7UYU

Crystal structure of TYK2 kinase domain in complex with compound 30


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Potent and selective TYK2-JH1 inhibitors highly efficacious in rodent model of psoriasis.

Leit, S.Greenwood, J.R.Mondal, S.Carriero, S.Dahlgren, M.Harriman, G.C.Kennedy-Smith, J.J.Kapeller, R.Lawson, J.P.Romero, D.L.Toms, A.V.Shelley, M.Wester, R.T.Westlin, W.McElwee, J.J.Miao, W.Edmondson, S.D.Masse, C.E.

(2022) Bioorg Med Chem Lett 73: 128891-128891

  • DOI: https://doi.org/10.1016/j.bmcl.2022.128891
  • Primary Citation of Related Structures:  
    7UYR, 7UYS, 7UYT, 7UYU, 7UYV, 7UYW

  • PubMed Abstract: 

    TYK2 is a member of the JAK family of kinases and a key mediator of IL-12, IL-23, and type I interferon signaling. These cytokines have been implicated in the pathogenesis of multiple inflammatory and autoimmune diseases such as psoriasis, rheumatoid arthritis, lupus, and inflammatory bowel diseases. Supported by compelling data from human genetic association studies, TYK2 inhibition is an attractive therapeutic strategy for these diseases. Herein, we report the discovery of a series of highly selective catalytic site TYK2 inhibitors designed using FEP+ and structurally enabled design starting from a virtual screen hit. We highlight the structure-based optimization to identify a lead candidate 30, a potent cellular TYK2 inhibitor with excellent selectivity, pharmacokinetic properties, and in vivo efficacy in a mouse psoriasis model.


  • Organizational Affiliation

    Nimbus Therapeutics, 130 Prospect St., Cambridge, MA 02139, United States. Electronic address: silvana.leit@nimbustx.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Non-receptor tyrosine-protein kinase TYK2289Homo 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
GTEx:  ENSG00000105397 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29597
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OV0 (Subject of Investigation/LOI)
Query on OV0

Download Ideal Coordinates CCD File 
B [auth A]2-(2,6-difluorophenyl)-4-[4-(pyrrolidine-1-carbonyl)anilino]-5H-pyrrolo[3,4-b]pyridin-5-one
C24 H18 F2 N4 O2
IIQPGWZFSIWDHM-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.174α = 90
b = 74.117β = 90
c = 104.788γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



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: 2022-08-24
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Structure summary