7K7O | pdb_00007k7o

CRYSTAL STRUCTURE OF TYROSINE KINASE 2 JH2 (PSEUDO KINASE DOMAIN) COMPLEXED WITH COMPOUND-12 AKA:6-[(cyclopropanecarbonyl)amino]-4-{[2-methoxy-3-(pyrimidin-2-yl)phenyl]amino}-N-methylpyridazine-3-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 
    0.252 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted VZJClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Discovery of BMS-986202: A Clinical Tyk2 Inhibitor that Binds to Tyk2 JH2.

Liu, C.Lin, J.Langevine, C.Smith, D.Li, J.Tokarski, J.S.Khan, J.Ruzanov, M.Strnad, J.Zupa-Fernandez, A.Cheng, L.Gillooly, K.M.Shuster, D.Zhang, Y.Thankappan, A.McIntyre, K.W.Chaudhry, C.Elzinga, P.A.Chiney, M.Chimalakonda, A.Lombardo, L.J.Macor, J.E.Carter, P.H.Burke, J.R.Weinstein, D.S.

(2021) J Med Chem 64: 677-694

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01698
  • Primary Citation of Related Structures:  
    7K7O, 7K7Q

  • PubMed Abstract: 

    A search for structurally diversified Tyk2 JH2 ligands from 6 (BMS-986165), a pyridazine carboxamide-derived Tyk2 JH2 ligand as a clinical Tyk2 inhibitor currently in late development for the treatment of psoriasis, began with a survey of six-membered heteroaryl groups in place of the N -methyl triazolyl moiety in 6 . The X-ray co-crystal structure of an early lead ( 12 ) revealed a potential new binding pocket. Exploration of the new pocket resulted in two frontrunners for a clinical candidate. The potential hydrogen bonding interaction with Thr599 in the pocket was achieved with a tertiary amide moiety, confirmed by the X-ray co-crystal structure of 29 . When the diversity search was extended to nicotinamides, a single fluorine atom addition was found to significantly enhance the permeability, which directly led to the discovery of 7 (BMS-986202) as a clinical Tyk2 inhibitor that binds to Tyk2 JH2. The preclinical studies of 7 , including efficacy studies in mouse models of IL-23-driven acanthosis, anti-CD40-induced colitis, and spontaneous lupus, will also be presented.


  • Organizational Affiliation

    Immunosciences Discovery Chemistry, Bristol-Myers Squibb Research & Development, P.O. Box 4000, Princeton, New Jersey 08543, 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
317Homo 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VZJ (Subject of Investigation/LOI)
Query on VZJ

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
6-[(cyclopropanecarbonyl)amino]-4-{[2-methoxy-3-(pyrimidin-2-yl)phenyl]amino}-N-methylpyridazine-3-carboxamide
C21 H21 N7 O3
XPHMHCUYKWFASJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
VZJ BindingDB:  7K7O IC50: min: 0.48, max: 53 (nM) from 3 assay(s)
EC50: 5.22 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.06α = 90
b = 66.62β = 112.94
c = 74.97γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted VZJClick on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2021-08-04 
  • Deposition Author(s): Khan, J.A.

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-04
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description