4GJ2

Tyk2 (JH1) in complex with 2,6-dichloro-N-[2-({[(1R,2R)-2-fluorocyclopropyl]carbonyl}amino)pyridin-4-yl]benzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Lead Optimization of a 4-Aminopyridine Benzamide Scaffold To Identify Potent, Selective, and Orally Bioavailable TYK2 Inhibitors.

Liang, J.van Abbema, A.Balazs, M.Barrett, K.Berezhkovsky, L.Blair, W.Chang, C.Delarosa, D.Devoss, J.Driscoll, J.Eigenbrot, C.Ghilardi, N.Gibbons, P.Halladay, J.Johnson, A.Kohli, P.B.Lai, Y.Liu, Y.Lyssikatos, J.Mantik, P.Menghrajani, K.Murray, J.Peng, I.Sambrone, A.Shia, S.Shin, Y.Smith, J.Sohn, S.Tsui, V.Ultsch, M.Wu, L.C.Xiao, Y.Yang, W.Young, J.Zhang, B.Zhu, B.Y.Magnuson, S.

(2013) J.Med.Chem. 56: 4521-4536

  • DOI: 10.1021/jm400266t
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Herein we report our lead optimization effort to identify potent, selective, and orally bioavailable TYK2 inhibitors, starting with lead molecule 3. We used structure-based design to discover 2,6-dichloro-4-cyanophenyl and (1R,2R)-2-fluorocyclopropyl ...

    Herein we report our lead optimization effort to identify potent, selective, and orally bioavailable TYK2 inhibitors, starting with lead molecule 3. We used structure-based design to discover 2,6-dichloro-4-cyanophenyl and (1R,2R)-2-fluorocyclopropylamide modifications, each of which exhibited improved TYK2 potency and JAK1 and JAK2 selectivity relative to 3. Further optimization eventually led to compound 37 that showed good TYK2 enzyme and interleukin-12 (IL-12) cell potency, as well as acceptable cellular JAK1 and JAK2 selectivity and excellent oral exposure in mice. When tested in a mouse IL-12 PK/PD model, compound 37 showed statistically significant knockdown of cytokine interferon-γ (IFNγ), suggesting that selective inhibition of TYK2 kinase activity might be sufficient to block the IL-12 pathway in vivo.


    Organizational Affiliation

    Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA. liang.jun@gene.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Non-receptor tyrosine-protein kinase TYK2
A
302Homo sapiensMutation(s): 6 
Gene Names: TYK2
EC: 2.7.10.2
Find proteins for P29597 (Homo sapiens)
Go to Gene View: TYK2
Go to UniProtKB:  P29597
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0XH
Query on 0XH

Download SDF File 
Download CCD File 
A
2,6-dichloro-N-[2-({[(1R,2R)-2-fluorocyclopropyl]carbonyl}amino)pyridin-4-yl]benzamide
C16 H12 Cl2 F N3 O2
RBNYBLHXBHWSCZ-JOYOIKCWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0XHKi: 2.5 nM BINDINGMOAD
0XHKi: 2.5 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.149α = 90.00
b = 74.077β = 90.00
c = 106.009γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
SCALAdata scaling
PHASERphasing
HKL-2000data collection
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-08-09 
  • Released Date: 2013-05-29 
  • Deposition Author(s): Ultsch, M.H.

Revision History 

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2013-06-26
    Type: Database references