4PY1 | pdb_00004py1

Crystal structure of Tyk2 in complex with compound 15, 6-((2,5-dimethoxyphenyl)thio)-3-(1-methyl-1H-pyrazol-4-yl)-[1,2,4]triazolo[4,3-b]pyridazine

• PDB DOI: https://doi.org/10.2210/pdb4PY1/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-03-25 Released: 2014-09-03 
• Deposition Author(s): Han, S., Knafels, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 
  0.236 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Kinase domain inhibition of leucine rich repeat kinase 2 (LRRK2) using a [1,2,4]triazolo[4,3-b]pyridazine scaffold.

Galatsis, P., Henderson, J.L., Kormos, B.L., Han, S., Kurumbail, R.G., Wager, T.T., Verhoest, P.R., Noell, G.S., Chen, Y., Needle, E., Berger, Z., Steyn, S.J., Houle, C., Hirst, W.D.

(2014) Bioorg Med Chem Lett 24: 4132-4140

• PubMed: 25113930 
• DOI: https://doi.org/10.1016/j.bmcl.2014.07.052
• Primary Citation Related Structures: 
  4PY1


• PubMed Abstract: 
  

  Leucine rich repeat kinase 2 (LRRK2) has been genetically linked to Parkinson's disease (PD). The most common mutant, G2019S, increases kinase activity, thus LRRK2 kinase inhibitors are potentially useful in the treatment of PD. We herein disclose the structure, potential ligand-protein binding interactions, and pharmacological profiling of potent and highly selective kinase inhibitors based on a triazolopyridazine chemical scaffold.

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Organizational Affiliation: 
• Worldwide Medicinal Chemistry, Pfizer Worldwide R&D, 610 Main St., Cambridge, MA 02139, United States. Electronic address: [e-mail].
Worldwide Medicinal Chemistry, Pfizer Worldwide R&D, 610 Main St., Cambridge, MA 02139, United States.
Worldwide Medicinal Chemistry, Pfizer Worldwide R&D, Eastern Point Rd., Groton, CT 06340, United States.
Primary Pharmacology Group, Pfizer Worldwide R&D, Eastern Point Rd., Groton, CT 06340, United States.
Neuroscience Research Unit, Pfizer Worldwide R&D, 610 Main St., Cambridge, MA 02139, United States.
Pharmacokinetics, Dynamics, and Metabolism, Pfizer Worldwide R&D, 610 Main St., Cambridge, MA 02139, United States.
Drug Safety R&D, Pfizer Worldwide R&D, Eastern Point Rd., Groton, CT 06340, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.92 kDa 
• Atom Count: 2,493 
• Modeled Residue Count: 290 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-receptor tyrosine-protein kinase TYK2	A	318	Homo sapiens	Mutation(s): 6  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2YK	B [auth A]	6-[(2,5-dimethoxyphenyl)sulfanyl]-3-(1-methyl-1H-pyrazol-4-yl)[1,2,4]triazolo[4,3-b]pyridazine C17 H16 N6 O2 S RAHGVIZTQAHVRX-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free:  0.236 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.47	α = 90
b = 73.51	β = 90
c = 103.63	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data collection
BUSTER	refinement
SCALA	data scaling
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-03 
Deposition Author(s): Han, S., Knafels, J.D.

Revision History  

• Version 1.0: 2014-09-03
  Type: Initial release
  
• Version 1.1: 2014-09-17
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary