Structure of PDB 7kpb Chain A Binding Site BS01

Receptor Information
>7kpb Chain A (length=153) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRTPSDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEG
LYLIYSQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRE
TPEGAEAKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGI
IAL
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 chain7kpb Chain C Residue 201 [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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PDB7kpb A conformation-selective monoclonal antibody against a small molecule-stabilised signalling-deficient form of TNF
Resolution3.0 Å
Binding residue
(original residue number in PDB)		L57 Y59 S60 Y119 L120 G121 L157
Binding residue
(residue number reindexed from 1)		L53 Y55 S56 Y115 L116 G117 L153
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:7kpb, PDBe:7kpb, PDBj:7kpb
PDBsum7kpb
PubMed33495445
UniProtP01375|TNFA_HUMAN Tumor necrosis factor (Gene Name=TNF)

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