5F9E

Structure of Protein Kinase C theta with compound 10: 2,2-dimethyl-7-(2-oxidanylidene-3~{H}-imidazo[4,5-b]pyridin-1-yl)-1-(phenylmethyl)-3~{H}-quinazolin-4-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report



Literature

Discovery and optimization of 1,7-disubstituted-2,2-dimethyl-2,3-dihydroquinazolin-4(1H)-ones as potent and selective PKC theta inhibitors.

Katoh, T.Takai, T.Yukawa, T.Tsukamoto, T.Watanabe, E.Mototani, H.Arita, T.Hayashi, H.Nakagawa, H.Klein, M.G.Zou, H.Sang, B.C.Snell, G.Nakada, Y.

(2016) Bioorg Med Chem 24: 2466-2475

  • DOI: 10.1016/j.bmc.2016.04.008
  • Primary Citation of Related Structures:  
    5F9E

  • PubMed Abstract: 
  • A high-throughput screening campaign helped us to identify an initial lead compound (1) as a protein kinase C-θ (PKCθ) inhibitor. Using the docking model of compound 1 bound to PKCθ as a model, structure-based drug design was employed and two regions ...

    A high-throughput screening campaign helped us to identify an initial lead compound (1) as a protein kinase C-θ (PKCθ) inhibitor. Using the docking model of compound 1 bound to PKCθ as a model, structure-based drug design was employed and two regions were identified that could be explored for further optimization, i.e., (a) a hydrophilic region around Thr442, unique to PKC family, in the inner part of the hinge region, and (b) a lipophilic region at the forefront of the ethyl moiety. Optimization of the hinge binder led us to find 1,3-dihydro-2H-imidazo[4,5-b]pyridin-2-one as a potent and selective hinge binder, which resulted in the discovery of compound 5. Filling the lipophilic region with a suitable lipophilic substituent boosted PKCθ inhibitory activity and led to the identification of compound 10. The co-crystal structure of compound 10 bound to PKCθ confirmed that both the hydrophilic and lipophilic regions were fully utilized. Further optimization of compound 10 led us to compound 14, which demonstrated an improved pharmacokinetic profile and inhibition of IL-2 production in a mouse.


    Organizational Affiliation

    Pharmaceutical Research Division, Takeda Pharmaceutical Company, Ltd, 26-1, Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein kinase C theta typeAB353Homo sapiensMutation(s): 0 
Gene Names: PRKCQPRKCT
EC: 2.7.11.13
Find proteins for Q04759 (Homo sapiens)
Explore Q04759 
Go to UniProtKB:  Q04759
NIH Common Fund Data Resources
PHAROS  Q04759
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5VS
Query on 5VS

Download Ideal Coordinates CCD File 
A, B
2,2-dimethyl-7-(2-oxidanylidene-3~{H}-imidazo[4,5-b]pyridin-1-yl)-1-(phenylmethyl)-3~{H}-quinazolin-4-one
C23 H21 N5 O2
LOPPJVYTMBRTCK-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A,BL-PEPTIDE LINKINGC3 H8 N O6 PSER
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5VSIC50:  0.46000000834465027   nM  Binding MOAD
5VSIC50:  0.46000000834465027   nM  BindingDB
5VSIC50:  16   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.603α = 90
b = 76.786β = 90
c = 149.304γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2015-12-09 
  • Released Date: 2016-05-11 
  • Deposition Author(s): Klein, M.

Revision History 

  • Version 1.0: 2016-05-11
    Type: Initial release