Structure of PDB 6npu Chain B Binding Site BS01

Receptor Information
>6npu 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 chain6npu Chain B Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6npu Identification and Optimization of Novel Small c-Abl Kinase Activators Using Fragment and HTS Methodologies.
Resolution2.33 Å
Binding residue
(original residue number in PDB)		L267 Y272 V275 A288 K290 E305 V308 M309 V318 I332 T334 F336 M337 I379 H380 A399 D400 F401
Binding residue
(residue number reindexed from 1)		L16 Y21 V24 A37 K39 E48 V51 M52 V61 I75 T77 F79 M80 I122 H123 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

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Molecular Function
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Biological Process
External links
PDB RCSB:6npu, PDBe:6npu, PDBj:6npu
PDBsum6npu
PubMed30689376
UniProtP00519|ABL1_HUMAN Tyrosine-protein kinase ABL1 (Gene Name=ABL1)

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