2UUE

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  2V22

  • 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
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
GVC-TETRAPEPTIDE INHIBITOR
E, F
5N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GVC
Query on GVC

Download SDF File 
Download CCD File 
E, F
1-(3,5-DICHLOROPHENYL)-5-METHYL-1H-1,2,4-TRIAZOLE-3-CARBOXYLIC ACID
C10 H7 Cl2 N3 O2
CZTNDZALWLHXBA-UHFFFAOYSA-N
 Ligand Interaction
MTZ
Query on MTZ

Download SDF File 
Download CCD File 
A, C
4-METHYL-5-{(2E)-2-[(4-MORPHOLIN-4-YLPHENYL)IMINO]-2,5-DIHYDROPYRIMIDIN-4-YL}-1,3-THIAZOL-2-AMINE
C18 H20 N6 O S
RPSZSAKYXPWBRR-PYCFMQQDSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
E, F
NON-POLYMERH2 N

--

PFF
Query on PFF
E, F
L-PEPTIDE LINKINGC9 H10 F N O2PHE
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MTZIC50: 740 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 74.563α = 90.00
b = 113.800β = 90.00
c = 155.031γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
MOLREPphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-27
    Type: Initial release
  • Version 1.1: 2012-09-05
    Type: Derived calculations, Non-polymer description, Other, Version format compliance