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 
  • R-Value Observed: 0.197 

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:  
    2V22, 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CELL DIVISION PROTEIN KINASE 2A, C298Homo sapiensMutation(s): 0 
Gene Names: CDK2CDKN2
EC: 2.7.11.1 (PDB Primary Data), 2.7.11.22 (UniProt)
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
NIH Common Fund Data Resources
PHAROS:  P24941
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CYCLIN A2B, D259Homo sapiensMutation(s): 0 
Gene Names: CCNA2CCN1CCNA
Find proteins for P20248 (Homo sapiens)
Explore P20248 
Go to UniProtKB:  P20248
NIH Common Fund Data Resources
PHAROS:  P20248
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
GVC-TETRAPEPTIDE INHIBITORE, F5synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MTZ
Query on MTZ

Download Ideal Coordinates CCD File 
G [auth A], H [auth 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
GVC
Query on GVC

Download Ideal Coordinates CCD File 
I [auth E], J [auth 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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PFF
Query on PFF
E, FL-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 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.563α = 90
b = 113.8β = 90
c = 155.031γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-27
    Type: Initial release
  • Version 1.1: 2012-09-05
    Changes: Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2019-10-09
    Changes: Data collection, Derived calculations, Other, Source and taxonomy