Structure of PDB 2pbw Chain A Binding Site BS01

Receptor Information
>2pbw Chain A (length=248) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RTLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFLYDV
KLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSK
PFMTLGISILYRKGTPIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKIST
YEKMWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCN
LTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWW
Ligand information
Ligand IDDOQ
InChIInChI=1S/C15H21NO6/c1-8(4-3-5-9(2)14(19)20)11-7-16-13(15(21)22)10(11)6-12(17)18/h3-5,9-11,13,16H,6-7H2,1-2H3,(H,17,18)(H,19,20)(H,21,22)/b5-3+,8-4-/t9-,10+,11-,13+/m1/s1
InChIKeyVZFRNCSOCOPNDB-AOKDLOFSSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C(/C=C/C=C(\C1C(C(C(=O)O)NC1)CC(=O)O)C)C
OpenEye OEToolkits 1.5.0CC(C=CC=C(C)C1CNC(C1CC(=O)O)C(=O)O)C(=O)O
OpenEye OEToolkits 1.5.0C[C@H](\C=C\C=C(\C)/[C@H]1CN[C@@H]([C@H]1CC(=O)O)C(=O)O)C(=O)O
CACTVS 3.341C[CH](C=CC=C(C)[CH]1CN[CH]([CH]1CC(O)=O)C(O)=O)C(O)=O
CACTVS 3.341C[C@H](\C=C\C=C(\C)[C@H]1CN[C@@H]([C@H]1CC(O)=O)C(O)=O)C(O)=O
FormulaC15 H21 N O6
Name(2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-1,3-HEXADIENYL]-3-PYRROLIDINEACETIC ACID;
(2S,3S,4S)-3-CARBOXYMETHYL-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-HEXA-1,3-DIENYL]-PYRROLIDINE-2-CARBOXYLIC ACID;
DOMOIC ACID
ChEMBLCHEMBL1232313
DrugBankDB02852
ZINCZINC000003995581
PDB chain2pbw Chain A Residue 401 [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]
PDB2pbw Partial agonism and antagonism of the ionotropic glutamate receptor iGLuR5: structures of the ligand-binding core in complex with domoic acid and 2-amino-3-[5-tert-butyl-3-(phosphonomethoxy)-4-isoxazolyl]propionic acid.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		E13 K60 Y61 P88 T90 R95 D139 G140 S141 T142 E190
Binding residue
(residue number reindexed from 1)		E10 K57 Y58 P85 T87 R92 D136 G137 S138 T139 E187
Annotation score1
Binding affinityMOAD: Ki=5.56nM
PDBbind-CN: -logKd/Ki=8.25,Ki=5.56nM
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:2pbw, PDBe:2pbw, PDBj:2pbw
PDBsum2pbw
PubMed17581823
UniProtP22756|GRIK1_RAT Glutamate receptor ionotropic, kainate 1 (Gene Name=Grik1)

[Back to BioLiP]