Structure of PDB 7kpa Chain C Binding Site BS01

Receptor Information
>7kpa Chain C (length=133) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SDKPVAHVVANAEGQLQWLNRNALLANGVELRDNQLVVPSEGLYLIYSQV
LFKGQGCPSTHVLLTHTISRIAVTKVNLLSAIKSPCAKPWYEPIYLGGVF
QLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL
Ligand information
Ligand IDD84
InChIInChI=1S/C31H26F2N4O4/c32-31(33)41-27-8-2-1-5-22(27)18-37-26-15-20(21-11-13-29(38)34-17-21)10-12-25(26)35-28(37)19-40-24-7-3-6-23(16-24)36-14-4-9-30(36)39/h1-3,5-8,10-13,15-17,31H,4,9,14,18-19H2,(H,34,38)
InChIKeyDNTKSNFCNRDJAC-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc(c(c1)Cn2c3cc(ccc3nc2COc4cccc(c4)N5CCCC5=O)C6=CNC(=O)C=C6)OC(F)F
ACDLabs 12.01c1(cc(ccc1)N2CCCC2=O)OCc5n(c4cc(C3=CNC(=O)C=C3)ccc4n5)Cc6c(cccc6)OC(F)F
CACTVS 3.385FC(F)Oc1ccccc1Cn2c(COc3cccc(c3)N4CCCC4=O)nc5ccc(cc25)C6=CNC(=O)C=C6
FormulaC31 H26 F2 N4 O4
Name5-(1-{[2-(difluoromethoxy)phenyl]methyl}-2-{[3-(2-oxopyrrolidin-1-yl)phenoxy]methyl}-1H-benzimidazol-6-yl)pyridin-2(1H)-one
ChEMBL
DrugBank
ZINC
PDB chain7kpa Chain C Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7kpa A conformation-selective monoclonal antibody against a small molecule-stabilised signalling-deficient form of TNF.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		L57 Y59 Y119 G121 G122 Y151
Binding residue
(residue number reindexed from 1)		L45 Y47 Y95 G97 G98 Y127
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005164 tumor necrosis factor receptor binding
Biological Process
GO:0006955 immune response
Cellular Component
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7kpa, PDBe:7kpa, PDBj:7kpa
PDBsum7kpa
PubMed33495445
UniProtP01375|TNFA_HUMAN Tumor necrosis factor (Gene Name=TNF)

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