Structure of PDB 4ymb Chain A Binding Site BS01

Receptor Information
>4ymb Chain A (length=252) 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
LTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRG
CP
Ligand information
Ligand ID4E7
InChIInChI=1S/C15H19NO4/c1-2-4-11-8-16-13(15(19)20)12(11)9-5-3-6-10(7-9)14(17)18/h3,5-7,11-13,16H,2,4,8H2,1H3,(H,17,18)(H,19,20)/t11-,12+,13+/m1/s1
InChIKeyOORLOXOWCACWSS-AGIUHOORSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CCCC1CNC(C1c2cccc(c2)C(=O)O)C(=O)O
CACTVS 3.385CCC[C@@H]1CN[C@@H]([C@H]1c2cccc(c2)C(O)=O)C(O)=O
ACDLabs 12.01N1C(C(C(C1)CCC)c2cc(ccc2)C(=O)O)C(O)=O
OpenEye OEToolkits 1.9.2CCC[C@@H]1CN[C@@H]([C@H]1c2cccc(c2)C(=O)O)C(=O)O
CACTVS 3.385CCC[CH]1CN[CH]([CH]1c2cccc(c2)C(O)=O)C(O)=O
FormulaC15 H19 N O4
Name(3R,4S)-3-(3-carboxyphenyl)-4-propyl-L-proline
ChEMBL
DrugBank
ZINCZINC000263620853
PDB chain4ymb Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ymb Structure-Activity Relationship Study of Ionotropic Glutamate Receptor Antagonist (2S,3R)-3-(3-Carboxyphenyl)pyrrolidine-2-carboxylic Acid.
Resolution1.93 Å
Binding residue
(original residue number in PDB)		Y61 P88 T90 R95 V137 T142 E190 S193 Y216
Binding residue
(residue number reindexed from 1)		Y58 P85 T87 R92 V134 T139 E187 S190 Y213
Annotation score1
Binding affinityMOAD: Ki=0.62uM
PDBbind-CN: -logKd/Ki=6.21,Ki=0.62uM
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
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Cellular Component
External links
PDB RCSB:4ymb, PDBe:4ymb, PDBj:4ymb
PDBsum4ymb
PubMed26200741
UniProtP22756|GRIK1_RAT Glutamate receptor ionotropic, kainate 1 (Gene Name=Grik1)

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