Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.14 kDa 
• Atom Count: 2,427 
• Modelled Residue Count: 288 
• Deposited Residue Count: 302 
• Unique protein chains: 1

 4GJ3

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

• PDB DOI:  https://doi.org/10.2210/pdb4GJ3/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


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

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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 

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

• PubMed: 23668484 
• DOI: https://doi.org/10.1021/jm400266t
• Primary Citation of Related Structures:  
  4GII, 4GJ2, 4GJ3


• 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-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.

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Organizational Affiliation: 

Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-receptor tyrosine-protein kinase TYK2	A	302	Homo sapiens	Mutation(s): 6  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0XP	B [auth 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

Binding Affinity Annotations
ID	Source	Binding Affinity
0XP	PDBBind:  4GJ3	Ki: 1.4 (nM) from 1 assay(s)
	Binding MOAD:  4GJ3	Ki: 1.4 (nM) from 1 assay(s)

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 = 36.229	α = 90
b = 74.203	β = 90
c = 105.891	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
BUSTER	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• 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