Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 124.45 kDa 
• Atom Count: 7714 
• Modelled Residue Count: 953 
• Deposited Residue Count: 1047 
• Unique protein chains: 1

3ZH8

A novel small molecule aPKC inhibitor

• PDB DOI: 10.2210/pdb3ZH8/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2012-12-20 Released: 2013-02-27 
• Deposition Author(s): Kjaer, S., Purkiss, A.G., Kostelecky, B., Knowles, P.P., Soriano, E., Murray-Rust, J., McDonald, N.Q.

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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 

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

• PubMed: 23418854 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN KINASE C IOTA TYPE	A, B, C	349	Homo sapiens	Mutation(s): 1  Gene Names: PRKCI, DXS1179E 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C58	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	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	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	AA [auth C], H [auth A], Q [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A, B, C	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Binding Affinity Annotations
ID	Source	Binding Affinity
C58	PDBBind:  3ZH8	Kd: 341 (nM) from 1 assay(s)

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 = 113.58	α = 90
b = 113.58	β = 90
c = 82.41	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-12-20 
• Released Date: 2013-02-27 
Deposition Author(s): Kjaer, S., Purkiss, A.G., Kostelecky, B., Knowles, P.P., Soriano, E., Murray-Rust, J., McDonald, N.Q.

Revision History  

• 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