5NEV

CDK2/Cyclin A in complex with compound 73

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

wwPDB Validation 3D Report Full Report



Literature

Cyclin-Dependent Kinase (CDK) Inhibitors: Structure-Activity Relationships and Insights into the CDK-2 Selectivity of 6-Substituted 2-Arylaminopurines.

Coxon, C.R., Anscombe, E., Harnor, S.J., Martin, M.P., Carbain, B., Golding, B.T., Hardcastle, I.R., Harlow, L.K., Korolchuk, S., Matheson, C.J., Newell, D.R., Noble, M.E., Sivaprakasam, M., Tudhope, S.J., Turner, D.M., Wang, L.Z., Wedge, S.R., Wong, C., Griffin, R.J., Endicott, J.A., Cano, C.

(2017) J Med Chem 60: 1746-1767

  • DOI: 10.1021/acs.jmedchem.6b01254
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • Purines and related heterocycles substituted at C-2 with 4'-sulfamoylanilino and at C-6 with a variety of groups have been synthesized with the aim of achieving selectivity of binding to CDK2 over CDK1. 6-Substituents that favor competitive inhibitio ...

    Purines and related heterocycles substituted at C-2 with 4'-sulfamoylanilino and at C-6 with a variety of groups have been synthesized with the aim of achieving selectivity of binding to CDK2 over CDK1. 6-Substituents that favor competitive inhibition at the ATP binding site of CDK2 were identified and typically exhibited 10-80-fold greater inhibition of CDK2 compared to CDK1. Most impressive was 4-((6-([1,1'-biphenyl]-3-yl)-9H-purin-2-yl)amino) benzenesulfonamide (73) that exhibited high potency toward CDK2 (IC 50 0.044 μM) but was ∼2000-fold less active toward CDK1 (IC 50 86 μM). This compound is therefore a useful tool for studies of cell cycle regulation. Crystal structures of inhibitor-kinase complexes showed that the inhibitor stabilizes a glycine-rich loop conformation that shapes the ATP ribose binding pocket and that is preferred in CDK2 but has not been observed in CDK1. This aspect of the active site may be exploited for the design of inhibitors that distinguish between CDK1 and CDK2.

    Organizational Affiliation: 

    Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Newcastle University , Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cyclin-A2
B, D
260Homo sapiensMutation(s): 0 
Gene Names: CCNA2, CCN1, CCNA
Find proteins for P20248 (Homo sapiens)
Go to UniProtKB:  P20248
NIH Common Fund Data Resources
PHAROS  P20248
GTEx  ENSG00000145386
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 2
A, C
303Homo sapiensMutation(s): 0 
Gene Names: CDK2, CDKN2
EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens)
Go to UniProtKB:  P24941
NIH Common Fund Data Resources
PHAROS  P24941
GTEx  ENSG00000123374
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
72L
Query on 72L
Download CCD File 
A, C
4-[[6-(3-phenylphenyl)-7~{H}-purin-2-yl]amino]benzenesulfonamide
C23 H18 N6 O2 S
FUGRWXRQJGJIER-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO		A,CL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.527α = 90
b = 132.053β = 90
c = 149.22γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-29
    Type: Initial release