Subsequent Events	6 Months Ended
Jun. 30, 2021
Subsequent Events.
Subsequent Events	Note 17. Subsequent Events Restated Janssen License and Collaboration Agreement On July 27, 2021, the Company entered into an amended and restated License and Collaboration Agreement (the “Restated Agreement”) with Janssen. The Restated Agreement amends and restates the License and Collaboration Agreement, dated May 27, 2017, by and between the Company and Janssen (as amended by Amendment No. 1 thereto, effective May 7, 2019, the “Original Agreement”). The Restated Agreement relates to the development, manufacture and commercialization of oral IL-23 receptor antagonist drug candidates. The candidates currently in development pursuant to the Restated Agreement include PTG-200, PN-232 and PN-235. PTG-200 is an oral, IL-23 receptor antagonist in Phase 2a development for the treatment of CD. PN-235 and PN-232 are second-generation oral IL-23 receptor antagonist candidates currently in Phase 1 studies. Janssen is primarily responsible for the conduct of the PTG-200 trial and the Company is primarily responsible for the conduct of the PN-232 and PN-235 Phase 1 studies. Pursuant to the Restated Agreement, the parties have: (a) amended development milestones to reflect Janssen’s expected development of collaboration compounds for multiple indications in the IL-23 pathway; (b) limited the Company’s further development and related expense obligations under the Restated Agreement to the ongoing PTG-200 Phase 2a study, and the ongoing Phase 1 studies in PN-232 and PN-235 described in the preceding paragraph; Janssen is responsible for all other future development and related expenses under the Restated Agreement; and (c) concluded the parties’ two-year research collaboration, while enabling Janssen to continue conducting additional research through July 2024 on compounds developed pursuant to the Original Agreement. The Company’s continuing development expense obligations under the Restated Agreement are as follows: (a) the Company will continue to fund 20% of the costs related to the ongoing Phase 2a study evaluating PTG-200 for the treatment of CD (subject to a $20.0 million cap on costs related to Phase 2a and 2b costs for PTG 200); (b) the Company is responsible for 50% of agreed-upon costs related to the ongoing Phase 1 study evaluating PN-235 incurred under the Original Agreement through January 4, 2021; (c) the Company is responsible for 100% of agreed-upon costs related to the ongoing Phase 1 study evaluating PN-232. Certain of the Company’s previous development expense obligations under the Original Agreement have been limited or eliminated as follows: (a) the Company’s previous $25.0 million obligation for 20% of costs related to Phase 2 studies for Second Generation Products has been eliminated; (b) the Company’s previous $5.0 million obligation for 50% of the costs of a potential third Phase 1 study evaluating a Second Generation Product has been eliminated; and (c) the Company has no obligation to fund any portion of any Phase 2b or other study evaluating PTG-200 beyond the ongoing Phase 2a study. One milestone for Second Generation Phase 2 development was reduced from $50.0 million to $25.0 million in the Restated Agreement; otherwise, the various milestone payment amounts in the Restated Agreement remain substantially the same as in the Original Agreement. To reflect parallel development of multiple indications in the IL-23 pathway, milestone payments under the Restated Agreement generally now correspond to the achievement of specified milestones in: (a) any initial indication (rather than CD, as in the Original Agreement); (b) any second indication (rather than UC, as in the Original Agreement); and (c) any third indication. With respect to Second Generation Products, milestone payments for second and third indications may be triggered by any Second Generation Product (i.e., not necessarily the Second Generation Product that triggered the initial payment for any indication, or the payment for a second indication). In addition, the opt-in payments contemplated by the Original Agreement related to the scope of Janssen’s license rights have been converted into development milestones in the Restated Agreement. The mid-single digit to ten percent tiered royalty rates payable pursuant to the Original Agreement remain the same in the Restated Agreement. The sales milestone payments in the Original Agreement also remain the same in the Restated Agreement. Following completion of the ongoing Phase 2a study for PTG-200 and the ongoing Phase 1 studies for PN-232 and PN-235, the Company has no further collaborative development obligations under the Restated Agreement. Any further research and development will be conducted by Janssen. Janssen retains exclusive, worldwide rights to develop and commercialize PTG-200 and any second-generation compounds derived from the research collaboration conducted under the Original Agreement, or Janssen’s further research under the Restated Agreement. Lease Amendment On July 2, 2021, the Company entered into an amendment (the “Second Lease Amendment”) to its facility lease agreement dated as of March 6, 2017, as amended, to lease approximately 15,000 square feet of additional office space in Newark, California. The Company expects to commence operations in the additional space in the third quarter of 2021. Under the Second Lease Amendment, the Company expects to pay additional base rent of approximately $1.5 million over the lease term, which expires in May 2024. The Company will be responsible for its proportional share of operating expenses and tax obligations. No additional security deposit is required.

Subsequent Events

6 Months Ended

Jun. 30, 2021

Note 17. Subsequent Events

Restated Janssen License and Collaboration Agreement

On July 27, 2021, the Company entered into an amended and restated License and Collaboration Agreement (the “Restated Agreement”) with Janssen. The Restated Agreement amends and restates the License and Collaboration Agreement, dated May 27, 2017, by and between the Company and Janssen (as amended by Amendment No. 1 thereto, effective May 7, 2019, the “Original Agreement”).

The Restated Agreement relates to the development, manufacture and commercialization of oral IL-23 receptor antagonist drug candidates. The candidates currently in development pursuant to the Restated Agreement include PTG-200, PN-232 and PN-235. PTG-200 is an oral, IL-23 receptor antagonist in Phase 2a development for the treatment of CD. PN-235 and PN-232 are second-generation oral IL-23 receptor antagonist candidates currently in

Phase 1 studies. Janssen is primarily responsible for the conduct of the PTG-200 trial and the Company is primarily responsible for the conduct of the PN-232 and PN-235 Phase 1 studies.

Pursuant to the Restated Agreement, the parties have:

(a) amended development milestones to reflect Janssen’s expected development of collaboration compounds for multiple indications in the IL-23 pathway;

(b) limited the Company’s further development and related expense obligations under the Restated Agreement to the ongoing PTG-200 Phase 2a study, and the ongoing Phase 1 studies in PN-232 and PN-235 described in the preceding paragraph; Janssen is responsible for all other future development and related expenses under the Restated Agreement; and

(c) concluded the parties’ two-year research collaboration, while enabling Janssen to continue conducting additional research through July 2024 on compounds developed pursuant to the Original Agreement.

The Company’s continuing development expense obligations under the Restated Agreement are as follows: (a) the Company will continue to fund 20% of the costs related to the ongoing Phase 2a study evaluating PTG-200 for the treatment of CD (subject to a $20.0 million cap on costs related to Phase 2a and 2b costs for PTG 200); (b) the Company is responsible for 50% of agreed-upon costs related to the ongoing Phase 1 study evaluating PN-235 incurred under the Original Agreement through January 4, 2021; (c) the Company is responsible for 100% of agreed-upon costs related to the ongoing Phase 1 study evaluating PN-232.

Certain of the Company’s previous development expense obligations under the Original Agreement have been limited or eliminated as follows: (a) the Company’s previous $25.0 million obligation for 20% of costs related to Phase 2 studies for Second Generation Products has been eliminated; (b) the Company’s previous $5.0 million obligation for 50% of the costs of a potential third Phase 1 study evaluating a Second Generation Product has been eliminated; and (c) the Company has no obligation to fund any portion of any Phase 2b or other study evaluating PTG-200 beyond the ongoing Phase 2a study.

One milestone for Second Generation Phase 2 development was reduced from $50.0 million to $25.0 million in the Restated Agreement; otherwise, the various milestone payment amounts in the Restated Agreement remain substantially the same as in the Original Agreement. To reflect parallel development of multiple indications in the IL-23 pathway, milestone payments under the Restated Agreement generally now correspond to the achievement of specified milestones in: (a) any initial indication (rather than CD, as in the Original Agreement); (b) any second indication (rather than UC, as in the Original Agreement); and (c) any third indication. With respect to Second Generation Products, milestone payments for second and third indications may be triggered by any Second Generation Product (i.e., not necessarily the Second Generation Product that triggered the initial payment for any indication, or the payment for a second indication). In addition, the opt-in payments contemplated by the Original Agreement related to the scope of Janssen’s license rights have been converted into development milestones in the Restated Agreement.

The mid-single digit to ten percent tiered royalty rates payable pursuant to the Original Agreement remain the same in the Restated Agreement. The sales milestone payments in the Original Agreement also remain the same in the Restated Agreement.

Following completion of the ongoing Phase 2a study for PTG-200 and the ongoing Phase 1 studies for PN-232 and PN-235, the Company has no further collaborative development obligations under the Restated Agreement. Any further research and development will be conducted by Janssen.

Janssen retains exclusive, worldwide rights to develop and commercialize PTG-200 and any second-generation compounds derived from the research collaboration conducted under the Original Agreement, or Janssen’s further research under the Restated Agreement.

Lease Amendment

On July 2, 2021, the Company entered into an amendment (the “Second Lease Amendment”) to its facility lease agreement dated as of March 6, 2017, as amended, to lease approximately 15,000 square feet of additional office space in Newark, California. The Company expects to commence operations in the additional space in the third quarter of 2021. Under the Second Lease Amendment, the Company expects to pay additional base rent of approximately $1.5 million over the lease term, which expires in May 2024. The Company will be responsible for its proportional share of operating expenses and tax obligations. No additional security deposit is required.