8S9A

Crystal structure of the TYK2 pseudokinase domain in complex with TAK-279


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of a Potent and Selective Tyrosine Kinase 2 Inhibitor: TAK-279.

Leit, S.Greenwood, J.Carriero, S.Mondal, S.Abel, R.Ashwell, M.Blanchette, H.Boyles, N.A.Cartwright, M.Collis, A.Feng, S.Ghanakota, P.Harriman, G.C.Hosagrahara, V.Kaila, N.Kapeller, R.Rafi, S.B.Romero, D.L.Tarantino, P.M.Timaniya, J.Toms, A.V.Wester, R.T.Westlin, W.Srivastava, B.Miao, W.Tummino, P.McElwee, J.J.Edmondson, S.D.Masse, C.E.

(2023) J Med Chem 66: 10473-10496

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00600
  • Primary Citation of Related Structures:  
    8S98, 8S99, 8S9A

  • PubMed Abstract: 

    TYK2 is a key mediator of IL12, IL23, and type I interferon signaling, and these cytokines have been implicated in the pathogenesis of multiple inflammatory and autoimmune diseases such as psoriasis, rheumatoid arthritis, lupus, and inflammatory bowel diseases. Supported by compelling data from human genome-wide association studies and clinical results, TYK2 inhibition through small molecules is an attractive therapeutic strategy to treat these diseases. Herein, we report the discovery of a series of highly selective pseudokinase (Janus homology 2, JH2) domain inhibitors of TYK2 enzymatic activity. A computationally enabled design strategy, including the use of FEP+, was instrumental in identifying a pyrazolo-pyrimidine core. We highlight the utility of computational physics-based predictions used to optimize this series of molecules to identify the development candidate 30 , a potent, exquisitely selective cellular TYK2 inhibitor that is currently in Phase 2 clinical trials for the treatment of psoriasis and psoriatic arthritis.


  • Organizational Affiliation

    Nimbus Therapeutics, 22 Boston Wharf Road, Floor 9, Boston, Massachusetts 02210, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Non-receptor tyrosine-protein kinase TYK2
A, B, C
295Homo sapiensMutation(s): 0 
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29597
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZSB (Subject of Investigation/LOI)
Query on ZSB

Download Ideal Coordinates CCD File 
D [auth A],
M [auth B],
R [auth C]
(8S)-N-[(1R,2R)-2-methoxycyclobutyl]-7-(methylamino)-5-{[(1P,2'P)-2-oxo-2H-[1,2'-bipyridin]-3-yl]amino}pyrazolo[1,5-a]pyrimidine-3-carboxamide
C23 H24 N8 O3
BWINBHTTZLVXGT-NVXWUHKLSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
J [auth A]
K [auth A]
L [auth A]
F [auth A],
G [auth A],
J [auth A],
K [auth A],
L [auth A],
O [auth B],
Q [auth B],
S [auth C],
U [auth C],
X [auth C],
Y [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
E [auth A]
H [auth A]
I [auth A]
N [auth B]
P [auth B]
E [auth A],
H [auth A],
I [auth A],
N [auth B],
P [auth B],
T [auth C],
V [auth C],
W [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.222α = 90
b = 112.94β = 90
c = 157.348γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-26
    Type: Initial release
  • Version 1.1: 2023-08-23
    Changes: Data collection, Database references