Structure of PDB 8eme Chain B Binding Site BS01

Receptor Information
>8eme Chain B (length=282) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREAT
SPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDY
VREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHV
KITDFGPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPA
SEISSILEKGERLPQPPICTIDVYMIMRKCWMIDADSRPKFRELIIEFSK
MARDPQRYLVIQGLPSPTDSNFYRALMDEEDM
Ligand information
Ligand IDZNL
InChIInChI=1S/C25H27N5O3S/c1-4-20(31)27-21-13-17(15-34-21)24(33)28-25-26-19-11-8-9-16(3)23(19)30(25)18-10-6-7-12-29(14-18)22(32)5-2/h4-5,8-9,11,13,15,18H,1-2,6-7,10,12,14H2,3H3,(H,27,31)(H,26,28,33)/t18-/m0/s1
InChIKeyDZTGCJZKRUDIGP-SFHVURJKSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1cccc2nc(NC(=O)c3csc(NC(=O)C=C)c3)n([CH]4CCCCN(C4)C(=O)C=C)c12
ACDLabs 12.01O=C(Nc1nc2cccc(C)c2n1C1CCCCN(C1)C(=O)C=C)c1cc(NC(=O)C=C)sc1
OpenEye OEToolkits 2.0.7Cc1cccc2c1n(c(n2)NC(=O)c3cc(sc3)NC(=O)C=C)[C@H]4CCCCN(C4)C(=O)C=C
CACTVS 3.385Cc1cccc2nc(NC(=O)c3csc(NC(=O)C=C)c3)n([C@H]4CCCCN(C4)C(=O)C=C)c12
OpenEye OEToolkits 2.0.7Cc1cccc2c1n(c(n2)NC(=O)c3cc(sc3)NC(=O)C=C)C4CCCCN(C4)C(=O)C=C
FormulaC25 H27 N5 O3 S
NameN-{7-methyl-1-[(3S)-1-(prop-2-enoyl)azepan-3-yl]-1H-benzimidazol-2-yl}-5-(prop-2-enamido)thiophene-3-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain8eme Chain B Residue 1101 [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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PDB8eme Dual-covalency small molecule inhibitors of the epidermal growth factor kinase
Resolution3.32 Å
Binding residue
(original residue number in PDB)		L718 V726 C775 M790 M793 P794 G796 C797 D800 R841 L844 T854
Binding residue
(residue number reindexed from 1)		L17 V25 C74 M89 M92 P93 G95 C96 D99 R140 L143 T153
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.10.1: receptor protein-tyrosine kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004713 protein tyrosine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8eme, PDBe:8eme, PDBj:8eme
PDBsum8eme
PubMed38947214
UniProtP00533|EGFR_HUMAN Epidermal growth factor receptor (Gene Name=EGFR)

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