Structure of PDB 3kfa Chain A Binding Site BS01

Receptor Information
>3kfa Chain A (length=284) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSPNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDT
MEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYL
RECNRQEVSAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLV
KVADFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGV
LLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQ
WNPSDRPSFAEIHQAFETMFQESSISDEVEKELG
Ligand information
Ligand IDB91
InChIInChI=1S/C29H25F3N8O/c1-17-3-4-20(9-19(17)7-8-39-16-36-25-26(37-22-5-6-22)33-14-34-27(25)39)28(41)38-23-10-21(29(30,31)32)11-24(12-23)40-13-18(2)35-15-40/h3-4,7-16,22H,5-6H2,1-2H3,(H,38,41)(H,33,34,37)/b8-7+
InChIKeyXQBYDVRVYRYLCH-BQYQJAHWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0Cc1ccc(cc1C=Cn2cnc3c2ncnc3NC4CC4)C(=O)Nc5cc(cc(c5)n6cc(nc6)C)C(F)(F)F
OpenEye OEToolkits 1.7.0Cc1ccc(cc1/C=C/n2cnc3c2ncnc3NC4CC4)C(=O)Nc5cc(cc(c5)n6cc(nc6)C)C(F)(F)F
ACDLabs 11.02FC(F)(F)c2cc(cc(n1cc(nc1)C)c2)NC(=O)c3cc(c(cc3)C)\C=C\n4c5ncnc(c5nc4)NC6CC6
CACTVS 3.352Cc1cn(cn1)c2cc(NC(=O)c3ccc(C)c(/C=C/n4cnc5c(NC6CC6)ncnc45)c3)cc(c2)C(F)(F)F
CACTVS 3.352Cc1cn(cn1)c2cc(NC(=O)c3ccc(C)c(C=Cn4cnc5c(NC6CC6)ncnc45)c3)cc(c2)C(F)(F)F
FormulaC29 H25 F3 N8 O
Name3-{(E)-2-[6-(cyclopropylamino)-9H-purin-9-yl]ethenyl}-4-methyl-N-[3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl]benzamide
ChEMBLCHEMBL539433
DrugBank
ZINCZINC000042919869
PDB chain3kfa Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3kfa Structural analysis of DFG-in and DFG-out dual Src-Abl inhibitors sharing a common vinyl purine template.
Resolution1.22 Å
Binding residue
(original residue number in PDB)		L248 A269 V270 E282 E286 V289 M290 I293 I313 T315 F317 M318 G321 F359 H361 L370 A380 D381 F382
Binding residue
(residue number reindexed from 1)		L21 A42 V43 E55 E59 V62 M63 I66 I86 T88 F90 M91 G94 F132 H134 L143 A153 D154 F155
Annotation score1
Binding affinityMOAD: ic50=25nM
PDBbind-CN: -logKd/Ki=7.60,IC50=25nM
Enzymatic activity
Catalytic site (original residue number in PDB) D363 A365 R367 N368 D381 P402
Catalytic site (residue number reindexed from 1) D136 A138 R140 N141 D154 P175
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
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Biological Process
External links
PDB RCSB:3kfa, PDBe:3kfa, PDBj:3kfa
PDBsum3kfa
PubMed19895503
UniProtP00520|ABL1_MOUSE Tyrosine-protein kinase ABL1 (Gene Name=Abl1)

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