4BCH

Structure of CDK9 in complex with cyclin T and a 2-amino-4-heteroaryl- pyrimidine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.958 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Comparative Structural and Functional Studies of 4-(Thiazol- 5-Yl)-2-(Phenylamino)Pyrimidine-5-Carbonitrile Cdk9 Inhibitors Suggest the Basis for Isotype Selectivity.

Hole, A.J.Baumli, S.Shao, H.Shi, S.Pepper, C.Fischer, P.M.Wang, S.Endicott, J.A.Noble, M.E.M.

(2013) J.Med.Chem. 56: 660

  • DOI: 10.1021/jm301495v
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cyclin-dependent kinase 9/cyclin T, the protein kinase heterodimer that constitutes positive transcription elongation factor b, is a well-validated target for treatment of several diseases, including cancer and cardiac hypertrophy. In order to aid in ...

    Cyclin-dependent kinase 9/cyclin T, the protein kinase heterodimer that constitutes positive transcription elongation factor b, is a well-validated target for treatment of several diseases, including cancer and cardiac hypertrophy. In order to aid inhibitor design and rationalize the basis for CDK9 selectivity, we have studied the CDK-binding properties of six different members of a 4-(thiazol-5-yl)-2-(phenylamino)pyrimidine-5-carbonitrile series that bind to both CDK9/cyclin T and CDK2/cyclin A. We find that for a given CDK, the melting temperature of a CDK/cyclin/inhibitor complex correlates well with inhibitor potency, suggesting that differential scanning fluorimetry (DSF) is a useful orthogonal measure of inhibitory activity for this series. We have used DSF to demonstrate that the binding of these compounds is independent of the presence or absence of the C-terminal tail region of CDK9, unlike the binding of the CDK9-selective inhibitor 5,6-dichlorobenzimidazone-1-β-d-ribofuranoside (DRB). Finally, on the basis of 11 cocrystal structures bound to CDK9/cyclin T or CDK2/cyclin A, we conclude that selective inhibition of CDK9/cyclin T by members of the 4-(thiazol-5-yl)-2-(phenylamino)pyrimidine-5-carbonitrile series results from the relative malleability of the CDK9 active site rather than from the formation of specific polar contacts.


    Organizational Affiliation

    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
T7Z
Query on T7Z

Download SDF File 
Download CCD File 
A
4-(4-methyl-2-methylimino-3H-1,3-thiazol-5-yl)-2-[(4-methyl-3-morpholin-4-ylsulfonyl-phenyl)amino]pyrimidine-5-carbonitrile
C21 H23 N7 O3 S2
SSEDQERECATUBR-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 %)
T7ZKi: 22 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.958 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.167 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 174.185α = 90.00
b = 174.185β = 90.00
c = 98.300γ = 120.00
Software Package:
Software NamePurpose
PHENIXphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-09
    Type: Initial release
  • Version 1.1: 2013-02-27
    Type: Database references