Structure of PDB 5gmp Chain A Binding Site BS01

Receptor Information
>5gmp Chain A (length=305) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIK
ELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPF
GCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLV
KTPQHVKITDFGLAKLLGAVPIKWMALESILHRIYTHQSDVWSYGVTVWE
LMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDAD
SRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPRALMDEEDMDDVVDAD
EYLIP
Ligand information
Ligand IDF62
InChIInChI=1S/C29H31N7O3/c1-5-26(37)31-20-7-6-8-22(16-20)36-27(38)15-19(2)23-18-30-29(33-28(23)36)32-24-10-9-21(17-25(24)39-4)35-13-11-34(3)12-14-35/h5-10,15-18H,1,11-14H2,2-4H3,(H,31,37)(H,30,32,33)
InChIKeyVJQPNQROUWVJQN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC1=CC(=O)N(c2c1cnc(n2)Nc3ccc(cc3OC)N4CCN(CC4)C)c5cccc(c5)NC(=O)C=C
CACTVS 3.385COc1cc(ccc1Nc2ncc3C(=CC(=O)N(c4cccc(NC(=O)C=C)c4)c3n2)C)N5CCN(C)CC5
FormulaC29 H31 N7 O3
NameN-[3-[2-[[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino]-5-methyl-7-oxidanylidene-pyrido[2,3-d]pyrimidin-8-yl]phenyl]prop-2-enamide
ChEMBLCHEMBL3633143
DrugBank
ZINCZINC000205907067
PDB chain5gmp Chain A 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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PDB5gmp A structure-guided optimization of pyrido[2,3-d]pyrimidin-7-ones as selective inhibitors of EGFR(L858R/T790M) mutant with improved pharmacokinetic properties.
Resolution2.797 Å
Binding residue
(original residue number in PDB)		L718 V726 A743 M790 Q791 L792 M793 P794 G796 C797 L844
Binding residue
(residue number reindexed from 1)		L23 V31 A48 M95 Q96 L97 M98 P99 G101 C102 L149
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=9.10,IC50=0.8nM
BindingDB: IC50=386nM
Enzymatic activity
Catalytic site (original residue number in PDB) D837 A839 R841 N842 D855
Catalytic site (residue number reindexed from 1) D142 A144 R146 N147 D160
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:5gmp, PDBe:5gmp, PDBj:5gmp
PDBsum5gmp
PubMed28033579
UniProtP00533|EGFR_HUMAN Epidermal growth factor receptor (Gene Name=EGFR)

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