6VNY

Crystal structure of TYK2 kinase with compound 10

• PDB DOI: https://doi.org/10.2210/pdb6VNY/pdb

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


• Deposited: 2020-01-29 Released: 2020-04-08 
• Deposition Author(s): Vajdos, F.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.229 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 

Starting Model: experimental

Literature

Design and optimization of a series of 4-(3-azabicyclo[3.1.0]hexan-3-yl)pyrimidin-2-amines: Dual inhibitors of TYK2 and JAK1.

Fensome, A., Ambler, C.M., Arnold, E., Banker, M.E., Clark, J.D., Dowty, M.E., Efremov, I.V., Flick, A., Gerstenberger, B.S., Gifford, R.S., Gopalsamy, A., Hegen, M., Jussif, J., Limburg, D.C., Lin, T.H., Pierce, B.S., Sharma, R., Trujillo, J.I., Vajdos, F.F., Vincent, F., Wan, Z.K., Xing, L., Yang, X., Yang, X.

(2020) Bioorg Med Chem 28: 115481-115481

• PubMed: 32253095 
• DOI: https://doi.org/10.1016/j.bmc.2020.115481
• Primary Citation of Related Structures:  
  6VNS, 6VNV, 6VNX, 6VNY, 6W8L


• PubMed Abstract: 
  

  Herein, we disclose a new series of TYK2/ JAK1 inhibitors based upon a 3.1.0 azabicyclic substituted pyrimidine scaffold. We illustrate the use of structure-based drug design for the initial design and subsequent optimization of this series of compounds. One advanced example 19 met program objectives for potency, selectivity and ADME, and demonstrated oral activity in the adjuvant-induced arthritis rat model.

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Organizational Affiliation: 

Medicine Design, Pfizer Inc, 1 Portland Street, Cambridge, MA 02139, United States. Electronic address: [e-mail].

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: 36.94 kDa 
• Atom Count: 2,470 
• Modelled Residue Count: 287 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-receptor tyrosine-protein kinase TYK2	A	318	Homo sapiens	Mutation(s): 5  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R4S (Subject of Investigation/LOI)	B [auth A]	N-[(1S,5R)-3-(5-fluoro-2-{[1-(2-hydroxyethyl)-1H-pyrazol-4-yl]amino}pyrimidin-4-yl)-3-azabicyclo[3.1.0]hexan-1-yl]cyclopropanecarboxamide C18 H22 F N7 O2 GYRPAYDYHMZXQT-KZULUSFZSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
R4S	BindingDB:  6VNY	IC50: min: 139, max: 2.00e+4 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.229 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.344	α = 90
b = 73.106	β = 90
c = 101.994	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-08 
Deposition Author(s): Vajdos, F.F.

Revision History  

• Version 1.0: 2020-04-08
  Type: Initial release
  
• Version 1.1: 2020-04-22
  Changes: Database references
• Version 1.2: 2020-04-29
  Changes: Database references
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection
• Version 1.5: 2024-11-06
  Changes: Structure summary