The structure of cyclin-dependent kinase 2 (CDK2) in complex with 4-[(6-amino-4-pyrimidinyl)amino]benzenesulfonamide

Experimental Data Snapshot

  • Resolution: 1.96 Å

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


The cyclin-dependent kinases cdk2 and cdk5 act by a random, anticooperative kinetic mechanism

Clare, P.M.Poorman, R.A.Kelley, L.C.Watenpaugh, K.D.Bannow, C.A.Leach, K.L.

(2001) J Biol Chem 276: 48292-48299

  • DOI: https://doi.org/10.1074/jbc.M102034200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    cdk2.cyclin E and cdk5.p25 are two members of the cyclin-dependent kinase family that are potential therapeutic targets for oncology and Alzheimer's disease, respectively. In this study we have investigated the mechanism for these enzymes. Kinases catalyze the transfer of phosphate from ATP to a protein acceptor, thus utilizing two substrates, ATP and the target protein. For a two-substrate reaction, possible kinetic mechanisms include: ping-pong, sequential random, or sequential ordered. To determine the kinetic mechanism of cdk2.GST-cyclin E and cdk5.GST-p25, kinase activity was measured in experiments in which concentrations of peptide and ATP substrates were varied in the presence of dead-end inhibitors. A peptide identical to the peptide substrate, but with a substitution of valine for the phosphoacceptor threonine, competed with substrate with a K(i) value of 0.6 mm. An aminopyrimidine, PNU 112455A, was identified in a screen for inhibitors of cdk2. Nonlinear least squares and Lineweaver-Burk analyses demonstrated that the inhibitor PNU 112455A was competitive with ATP with a K(i) value of 2 microm. In addition, a co-crystal of PNU 112455A with cdk2 showed that the inhibitor binds in the ATP binding pocket of the enzyme. Analysis of the inhibitor data demonstrated that both kinases use a sequential random mechanism, in which either ATP or peptide may bind first to the enzyme active site. For both kinases, the binding of the second substrate was shown to be anticooperative, in that the binding of the first substrate decreases the affinity of the second substrate. For cdk2.GST-cyclin E the kinetic parameters were determined to be K(m, ATP) = 3.6 +/- 1.0 microm, K(m, peptide) = 4.6 +/- 1.4 microm, and the anticooperativity factor, alpha = 130 +/- 44. For cdk5.GST-p25, the K(m, ATP) = 3.2 +/- 0.7 microm, K(m, peptide) = 1.6 +/- 0.3 microm, and alpha = 7.2 +/- 1.8.

  • Organizational Affiliation

    Department of Cell and Molecular Biology, Pharmacia Corporation, Kalamazoo, Michigan 49007-4940, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CELL DIVISION PROTEIN KINASE 2298Homo sapiensMutation(s): 0 
Gene Names: CDK2CDKN2
EC: 2.7.1 (PDB Primary Data), (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
PHAROS:  P24941
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24941
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on U55

Download Ideal Coordinates CCD File 
C10 H11 N5 O2 S
Binding Affinity Annotations 
IDSourceBinding Affinity
U55 PDBBind:  1JSV Ki: 2000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.96 Å
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.032α = 90
b = 72.058β = 90
c = 72.197γ = 90
Software Package:
Software NamePurpose
Siemensdata collection
SAINTdata reduction
SIEMENSdata reduction
SAINTdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-08-29
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2018-04-04
    Changes: Data collection