6NZH

CRYSTAL STRUCTURE OF TYROSINE KINASE 2 JH2 (PSEUDO KINASE DOMAIN) COMPLEXED WITH Compound_40 AKA 6-cyclopropaneamido-4-[(2-methanesulfonylphenyl)amino]-N-methylpyridine-3-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Identification ofN-Methyl Nicotinamide andN-Methyl Pyridazine-3-Carboxamide Pseudokinase Domain Ligands as Highly Selective Allosteric Inhibitors of Tyrosine Kinase 2 (TYK2).

Moslin, R.Zhang, Y.Wrobleski, S.T.Lin, S.Mertzman, M.Spergel, S.Tokarski, J.S.Strnad, J.Gillooly, K.McIntyre, K.W.Zupa-Fernandez, A.Cheng, L.Sun, H.Chaudhry, C.Huang, C.D'Arienzo, C.Heimrich, E.Yang, X.Muckelbauer, J.K.Chang, C.Tredup, J.Mulligan, D.Xie, D.Aranibar, N.Chiney, M.Burke, J.R.Lombardo, L.Carter, P.H.Weinstein, D.S.

(2019) J Med Chem 62: 8953-8972

  • DOI: 10.1021/acs.jmedchem.9b00443
  • Primary Citation of Related Structures:  
    6NZE, 6NZF, 6NZH

  • PubMed Abstract: 
  • As a member of the Janus (JAK) family of nonreceptor tyrosine kinases, TYK2 plays an important role in mediating the signaling of pro-inflammatory cytokines including IL-12, IL-23, and type 1 interferons. The nicotinamide 4 , identified by a SPA-based high-throughput screen targeting the TYK2 pseudokinase domain, potently inhibits IL-23 and IFNα signaling in cellular assays ...

    As a member of the Janus (JAK) family of nonreceptor tyrosine kinases, TYK2 plays an important role in mediating the signaling of pro-inflammatory cytokines including IL-12, IL-23, and type 1 interferons. The nicotinamide 4 , identified by a SPA-based high-throughput screen targeting the TYK2 pseudokinase domain, potently inhibits IL-23 and IFNα signaling in cellular assays. The described work details the optimization of this poorly selective hit ( 4 ) to potent and selective molecules such as 47 and 48 . The discoveries described herein were critical to the eventual identification of the clinical TYK2 JH2 inhibitor (see following report in this issue). Compound 48 provided robust inhibition in a mouse IL-12-induced IFNγ pharmacodynamic model as well as efficacy in an IL-23 and IL-12-dependent mouse colitis model. These results demonstrate the ability of TYK2 JH2 domain binders to provide a highly selective alternative to conventional TYK2 orthosteric inhibitors.


    Organizational Affiliation

    Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Non-receptor tyrosine-protein kinase TYK2A, B317Homo sapiensMutation(s): 0 
Gene Names: TYK2
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P29597 (Homo sapiens)
Explore P29597 
Go to UniProtKB:  P29597
PHAROS:  P29597
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L9A (Subject of Investigation/LOI)
Query on L9A

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]6-[(cyclopropanecarbonyl)amino]-N-methyl-4-{[2-(methylsulfonyl)phenyl]amino}pyridine-3-carboxamide
C18 H20 N4 O4 S
YGFJMLGZTAWLOO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.71α = 90
b = 65.53β = 112.71
c = 74.43γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2019-02-13 
  • Released Date: 2019-07-24 
  • Deposition Author(s): Muckelbauer, J.M.

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Database references