1DM2

HUMAN CYCLIN-DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR HYMENIALDISINE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.192 
  • R-Value Observed: 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

  • DOI: 10.1016/s1074-5521(00)00063-6
  • Primary Citation of Related Structures:  
    1DM2

  • 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.

    Related Citations: 
    • 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
    • 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
    • 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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYCLIN-DEPENDENT KINASE 2 A298Homo sapiensMutation(s): 0 
Gene Names: CDK2, CDKN2
EC: 2.7.1 (PDB Primary Data), 2.7.11.22 (UniProt)
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
NIH Common Fund Data Resources
PHAROS:  P24941
GTEx:  ENSG00000123374
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HMD
Query on HMD
Download Ideal Coordinates 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
C11 H10 Br N5 O2
QPCBNXNDVYOBIP-WHFBIAKZSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HMDIC50 :  70   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.39α = 90
b = 70.67β = 90
c = 72.26γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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