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 

Starting Model: experimental
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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 (PDB Primary Data), 2.7.11.22 (UniProt)
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
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)
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

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Ligand Structure Quality Assessment 


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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