3ZH8

A novel small molecule aPKC inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.739 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Adenosine-Binding Motif Mimicry and Cellular Effects of a Thieno[2,3-D]Pyrimidine-Based Chemical Inhibitor of Atypical Protein Kinase C Isozymes.

Kjaer, S., Linch, M., Purkiss, A., Kostelecky, B., Knowles, P.P., Rosse, C., Riou, P., Soudy, C., Kaye, S., Patel, B., Soriano, E., Murray-Rust, J., Barton, C., Dillon, C., Roffey, J., Parker, P.J., Mcdonald, N.Q.

(2013) Biochem.J. 451: 329

  • DOI: 10.1042/BJ20121871

  • PubMed Abstract: 

    • The aPKC [atypical PKC (protein kinase C)] isoforms ι and ζ play crucial roles in the formation and maintenance of cell polarity and represent attractive anti-oncogenic drug targets in Ras-dependent tumours. To date, few isoform-specific chemical bio ...

    The aPKC [atypical PKC (protein kinase C)] isoforms ι and ζ play crucial roles in the formation and maintenance of cell polarity and represent attractive anti-oncogenic drug targets in Ras-dependent tumours. To date, few isoform-specific chemical biology tools are available to inhibit aPKC catalytic activity. In the present paper, we describe the identification and functional characterization of potent and selective thieno[2,3-d]pyrimidine-based chemical inhibitors of aPKCs. A crystal structure of human PKCι kinase domain bound to a representative compound, CRT0066854, reveals the basis for potent and selective chemical inhibition. Furthermore, CRT0066854 displaces a crucial Asn-Phe-Asp motif that is part of the adenosine-binding pocket and engages an acidic patch used by arginine-rich PKC substrates. We show that CRT0066854 inhibits the LLGL2 (lethal giant larvae 2) phosphorylation in cell lines and exhibits phenotypic effects in a range of cell-based assays. We conclude that this compound can be used as a chemical tool to modulate aPKC activity in vitro and in vivo and may guide the search for further aPKC-selective inhibitors.

    Organizational Affiliation: 

    Structural Biology, Cancer Research UK, 44 Lincoln's Inn Fields, London WC2A 3LY, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN KINASE C IOTA TYPE
A, B, C
349Homo sapiensMutations: S348C
Gene Names: PRKCI (DXS1179E)
EC: 2.7.11.13
Find proteins for P41743 (Homo sapiens)
Go to Gene View: PRKCI
Go to UniProtKB:  P41743
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C58
Query on C58
Download SDF File 
Download CCD File 
A, B, C
(2S)-3-phenyl-N~1~-[2-(pyridin-4-yl)-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4-yl]propane-1,2-diamine
C24 H25 N5 S
NRHASZRDWOUMFD-SFHVURJKSA-N
 Ligand Interaction
IOD
Query on IOD
Download SDF File 
Download CCD File 
A, B, C
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL
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Download CCD File 
A, B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO
Download SDF File 
Download CCD File 
A, B, C
ethane-1,2-diol
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A, B, C
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
C58Kd: 341 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.739 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.210 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 113.580α = 90.00
b = 113.580β = 90.00
c = 82.410γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
iMOSFLMdata reduction
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-04-17
    Type: Database references