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 

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

  • 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-di ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CELL DIVISION PROTEIN KINASE 2
A, C
298Homo sapiensMutation(s): 0 
Gene Names: CDK2 (CDKN2)
EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens)
Go to Gene View: CDK2
Go to UniProtKB:  P24941
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CYCLIN-A2
B, D
261Homo sapiensMutation(s): 0 
Gene Names: CCNA2 (CCN1, CCNA)
Find proteins for P20248 (Homo sapiens)
Go to Gene View: CCNA2
Go to UniProtKB:  P20248
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ACE-LEU-ASN-PFF-NH2
H
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
X1N
Query on X1N

Download SDF File 
Download CCD File 
A, 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  3 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
H
NON-POLYMERH2 N

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PFF
Query on PFF
H
L-PEPTIDE LINKINGC9 H10 F N O2PHE
ACE
Query on ACE
H
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 74.558α = 90.00
b = 114.257β = 90.00
c = 157.277γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOLREPphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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