠ D107), A110 (≠ N108), Y114 (≠ L112)
binding magnesium ion: E203 (= E205), G207 (≠ F209), D209 (= D211)
binding pyridoxal-5'-phosphate: F51 (= F49), K52 (= K50), N79 (= N77), G178 (= G180), G179 (= G181), G180 (= G182), G181 (= G183), G231 (≠ A234), E276 (= E279), T278 (≠ G281), S303 (= S306)

1v71A Crystal structure of s.Pombe serine racemase
39% identity, 97% coverage: 6:321/325 of query aligns to 8:318/318 of 1v71A

query
sites
1v71A

I

V

E

A

A

S

A

A

A

S

G

E

R

R

L

I

K

K

G

K

H

F

A

A

R

N

V

K

T

T

P

P

L

V

L

L

S

T

S

S

P

S

F

T

L

V

D

N

D

K

I

E

A

F

G

V

R

A

R

E

V

V

L

F

V

F

K

K

A

C

E

E

C

N

L

F

Q

Q

H

K

T

M

G

G

S

A

F
|
F

K
|
K

Y

F

R

R

G

G

A

A

R

L

S

N

A

A

V

L

S

S

A

Q

L

L

P

N

E

E

D

A

K

Q

R

R

K

K

N

A

G

G

V

V

I

L

A

T

Y

F

S

S

S
|
S

G

G

N
|
N

H

H

A

A

Q

Q

G

A

V

I

A

A

L

L

A

S

A

A

R

K

Q

I

F

L

G

G

V

I

A

P

A

A

V

K

I

I

V

I

M

M

P

P

S

L

D

D

A

A

P

P

K

E

M

A

K

K

I

V

D

A

N

A

T

T

R

K

A

G

L

Y

G

G

A

G

E

Q

V

V

V

I

L

M

Y

Y

D

D

R

R

A

Y

N

K

E

D

D

D

R

R

D

E

A

K

I

M

G

A

T

K

K

E

L

I

S

S

E

E

E

R

R

E

G

G

L

L

T

T

L

I

I

I

R

P

P

P

F

Y

D

D

E

H

P

P

E

H

V

V

I

L

A

A

G

G

Q

Q

G

G

T

T

C

A

G

A

L

K

E

E

I

L

A

F

A

E

Q

E

A

V

A

G

E

P

L

L

G

D

V

A

T

-

E

-

A

-

D

-

V

L

I

F

V

V

C

C

C

L

G
|
G

L

L

T

L

S

S

G

G

I

S

A

A

L

L

A

A

L

A

E

R

A

H

R

F

A

A

P

P

G

N

M

C

R

E

V

V

R

Y

P

G

A

V

E
|
E

P

P

E

E

G

A

F
x
G

D

N

D
|
D

V

G

T

Q

R

Q

S

S

L

F

A

R

S

K

G

G

R

S

I

I

E

V

H

H

N

-

A

I

S

D

S

T

A

P

N

K

G

T

L

I

C

A

D

D

A
x
G

I

A

V

Q

T

T

P

Q

Q

H

P

L

G

G

N

N

L

Y

T

T

F

F

P

S

I

I

M

I

N

K

R

E

L

K

C

V

G

D

P

D

G

I

I

L

V

T

V

V

T

S

D

D

D

E

E

E

A

L

Q

I

M

D

A

C

M

L

A

K

Q

F

A

Y

F

A

S

A

R

R

L

M

K

K

L

I

V

V

A

V

E
|
E

P

P

G
x
T

G

G

A

C

V

L

A

S

L

F

A

A

L

R

Y

A

H

M

G

K

D

E

Q

K

L

L

D

K

G

N

D

K

A

R

V

I

I

G

C

I

T

I

I
|
I

S
|
S

G
|
G

G

G

N

N

V

V

D

D

R

I

A

E

V

R

F

Y

L

A

R

H

A

F

L

L

E

S

Q

Q

active site: K52 (= K50), S77 (= S75), E203 (= E205), G207 (≠ F209), D209 (= D211), G231 (≠ A234), I302 (= I305), S303 (= S306)
binding magnesium ion: E203 (= E205), G207 (≠ F209), D209 (= D211)
binding pyridoxal-5'-phosphate: F51 (= F49), K52 (= K50), N79 (= N77), G178 (= G180), G179 (= G181), G180 (= G182), G181 (= G183), G231 (≠ A234), E276 (= E279), T278 (≠ G281), S303 (= S306), G304 (= G307)

5cvcA Structure of maize serine racemase (see paper)
37% identity, 99% coverage: 2:324/325 of query aligns to 4:325/329 of 5cvcA

query
sites
5cvcA

D

D

I

I

E

D

R

S

I

I

E

R

A

E

A

A

A

Q

G

A

R

R

L

I

K

A

G

P

H

Y

A

V

R

H

V

R

T

T

P

P

L

V

L

M

S

S

P

T

F

S

L

I

D

D

D

A

I

M

A

V

G

G

R

K

V

L

L

F

V

F

K

K

A

C

E

E

C

C

L

F

Q

Q

H

K

T

A

G

G

S

A

F
|
F

K
|
K

Y

I

R

R

G

G

A

A

R

S

S

N

A

S

V

I

S

F

A

A

L

L

P

D

E

D

D

E

K

Q

R

V

K

S

N

K

G

G

V

V

I

V

A

T

Y

H

S

S

S
|
S

G

G

N
|
N

H

H

A

A

Q

A

G

A

V

V

A

A

L

L

A

A

R

K

Q

L

F

R

G

G

V

I

A

P

A

A

V

H

I

I

V

V

M

I

P

P

S

R

D

N

A

A

P

P

K

A

M

S

K

K

I

V

D

E

N

N

T

V

R

K

A

C

L

Y

G

G

A

G

E

H

V

I

L

W

Y

S

D

D

R

A

A

S

N

I

E

E

D

S

R

R

D

E

A

Y

I

V

G

S

T

K

K

R

L

V

S

Q

E

E

R

T

G

G

L

A

T

V

L

L

I

I

R

H

P

P

F

I

D

N

E

S

P

K

E

Y

V

T

I

I

A

S

G

G

Q

Q

G

G

T

T

C

V

G

S

L

L

E

E

I

L

A

L

A

E

Q

Q

A

V

A

P

E

E

L

I

G

D

V

T

T

-

E

-

A

-

D

-

V

I

I

I

V

V

C

P

C

I

G
x
S

G
|
G

L

L

T

I

S

S

G

G

I

V

A

A

L

L

A

A

L

A

E

K

A

A

R

I

A

N

P

P

G

S

M

I

R

R

V

I

R

L

P

A

A

A

E
|
E

P

P

E

K

G

G

F
x
A

D

D

D
|
D

V

S

T

A

R

Q

S

S

L

K

A

A

S

A

G

G

R

K

I

I

E

I

H

-

N

T

A

L

S

P

S

S

A

T

N

N

G

T

L

I

C

A

D

D

A
x
G

I
x
L

V

-

T

R

P

A

Q

F

P

L

G

G

N

D

L

L

T

T

F

W

P

P

I

V

M

V

N

R

R

D

L

L

C

V

G

D

P

D

G

V

I

I

V

V

T

D

D

D

D

T

E

A

A

I

Q

V

M

D

A

A

M

M

A

K

Q

M

A

C

F

Y

S

E

R

I

L

L

K

K

L

V

V

A

A

V

E
|
E

P

P

G

S

G

G

A

A

V

I

A

G

L

L

A

A

L

L

Y

-

H

-

G

S

D

D

Q

E

L

F

-

K

-

Q

-

S

-

A

-

W

-

H

D

E

G

S

D

S

A

K

V

I

I

G

C

I

T

I

I
x
V

S
|
S

G
|
G

G

G

N

N

V

V

D

D

R

L

A

G

V

T

F

L

L

W

R

Q

A

S

L

M

E

Y

Q

K

F

H

G

L

E

E

active site: K52 (= K50), S77 (= S75), E203 (= E205), A207 (≠ F209), D209 (= D211), G231 (≠ A234), V306 (≠ I305), S307 (= S306)
binding magnesium ion: E203 (= E205), A207 (≠ F209), D209 (= D211)
binding pyridoxal-5'-phosphate: F51 (= F49), K52 (= K50), N79 (= N77), S178 (≠ G180), G179 (= G181), G180 (= G182), G181 (= G183), L232 (≠ I235), E275 (= E279), S307 (= S306), G308 (= G307)

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)
35% identity, 97% coverage: 6:321/325 of query aligns to 12:328/340 of Q9GZT4

query
sites
Q9GZT4

I

V

E
|
E

A

K

A

A

A

H

G

I

R

N

L

I

K

R

G

D

H

S

A

I

R

H

V

L

T

T

P

P

L

V

L

L

S

T

S
|
S

P
x
S

F
x
I

L

L

D

N

D

Q

I

L

A

T

G

G

R

R

R

N

V

L

L

F

V

F

K

K

A

C

E

E

C

L

L

F

Q

Q

H
x
K

T
|
T

G

G

S

S

F

F

K
|
K

Y

I

R

R

G

G

A

A

R

L

S

N

A

A

V

V

S

R

A

S

L

L

P

V

E
x
P

D

D

-

A

-

L

-

E

K

R

R

K

K

P

N

K

G

A

V

V

I

V

A
x
T

Y

H

S

S

G

G

N
|
N

H

H

A

G

Q
|
Q

G

A

V

L

A

T

L

Y

A

A

R

K

Q

L

F

E

G

G

V

I

A

P

A

A

V

Y

I

I

V

V

M

V

P

P

S

Q

D

T

A

A

P

P

K

D

M

C

K

K

I

K

D

L

N

A

T

I

R

Q

A

A

L
x
Y

G

G

A

A

E

S

V

I

V

V

L

Y

Y

C

D

E

R

P

A

S

N

D

E

E

D

S

R

R

D

E

A

N

I

V

G

A

T

K

K

R

L

V

S

T

E

E

R

T

G

E

L

G

T

I

L

M

I

V

R

H

P

P

F

N

D

Q

E

E

P

P

E

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

C

I

G

A

L

L

E

E

I

V

A

L

A

N

Q

Q

A

V

A

P

E

L

L

V

G
x
D

V

A

T

-

E

-

A

-

D

-

V

L

I

V

V

V

C

P

C

V

G
|
G

L
x
M

T

L

S

A

G

G

I

I

A

A

L

I

A

T

L

V

E

K

A

A

R

L

A

K

P

P

G

S

M

V

R

K

V

V

R

Y

P

A

A

A

E
|
E

P

P

E

S

G

N

F
x
A

D

D

D
|
D

V

C

T

Y

R

Q

S

S

L

K

A

L

S

K

G

G

R

K

I

L

E

M

H

P

N

N

A

L

S

Y

S

P

A

P

N

E

G

T

L

I

C

A

D

D

A

G

I

-

V

V

T

K

P

S

Q

S

P

I

G

G

N

L

L
x
N

T

T

F

W

P

P

I

I

M

I

N

R

R

D

L

L

C

V

G

D

P

D

G

I

I

F

V

T

V

V

T

T

D

E

D

D

E

E

A

I

Q

K

M

C

A

A

M

T

A

Q

Q

L

A

V

F

W

S

E

R

R

L

M

K
|
K

L

L

V

L

A

I

E

E

P

P

G

T

G

A

A

G

V

V

A

G

L

V

A

A

A

V

L

L

Y

S

H

Q

G

H

D

F

Q

Q

L

T

D

V

G

S

D

P

A

E

V

V

-

K

-

N

I

I

C

C

T

I

I

V

-

L

S
|
S

G

G

N
|
N

V

V

D

D

R

L

A

T

V

S

F

S

L

I

R

T

A

W

L

V

E

K

Q

Q

E13 (= E7) binding Mg(2+)
S31 (= S25) binding ATP
S32 (≠ P26) binding ATP
I33 (≠ F27) binding ATP
K51 (≠ H45) binding ATP
T52 (= T46) binding ATP
K56 (= K50) modified: N6-(pyridoxal phosphate)lysine
P69 (≠ E63) binding Ca(2+)
T81 (≠ A72) binding Ca(2+)
N86 (= N77) binding pyridoxal 5'-phosphate
Q89 (= Q80) binding ATP
Y121 (≠ L112) binding ATP
D178 (≠ G169) binding Mg(2+)
G185 (= G180) binding pyridoxal 5'-phosphate
G186 (= G181) binding pyridoxal 5'-phosphate
G187 (= G182) binding pyridoxal 5'-phosphate
G188 (= G183) binding pyridoxal 5'-phosphate
M189 (≠ L184) binding pyridoxal 5'-phosphate
E210 (= E205) binding Ca(2+); binding Mg(2+); binding Mn(2+)
A214 (≠ F209) binding Ca(2+); binding Mg(2+); binding Mn(2+)
D216 (= D211) binding Ca(2+); binding Mg(2+); binding Mn(2+)
N247 (≠ L243) binding Ca(2+); binding Mg(2+)
K279 (= K275) binding ATP
S313 (= S306) binding pyridoxal 5'-phosphate
N316 (= N309) binding ATP

7nbhAAA structure of human serine racemase in complex with DSiP fragment Z26781964, XChem fragment screen (see paper)
36% identity, 94% coverage: 6:311/325 of query aligns to 9:315/320 of 7nbhAAA

query
sites
7nbhAAA

I

V

E

E

A

K

A

A

A

H

G

I

R

N

L

I

K

R

G

D

H

S

A

I

R

H

V

L

T

T

P

P

L

V

L

L

S

T

S

S

P

S

F

I

L

L

D

N

D

Q

I

L

A

T

G

G

R

R

R

N

V

L

L

F

V

F

K

K

A

C

E

E

C

L

L

F

Q

Q

H

K

T

T

G

G

S

S

F

F

K
|
K

Y

I

R

R

G

G

A

A

R

L

S

N

A

A

V

V

S

R

A

S

L

L

P

V

E

P

D

D

-

A

-

L

-

E

K

R

R

K

K

P

N

K

G

A

V

V

I

V

A

T

Y

H

S

S

S
|
S

G

G

N

N

H

H

A
x
G

Q
|
Q

G

A

V

L

A

T

L

Y

A

A

R

K

Q

L

F

E

G

G

V

I

A

P

A

A

V

Y

I

I

V

V

M

V

P

P

S

Q

D

T

A

A

P

P

K

D

M

C

K
|
K

I

K

D

L

N

A

T
x
I

R

Q

A

A

L
x
Y

G

G

A

A

E

S

V

I

V

V

L

Y

Y

C

D

E

R

P

A

S

N

D

E

E

D

S

R

R

D

E

A

N

I

V

G

A

T

K

K

R

L

V

S

T

E

E

R

T

G

E

L

G

T

I

L

M

I

V

R

H

P

P

F

N

D

Q

E

E

P

P

E

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

C

I

G

A

L

L

E

E

I

V

A

L

A

N

Q

Q

A

V

A

P

E

L

L

V

G

D

V

A

T

-

E

-

A

-

D

-

V

L

I

V

V

V

C

P

C

V

G

G

L

M

T

L

S

A

G

G

I

I

A

A

L

I

A

T

L

V

E

K

A

A

R

L

A

K

P

P

G

S

M

V

R

K

V

V

R

Y

P

A

A

A

E
|
E

P

P

E

S

G

N

F
x
A

D

D

D
|
D

V

C

T

Y

R

Q

S

S

L

K

A

L

S

K

G

G

R

K

I

L

E

M

H

P

N

N

A

L

S

Y

S

P

A

P

N

E

G

T

L

I

C

A

D
|
D

A
x
G

I

-

V

V

T

K

P

S

Q

S

P

I

G

G

N

L

L

N

T

T

F

W

P

P

I

I

M

I

N

R

R

D

L

L

C

V

G

D

P

D

G

I

I

F

V

T

V

V

T

T

D

E

D

D

E

E

A

I

Q

K

M

C

A

A

M

T

A

Q

Q

L

A

V

F

W

S

E

R

R

L

M

K

K

L

L

V

L

A

I

E

E

P
|
P

G

T

G

A

A

G

V

V

A

G

L

V

A

A

A

V

L

L

Y

S

H

Q

G

H

D

F

Q

Q

L

T

D

V

G

S

D

P

A

E

V

V

-

K

-

N

I

I

C

C

T

I

I

V

-
x
L

S
|
S

G

G

N
|
N

V
|
V

D
|
D

active site: K53 (= K50), S81 (= S75), E207 (= E205), A211 (≠ F209), D213 (= D211), G236 (≠ A234), L309 (vs. gap), S310 (= S306)
binding calcium ion: E207 (= E205), A211 (≠ F209), D213 (= D211)
binding N-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide: S81 (= S75), G85 (≠ A79), Q86 (= Q80), K111 (= K105), I115 (≠ T109), Y118 (≠ L112), D235 (= D233), P281 (= P280), N313 (= N309), V314 (= V310), D315 (= D311)

7nbfAAA structure of human serine racemase in complex with DSiP fragment Z126932614, XChem fragment screen (see paper)
36% identity, 94% coverage: 6:311/325 of query aligns to 9:315/323 of 7nbfAAA

query
sites
7nbfAAA

I

V

E

E

A

K

A

A

A

H

G

I

R

N

L

I

K

R

G

D

H

S

A

I

R
x
H

V
x
L

T
|
T

P
|
P

L

V

L
|
L

S
x
T

S

S

P

S

F

I

L

L

D

N

D

Q

I

L

A

T

G

G

R

R

R

N

V

L

L

F

V

F

K

K

A

C

E

E

C

L

L
x
F

Q

Q

H

K

T

T

G

G

S

S

F
|
F

K
|
K

Y

I

R

R

G

G

A

A

R

L

S

N

A

A

V

V

S

R

A

S

L

L

P

V

E

P

D

D

-

A

-

L

-

E

K

R

R

K

K

P

N

K

G

A

V

V

I

V

A

T

Y

H

S

S

S
|
S

G

G

N
|
N

H

H

A

G

Q

Q

G

A

V

L

A

T

L

Y

A

A

R

K

Q

L

F

E

G

G

V

I

A

P

A

A

V

Y

I

I

V

V

M

V

P

P

S

Q

D

T

A

A

P

P

K

D

M

C

K

K

I

K

D

L

N

A

T

I

R

Q

A

A

L

Y

G

G

A

A

E

S

V

I

V

V

L

Y

Y

C

D

E

R

P

A

S

N

D

E

E

D

S

R

R

D

E

A

N

I

V

G

A

T

K

K

R

L

V

S

T

E

E

R

T

G

E

L

G

T

I

L

M

I

V

R

H

P

P

F

N

D

Q

E

E

P

P

E

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

C

I

G

A

L

L

E

E

I

V

A

L

A

N

Q

Q

A

V

A

P

E

L

L

V

G

D

V

A

T

-

E

-

A

-

D

-

V

L

I

V

V

V

C

P

C

V

G
|
G

L
x
M

T

L

S

A

G

G

I

I

A

A

L

I

A

T

L

V

E

K

A

A

R

L

A

K

P

P

G

S

M

V

R

K

V

V

R

Y

P

A

A

A

E
|
E

P

P

E

S

G

N

F
x
A

D

D

D
|
D

V

C

T

Y

R

Q

S

S

L

K

A

L

S

K

G

G

R

K

I

L

E

M

H

P

N

N

A

L

S

Y

S

P

A

P

N

E

G

T

L

I

C

A

D

D

A
x
G

I

-

V
|
V

T

K

P

S

Q

S

P

I

G

G

N

L

L
x
N

T

T

F

W

P

P

I

I

M

I

N

R

R

D

L

L

C

V

G

D

P

D

G

I

I

F

V

T

V

V

T

T

D

E

D

D

E

E

A

I

Q

K

M

C

A

A

M

T

A

Q

Q

L

A

V

F

W

S

E

R

R

L

M

K

K

L

L

V

L

A

I

E

E

P

P

G
x
T

G

A

A

G

V

V

A

G

L

V

A

A

A

V

L

L

Y

S

H

Q

G

H

D

F

Q

Q

L

T

D

V

G

S

D

P

A

E

V

V

-

K

-

N

I

I

C

C

T

I

I

V

-
x
L

S
|
S

G
|
G

G

G

N

N

V

V

D

D

active site: K53 (= K50), S81 (= S75), E207 (= E205), A211 (≠ F209), D213 (= D211), G236 (≠ A234), L309 (vs. gap), S310 (= S306)
binding calcium ion: E207 (= E205), A211 (≠ F209), D213 (= D211)
binding magnesium ion: N244 (≠ L243)
binding pyridoxal-5'-phosphate: F52 (= F49), K53 (= K50), N83 (= N77), G182 (= G180), G183 (= G181), G184 (= G182), G185 (= G183), M186 (≠ L184), G236 (≠ A234), V237 (= V236), T282 (≠ G281), S310 (= S306), G311 (= G307)
binding 2-[(methylsulfonyl)methyl]-1H-benzimidazole: H21 (≠ R18), L22 (≠ V19), T23 (= T20), P24 (= P21), L26 (= L23), T27 (≠ S24), F46 (≠ L43)

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)
36% identity, 94% coverage: 6:311/325 of query aligns to 9:315/323 of 7nbdAAA

query
sites
7nbdAAA

I

V

E

E

A

K

A

A

A

H

G

I

R

N

L

I

K

R

G

D

H

S

A

I

R

H

V

L

T

T

P

P

L

V

L

L

S

T

S

S

P

S

F

I

L

L

D

N

D

Q

I

L

A

T

G

G

R

R

R

N

V

L

L

F

V

F

K

K

A

C

E

E

C

L

L

F

Q

Q

H

K

T

T

G

G

S

S

F
|
F

K
|
K

Y

I

R

R

G

G

A

A

R

L

S

N

A

A

V

V

S

R

A

S

L

L

P

V

E

P

D

D

-

A

-

L

-

E

K

R

R

K

K

P

N

K

G

A

V

V

I

V

A

T

Y

H

S

S

S
|
S

G

G

N
|
N

H

H

A

G

Q

Q

G

A

V

L

A

T

L

Y

A

A

R

K

Q

L

F

E

G

G

V

I

A

P

A

A

V

Y

I

I

V

V

M

V

P

P

S

Q

D

T

A

A

P

P

K

D

M

C

K

K

I

K

D

L

N

A

T

I

R

Q

A

A

L

Y

G

G

A

A

E

S

V

I

V

V

L

Y

Y

C

D

E

R

P

A

S

N

D

E

E

D

S

R

R

D

E

A

N

I

V

G

A

T

K

K

R

L

V

S

T

E

E

R

T

G

E

L

G

T

I

L

M

I

V

R

H

P

P

F

N

D

Q

E

E

P

P

E

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

C

I

G

A

L

L

E

E

I

V

A

L

A

N

Q

Q

A

V

A

P

E

L

L

V

G

D

V

A

T

-

E

-

A

-

D

-

V

L

I

V

V

V

C

P

C

V

G
|
G

L
x
M

T

L

S

A

G

G

I

I

A

A

L

I

A

T

L

V

E

K

A

A

R

L

A

K

P

P

G

S

M

V

R

K

V

V

R

Y

P

A

A

A

E
|
E

P

P

E

S

G

N

F
x
A

D

D

D
|
D

V

C

T

Y

R

Q

S

S

L

K

A

L

S

K

G

G

R

K

I

L

E

M

H

P

N

N

A

L

S

Y

S

P

A

P

N

E

G

T

L

I

C

A

D

D

A
x
G

I

-

V
|
V

T

K

P

S

Q

S

P

I

G

G

N

L

L
x
N

T

T

F

W

P

P

I

I

M

I

N

R

R

D

L

L

C

V

G

D

P

D

G

I

I

F

V

T

V

V

T

T

D

E

D

D

E

E

A

I

Q

K

M

C

A

A

M

T

A

Q

Q

L

A

V

F
x
W

S

E

R

R

L

M

K

K

L

L

V
x
L

A

I

E
|
E

P

P

G
x
T

G

A

A

G

V

V

A

G

L

V

A

A

A

V

L

L

Y

S

H

Q

G

H

D

F

Q

Q

L

T

D

V

G

S

D

P

A

E

V

V

-

K

-

N

I

I

C

C

T

I

I

V

-
x
L

S
|
S

G
|
G

G

G

N

N

V
|
V

D

D

active site: K53 (= K50), S81 (= S75), E207 (= E205), A211 (≠ F209), D213 (= D211), G236 (≠ A234), L309 (vs. gap), S310 (= S306)
binding calcium ion: E207 (= E205), A211 (≠ F209), D213 (= D211)
binding [4-(1H-benzimidazol-1-yl)phenyl]methanol: W272 (≠ F271), L278 (≠ V277), V314 (= V310)
binding magnesium ion: N244 (≠ L243)
binding pyridoxal-5'-phosphate: F52 (= F49), K53 (= K50), N83 (= N77), G182 (= G180), G183 (= G181), G184 (= G182), G185 (= G183), M186 (≠ L184), G236 (≠ A234), V237 (= V236), E280 (= E279), T282 (≠ G281), S310 (= S306), G311 (= G307)

Sites not aligning to the query:

7nbcCCC structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen (see paper)
36% identity, 94% coverage: 6:311/325 of query aligns to 9:315/323 of 7nbcCCC

query
sites
7nbcCCC

I

V

E

E

A

K

A

A

A

H

G

I

R

N

L

I

K

R

G

D

H

S

A

I

R

H

V

L

T

T

P

P

L

V

L

L

S

T

S

S

P

S

F

I

L

L

D

N

D

Q

I

L

A

T

G

G

R

R

R

N

V

L

L

F

V

F

K

K

A

C

E

E

C

L

L

F

Q

Q

H

K

T

T

G

G

S

S

F
|
F

K
|
K

Y

I

R

R

G

G

A

A

R

L

S

N

A

A

V

V

S

R

A

S

L

L

P

V

E

P

D

D

-

A

-

L

-

E

K

R

R

K

K

P

N

K

G

A

V

V

I

V

A
x
T

Y
x
H

S

S

S
|
S

G

G

N
|
N

H
|
H

A

G

Q

Q

G

A

V

L

A

T

L

Y

A

A

R

K

Q

L

F

E

G

G

V

I

A

P

A

A

V

Y

I

I

V

V

M

V

P

P

S

Q

D

T

A

A

P

P

K

D

M

C

K

K

I

K

D

L

N

A

T

I

R

Q

A

A

L

Y

G

G

A

A

E

S

V

I

V

V

L

Y

Y

C

D

E

R

P

A

S

N

D

E

E

D

S

R

R

D

E

A

N

I

V

G

A

T

K

K

R

L

V

S

T

E

E

R

T

G

E

L

G

T

I

L

M

I
x
V

R
x
H

P
|
P

F

N

D

Q

E

E

P

P

E

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

C

I

G

A

L

L

E

E

I

V

A

L

A

N

Q

Q

A

V

A

P

E

L

L

V

G

D

V

A

T

-

E

-

A

-

D

-

V

L

I

V

V

V

C

P

C

V

G
|
G

L
x
M

T

L

S

A

G

G

I

I

A

A

L

I

A

T

L

V

E

K

A

A

R

L

A

K

P

P

G

S

M

V

R

K

V

V

R

Y

P

A

A

A

E
|
E

P

P

E

S

G

N

F
x
A

D

D

D
|
D

V

C

T

Y

R

Q

S

S

L

K

A

L

S

K

G

G

R

K

I

L

E

M

H

P

N

N

A

L

S

Y

S

P

A

P

N

E

G

T

L

I

C

A

D

D

A
x
G

I

-

V
|
V

T

K

P

S

Q

S

P

I

G

G

N

L

L

N

T

T

F

W

P

P

I

I

M

I

N

R

R

D

L

L

C

V

G

D

P

D

G

I

I

F

V

T

V

V

T

T

D

E

D

D

E

E

A

I

Q

K

M

C

A

A

M

T

A

Q

Q

L

A

V

F

W

S

E

R

R

L

M

K

K

L

L

V

L

A

I

E

E

P

P

G
x
T

G

A

A

G

V

V

A

G

L

V

A

A

A

V

L

L

Y

S

H

Q

G

H

D

F

Q

Q

L

T

D

V

G

S

D

P

A

E

V

V

-

K

-

N

I

I

C

C

T

I

I

V

-
x
L

S
|
S

G
|
G

G

G

N

N

V

V

D

D

active site: K53 (= K50), S81 (= S75), E207 (= E205), A211 (≠ F209), D213 (= D211), G236 (≠ A234), L309 (vs. gap), S310 (= S306)
binding biphenyl-4-ylacetic acid: T78 (≠ A72), H79 (≠ Y73), H84 (= H78), V148 (≠ I142), H149 (≠ R143), P150 (= P144)
binding calcium ion: E207 (= E205), A211 (≠ F209), D213 (= D211)
binding pyridoxal-5'-phosphate: F52 (= F49), K53 (= K50), N83 (= N77), G182 (= G180), G183 (= G181), G184 (= G182), G185 (= G183), M186 (≠ L184), G236 (≠ A234), V237 (= V236), T282 (≠ G281), S310 (= S306), G311 (= G307)

7nbcAAA structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen (see paper)
36% identity, 94% coverage: 6:311/325 of query aligns to 9:315/323 of 7nbcAAA

query
sites
7nbcAAA

I

V

E

E

A

K

A

A

A

H

G

I

R

N

L

I

K

R

G

D

H

S

A

I

R

H

V

L

T

T

P

P

L

V

L

L

S

T

S

S

P

S

F

I

L

L

D

N

D

Q

I

L

A

T

G

G

R

R

R

N

V

L

L

F

V

F

K

K

A

C

E

E

C

L

L

F