Structure of PDB 3pyy Chain B Binding Site BS01

Receptor Information
>3pyy Chain B (length=257) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLVEEFLKEAA
VMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLRECNRQEVNAV
VLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGAKFPI
KWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLE
KDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQESSIS
DEVEKEL
Ligand information
Ligand IDSTI
InChIInChI=1S/C29H31N7O/c1-21-5-10-25(18-27(21)34-29-31-13-11-26(33-29)24-4-3-12-30-19-24)32-28(37)23-8-6-22(7-9-23)20-36-16-14-35(2)15-17-36/h3-13,18-19H,14-17,20H2,1-2H3,(H,32,37)(H,31,33,34)
InChIKeyKTUFNOKKBVMGRW-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1ccc(cc1Nc2nccc(n2)c3cccnc3)NC(=O)c4ccc(cc4)CN5CCN(CC5)C
CACTVS 3.341CN1CCN(CC1)Cc2ccc(cc2)C(=O)Nc3ccc(C)c(Nc4nccc(n4)c5cccnc5)c3
ACDLabs 10.04O=C(Nc3ccc(c(Nc2nc(c1cccnc1)ccn2)c3)C)c4ccc(cc4)CN5CCN(CC5)C
FormulaC29 H31 N7 O
Name4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE;
STI-571;
IMATINIB
ChEMBLCHEMBL941
DrugBankDB00619
ZINCZINC000019632618
PDB chain3pyy Chain B Residue 4 [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]
PDB3pyy Discovery and Characterization of a Cell-Permeable, Small-Molecule c-Abl Kinase Activator that Binds to the Myristoyl Binding Site.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		Y272 V275 K290 E305 M309 I332 T334 F336 M337 I379 H380 L389 A399 D400 F401
Binding residue
(residue number reindexed from 1)		Y21 V24 K39 E48 M52 I75 T77 F79 M80 I122 H123 L132 A142 D143 F144
Annotation score1
Binding affinityBindingDB: IC50=38nM,Kd=44nM,Ki=13nM,EC50=7e+1nM
Enzymatic activity
Catalytic site (original residue number in PDB) D382 A384 R386 N387 D400 P421
Catalytic site (residue number reindexed from 1) D125 A127 R129 N130 D143 P149
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:3pyy, PDBe:3pyy, PDBj:3pyy
PDBsum3pyy
PubMed21338916
UniProtP00519|ABL1_HUMAN Tyrosine-protein kinase ABL1 (Gene Name=ABL1)

[Back to BioLiP]