8UAK

Crystal structure of the catalytic domain of human PKC alpha (D463N, V568I, S657E) in complex with Darovasertib (NVP-LXS196) at 2.82-A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

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Literature

Discovery of Darovasertib (NVP-LXS196), a Pan-PKC Inhibitor for the Treatment of Metastatic Uveal Melanoma.

Visser, M.Papillon, J.P.N.Luzzio, M.LaMarche, M.J.Fan, J.Michael, W.Wang, D.Zhang, A.Straub, C.Mathieu, S.Kato, M.Palermo, M.Chen, C.Ramsey, T.Joud, C.Barrett, R.Vattay, A.Guo, R.Bric, A.Chung, F.Liang, G.Romanowski, M.J.Lam, J.Thohan, S.Atassi, F.Wylie, A.Cooke, V.G.

(2024) J Med Chem 67: 1447-1459

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c02002
  • Primary Citation of Related Structures:  
    8U37, 8UAK

  • PubMed Abstract: 

    Uveal melanoma (UM) is the most common primary intraocular malignancy in the adult eye. Despite the aggressive local management of primary UM, the development of metastases is common with no effective treatment options for metastatic disease. Genetic analysis of UM samples reveals the presence of mutually exclusive activating mutations in the Gq alpha subunits GNAQ and GNA11. One of the key downstream targets of the constitutively active Gq alpha subunits is the protein kinase C (PKC) signaling pathway. Herein, we describe the discovery of darovasertib (NVP-LXS196), a potent pan-PKC inhibitor with high whole kinome selectivity. The lead series was optimized for kinase and off target selectivity to afford a compound that is rapidly absorbed and well tolerated in preclinical species. LXS196 is being investigated in the clinic as a monotherapy and in combination with other agents for the treatment of uveal melanoma (UM), including primary UM and metastatic uveal melanoma (MUM).


  • Organizational Affiliation

    Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein kinase C alpha type354Homo sapiensMutation(s): 3 
Gene Names: PRKCAPKCAPRKACA
EC: 2.7.11.13
UniProt & NIH Common Fund Data Resources
Find proteins for P17252 (Homo sapiens)
Explore P17252 
Go to UniProtKB:  P17252
PHAROS:  P17252
GTEx:  ENSG00000154229 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17252
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
W39 (Subject of Investigation/LOI)
Query on W39

Download Ideal Coordinates CCD File 
B [auth A](6M)-3-amino-N-[3-(4-amino-4-methylpiperidin-1-yl)pyridin-2-yl]-6-[3-(trifluoromethyl)pyridin-2-yl]pyrazine-2-carboxamide
C22 H23 F3 N8 O
XXJXHXJWQSCNPX-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.818α = 90
b = 44.532β = 114.04
c = 85.691γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-24
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Database references