1G5S

CRYSTAL STRUCTURE OF HUMAN CYCLIN DEPENDENT KINASE 2 (CDK2) IN COMPLEX WITH THE INHIBITOR H717


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of human cyclin-dependent kinase 2 in complex with the adenine-derived inhibitor H717.

Dreyer, M.K.Borcherding, D.R.Dumont, J.A.Peet, N.P.Tsay, J.T.Wright, P.S.Bitonti, A.J.Shen, J.Kim, S.H.

(2001) J.Med.Chem. 44: 524-530


  • PubMed Abstract: 
  • Cyclin-dependent kinases (CDKs) are regulatory proteins of the eukaryotic cell cycle. They act after association with different cyclins, the concentrations of which vary throughout the progression of the cell cycle. As central mediators of cell growt ...

    Cyclin-dependent kinases (CDKs) are regulatory proteins of the eukaryotic cell cycle. They act after association with different cyclins, the concentrations of which vary throughout the progression of the cell cycle. As central mediators of cell growth, CDKs are potential targets for inhibitory molecules that would allow disruption of the cell cycle in order to evoke an antiproliferative effect and may therefore be useful as cancer therapeutics. We synthesized several inhibitory 2,6,9-trisubstituted purine derivatives and solved the crystal structure of one of these compounds, H717, in complex with human CDK2 at 2.6 A resolution. The orientation of the C2-p-diaminocyclohexyl portion of the inhibitor is strikingly different from those of similar moieties in other related inhibitor complexes. The N9-cyclopentyl ring fully occupies a space in the enzyme which is otherwise empty, while the C6-N-aminobenzyl substituent points out of the ATP-binding site. The structure provides a basis for the further development of more potent inhibitory drugs.


    Related Citations: 
    • Purification and crystallization of human cyclin-dependent kinase 2
      Rosenblatt, J.,DeBondt, H.,Jancarik, J.,Morgan, D.O.,Kim, S.-H.
      (1993) J.Mol.Biol. 230: 1317


    Organizational Affiliation

    Department of Chemistry and Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, USA. dreyer@biozentrum.uni.wuerzburg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CELL DIVISION PROTEIN KINASE 2
A
298Homo sapiensGene Names: CDK2 (CDKN2)
EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens)
Go to Gene View: CDK2
Go to UniProtKB:  P24941
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I17
Query on I17

Download SDF File 
Download CCD File 
A
2-[TRANS-(4-AMINOCYCLOHEXYL)AMINO]-6-(BENZYL-AMINO)-9-CYCLOPENTYLPURINE
C23 H31 N7
JTVILUUAQWQWBK-IYARVYRRSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
I17IC50: 48 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.180α = 90.00
b = 72.840β = 90.00
c = 73.470γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORphasing
X-PLORmodel building
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description