Crystal structure of JAK1 kinase with compound 10

Experimental Data Snapshot

  • Resolution: 2.11 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


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

  • 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: Andrew.Fensome@Pfizer.Com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase JAK1316Homo sapiensMutation(s): 0 
Gene Names: JAK1JAK1AJAK1B
UniProt & NIH Common Fund Data Resources
Find proteins for P23458 (Homo sapiens)
Explore P23458 
Go to UniProtKB:  P23458
GTEx:  ENSG00000162434 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23458
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R4S (Subject of Investigation/LOI)
Query on R4S

Download Ideal Coordinates CCD File 
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
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PTR
Binding Affinity Annotations 
IDSourceBinding Affinity
R4S Binding MOAD:  6W8L IC50: 774 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • 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 = 45.92α = 90
b = 88.83β = 90
c = 146.76γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • 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