Biological Assembly 1  

 3D View: Structure | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.38 kDa 
• Atom Count: 2272 
• Modelled Residue Count: 275 
• Deposited Residue Count: 298 
• Unique protein chains: 1

1G5S

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

• DOI: 10.2210/pdb1G5S/pdb

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


• Deposited: 2000-11-02 Released: 2001-11-02 
• Deposition Author(s): 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.

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Experimental Data Snapshot

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

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: 11170642 
• DOI: 10.1021/jm001043t
• Primary Citation of Related Structures:  
  1G5S


• 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 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.

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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

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Organizational Affiliation: 

Department of Chemistry and Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CELL DIVISION PROTEIN 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 GTEx:  ENSG00000123374

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I17 (Subject of Investigation/LOI)	B [auth A]	2-[TRANS-(4-AMINOCYCLOHEXYL)AMINO]-6-(BENZYL-AMINO)-9-CYCLOPENTYLPURINE C23 H31 N7 JTVILUUAQWQWBK-IYARVYRRSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
I17	BindingDB:  1G5S	IC50: 48 (nM) from 1 assay(s)
	PDBBind:  1G5S	IC50: 48 (nM) from 1 assay(s)

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 = 54.18	α = 90
b = 72.84	β = 90
c = 73.47	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-11-02 
• Released Date: 2001-11-02 
Deposition Author(s): 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.

Revision History  

• Version 1.0: 2001-11-02
  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: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2018-04-04
  Changes: Data collection