Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 129028.45 
• Atom Count: 9034 
• Residue Count: 1114 
• Unique protein chains: 2

2V22

REPLACE: A strategy for Iterative Design of Cyclin Binding Groove Inhibitors

• DOI: 10.2210/pdb2V22/pdb

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


• Deposited: 2007-05-31 Released: 2008-01-29 
• Deposition Author(s): Andrews, M.J., Kontopidis, G., McInnes, C., Plater, A., Innes, L., Cowan, A., Jewsbury, P., Fischer, P.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.277 
• R-Value Work: 0.171 

Literature

Replace: A Strategy for Iterative Design of Cyclin- Binding Groove Inhibitors

Andrews, M.J., Kontopidis, G., Mcinnes, C., Plater, A., Innes, L., Cowan, A., Jewsbury, P., Fischer, P.M.

(2006) Chembiochem 7: 1909

• PubMed: 17051658 
• DOI: 10.1002/cbic.200600189
• Primary Citation of Related Structures:  
  2UUE


• PubMed Abstract: 
  

We describe a drug-design strategy termed REPLACE (REplacement with Partial Ligand Alternatives through Computational Enrichment) in which nonpeptidic surrogates for specific determinants of known peptide ligands are identified in silico by using a core peptide-bound protein structure as a design anchor. In the REPLACE application example, we present the effective replacement of two critical binding motifs in a lead protein-protein interaction inhibitor pentapeptide with more druglike phenyltriazole and diphenyl ether groups. These were identified through docking of fragment libraries into the volume of the cyclin-binding groove of CDK2/cyclin A vacated through truncation of the inhibitor peptide-binding determinants. Proof of concept for this strategy was obtained through the generation of potent peptide-small-molecule hybrids and by the confirmation of inhibitor-binding modes in X-ray crystal structures. This method therefore allows nonpeptide fragments to be identified without the requirement for a high-sensitivity binding assay and should be generally applicable in replacing amino acids as individual residues or groups in peptide inhibitors to generate pharmaceutically acceptable lead molecules.

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Related Citations: 

• Differential Binding of Inhibitors to Active and Inactive Cdk2 Provides Insights for Drug Design
  Kontopidis, G.,Mcinnes, C.,Pandalaneni, S.R.,Mcnae, I.,Gibson, D.,Mezna, M.,Thomas, M.,Wood, G.,Wang, S.,Walkinshaw, M.D.,Fische, P.M.
  (2006) Chem.Biol. 13: 201




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Organizational Affiliation: 

Cyclacel Limited, James Lindsay Place, Dundee, DD1 5JJ, UK. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CELL DIVISION PROTEIN KINASE 2	A, C	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
CYCLIN-A2	B, D	259	Homo sapiens	Mutation(s): 0  Gene Names: CCNA2 (CCN1, CCNA)
Find proteins for P20248 (Homo sapiens) Go to Gene View: CCNA2 Go to UniProtKB:  P20248

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
C35	B, D	N~2~-{[1-(4-CHLOROPHENYL)-5-METHYL-1H-1,2,4-TRIAZOL-3-YL]CARBONYL}-N~5~-(DIAMINOMETHYLIDENE)-L-ORNITHYL-L-LEUCYL-L-ISOLEUCYL-4-FLUORO-L-PHENYLALANINAMIDE C37 H51 Cl F N11 O5 KPJZLROHGAJEAN-WRTIUAHLSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
C35	IC50: 4100 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.277 
• R-Value Work: 0.171 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 74.693	α = 90.00
b = 113.571	β = 90.00
c = 156.025	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-05-31 
• Released Date: 2008-01-29 
• Deposition Author(s): Andrews, M.J., Kontopidis, G., McInnes, C., Plater, A., Innes, L., Cowan, A., Jewsbury, P., Fischer, P.M.

Revision History 

• Version 1.0: 2008-01-29
  Type: Initial release
• Version 1.1: 2011-05-08
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance