2UZN

Crystal structure of human CDK2 complexed with a thiazolidinone inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1016/j.bmcl.2007.04.110
  • Primary Citation of Related Structures:  

  • 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 model ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CELL DIVISION PROTEIN KINASE 2
A
298Homo sapiensMutation(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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C96
Query on C96

Download SDF File 
Download CCD File 
A
4-{5-[(1Z)-1-(2-IMINO-4-OXO-1,3-THIAZOLIDIN-5-YLIDENE)ETHYL]-2-FURYL}BENZENESULFONAMIDE
C15 H13 N3 O4 S2
AKFVRSQELXTCFW-JYRVWZFOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
C96IC50: 30 nM BINDINGMOAD
C96IC50: 30 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.591α = 90.00
b = 71.454β = 90.00
c = 72.284γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata scaling
CrystalCleardata reduction
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance