4BCG

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Substituted 4-(Thiazol-5-Yl)-2-(Phenylamino)Pyrimidines are Highly Active Cdk9 Inhibitors: Synthesis, X-Ray Crystal Structure, Sar and Anti-Cancer Activities.

Shao, H., Shi, S., Huang, S., Hole, A., Abbas, A.Y., Baumli, S., Liu, X., Lam, F., Foley, D.W., Fischer, P.M., Noble, M., Endicott, J.A., Pepper, C., Wang, S.

(2013) J Med Chem 56: 640

  • DOI: 10.1021/jm301475f
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • Cancer cells often have a high demand for antiapoptotic proteins in order to resist programmed cell death. CDK9 inhibition selectively targets survival proteins and reinstates apoptosis in cancer cells. We designed a series of 4-thiazol-2-anilinopyrimidine derivatives with functional groups attached to the C5-position of the pyrimidine or to the C4-thiazol moiety and investigated their effects on CDK9 potency and selectivity ...

    Cancer cells often have a high demand for antiapoptotic proteins in order to resist programmed cell death. CDK9 inhibition selectively targets survival proteins and reinstates apoptosis in cancer cells. We designed a series of 4-thiazol-2-anilinopyrimidine derivatives with functional groups attached to the C5-position of the pyrimidine or to the C4-thiazol moiety and investigated their effects on CDK9 potency and selectivity. One of the most selective compounds, 12u inhibits CDK9 with IC(50) = 7 nM and shows over 80-fold selectivity for CDK9 versus CDK2. X-ray crystal structures of 12u bound to CDK9 and CDK2 provide insights into the binding modes. This work, together with crystal structures of selected inhibitors in complex with both enzymes described in a companion paper, (34) provides a rationale for the observed SAR. 12u demonstrates potent anticancer activity against primary chronic lymphocytic leukemia cells with a therapeutic window 31- and 107-fold over those of normal B- and T-cells.

    Organizational Affiliation: 

    School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYCLIN-DEPENDENT KINASE 9A331Homo sapiensMutation(s): 0 
Gene Names: CDK9, CDC2L4, 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T3C
Query on T3C
Download CCD File 
A
2-[[3-(1,4-diazepan-1-yl)phenyl]amino]-4-[4-methyl-2-(methylamino)-1,3-thiazol-5-yl]pyrimidine-5-carbonitrile
C21 H24 N8 S
BKOYUSKBPMSUBK-UHFFFAOYSA-N		 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 %)
T3CKi:  7   nM  BindingDB
T3CKi :  7   nM  PDBBind
T3CIC50:  14   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.8α = 90
b = 172.8β = 90
c = 98.88γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-17
    Type: Initial release
  • Version 1.1: 2019-05-15
    Changes: Data collection, Derived calculations, Experimental preparation, Other