3MY1

Structure of CDK9/cyclinT1 in complex with DRB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Halogen bonds form the basis for selective P-TEFb inhibition by DRB

Baumli, S.Endicott, J.A.Johnson, L.N.

(2010) Chem Biol 17: 931-936

  • DOI: https://doi.org/10.1016/j.chembiol.2010.07.012
  • Primary Citation of Related Structures:  
    3MY1, 3MY5

  • PubMed Abstract: 

    Cdk9, the kinase of the positive transcription elongation factor b, is required for processive transcription elongation by RNA polymerase II. Cdk9 inhibition contributes to the anticancer activity of many Cdk inhibitors under clinical investigation and hence there is interest in selective Cdk9 inhibitors. DRB (5,6-dichlorobenzimidazone-1-β-D-ribofuranoside) is a commonly used reagent for Cdk9 inhibition in cell biology studies. The crystal structures of Cdk9 and Cdk2 in complex with DRB reported here describe the molecular basis for the DRB selectivity toward Cdk9. The DRB chlorine atoms form halogen bonds that are specific for the Cdk9 kinase hinge region. Kinetic and thermodynamic experiments validate the structural findings and implicate the C-terminal residues of Cdk9 in contributing to the affinity for DRB. These results open the possibility to exploit halogen atoms in inhibitor design to specifically target Cdk9.


  • Organizational Affiliation

    Department of Biochemistry/Laboratory of Molecular Biophysics, University of Oxford, UK. Sonja.baumli@bioch.ox.ac.uk


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division protein kinase 9331Homo sapiensMutation(s): 0 
Gene Names: CDC2L4CDK9
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P50750 (Homo sapiens)
Go to UniProtKB:  P50750
PHAROS:  P50750
GTEx:  ENSG00000136807 
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-T1260Homo sapiensMutation(s): 3 
Gene Names: CCNT1
UniProt & NIH Common Fund Data Resources
Find proteins for O60563 (Homo sapiens)
Go to UniProtKB:  O60563
PHAROS:  O60563
GTEx:  ENSG00000129315 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Binding Affinity Annotations 
IDSourceBinding Affinity
RFZ BindingDB:  3MY1 Ki: 340 (nM) from 1 assay(s)
PDBBind:  3MY1 IC50: 3580 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.789α = 90
b = 173.789β = 90
c = 99.221γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXmodel building
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-30
    Changes: Structure summary