Structure of PDB 5nkd Chain A Binding Site BS01

Receptor Information
>5nkd Chain A (length=287) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AVLKFTTEIHPSCVTRQKVIGAGEFGEVYKGMLKEVPVAIKTLKAGYTEK
QRVDFLGEAGIMGQFSHHNIIRLEGVISKYKPMMIITEYMENGALDKFLR
EKDGEFSVLQLVGMLRGIAAGMKYLANMNYVHRDLAARNILVNSNLVCKV
SDFGLSRVLEDDPEATYGKIPIRWTAPEAISYRKFTSASDVWSFGIVMWE
VMTYGERPYWELSNHEVMKAINDGFRLPTPMDCPSAIYQLMMQCWQQERA
RRPKFADIVSILDKLIRAPDSLKTLADFDPRVSIRLP
Ligand information
Ligand ID91K
InChIInChI=1S/C24H23ClN4O4S/c1-14-4-2-7-18(25)21(14)28-22(32)19-12-26-24(34-19)27-17-6-3-5-16(11-17)23(33)29-9-8-15(13-29)10-20(30)31/h2-7,11-12,15H,8-10,13H2,1H3,(H,26,27)(H,28,32)(H,30,31)/t15-/m1/s1
InChIKeyVNOJDMNSDQAVOE-OAHLLOKOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1cccc(c1NC(=O)c2cnc(s2)Nc3cccc(c3)C(=O)N4CC[C@@H](C4)CC(=O)O)Cl
CACTVS 3.385Cc1cccc(Cl)c1NC(=O)c2sc(Nc3cccc(c3)C(=O)N4CC[C@@H](C4)CC(O)=O)nc2
OpenEye OEToolkits 2.0.6Cc1cccc(c1NC(=O)c2cnc(s2)Nc3cccc(c3)C(=O)N4CCC(C4)CC(=O)O)Cl
CACTVS 3.385Cc1cccc(Cl)c1NC(=O)c2sc(Nc3cccc(c3)C(=O)N4CC[CH](C4)CC(O)=O)nc2
FormulaC24 H23 Cl N4 O4 S
Name2-[(3~{R})-1-[3-[[5-[(2-chloranyl-6-methyl-phenyl)carbamoyl]-1,3-thiazol-2-yl]amino]phenyl]carbonylpyrrolidin-3-yl]ethanoic acid
ChEMBL
DrugBank
ZINC
PDB chain5nkd Chain A Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5nkd Chemoproteomics-Aided Medicinal Chemistry for the Discovery of EPHA2 Inhibitors.
Resolution1.408 Å
Binding residue
(original residue number in PDB)		K617 I619 A644 K646 E663 I690 T692 Y694 M695 G698 L746
Binding residue
(residue number reindexed from 1)		K18 I20 A39 K41 E58 I85 T87 Y89 M90 G93 L141
Annotation score1
Binding affinityMOAD: Kd=26.3nM
PDBbind-CN: -logKd/Ki=7.59,Kd=26nM
Enzymatic activity
Catalytic site (original residue number in PDB) D739 A741 R743 N744 D757 D766 P780
Catalytic site (residue number reindexed from 1) D134 A136 R138 N139 D152 D161 P171
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:5nkd, PDBe:5nkd, PDBj:5nkd
PDBsum5nkd
PubMed28544567
UniProtP29317|EPHA2_HUMAN Ephrin type-A receptor 2 (Gene Name=EPHA2)

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