3ZH8

A novel small molecule aPKC inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.2 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
  • Primary Citation of Related Structures:  
    3ZH8

  • 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 biology tools are available to inhibit aPKC catalytic activity ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN KINASE C IOTA TYPEA, B, C349Homo sapiensMutation(s): 1 
Gene Names: PRKCI, DXS1179E
EC: 2.7.11.13
Find proteins for P41743 (Homo sapiens)
Explore P41743 
Go to UniProtKB:  P41743
NIH Common Fund Data Resources
PHAROS:  P41743
GTEx:  ENSG00000163558
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C58
Query on C58
Download Ideal Coordinates CCD File 
 BA [auth C], I [auth A], R [auth B](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 Ideal Coordinates CCD File 
D [auth A] , E [auth A] , F [auth A] , G [auth A] , M [auth B] , N [auth B] , O [auth B] , P [auth B] , 
D [auth A],  E [auth A],  F [auth A],  G [auth A],  M [auth B],  N [auth B],  O [auth B],  P [auth B],  W [auth C],  X [auth C],  Y [auth C],  Z [auth C]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
CA [auth C] , DA [auth C] , EA [auth C] , J [auth A] , K [auth A] , L [auth A] , S [auth B] , T [auth B] , 
CA [auth C],  DA [auth C],  EA [auth C],  J [auth A],  K [auth A],  L [auth A],  S [auth B],  T [auth B],  U [auth B],  V [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
 AA [auth C], H [auth A], Q [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO		A, B, CL-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: 2.74 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.58α = 90
b = 113.58β = 90
c = 82.41γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-04-17
    Changes: Database references
  • Version 1.2: 2019-04-03
    Changes: Data collection, Derived calculations, Other, Source and taxonomy