Structure of PDB 7nbf Chain DDD Binding Site BS04

Receptor Information
>7nbf Chain DDD (length=317) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QYDISFADVEKAHINIRDSIHLTPVLTSSILNQLTGRNLFFKCELFQKTG
SFKIRGALNAVRSLVRKPKAVVTHSSGNHGQALTYAAKLEGIPAYIVVPQ
TAPDCKKLAIQAYGASIVYCEPSDESRENVAKRVTEETEGIMVHPNQEPA
VIAGQGTIALEVLNQVPLVDALVVPVGGGGMLAGIAITVKALKPSVKVYA
AEPSNADDCYQSKLKGKLMPNLYPPETIADGVKSSIGLNTWPIIRDLVDD
IFTVTEDEIKCATQLVWERMKLLIEPTAGVGVAAVLSQHFQTVSPEVKNI
CIVLSGGNVDLTSSITW
Ligand information
Ligand IDT6J
InChIInChI=1S/C9H10N2O2S/c1-14(12,13)6-9-10-7-4-2-3-5-8(7)11-9/h2-5H,6H2,1H3,(H,10,11)
InChIKeyWCWTYTQSZZWNEW-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CS(=O)(=O)Cc1[nH]c2ccccc2n1
CACTVS 3.385C[S](=O)(=O)Cc1[nH]c2ccccc2n1
ACDLabs 12.01n1c(nc2ccccc12)CS(C)(=O)=O
FormulaC9 H10 N2 O2 S
Name2-[(methylsulfonyl)methyl]-1H-benzimidazole
ChEMBL
DrugBank
ZINCZINC000003888556
PDB chain7nbf Chain DDD Residue 405 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB7nbf Tyrosine 121 moves revealing a ligandable pocket that couples catalysis to ATP-binding in serine racemase.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		H24 L25 P27 F49
Binding residue
(residue number reindexed from 1)		H21 L22 P24 F46
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K56 S84 E210 A214 D216 G239 L312 S313
Catalytic site (residue number reindexed from 1) K53 S76 E202 A206 D208 G231 L304 S305
Enzyme Commision number 4.3.1.17: L-serine ammonia-lyase.
4.3.1.18: D-serine ammonia-lyase.
5.1.1.18: serine racemase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0003941 L-serine ammonia-lyase activity
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008721 D-serine ammonia-lyase activity
GO:0016594 glycine binding
GO:0016829 lyase activity
GO:0016853 isomerase activity
GO:0018114 threonine racemase activity
GO:0030165 PDZ domain binding
GO:0030170 pyridoxal phosphate binding
GO:0030378 serine racemase activity
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
Biological Process
GO:0006520 amino acid metabolic process
GO:0006563 L-serine metabolic process
GO:0009069 serine family amino acid metabolic process
GO:0009410 response to xenobiotic stimulus
GO:0014070 response to organic cyclic compound
GO:0032496 response to lipopolysaccharide
GO:0042866 pyruvate biosynthetic process
GO:0070178 D-serine metabolic process
GO:0070179 D-serine biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0043025 neuronal cell body
GO:0045177 apical part of cell

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7nbf, PDBe:7nbf, PDBj:7nbf
PDBsum7nbf
PubMed35410329
UniProtQ9GZT4|SRR_HUMAN Serine racemase (Gene Name=SRR)

[Back to BioLiP]