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 

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
  • Structures With Same Primary Citation

  • 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 9A331Homo sapiensMutation(s): 0 
Gene Names: CDC2L4, CDK9, TAK
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
Find proteins for P50750 (Homo sapiens)
Explore P50750 
Go to UniProtKB:  P50750
NIH Common Fund Data Resources
PHAROS  P50750
GTEx  ENSG00000136807
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cyclin-T1B260Homo sapiensMutation(s): 3 
Gene Names: CCNT1
Find proteins for O60563 (Homo sapiens)
Explore O60563 
Go to UniProtKB:  O60563
NIH Common Fund Data Resources
PHAROS  O60563
GTEx  ENSG00000129315
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RFZ
Query on RFZ
Download CCD File 
A
5,6-dichloro-1-beta-D-ribofuranosyl-1H-benzimidazole
C12 H12 Cl2 N2 O4
XHSQDZXAVJRBMX-DDHJBXDOSA-N		 Ligand Interaction
PO4
Query on PO4
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
GOL
Query on GOL
Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO		AL-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: 2.80 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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Entry History 

Deposition Data

Revision History 

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