2UZD

Crystal structure of human CDK2 complexed with a thiazolidinone inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 
    0.269 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted C85Click on this verticalbar to view details

This is version 1.5 of the entry. See complete history


Literature

Discovery of a Potent Cdk2 Inhibitor with a Novel Binding Mode, Using Virtual Screening and Initial, Structure-Guided Lead Scoping.

Richardson, C.M.Nunns, C.L.Williamson, D.S.Parratt, M.J.Dokurno, P.Howes, R.Borgognoni, J.Drysdale, M.J.Finch, H.Hubbard, R.E.Jackson, P.S.Kierstan, P.Lentzen, G.Moore, J.D.Murray, J.B.Simmonite, H.Surgenor, A.E.Torrance, C.J.

(2007) Bioorg Med Chem Lett 17: 3880

  • DOI: https://doi.org/10.1016/j.bmcl.2007.04.110
  • Primary Citation of Related Structures:  
    2UZB, 2UZD, 2UZE, 2UZL, 2UZN, 2UZO, 2V0D

  • PubMed Abstract: 

    Virtual screening against a pCDK2/cyclin A crystal structure led to the identification of a potent and novel CDK2 inhibitor, which exhibited an unusual mode of interaction with the kinase binding motif. With the aid of X-ray crystallography and modelling, a medicinal chemistry strategy was implemented to probe the interactions seen in the crystal structure and to establish SAR. A fragment-based approach was also considered but a different, more conventional, binding mode was observed. Compound selectivity against GSK-3beta was improved using a rational design strategy, with crystallographic verification of the CDK2 binding mode.


  • Organizational Affiliation

    Vernalis (R&D) Ltd, Granta Park, Cambridge CB21 6GB, UK. c.richardson@vernalis.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CELL DIVISION PROTEIN KINASE 2
A, C
298Homo sapiensMutation(s): 0 
EC: 2.7.11.22 (PDB Primary Data), 2.7.1.37 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
PHAROS:  P24941
GTEx:  ENSG00000123374 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24941
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CYCLIN A2
B, D
258Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P20248 (Homo sapiens)
Explore P20248 
Go to UniProtKB:  P20248
PHAROS:  P20248
GTEx:  ENSG00000145386 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20248
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C85
Query on C85

Download Ideal Coordinates CCD File 
E [auth A],
F [auth C]
4-{5-[(Z)-(2-IMINO-4-OXO-1,3-THIAZOLIDIN-5-YLIDENE)METHYL]FURAN-2-YL}BENZENESULFONAMIDE
C14 H11 N3 O4 S2
BKUMVXIXUVYKDQ-GHXNOFRVSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A, C
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Binding Affinity Annotations 
IDSourceBinding Affinity
C85 BindingDB:  2UZD IC50: 180 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free:  0.269 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.559α = 90
b = 160.292β = 90
c = 66.509γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted C85Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-26
    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
  • Version 1.4: 2019-04-03
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2024-11-13
    Changes: Data collection, Database references, Other, Structure summary