Structure of PDB 3cs9 Chain D Binding Site BS01

Receptor Information
>3cs9 Chain D (length=263) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DKWEMERTDITMKHKLGGGQYGEVYEGVWTVAVKTLKEDTMEVEEFLKEA
AVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLRECNRQEVNA
VVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRL
MTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGM
SPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFA
EIHQAFETMFQES
Ligand information
Ligand IDNIL
InChIInChI=1S/C28H22F3N7O/c1-17-5-6-19(10-25(17)37-27-33-9-7-24(36-27)20-4-3-8-32-14-20)26(39)35-22-11-21(28(29,30)31)12-23(13-22)38-15-18(2)34-16-38/h3-16H,1-2H3,(H,35,39)(H,33,36,37)
InChIKeyHHZIURLSWUIHRB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cn(cn1)c2cc(NC(=O)c3ccc(C)c(Nc4nccc(n4)c5cccnc5)c3)cc(c2)C(F)(F)F
OpenEye OEToolkits 1.5.0Cc1ccc(cc1Nc2nccc(n2)c3cccnc3)C(=O)Nc4cc(cc(c4)n5cc(nc5)C)C(F)(F)F
ACDLabs 10.04FC(F)(F)c1cc(cc(c1)n2cc(nc2)C)NC(=O)c5ccc(c(Nc4nc(c3cccnc3)ccn4)c5)C
FormulaC28 H22 F3 N7 O
NameNilotinib;
4-methyl-N-[3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl]-3-[(4-pyridin-3-ylpyrimidin-2-yl)amino]benzamide
ChEMBLCHEMBL255863
DrugBankDB04868
ZINCZINC000006716957
PDB chain3cs9 Chain D Residue 600 [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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PDB3cs9 Characterization of AMN107, a selective inhibitor of native and mutant Bcr-Abl
Resolution2.21 Å
Binding residue
(original residue number in PDB)		L248 Y253 A269 K271 E286 V289 M290 T315 F317 M318 H361 A380 D381 F382
Binding residue
(residue number reindexed from 1)		L16 Y21 A32 K34 E49 V52 M53 T78 F80 M81 H124 A143 D144 F145
Annotation score1
Binding affinityMOAD: ic50<33uM
BindingDB: Kd=10nM,IC50=20nM,Ki=1nM
Enzymatic activity
Catalytic site (original residue number in PDB) D363 A365 R367 N368 D381 P402
Catalytic site (residue number reindexed from 1) D126 A128 R130 N131 D144 P165
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:3cs9, PDBe:3cs9, PDBj:3cs9
PDBsum3cs9
PubMed15710326
UniProtP00519|ABL1_HUMAN Tyrosine-protein kinase ABL1 (Gene Name=ABL1)

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