Structure of PDB 5nk3 Chain A Binding Site BS01

Receptor Information
>5nk3 Chain A (length=281) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VLKFTTEIHPSCVTRQKVIGAGEFGEVYKGMLKTKEVPVAIKTLKAGYTE
KQRVDFLGEAGIMGQFSHHNIIRLEGVISKYKPMMIITEYMENGALDKFL
REKDGEFSVLQLVGMLRGIAAGMKYLANMNYVHRDLAARNILVNSNLVCK
VSDFGLSRVLEDDPEATYTGKIPIRWTAPEAISYRKFTSASDVWSFGIVM
WEVMTYGERPYWELSNHEVMKAINDGFRLPTPMDCPSAIYQLMMQCWQQE
RARRPKFADIVSILDKLIRAPDSLKTLADFD
Ligand information
Ligand ID92Q
InChIInChI=1S/C22H22ClN5O2S/c1-13-4-2-7-17(23)19(13)28-21(30)18-12-25-22(31-18)27-15-6-3-5-14(10-15)20(29)26-16-8-9-24-11-16/h2-7,10,12,16,24H,8-9,11H2,1H3,(H,25,27)(H,26,29)(H,28,30)/t16-/m0/s1
InChIKeyNFJBJEVYNAEEOP-INIZCTEOSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1cccc(Cl)c1NC(=O)c2sc(Nc3cccc(c3)C(=O)N[CH]4CCNC4)nc2
OpenEye OEToolkits 2.0.6Cc1cccc(c1NC(=O)c2cnc(s2)Nc3cccc(c3)C(=O)NC4CCNC4)Cl
OpenEye OEToolkits 2.0.6Cc1cccc(c1NC(=O)c2cnc(s2)Nc3cccc(c3)C(=O)N[C@H]4CCNC4)Cl
CACTVS 3.385Cc1cccc(Cl)c1NC(=O)c2sc(Nc3cccc(c3)C(=O)N[C@H]4CCNC4)nc2
FormulaC22 H22 Cl N5 O2 S
Name~{N}-(2-chloranyl-6-methyl-phenyl)-2-[[3-[[(3~{S})-pyrrolidin-3-yl]carbamoyl]phenyl]amino]-1,3-thiazole-5-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain5nk3 Chain A Residue 1001 [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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PDB5nk3 Chemoproteomics-Aided Medicinal Chemistry for the Discovery of EPHA2 Inhibitors.
Resolution1.586 Å
Binding residue
(original residue number in PDB)		I619 A644 I645 K646 M667 I690 T692 Y694 M695 G698 A699 L746
Binding residue
(residue number reindexed from 1)		I19 A40 I41 K42 M63 I86 T88 Y90 M91 G94 A95 L142
Annotation score1
Binding affinityMOAD: Kd=38.02nM
PDBbind-CN: -logKd/Ki=7.42,Kd=38nM
Enzymatic activity
Catalytic site (original residue number in PDB) D739 A741 R743 N744 D757 D766 P780
Catalytic site (residue number reindexed from 1) D135 A137 R139 N140 D153 D162 P173
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:5nk3, PDBe:5nk3, PDBj:5nk3
PDBsum5nk3
PubMed28544567
UniProtP29317|EPHA2_HUMAN Ephrin type-A receptor 2 (Gene Name=EPHA2)

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