3TN8

CDK9/cyclin T in complex with CAN508


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The CDK9 C-helix Exhibits Conformational Plasticity That May Explain the Selectivity of CAN508.

Baumli, S.Hole, A.J.Noble, M.E.Endicott, J.A.

(2012) Acs Chem.Biol. 7: 811-816

  • DOI: 10.1021/cb2004516
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • CDK9 is the kinase of positive transcription elongation factor b and facilitates the transition of paused RNA polymerase II to processive transcription elongation. CDK9 is a validated target for the treatment of cancer, cardiac hypertrophy, and human ...

    CDK9 is the kinase of positive transcription elongation factor b and facilitates the transition of paused RNA polymerase II to processive transcription elongation. CDK9 is a validated target for the treatment of cancer, cardiac hypertrophy, and human immunodeficiency virus. Here we analyze different CDK9/cyclin T variants to identify a form of the complex amenable to use in inhibitor design. To demonstrate the utility of this system, we have determined the crystal structures of CDK9/cyclin T and CDK2/cyclin A bound to the CDK9-specific inhibitor CAN508. Comparison of the structures reveals CDK9-specific conformational changes and identifies a CDK9-specific hydrophobic pocket, adjacent to the αC-helix. By comparison with a previously published structure of CDK9/cyclin T/human immunodeficiency virus TAT we find that the CDK9 αC-helix has a degree of conformational variability that has the potential to be exploited for inhibitor design.


    Organizational Affiliation

    Northern Institute for Cancer Research, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K. sonja.baumli@ncl.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent 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, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
F18
Query on F18

Download SDF File 
Download CCD File 
A
4-[(E)-(3,5-DIAMINO-1H-PYRAZOL-4-YL)DIAZENYL]PHENOL
CAN508
C9 H10 N6 O
AYZRKFOEZQBUEA-SEYXRHQNSA-N
 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
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 %)
F18IC50: 350 nM (100) BINDINGDB
F18IC50: 740 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.176 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 173.420α = 90.00
b = 173.420β = 90.00
c = 97.891γ = 120.00
Software Package:
Software NamePurpose
ADSCdata collection
MOSFLMdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2012-06-13
    Type: Database references