Structure of PDB 4ybj Chain A Binding Site BS01

Receptor Information
>4ybj Chain A (length=255) Species: 9031 (Gallus gallus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AWEIPRESLRLEVKLGQGGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQE
AQVMKKLRHEKLVQLYAVVSEEPIYIVTEYMSKGSLLDFLKGEMGKYLRL
PQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVADFGPIKW
TAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERG
YRMPCPPECPESLHDLMCQCWRKDPEERPTFEYLQAFLEDYFTSTEPQYQ
PGENL
Ligand information
Ligand ID4A9
InChIInChI=1S/C29H29F3N8O3S/c1-18-34-24(16-25(35-18)40-10-8-39(9-11-40)12-13-41)38-28-33-17-23(44-28)27(43)37-22-7-3-6-21(15-22)36-26(42)19-4-2-5-20(14-19)29(30,31)32/h2-7,14-17,41H,8-13H2,1H3,(H,36,42)(H,37,43)(H,33,34,35,38)
InChIKeyGWJVXYZDNRXACJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1nc(Nc2sc(cn2)C(=O)Nc3cccc(NC(=O)c4cccc(c4)C(F)(F)F)c3)cc(n1)N5CCN(CCO)CC5
OpenEye OEToolkits 1.9.2Cc1nc(cc(n1)N2CCN(CC2)CCO)Nc3ncc(s3)C(=O)Nc4cccc(c4)NC(=O)c5cccc(c5)C(F)(F)F
ACDLabs 12.01FC(F)(F)c1cccc(c1)C(=O)Nc2cccc(c2)NC(=O)c3sc(nc3)Nc5nc(nc(N4CCN(CCO)CC4)c5)C
FormulaC29 H29 F3 N8 O3 S
Name2-({6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-methylpyrimidin-4-yl}amino)-N-(3-{[3-(trifluoromethyl)benzoyl]amino}phenyl)-1,3-thiazole-5-carboxamide
ChEMBL
DrugBank
ZINCZINC000584904642
PDB chain4ybj Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4ybj Conformation-Selective Analogues of Dasatinib Reveal Insight into Kinase Inhibitor Binding and Selectivity.
Resolution2.61 Å
Binding residue
(original residue number in PDB)		L273 A293 K295 E310 M314 I336 T338 Y340 M341 S342 G344 L393 V402 A403 D404 F405
Binding residue
(residue number reindexed from 1)		L15 A33 K35 E50 M54 I76 T78 Y80 M81 S82 G84 L133 V142 A143 D144 F145
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=9.28,Kd=0.53nM
Enzymatic activity
Catalytic site (original residue number in PDB) D386 R388 A390 N391 D404
Catalytic site (residue number reindexed from 1) D126 R128 A130 N131 D144
Enzyme Commision number 2.7.10.2: non-specific 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:4ybj, PDBe:4ybj, PDBj:4ybj
PDBsum4ybj
PubMed26895387
UniProtP00523|SRC_CHICK Proto-oncogene tyrosine-protein kinase Src (Gene Name=SRC)

[Back to BioLiP]