2XMY | pdb_00002xmy

Discovery and Characterisation of 2-Anilino-4-(thiazol-5-yl) pyrimidine Transcriptional CDK Inhibitors as Anticancer Agents


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.271 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery and Characterisation of 2-Anilino-4-(Thiazol-5-Yl)Pyrimidine Transcriptional Cdk Inhibitors as Anticancer Agents

Wang, S.Griffiths, G.Midgley, C.A.Barnett, A.L.Cooper, M.Grabarek, J.Ingram, L.Jackson, W.Kontopidis, G.Mcclue, S.J.Mcinnes, C.Mclachlan, J.Meades, C.Mezna, M.Stuart, I.Thomas, M.P.Zheleva, D.I.Lane, D.P.Jackson, R.C.Glover, D.M.Blake, D.G.Fischer, P.M.

(2010) Chem Biol 17: 1111

  • DOI: https://doi.org/10.1016/j.chembiol.2010.07.016
  • Primary Citation Related Structures: 
    2XMY, 2XNB

  • PubMed Abstract: 

    The main difficulty in the development of ATP antagonist kinase inhibitors is target specificity, since the ATP-binding motif is present in many proteins. We introduce a strategy that has allowed us to identify compounds from a kinase inhibitor library that block the cyclin-dependent kinases responsible for regulating transcription, i.e., CDK7 and especially CDK9. The screening cascade employs cellular phenotypic assays based on mitotic index and nuclear p53 protein accumulation. This permitted us to classify compounds into transcriptional, cell cycle, and mitotic inhibitor groups. We describe the characterization of the transcriptional inhibitor class in terms of kinase inhibition profile, cellular mode of action, and selectivity for transformed cells. A structural selectivity rationale was used to optimize potency and biopharmaceutical properties and led to the development of a transcriptional inhibitor, 3,4-dimethyl-5-[2-(4-piperazin-1-yl-phenylamino)-pyrimidin-4-yl]-3H-thiazol-2-one, with anticancer activity in animal models.


  • Organizational Affiliation
    • Cyclacel Limited, Dundee DD15JJ, Scotland, UK.

Macromolecule Content 

  • Total Structure Weight: 34.41 kDa 
  • Atom Count: 2,717 
  • Modeled Residue Count: 295 
  • Deposited Residue Count: 298 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 (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

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDK

Query on CDK



Download:Ideal Coordinates CCD File
B [auth A]4-[4-(3,4-DIMETHYL-2-OXO-2,3-DIHYDRO-THIAZOL-5-YL)-PYRIMIDIN-2-YLAMINO]-N-(2-METHOXY-ETHYL)-BENZENESULFONAMIDE
C18 H21 N5 O4 S2
WQZVTNFUNLTGDW-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
CDK BindingDB:  2XMY Ki: 0.11 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.271 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.118α = 90
b = 71.498β = 90
c = 71.642γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-10
    Type: Initial release
  • Version 1.1: 2012-03-28
    Changes: Database references, Other, Refinement description, Source and taxonomy, Version format compliance
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description