Structure of PDB 4nf6 Chain B Binding Site BS01

Receptor Information
>4nf6 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]
DDNHLSIVTLEEAPFVIVEDIDTETCVRNTVPCRKFVKINNSTNEGMNVK
KCCKGFCIDILKKLSRTVKFTYDLYLVTNGKHGKKVNNVWNGMIGEVVYQ
RAVMAVGSLTINEERSEVVDFSVPFVETGISVMVSRGTQVTGLSDKKFQR
PHDYSPPFRFGTVPNGSTERNIRNNYPYMHQYMTRFNQRGVEDALVSLKT
GKLDAFIYDAAVLNYKAGRDEGCKLVTIGSGYIFATTGYGIALQKGSPWK
RQIDLALLQFVGDGEMEELETLWLTGIC
Ligand information
Ligand ID2JL
InChIInChI=1S/C21H18N2O5/c24-19(23-10-9-22-17(20(25)26)18(23)21(27)28)14-7-8-16-13(11-14)6-5-12-3-1-2-4-15(12)16/h1-8,11,17-18,22H,9-10H2,(H,25,26)(H,27,28)/t17-,18+/m1/s1
InChIKeyIWWXIZOMXGOTPP-MSOLQXFVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1ccc2c(c1)ccc3c2ccc(c3)C(=O)N4CCN[C@H]([C@H]4C(=O)O)C(=O)O
CACTVS 3.385OC(=O)[CH]1NCCN([CH]1C(O)=O)C(=O)c2ccc3c(ccc4ccccc34)c2
OpenEye OEToolkits 1.7.6c1ccc2c(c1)ccc3c2ccc(c3)C(=O)N4CCNC(C4C(=O)O)C(=O)O
ACDLabs 12.01O=C(c3cc2ccc1ccccc1c2cc3)N4C(C(=O)O)C(C(=O)O)NCC4
CACTVS 3.385OC(=O)[C@@H]1NCCN([C@@H]1C(O)=O)C(=O)c2ccc3c(ccc4ccccc34)c2
FormulaC21 H18 N2 O5
Name(2S,3R)-1-(phenanthren-2-ylcarbonyl)piperazine-2,3-dicarboxylic acid
ChEMBLCHEMBL1950808
DrugBank
ZINCZINC000013831227
PDB chain4nf6 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

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PDB4nf6 Structural Insights into Competitive Antagonism in NMDA Receptors.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		E16 A17 H88 S114 L115 T116 R121 S173 Y214 V218 K222 Y245
Binding residue
(residue number reindexed from 1)		E12 A13 H82 S108 L109 T110 R115 S167 Y208 V212 K216 Y239
Annotation score1
Binding affinityMOAD: Ki=0.82uM
BindingDB: Ki=210nM
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:4nf6, PDBe:4nf6, PDBj:4nf6
PDBsum4nf6
PubMed24462099
UniProtQ00959|NMDE1_RAT Glutamate receptor ionotropic, NMDA 2A (Gene Name=Grin2a)

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