Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.55 kDa 
• Atom Count: 2343 
• Modelled Residue Count: 274 
• Deposited Residue Count: 298 
• Unique protein chains: 1

1DM2

HUMAN CYCLIN-DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR HYMENIALDISINE

• PDB DOI: 10.2210/pdb1DM2/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• 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: 2.10 Å
• R-Value Free: 0.267 
• R-Value Work: 0.192 
• R-Value Observed: 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 
• 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLIN-DEPENDENT KINASE 2	A	298	Homo sapiens	Mutation(s): 0  Gene Names: CDK2, CDKN2 EC: 2.7.1 (PDB Primary Data), 2.7.11.22 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens) Explore P24941  Go to UniProtKB:  P24941
PHAROS:  P24941

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HMD	B [auth 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
EDO	C [auth A], D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
HMD	PDBBind:  1DM2	IC50: 70 (nM) from 1 assay(s)

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 = 53.39	α = 90
b = 70.67	β = 90
c = 72.26	γ = 90

Software Package:

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

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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-31
  Changes: Database references