2V22

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • 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 c ...

    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.


    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


    Organizational Affiliation

    Cyclacel Limited, James Lindsay Place, Dundee, DD1 5JJ, UK. martin.andrews@glpg.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CELL DIVISION PROTEIN KINASE 2
A, C
298Homo sapiensGene 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
MoleculeChainsSequence LengthOrganismDetails
CYCLIN-A2
B, D
259Homo sapiensGene Names: CCNA2 (CCN1, CCNA)
Find proteins for P20248 (Homo sapiens)
Go to Gene View: CCNA2
Go to UniProtKB:  P20248
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C35
Query on C35

Download SDF File 
Download CCD File 
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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
C35IC50: 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 = 74.693α = 90.00
b = 113.571β = 90.00
c = 156.025γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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