3ZH8 | pdb_00003zh8

A novel small molecule aPKC inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 
    0.257 (Depositor), 0.265 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.213 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3ZH8

Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1042/BJ20121871
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 124.45 kDa 
  • Atom Count: 7,714 
  • Modeled Residue Count: 953 
  • Deposited Residue Count: 1,047 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN KINASE C IOTA TYPE
A, B, C
349Homo sapiensMutation(s): 1 
EC: 2.7.11.13
UniProt & NIH Common Fund Data Resources
Find proteins for P41743 (Homo sapiens)
Explore P41743 
Go to UniProtKB:  P41743
PHAROS:  P41743
GTEx:  ENSG00000163558 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41743
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / 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
IOD

Query on IOD



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
M [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
EDO

Query on EDO



Download:Ideal Coordinates CCD File
CA [auth C]
DA [auth C]
EA [auth C]
J [auth A]
K [auth A]
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
CL

Query on CL



Download:Ideal Coordinates CCD File
AA [auth C],
H [auth A],
Q [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A, B, C
L-PEPTIDE LINKINGC4 H10 N O6 PTHR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free:  0.257 (Depositor), 0.265 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.213 (Depositor) 
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

View Full Validation Report



Ligand Structure Quality Assessment 


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
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary