3MY1

Structure of CDK9/cyclinT1 in complex with DRB

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.chembiol.2010.07.012
  • Primary Citation of Related Structures:  

  • 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 a ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cell division protein kinase 9
A
331Homo sapiensMutation(s): 0 
Gene Names: CDK9 (CDC2L4, TAK)
EC: 2.7.11.22, 2.7.11.23
Find proteins for P50750 (Homo sapiens)
Go to Gene View: CDK9
Go to UniProtKB:  P50750
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cyclin-T1
B
260Homo sapiensMutation(s): 3 
Gene Names: CCNT1
Find proteins for O60563 (Homo sapiens)
Go to Gene View: CCNT1
Go to UniProtKB:  O60563
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
RFZ
Query on RFZ
Download SDF File 
Download CCD File 
A
5,6-dichloro-1-beta-D-ribofuranosyl-1H-benzimidazole
C12 H12 Cl2 N2 O4
XHSQDZXAVJRBMX-DDHJBXDOSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RFZIC50: 3580 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.173 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 173.789α = 90.00
b = 173.789β = 90.00
c = 99.221γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
ADSCdata collection
PHENIXphasing
PHENIXmodel building
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance