Structure of PDB 2qs2 Chain B Binding Site BS01

Receptor Information
>2qs2 Chain B (length=251) 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
N
Ligand information
Ligand IDUBF
InChIInChI=1S/C13H12BrN3O6S/c14-7-4-16(5-8(15)11(19)20)13(23)17(10(7)18)3-6-1-2-24-9(6)12(21)22/h1-2,4,8H,3,5,15H2,(H,19,20)(H,21,22)/t8-/m0/s1
InChIKeyKKTBJRLDYITGOV-QMMMGPOBSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[C@@H](CN1C=C(Br)C(=O)N(Cc2ccsc2C(O)=O)C1=O)C(O)=O
OpenEye OEToolkits 1.5.0c1csc(c1CN2C(=O)C(=CN(C2=O)C[C@@H](C(=O)O)N)Br)C(=O)O
ACDLabs 10.04O=C(O)C(N)CN1C(=O)N(C(=O)C(Br)=C1)Cc2c(scc2)C(=O)O
CACTVS 3.341N[CH](CN1C=C(Br)C(=O)N(Cc2ccsc2C(O)=O)C1=O)C(O)=O
OpenEye OEToolkits 1.5.0c1csc(c1CN2C(=O)C(=CN(C2=O)CC(C(=O)O)N)Br)C(=O)O
FormulaC13 H12 Br N3 O6 S
Name3-({3-[(2S)-2-amino-2-carboxyethyl]-5-bromo-2,6-dioxo-3,6-dihydropyrimidin-1(2H)-yl}methyl)thiophene-2-carboxylic acid
ChEMBLCHEMBL221321
DrugBank
ZINCZINC000035323735
PDB chain2qs2 Chain B Residue 602 [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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PDB2qs2 Binding site and ligand flexibility revealed by high resolution crystal structures of GluK1 competitive antagonists.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		E13 Y61 P88 L89 T90 R95 V137 S141 T142 Y216
Binding residue
(residue number reindexed from 1)		E10 Y58 P85 L86 T87 R92 V134 S138 T139 Y213
Annotation score1
Binding affinityMOAD: Kd=186nM
BindingDB: Kd=25nM
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:2qs2, PDBe:2qs2, PDBj:2qs2
PDBsum2qs2
PubMed20558186
UniProtP22756|GRIK1_RAT Glutamate receptor ionotropic, kainate 1 (Gene Name=Grik1)

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