2X1N

Truncation and Optimisation of Peptide Inhibitors of CDK2, Cyclin A Through Structure Guided Design

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Design, Synthesis, and Evaluation of 2-Methyl- and 2-Amino-N-Aryl-4,5-Dihydrothiazolo[4,5-H]Quinazolin-8-Amines as Ring-Constrained 2-Anilino-4-(Thiazol-5-Yl)Pyrimidine Cyclin-Dependent Kinase Inhibitors.

Mcintyre, N.A., Mcinnes, C., Griffiths, G., Barnett, A.L., Kontopidis, G., Slawin, A.M.Z., Jackson, W., Thomas, M., Zheleva, D.I., Wang, S., Blake, D.G., Westwood, N.J., Fischer, P.M.

(2010) J Med Chem 53: 2136

  • DOI: 10.1021/jm901660c
  • Primary Citation of Related Structures:  
    2X1N

  • PubMed Abstract: 

    • Following the recent discovery and development of 2-anilino-4-(thiazol-5-yl)pyrimidine cyclin dependent kinase (CDK) inhibitors, a program was initiated to evaluate related ring-constrained analogues, specifically, 2-methyl- and 2-amino-N-aryl-4,5-dihydrothiazolo[4,5-h]quinazolin-8-amines for inhibition of CDKs ...

    Following the recent discovery and development of 2-anilino-4-(thiazol-5-yl)pyrimidine cyclin dependent kinase (CDK) inhibitors, a program was initiated to evaluate related ring-constrained analogues, specifically, 2-methyl- and 2-amino-N-aryl-4,5-dihydrothiazolo[4,5-h]quinazolin-8-amines for inhibition of CDKs. Here we report the rational design, synthesis, structure-activity relationships (SARs), and cellular mode-of-action profile of these second generation CDK inhibitors. Many of the analogues from this chemical series inhibit CDKs with very low nanomolar K(i) values. The most potent compound reported in this study inhibits CDK2 with an IC(50) of 0.7 nM ([ATP] = 100 microM). Furthermore, an X-ray crystal structure of 2-methyl-N-(3-(nitro)phenyl)-4,5-dihydrothiazolo[4,5-h]quinazolin-8-amine (11g), a representative from the chemical series in complex with cyclin A-CDK2, is reported, confirming the design rationale and expected binding mode within the CDK2 ATP binding pocket.

    Related Citations: 
    • Truncation and Optimisation of Peptide Inhibitors of Cyclin-Dependent Kinase 2-Cyclin a Through Structure-Guided Design.
      Kontopidis, G., Andrews, M.J., Mcinnes, C., Plater, A., Innes, L., Renachowski, S., Cowan, A., Fischer, P.M.
      (2009) ChemMedChem 4: 1120
    Organizational Affiliation: 

    School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CELL DIVISION PROTEIN KINASE 2A, C298Homo sapiensMutation(s): 0 
Gene Names: CDK2, CDKN2
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.22 (UniProt)
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
NIH Common Fund Data Resources
PHAROS:  P24941
GTEx:  ENSG00000123374
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CYCLIN-A2B, D261Homo sapiensMutation(s): 0 
Gene Names: CCNA2, CCN1, CCNA
Find proteins for P20248 (Homo sapiens)
Explore P20248 
Go to UniProtKB:  P20248
NIH Common Fund Data Resources
PHAROS:  P20248
GTEx:  ENSG00000145386
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ACE-LEU-ASN-PFF-NH2E [auth H]5synthetic constructMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
X1N
Query on X1N
Download Ideal Coordinates CCD File 
 F [auth A], G [auth C]2-METHYL-N-[(1Z)-3-NITROCYCLOHEXA-2,4-DIEN-1-YLIDENE]-4,5-DIHYDRO[1,3]THIAZOLO[4,5-H]QUINAZOLIN-8-AMINE
C16 H13 N5 O2 S
CMWWYSDXIZEJPA-ODLFYWEKSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PFF
Query on PFF		E [auth H]L-PEPTIDE LINKINGC9 H10 F N O2PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.558α = 90
b = 114.257β = 90
c = 157.277γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2016-12-14
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2017-03-29
    Changes: Other