4BCP

Structure of CDK2 in complex with cyclin A and a 2-amino-4-heteroaryl- pyrimidine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.181 

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
  • Primary Citation of Related Structures:  4BCG

  • 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-anilinopyri ...

    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 2
A, C
300Homo sapiensGene Names: CDK2 (CDKN2)
EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens)
Go to Gene View: CDK2
Go to UniProtKB:  P24941
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CYCLIN-A2
B, D
262Homo sapiensGene Names: CCNA2 (CCN1, CCNA)
Find proteins for P20248 (Homo sapiens)
Go to Gene View: CCNA2
Go to UniProtKB:  P20248
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T3C
Query on T3C

Download SDF File 
Download CCD File 
A, C
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
SGM
Query on SGM

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Download CCD File 
B, D
MONOTHIOGLYCEROL
C3 H8 O2 S
PJUIMOJAAPLTRJ-GSVOUGTGSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
B, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A, C
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
T3CIC50: 1126 nM (100) BINDINGDB
T3CKi: 568 nM (100) BINDINGDB
T3CKi: 568 nM BINDINGMOAD
T3CKi: 568 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 73.810α = 90.00
b = 134.553β = 90.00
c = 149.168γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-17
    Type: Initial release
  • Version 1.1: 2013-08-07
    Type: Refinement description