1Y91

Crystal structure of human CDK2 complexed with a pyrazolo[1,5-a]pyrimidine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.201 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure-guided design of pyrazolo[1,5-a]pyrimidines as inhibitors of human cyclin-dependent kinase 2.

Williamson, D.S.Parratt, M.J.Bower, J.F.Moore, J.D.Richardson, C.M.Dokurno, P.Cansfield, A.D.Francis, G.L.Hebdon, R.J.Howes, R.Jackson, P.S.Lockie, A.M.Murray, J.B.Nunns, C.L.Powles, J.Robertson, A.Surgenor, A.E.Torrance, C.J.

(2005) Bioorg Med Chem Lett 15: 863-867

  • DOI: https://doi.org/10.1016/j.bmcl.2004.12.073
  • Primary Citation of Related Structures:  
    1Y8Y, 1Y91

  • PubMed Abstract: 

    The protein structure guided design of a series of pyrazolo[1,5-a]pyrimidines with high potency for human cyclin-dependent kinase 2 (CDK2) is described. Some examples were shown to inhibit the growth of human colon tumour cells, were equipotent for CDK1 and were selective against GSK-3beta and other kinases.


  • Organizational Affiliation

    Vernalis (R&D) Ltd, Granta Park, Great Abington, Cambridge CB1 6GB, United Kingdom. d.williamson@vernalis.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division protein kinase 2298Homo sapiensMutation(s): 0 
Gene Names: CDK2
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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CT9
Query on CT9

Download Ideal Coordinates CCD File 
B [auth A]4-[5-(TRANS-4-AMINOCYCLOHEXYLAMINO)-3-ISOPROPYLPYRAZOLO[1,5-A]PYRIMIDIN-7-YLAMINO]-N,N-DIMETHYLBENZENESULFONAMIDE
C23 H33 N7 O2 S
MDIWBYRNTPTYQI-QAQDUYKDSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
CT9 BindingDB:  1Y91 IC50: 59 (nM) from 1 assay(s)
PDBBind:  1Y91 IC50: 59 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.372α = 90
b = 71.423β = 90
c = 72.004γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
d*TREKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2005-02-08
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description