Structure of PDB 5dex Chain B Binding Site BS01

Receptor Information
>5dex Chain B (length=279) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DNHLSIVTLEEAPFVIVEDIDPTETCVRNTVPCRKFVKINNSTNEGMNVK
KCCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQ
RAVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRGTQVTGLSDKKFQR
PHDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTRFNQRGVEDALVSLKT
GKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATTGYGIALQKGSPWK
RQIDLALLQFVGDGEMEELETLWLTGICH
Ligand information
Ligand ID5E0
InChIInChI=1S/C13H13N3O4/c14-10(12(17)18)6-9-7-11(13(19)20)15-16(9)8-4-2-1-3-5-8/h1-5,7,10H,6,14H2,(H,17,18)(H,19,20)/t10-/m1/s1
InChIKeyMAXWODHGWOEWBN-SNVBAGLBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2c1ccc(cc1)n2c(cc(n2)C(=O)O)C[C@H](C(=O)O)N
ACDLabs 12.01c1c(cccc1)n2c(CC(N)C(O)=O)cc(C(=O)O)n2
CACTVS 3.385N[CH](Cc1cc(nn1c2ccccc2)C(O)=O)C(O)=O
OpenEye OEToolkits 1.9.2c1ccc(cc1)n2c(cc(n2)C(=O)O)CC(C(=O)O)N
CACTVS 3.385N[C@H](Cc1cc(nn1c2ccccc2)C(O)=O)C(O)=O
FormulaC13 H13 N3 O4
Name5-[(2R)-2-amino-2-carboxyethyl]-1-phenyl-1H-pyrazole-3-carboxylic acid
ChEMBL
DrugBank
ZINCZINC000584904808
PDB chain5dex 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]
PDB5dex 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)		H82 T110 R115 T128 G129 G166 S167 T168 Y208 D209
Annotation score1
Binding affinityMOAD: Ki=22.6nM
PDBbind-CN: -logKd/Ki=7.65,Ki=22.6nM
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:5dex, PDBe:5dex, PDBj:5dex
PDBsum5dex
PubMed28760974
UniProtQ00959|NMDE1_RAT Glutamate receptor ionotropic, NMDA 2A (Gene Name=Grin2a)

[Back to BioLiP]