Structure of PDB 6ooy Chain C Binding Site BS01

Receptor Information
>6ooy Chain C (length=134) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYS
QVLFKGQGCHVLLTHTISRIAVSYQTKVNLLSAIKSPCKPWYEPIYLGGV
FQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL
Ligand information
Ligand IDA7M
InChIInChI=1S/C17H18N2O/c1-12-7-8-13(2)14(9-12)10-19-16-6-4-3-5-15(16)18-17(19)11-20/h3-9,20H,10-11H2,1-2H3
InChIKeyRZRPPZWEPMDGEI-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ccc(C)c(Cn2c(CO)nc3ccccc23)c1
ACDLabs 12.01c3(Cn1c(CO)nc2ccccc12)cc(C)ccc3C
OpenEye OEToolkits 2.0.6Cc1ccc(c(c1)Cn2c3ccccc3nc2CO)C
FormulaC17 H18 N2 O
Name{1-[(2,5-dimethylphenyl)methyl]-1H-benzimidazol-2-yl}methanol
ChEMBLCHEMBL1477600
DrugBank
ZINCZINC000000572604
PDB chain6ooy 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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PDB6ooy Small molecules that inhibit TNF signalling by stabilising an asymmetric form of the trimer.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		Y59 S60 Y119 Y151
Binding residue
(residue number reindexed from 1)		Y49 S50 Y96 Y128
Annotation score1
Binding affinityMOAD: Kd=22uM
PDBbind-CN: -logKd/Ki=4.66,Kd=22uM
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:6ooy, PDBe:6ooy, PDBj:6ooy
PDBsum6ooy
PubMed31857588
UniProtP01375|TNFA_HUMAN Tumor necrosis factor (Gene Name=TNF)

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