Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 34222.80 
• Atom Count: 2314 
• Residue Count: 298 
• Unique protein chains: 1

1H0W

Human cyclin dependent protein kinase 2 in complex with the inhibitor 2-Amino-6-[cyclohex-3-enyl]methoxypurine

• DOI: 10.2210/pdb1H0W/pdb

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


• Deposited: 2002-06-27 Released: 2003-06-27 
• Deposition Author(s): Gibson, A.E., Arris, C.E., Bentley, J., Boyle, F.T., Curtin, N.J., Davies, T.G., Endicott, J.A., Golding, B.T., Grant, S., Griffin, R.J., Jewsbury, P., Johnson, L.N., Mesguiche, V., Newell, D.R., Noble, M.E.M., Tucker, J.A., Whitfield, H.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.287 
• R-Value Work: 0.210 

Literature

Probing the ATP Ribose-Binding Domain of Cyclin-Dependent Kinases 1 and 2 with O(6)-Substituted Guanine Derivatives

Gibson, A.E., Arris, C.E., Bentley, J., Boyle, F.T., Curtin, N.J., Davies, T.G., Endicott, J.A., Golding, B.T., Grant, S., Griffin, R.J., Jewsbury, P., Johnson, L.N., Mesguiche, V., Newell, D.R., Noble, M.E.M., Tucker, J.A., Whitfield, H.J.

(2002) J.Med.Chem. 45: 3381

• PubMed: 12139449 
• Primary Citation of Related Structures:  
  1H0V, 1GZ8


• PubMed Abstract: 
  

O(6)-substituted guanines are adenosine 5'-triphosphate (ATP) competitive inhibitors of CDK1/cyclin B1 and CDK2/cyclin A, the O(6) substituent occupying the kinase ribose binding site. Fifty-eight O(6)-substituted guanines were prepared to probe the ribose pocket, and the structures of four representative compounds bound to monomeric CDK2 were determined by X-ray crystallography. Optimum binding occurs with a moderately sized aliphatic O(6) substituent that packs tightly against the hydrophobic patch presented by the glycine loop, centered on Val18, an interaction promoted by the conformational restraints imposed in a cyclohexylmethyl or cyclohexenylmethyl ring. Structure-based design generated (R)-(2-amino-9H-purin-6-yloxymethyl)pyrrolidin-2-one (56), which reproduces the reported hydrogen bonds formed between ATP and Asp86 and Gln131 but failed to improve inhibitory potency. Thus, the parent compound O(6)-cyclohexylmethylguanine (NU2058, 25) is the preferred starting point for exploring other areas of the kinase active site.

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Organizational Affiliation: 

Department of Chemistry and Cancer Research Unit, University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CELL DIVISION PROTEIN 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
207	A	1-AMINO-6-CYCLOHEX-3-ENYLMETHYLOXYPURINE C13 H18 N4 O VPUIDVRYMVIXGO-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
207	IC50: 13000 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.287 
• R-Value Work: 0.210 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 53.422	α = 90.00
b = 72.264	β = 90.00
c = 72.375	γ = 90.00

Software Package:

Software Name	Purpose
CCP4	phasing
DENZO	data reduction
REFMAC	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-06-27 
• Released Date: 2003-06-27 
• Deposition Author(s): Gibson, A.E., Arris, C.E., Bentley, J., Boyle, F.T., Curtin, N.J., Davies, T.G., Endicott, J.A., Golding, B.T., Grant, S., Griffin, R.J., Jewsbury, P., Johnson, L.N., Mesguiche, V., Newell, D.R., Noble, M.E.M., Tucker, J.A., Whitfield, H.J.

Revision History 

• Version 1.0: 2003-06-27
  Type: Initial release
• Version 1.1: 2011-05-08
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2019-03-06
  Type: Data collection, Derived calculations, Experimental preparation, Other