Structure of PDB 5cmk Chain B Binding Site BS01

Receptor Information
>5cmk Chain B (length=253) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SNRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTY
EIRLVEDGKYGAQDDVNGQWNGMVRELIDHKADLAVAPLTITYVREKVID
FSKPFMTLGISILYRKGTPIDSADDLAKQTKIEYGAVEDGSTMTFFKKSK
ISTYDKMWAFMSSRRQSVLVKSSEEGIQRVLTSDYALLMESTTIEFVTQR
NCNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAILQLQEEGKLHMMKEKW
WRG
Ligand information
Ligand IDLY5
InChIInChI=1S/C16H24F2N2O4/c17-16(18)5-13(15(23)24)20(8-16)7-9-1-2-10-6-19-12(14(21)22)4-11(10)3-9/h9-13,19H,1-8H2,(H,21,22)(H,23,24)/t9-,10-,11+,12-,13-/m0/s1
InChIKeyOXQXJYQSWZFDBB-WJTVCTBASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C1C[C@H]2CN[C@@H](C[C@H]2C[C@H]1CN3CC(C[C@H]3C(=O)O)(F)F)C(=O)O
OpenEye OEToolkits 1.7.6C1CC2CNC(CC2CC1CN3CC(CC3C(=O)O)(F)F)C(=O)O
CACTVS 3.385OC(=O)[CH]1C[CH]2C[CH](CC[CH]2CN1)CN3CC(F)(F)C[CH]3C(O)=O
CACTVS 3.385OC(=O)[C@@H]1C[C@H]2C[C@H](CC[C@H]2CN1)CN3CC(F)(F)C[C@H]3C(O)=O
ACDLabs 12.01FC1(CN(C(C1)C(O)=O)CC2CC3C(CC2)CNC(C(O)=O)C3)F
FormulaC16 H24 F2 N2 O4
Name(3S,4aR,6S,8aR)-6-{[(2S)-2-carboxy-4,4-difluoropyrrolidin-1-yl]methyl}decahydroisoquinoline-3-carboxylic acid;
LY466195
ChEMBLCHEMBL1234118
DrugBank
ZINCZINC000003989289
PDB chain5cmk 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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PDB5cmk Structural basis of kainate subtype glutamate receptor desensitization.
Resolution1.801 Å
Binding residue
(original residue number in PDB)
Y61 P89 T91 R96 S142 T143 E191 Y217
Binding residue
(residue number reindexed from 1)
Y60 P88 T90 R95 S141 T142 E190 Y216
Annotation score1
Binding affinityMOAD: ic50=30nM
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:5cmk, PDBe:5cmk, PDBj:5cmk
PDBsum5cmk
PubMed27580033
UniProtP42260|GRIK2_RAT Glutamate receptor ionotropic, kainate 2 (Gene Name=Grik2)

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