Structure of PDB 7nbh Chain DDD Binding Site BS02

Receptor Information
>7nbh Chain DDD (length=315) 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
CIVLSGGNVDLTSSW
Ligand information
Ligand IDW0D
InChIInChI=1S/C13H11N3O2/c17-13(11-6-3-7-18-11)14-8-12-15-9-4-1-2-5-10(9)16-12/h1-7H,8H2,(H,14,17)(H,15,16)
InChIKeyWFEIYWNIMQWEHE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01n2c(CNC(=O)c1ccco1)nc3ccccc23
OpenEye OEToolkits 2.0.7c1ccc2c(c1)[nH]c(n2)CNC(=O)c3ccco3
CACTVS 3.385O=C(NCc1[nH]c2ccccc2n1)c3occc3
FormulaC13 H11 N3 O2
NameN-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide
ChEMBLCHEMBL1904688
DrugBank
ZINCZINC000000508336
PDB chain7nbh Chain DDD Residue 411 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7nbh Tyrosine 121 moves revealing a ligandable pocket that couples catalysis to ATP-binding in serine racemase.
Resolution1.77 Å
Binding residue
(original residue number in PDB)		S84 Q89 K114 Y121
Binding residue
(residue number reindexed from 1)		S76 Q81 K106 Y113
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7nbh, PDBe:7nbh, PDBj:7nbh
PDBsum7nbh
PubMed35410329
UniProtQ9GZT4|SRR_HUMAN Serine racemase (Gene Name=SRR)

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