2C69

Crystal structure of the human CDK2 complexed with the triazolopyrimidine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Triazolo[1,5-a]pyrimidines as novel CDK2 inhibitors: protein structure-guided design and SAR.

Richardson, C.M.Williamson, D.S.Parratt, M.J.Borgognoni, J.Cansfield, A.D.Dokurno, P.Francis, G.L.Howes, R.Moore, J.D.Murray, J.B.Robertson, A.Surgenor, A.E.Torrance, C.J.

(2006) Bioorg Med Chem Lett 16: 1353-1357

  • DOI: https://doi.org/10.1016/j.bmcl.2005.11.048
  • Primary Citation of Related Structures:  
    2C68, 2C69, 2C6I, 2C6K, 2C6L, 2C6M, 2C6O, 2C6T

  • PubMed Abstract: 

    Crystallographic and modelling data, in conjunction with a medicinal chemistry template-hopping approach, led to the identification of a series of novel and potent inhibitors of human cyclin-dependent kinase 2 (CDK2), with selectivity over glycogen synthase kinase-3beta (GSK-3beta). One example had a CDK2 IC(50) of 120 nM and showed selectivity over GSK-3beta of 167-fold.


  • Organizational Affiliation

    Vernalis (R&D) Ltd, Granta Park, Great Abington, Cambridge CB1 6GB, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CELL DIVISION PROTEIN KINASE 2298Homo sapiensMutation(s): 0 
EC: 2.7.1.37
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CT8
Query on CT8

Download Ideal Coordinates CCD File 
B [auth A](5Z)-5-(3-BROMOCYCLOHEXA-2,5-DIEN-1-YLIDENE)-N-(PYRIDIN-4-YLMETHYL)-1,5-DIHYDRO[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-AMINE
C17 H14 Br N6
YWBFPKPWMSWWEA-UHFFFAOYSA-O
Binding Affinity Annotations 
IDSourceBinding Affinity
CT8 PDBBind:  2C69 IC50: 2.60e+4 (nM) from 1 assay(s)
Binding MOAD:  2C69 IC50: 2.60e+4 (nM) from 1 assay(s)
BindingDB:  2C69 IC50: 2.60e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.578α = 90
b = 71.611β = 90
c = 72.296γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
d*TREKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-07
    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: 2018-02-28
    Changes: Database references, Source and taxonomy
  • Version 1.4: 2019-01-30
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2019-04-24
    Changes: Data collection, Source and taxonomy
  • Version 1.6: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description