Structure of PDB 5nf5 Chain B Binding Site BS01

Receptor Information
>5nf5 Chain B (length=255) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NRTLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFLYD
VKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFS
KPFMTLGISILYRKGTPIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKIS
TYEKMWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNC
NLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWR
GNGCP
Ligand information
Ligand ID8VN
InChIInChI=1S/C7H8N2O5/c10-6(11)4-3-2(1-8-4)14-9-5(3)7(12)13/h2-4,8H,1H2,(H,10,11)(H,12,13)/t2-,3-,4-/m0/s1
InChIKeyJMTZNIDIUDLCMK-HZLVTQRSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6C1C2C(C(N1)C(=O)O)C(=NO2)C(=O)O
CACTVS 3.385OC(=O)[CH]1NC[CH]2ON=C([CH]12)C(O)=O
CACTVS 3.385OC(=O)[C@H]1NC[C@@H]2ON=C([C@H]12)C(O)=O
OpenEye OEToolkits 2.0.6C1[C@H]2[C@@H]([C@H](N1)C(=O)O)C(=NO2)C(=O)O
FormulaC7 H8 N2 O5
Name(3~{a}~{S},4~{S},6~{a}~{R})-4,5,6,6~{a}-tetrahydro-3~{a}~{H}-pyrrolo[3,4-d][1,2]oxazole-3,4-dicarboxylic acid
ChEMBLCHEMBL125440
DrugBank
ZINC
PDB chain5nf5 Chain B Residue 303 [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]
PDB5nf5 Structure and Affinity of Two Bicyclic Glutamate Analogues at AMPA and Kainate Receptors.
Resolution2.85 Å
Binding residue
(original residue number in PDB)		Y61 P88 T90 R95 S141 T142 E190
Binding residue
(residue number reindexed from 1)		Y59 P86 T88 R93 S139 T140 E188
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.82,Ki=152nM
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:5nf5, PDBe:5nf5, PDBj:5nf5
PDBsum5nf5
PubMed28691798
UniProtP22756|GRIK1_RAT Glutamate receptor ionotropic, kainate 1 (Gene Name=Grik1)

[Back to BioLiP]