1DM2

HUMAN CYCLIN-DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR HYMENIALDISINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Inhibition of cyclin-dependent kinases, GSK-3beta and CK1 by hymenialdisine, a marine sponge constituent.

Meijer, L.Thunnissen, A.M.White, A.W.Garnier, M.Nikolic, M.Tsai, L.H.Walter, J.Cleverley, K.E.Salinas, P.C.Wu, Y.Z.Biernat, J.Mandelkow, E.M.Kim, S.H.Pettit, G.R.

(2000) Chem.Biol. 7: 51-63


  • PubMed Abstract: 
  • Over 2000 protein kinases regulate cellular functions. Screening for inhibitors of some of these kinases has already yielded some potent and selective compounds with promising potential for the treatment of human diseases.

    Over 2000 protein kinases regulate cellular functions. Screening for inhibitors of some of these kinases has already yielded some potent and selective compounds with promising potential for the treatment of human diseases.


    Related Citations: 
    • Inhibition of Cyclin-Dependent Kinases by Purine Analogues-Crystal Structure of Human Cdk2 Complexed with Roscovitine
      De Azevedo, W.F.,Leclerc, S.,Meijer, L.,Havlicek, L.,Strnad, M.,Kim, S.-H.
      (1997) Eur.J.Biochem. 243: 518
    • Multiple Modes of Ligand Recognition: Crystal Structures of Cyclin-Dependent Protein Kinase 2 in Complex with ATP and Two Inhibitors, Olomoucine and Isopentenyladenine
      Schultze-Gahmen, U.,Brandsen, J.,Jones, H.D.,Morgan, D.O.,Meijer, L.,Vesely, J.,Kim, S.-H.
      (1995) Proteins 22: 378
    • Exploiting Chemical Libraries, Structure, and Genomics in the Search for Kinase Inhibitors
      Gray, N.S.,Wodicka, L.,Thunnissen, A.M.W.H.,Norman, T.C.,Kwon, S.,Espinoza, F.H.,Morgan, D.O.,Barnes, G.,Leclerc, S.,Meijer, L.,Kim, S.-H.,Lockhart, D.J.,Schultz, P.G.
      (1998) Science 281: 533
    • Crystal Structure of Cyclin-Dependent Kinase 2
      De Bondt, H.L.,Rosenblatt, J.,Jancarik, J.,Jones, H.D.,Morgan, D.O.,Kim, S.-H.
      (1993) Nature 363: 595


    Organizational Affiliation

    CNRS, Station Biologique, Roscoff cedex, 29682, France. meijer@sb-roscoff.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYCLIN-DEPENDENT KINASE 2
A
298Homo sapiensMutation(s): 0 
Gene 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
HMD
Query on HMD

Download SDF File 
Download CCD File 
A
4-(5-AMINO-4-OXO-4H-PYRAZOL-3-YL)-2-BROMO-4,5,6,7-TETRAHYDRO-3AH-PYRROLO[2,3-C]AZEPIN-8-ONE
HYMENIALDISINE
C11 H10 Br N5 O2
QPCBNXNDVYOBIP-WHFBIAKZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HMDIC50: 70 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.390α = 90.00
b = 70.670β = 90.00
c = 72.260γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
SCALEPACKdata scaling
DENZOdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-05-31
    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: 2018-01-31
    Type: Database references