6OVA | pdb_00006ova

Crystal Structure of TYK2 with novel pyrrolidinone inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6OVA/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2019-05-07 Released: 2020-02-12 
• Deposition Author(s): Skene, R.J., Hoffman, I.D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.251 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Efficient synthesis of tert-butyl 3-cyano-3-cyclopropyl-2-oxopyrrolidine-4-carboxylates: Highly functionalized 2-pyrrolidinone enabling access to novel macrocyclic Tyk2 inhibitors.

Sasaki, Y., Tokuhara, H., Ohba, Y., Okabe, A., Nakayama, M., Nakagawa, H., Skene, R., Hoffman, I., Zou, H., Yoshida, M.

(2020) Bioorg Med Chem Lett 30: 126963-126963

• PubMed: 31980341 
• DOI: https://doi.org/10.1016/j.bmcl.2020.126963
• Primary Citation Related Structures: 
  6OVA


• PubMed Abstract: 
  

  Herein we report an efficient method for the synthesis of a highly functionalized 2-pyrrolidinone, tert-butyl 3-cyano-3-cyclopropyl-2-oxopyrrolidine-4-carboxylate, from readily available starting materials. Utility of this compound was demonstrated in the synthesis of a novel series of macrocyclic Tyk2 inhibitors, leading to the identification of a potent and selective macrocyclic Tyk2 inhibitor (26).

---

Organizational Affiliation: 
• Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26‑1, Muraoka‑Higashi 2‑chome, Fujisawa, Kanagawa 251‑8555, Japan. Electronic address: [e-mail].
Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26‑1, Muraoka‑Higashi 2‑chome, Fujisawa, Kanagawa 251‑8555, Japan.
Takeda California, Inc., 10410 Science Center Drive, San Diego, CA 92121, 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: 35.24 kDa 
• Atom Count: 2,312 
• Modeled Residue Count: 273 
• Deposited Residue Count: 301 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-receptor tyrosine-protein kinase TYK2	A	301	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
N9G (Subject of Investigation/LOI)	B [auth A]	6-({4-[(3S)-3-cyano-3-cyclopropyl-2-oxopyrrolidin-1-yl]pyridin-2-yl}amino)-N,N-dimethylpyridine-3-carboxamide C21 H22 N6 O2 CFHPNFDEUWSEIR-OAQYLSRUSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
N9G	BindingDB:  6OVA	IC50: 1.1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.251 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.073	α = 90
b = 48.073	β = 90
c = 475.025	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-02-12 
Deposition Author(s): Skene, R.J., Hoffman, I.D.

Revision History  

• Version 1.0: 2020-02-12
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references