Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 34.22 kDa 
• Atom Count: 2447 
• Modelled Residue Count: 283 
• Deposited 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
• Mutation(s): No 


• 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: 2.10 Å
• R-Value Free: 0.287 
• R-Value Work: 0.210 
• R-Value Observed: 0.214 

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 
• DOI: 10.1021/jm020056z
• Primary Citation of Related Structures:  
  1GZ8, 1H0V, 1H0W


• 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

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: 2.7.1.37 (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
207 (Subject of Investigation/LOI)	B [auth A]	1-AMINO-6-CYCLOHEX-3-ENYLMETHYLOXYPURINE C13 H18 N4 O VPUIDVRYMVIXGO-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
207	PDBBind:  1H0W	IC50: 1.30e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.287 
• R-Value Work: 0.210 
• R-Value Observed: 0.214 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.422	α = 90
b = 72.264	β = 90
c = 72.375	γ = 90

Software Package:

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

Structure Validation

Ligand Structure Quality Assessment  

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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-03-06
  Changes: Data collection, Derived calculations, Experimental preparation, Other