Jak1 with compound 23

Experimental Data Snapshot

  • Resolution: 2.48 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


Dual Inhibition of TYK2 and JAK1 for the Treatment of Autoimmune Diseases: Discovery of (( S)-2,2-Difluorocyclopropyl)((1 R,5 S)-3-(2-((1-methyl-1 H-pyrazol-4-yl)amino)pyrimidin-4-yl)-3,8-diazabicyclo[3.2.1]octan-8-yl)methanone (PF-06700841).

Fensome, A.Ambler, C.M.Arnold, E.Banker, M.E.Brown, M.F.Chrencik, J.Clark, J.D.Dowty, M.E.Efremov, I.V.Flick, A.Gerstenberger, B.S.Gopalsamy, A.Hayward, M.M.Hegen, M.Hollingshead, B.D.Jussif, J.Knafels, J.D.Limburg, D.C.Lin, D.Lin, T.H.Pierce, B.S.Saiah, E.Sharma, R.Symanowicz, P.T.Telliez, J.B.Trujillo, J.I.Vajdos, F.F.Vincent, F.Wan, Z.K.Xing, L.Yang, X.Yang, X.Zhang, L.

(2018) J Med Chem 61: 8597-8612

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b00917
  • Primary Citation of Related Structures:  
    6DBK, 6DBM, 6DBN

  • PubMed Abstract: 

    Cytokine signaling is an important characteristic of autoimmune diseases. Many pro-inflammatory cytokines signal through the Janus kinase (JAK)/Signal transducer and activator of transcription (STAT) pathway. JAK1 is important for the γ-common chain cytokines, interleukin (IL)-6, and type-I interferon (IFN) family, while TYK2 in addition to type-I IFN signaling also plays a role in IL-23 and IL-12 signaling. Intervention with monoclonal antibodies (mAbs) or JAK1 inhibitors has demonstrated efficacy in Phase III psoriasis, psoriatic arthritis, inflammatory bowel disease, and rheumatoid arthritis studies, leading to multiple drug approvals. We hypothesized that a dual JAK1/TYK2 inhibitor will provide additional efficacy, while managing risk by optimizing selectivity against JAK2 driven hematopoietic changes. Our program began with a conformationally constrained piperazinyl-pyrimidine Type 1 ATP site inhibitor, subsequent work led to the discovery of PF-06700841 (compound 23), which is in Phase II clinical development (NCT02969018, NCT02958865, NCT03395184, and NCT02974868).

  • Organizational Affiliation

    Medicine Design, Pfizer Inc., 1 Portland Street , Cambridge , Massachusetts 02139 , United States.

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
PHAROS:  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
G4J (Subject of Investigation/LOI)
Query on G4J

Download Ideal Coordinates CCD File 
B [auth A][(1S)-2,2-difluorocyclopropyl][(1R,5S)-3-{2-[(1-methyl-1H-pyrazol-4-yl)amino]pyrimidin-4-yl}-3,8-diazabicyclo[3.2.1]octan-8-yl]methanone
C18 H21 F2 N7 O
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PTR
Binding Affinity Annotations 
IDSourceBinding Affinity
G4J BindingDB:  6DBN IC50: min: 17, max: 641 (nM) from 10 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.48 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.190 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.51α = 90
b = 88.422β = 90
c = 145.914γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2018-08-29 
  • Deposition Author(s): Vajdos, F.F.

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-11-07
    Changes: Data collection, Database references