Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34548.89 
• Atom Count: 2258 
• Residue Count: 298 
• Unique protein chains: 1

1DM2

HUMAN CYCLIN-DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR HYMENIALDISINE

• DOI: 10.2210/pdb1DM2/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda


• Deposited: 1999-12-13 Released: 2000-05-31 
• Deposition Author(s): Thunnissen, A.M., Kim, S.-H.

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Experimental Data Snapshot

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

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: 10662688 


• 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.

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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




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Organizational Affiliation: 

CNRS, Station Biologique, Roscoff cedex, 29682, France. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CYCLIN-DEPENDENT KINASE 2	A	298	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
HMD	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
HMD	IC50: 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 = 53.390	α = 90.00
b = 70.670	β = 90.00
c = 72.260	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	phasing
SCALEPACK	data scaling
DENZO	data reduction
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-12-13 
• Released Date: 2000-05-31 
• Deposition Author(s): Thunnissen, A.M., Kim, S.-H.

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