Structure of PDB 5vih Chain B Binding Site BS01

Receptor Information
>5vih Chain B (length=278) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DNHLSIVTLEEAPFVIVEDIDPLTCVRNTVPCRKFVKINNSTNEGMNVKK
CCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQR
AVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRGTQVTGLSDKKFQRP
HDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTRFNQRGVEDALVSLKTG
KLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATTGYGIALQKGSPWKR
QIDLALLQFVGDGEMEELETLWLTGICH
Ligand information
Ligand ID5DZ
InChIInChI=1S/C13H12FN3O4/c14-7-1-3-8(4-2-7)17-9(5-10(15)12(18)19)6-11(16-17)13(20)21/h1-4,6,10H,5,15H2,(H,18,19)(H,20,21)/t10-/m1/s1
InChIKeyFSQWUEIVHBDCAC-SNVBAGLBSA-N
SMILES
SoftwareSMILES
CACTVS 3.385N[CH](Cc1cc(nn1c2ccc(F)cc2)C(O)=O)C(O)=O
OpenEye OEToolkits 1.9.2c1cc(ccc1n2c(cc(n2)C(=O)O)CC(C(=O)O)N)F
OpenEye OEToolkits 1.9.2c1cc(ccc1n2c(cc(n2)C(=O)O)C[C@H](C(=O)O)N)F
CACTVS 3.385N[C@H](Cc1cc(nn1c2ccc(F)cc2)C(O)=O)C(O)=O
ACDLabs 12.01C(O)(=O)C(N)Cc2cc(C(=O)O)nn2c1ccc(F)cc1
FormulaC13 H12 F N3 O4
Name5-[(2R)-2-amino-2-carboxyethyl]-1-(4-fluorophenyl)-1H-pyrazole-3-carboxylic acid
ChEMBL
DrugBank
ZINCZINC000584904776
PDB chain5vih Chain B Residue 301 [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]
PDB5vih Structural basis of subunit selectivity for competitive NMDA receptor antagonists with preference for GluN2A over GluN2B subunits.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		H88 T116 R121 T134 G135 G172 S173 T174 Y214 D215
Binding residue
(residue number reindexed from 1)		H81 T109 R114 T127 G128 G165 S166 T167 Y207 D208
Annotation score1
Binding affinityMOAD: Ki=32.2nM
PDBbind-CN: -logKd/Ki=7.49,Ki=32.2nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0015276 ligand-gated monoatomic ion channel activity
Cellular Component
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:5vih, PDBe:5vih, PDBj:5vih
PDBsum5vih
PubMed28760974
UniProtQ00959|NMDE1_RAT Glutamate receptor ionotropic, NMDA 2A (Gene Name=Grin2a)

[Back to BioLiP]