4GJ3

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.212 

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:  
    4GJ2, 4GJ3, 4GII

  • 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-fluorocyclopropylamid ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Non-receptor tyrosine-protein kinase TYK2 A302Homo sapiensMutation(s): 6 
Gene Names: TYK2
EC: 2.7.10.2
Find proteins for P29597 (Homo sapiens)
Explore P29597 
Go to UniProtKB:  P29597
NIH Common Fund Data Resources
PHAROS:  P29597
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0XP
Query on 0XP

Download Ideal Coordinates CCD File 
A
2,6-dichloro-4-cyano-N-[2-({[(1R,2R)-2-fluorocyclopropyl]carbonyl}amino)pyridin-4-yl]benzamide
C17 H11 Cl2 F N4 O2
TZBYGJGLZFYXII-GXFFZTMASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0XPKi :  1.399999976158142   nM  PDBBind
0XPKi:  1.399999976158142   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.229α = 90
b = 74.203β = 90
c = 105.891γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



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
    Changes: Database references