6DBK

Tyk2 with compound 8

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

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 ...

    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.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Non-receptor tyrosine-protein kinase TYK2A318Homo sapiensMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29597
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G5D (Subject of Investigation/LOI)
Query on G5D
Download Ideal Coordinates CCD File 
B [auth A]4-({4-[(1S,4S)-5-(cyanoacetyl)-2,5-diazabicyclo[2.2.1]heptan-2-yl]pyrimidin-2-yl}amino)-N-ethylbenzamide
C21 H23 N7 O2
YUJXKTRZTBIDCL-IRXDYDNUSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR		A L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Binding Affinity Annotations 
IDSourceBinding Affinity
G5D Binding MOAD:  6DBK IC50: 23 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.483α = 90
b = 73.139β = 90
c = 103.026γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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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