6W8L

Crystal structure of JAK1 kinase with compound 10

• PDB DOI: https://doi.org/10.2210/pdb6W8L/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2020-03-20 Released: 2020-04-08 
• Deposition Author(s): Vajdos, F.F.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.226 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 

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.

---

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: 36.8 kDa 
• Atom Count: 2,340 
• Modelled Residue Count: 280 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase JAK1	A	316	Homo sapiens	Mutation(s): 0  Gene Names: JAK1, JAK1A, JAK1B EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P23458 (Homo sapiens) Explore P23458  Go to UniProtKB:  P23458
PHAROS:  P23458 GTEx:  ENSG00000162434

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	Binding MOAD:  6W8L	IC50: 774 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.226 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.92	α = 90
b = 88.83	β = 90
c = 146.76	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	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: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection