Structure of PDB 3my1 Chain A Binding Site BS01

Receptor Information
>3my1 Chain A (length=315) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DSVECPFCDEVSKYEKLAKIGQGTFGEVFKARHRKTGQKVALKKVLMENE
KEGFPITALREIKILQLLKHENVVNLIEICRTKKGSIYLVFDFCEHDLAG
LLSNVLVKFTLSEIKRVMQMLLNGLYYIHRNKILHRDMKAANVLITRDGV
LKLADFGLARAFSLAKNSQPNRYTNRVVTLWYRPPELLLGERDYGPPIDL
WGAGCIMAEMWTRSPIMQGNTEQHQLALISQLCGSITPEVWPNVDNYELY
EKLELVKGQKRKVKDRLKAYVRDPYALDLIDKLLVLDPAQRIDSDDALNH
DFFWSDPMPSDLKGM
Ligand information
Ligand IDRFZ
InChIInChI=1S/C12H12Cl2N2O4/c13-5-1-7-8(2-6(5)14)16(4-15-7)12-11(19)10(18)9(3-17)20-12/h1-2,4,9-12,17-19H,3H2/t9-,10-,11-,12-/m1/s1
InChIKeyXHSQDZXAVJRBMX-DDHJBXDOSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3cc(Cl)c(Cl)cc23
OpenEye OEToolkits 1.5.0c1c2c(cc(c1Cl)Cl)n(cn2)C3C(C(C(O3)CO)O)O
OpenEye OEToolkits 1.5.0c1c2c(cc(c1Cl)Cl)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O
CACTVS 3.341OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3cc(Cl)c(Cl)cc23
ACDLabs 10.04Clc2cc1ncn(c1cc2Cl)C3OC(C(O)C3O)CO
FormulaC12 H12 Cl2 N2 O4
Name5,6-dichloro-1-beta-D-ribofuranosyl-1H-benzimidazole
ChEMBLCHEMBL375530
DrugBankDB08473
ZINCZINC000003873418
PDB chain3my1 Chain A Residue 336 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3my1 Halogen bonds form the basis for selective P-TEFb inhibition by DRB
Resolution2.8 Å
Binding residue
(original residue number in PDB)		A46 D104 F105 C106 L156 D167
Binding residue
(residue number reindexed from 1)		A41 D92 F93 C94 L144 D155
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.45,IC50=3.58uM
Enzymatic activity
Catalytic site (original residue number in PDB) D149 K151 A153 N154 D167 S180 T191
Catalytic site (residue number reindexed from 1) D137 K139 A141 N142 D155 S168 T179
Enzyme Commision number 2.7.11.22: cyclin-dependent kinase.
2.7.11.23: [RNA-polymerase]-subunit kinase.
Gene Ontology
Molecular Function
GO:0004672 protein 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:3my1, PDBe:3my1, PDBj:3my1
PDBsum3my1
PubMed20851342
UniProtP50750|CDK9_HUMAN Cyclin-dependent kinase 9 (Gene Name=CDK9)

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