3TXO | pdb_00003txo

PKC eta kinase in complex with a naphthyridine

• PDB DOI: https://doi.org/10.2210/pdb3TXO/pdb

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


• Deposited: 2011-09-23 Released: 2011-11-30 
• Deposition Author(s): Stark, W., Rummel, G., Cowan-Jacob, S.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

2,6-Naphthyridines as potent and selective inhibitors of the novel protein kinase C isozymes.

van Eis, M.J., Evenou, J.P., Floersheim, P., Gaul, C., Cowan-Jacob, S.W., Monovich, L., Rummel, G., Schuler, W., Stark, W., Strauss, A., Matt, A., Vangrevelinghe, E., Wagner, J., Soldermann, N.

(2011) Bioorg Med Chem Lett 21: 7367-7372

• PubMed: 22078216 
• DOI: https://doi.org/10.1016/j.bmcl.2011.10.025
• Primary Citation of Related Structures:  
  3TXO


• PubMed Abstract: 
  

  The present study describes a novel series of ATP-competitive PKC inhibitors based on the 2,6-naphthyridine template. Example compounds potently inhibit the novel Protein Kinase C (PKC) isotypes δ, ε, η, θ (in particular PKCε/η, and display a 10-100-fold selectivity over the classical PKC isotypes. The prototype compound 11 was found to inhibit PKCθ-dependent pathways in vitro and in vivo. In vitro, a-CD3/a-CD28-induced lymphocyte proliferation could be effectively blocked in 10% rat whole blood. In mice, 11 dose-dependently inhibited Staphylococcus aureus enterotoxin B-triggered IL-2 serum levels after oral dosing.

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Organizational Affiliation: 

Novartis Institutes for BioMedical Research, Forum 1, Novartis Campus, CH-4056 Basel, Switzerland. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40.79 kDa 
• Atom Count: 2,755 
• Modelled Residue Count: 318 
• Deposited Residue Count: 353 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein kinase C eta type	A	353	Homo sapiens	Mutation(s): 1  Gene Names: PRKCH, PKCL, PRKCL EC: 2.7.11.13
UniProt & NIH Common Fund Data Resources
Find proteins for P24723 (Homo sapiens) Explore P24723  Go to UniProtKB:  P24723
PHAROS:  P24723 GTEx:  ENSG00000027075

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
07U	B [auth A]	2-methyl-N~1~-[3-(pyridin-4-yl)-2,6-naphthyridin-1-yl]propane-1,2-diamine C17 H19 N5 WNDOFCPEDZYDPL-UHFFFAOYSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
07U	BindingDB:  3TXO	IC50: 9 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.533	α = 90
b = 56.861	β = 90
c = 63.367	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-30 
Deposition Author(s): Stark, W., Rummel, G., Cowan-Jacob, S.W.

Revision History  

• Version 1.0: 2011-11-30
  Type: Initial release
  
• Version 1.1: 2011-12-07
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary