Organization and Summary of Significant Accounting Policies | 1. Organization and Summary of Significant Accounting Policies Business Activities and Organization Pfenex Inc. (the Company or Pfenex) is a clinical-stage development and licensing biotechnology company focused on leveraging its Pf ® Pf Pf ® ® ® Product Candidates and Collaborations The following table summarizes certain information about the Company’s lead product candidates and collaborations: Product Candidate Branded Reference Drug Program Indication Proposed Therapeutic Equivalent PF708 – Teriparatide Forteo • Licensed in the United States to Alvogen; • Licensed in Mainland China, Hong Kong, Singapore, Malaysia, Thailand to NT Pharma; • Wholly-Owned Rest of World Osteoporosis Multiple Hematology/Oncology Various • Jazz Pharmaceuticals Ireland Limited Various Novel Vaccines Px563L and RPA563 – rPA based anthrax vaccines N/A • U.S. Government Funded Anthrax post-exposure prophylaxis Proposed Therapeutic Equivalent : PF708 – Teriparatide PF708 is being developed as a therapeutic equivalent candidate to Forteo, which is approved and marketed by Eli Lilly and Company for the treatment of osteoporosis patients at a high risk of fracture. In April 2018, the Company and NT Pharma entered into a Development and License Agreement (NT Pharma Agreement), pursuant to which the Company granted an exclusive license to NT Pharma to commercialize PF708 in Mainland China, Hong Kong, Singapore, Malaysia and Thailand and a non-exclusive Collaboration Partner: Jazz Pharmaceuticals Ireland Limited In July 2016, the Company and Jazz announced an agreement under which the Company granted Jazz worldwide rights to develop and commercialize multiple early stage hematology/oncology product candidates, including PF743, a recombinant crisantaspase, and PF745, a recombinant crisantaspase with half-life extension technology. In December 2017, the parties amended the Jazz agreement, bringing the total value of payments and potential payments associated with the collaboration to $224.5 million. In addition, the Company may be eligible to receive tiered royalties on worldwide sales of any products resulting from the collaboration at rates reduced from those under the 2016 agreement. Novel Vaccines: Px563L and RPA563 – rPA based anthrax vaccines The Company is also developing Px563L and RPA563, novel anthrax vaccine candidates, in response to the United States government’s unmet demand for increased quantity, stability and dose-sparing regimens of anthrax vaccine . Pf ē nex Expression Technology Licenses: CRM197 The Company has several development and commercial partnerships in place for CRM197, which is a non-toxic non-GMP . The Company’s revenue in the near term is primarily related to monetizing its protein production platform through CRM197 product sales, commercial license agreements, service agreements, and government contracts, which may provide for various types of payments, including upfront payments, funding of research and development, milestone payments, intellectual property access fees and licensing fees. Other Pipeline Products In addition to the Company’s lead product candidates, its pipeline includes various other biosimilar candidates, including PF582, the Company’s biosimilar candidate to Lucentis, and PF529, the Company’s biosimilar candidate to Neulasta, as well as vaccines and next generation biologic candidates. Following its strategic review in November 2017, the Company decided to pause its development activities for PF582 and PF529 and focus the Company’s efforts and resources elsewhere in its product portfolio. At the Market Offering Program In March 2018, the Company entered into an equity sales agreement (Sales Agreement) with William Blair & Company, L.L.C. (William Blair) to sell shares of the Company’s common stock having aggregate sales proceeds of up to $20.0 million, from time to time, through an “at the market” equity offering program under which William Blair will act as sales agent. Under the Sales Agreement, the Company sets the parameters for the sale of shares, including the number of shares to be issued, the time period during which sales are requested to be made, limitation on the number of shares that may be sold in any one trading day and any minimum price below which sales may not be made. As of September 30, 2018, the Company had not sold any shares under the Sales Agreement. Follow-on In May 2018, the Company completed a public offering of common stock in which it sold 7,820,000 shares of its common stock at an offering price of $5.50 per share, which included the full exercise by the underwriters of their option to purchase an additional 1,020,000 shares, pursuant to the Company’s existing shelf registration statement. The net proceeds generated from this transaction, after underwriting discounts and commissions and offering costs, were approximately $39.5 million. Basis of Presentation The accompanying unaudited consolidated financial statements have been prepared in accordance with United States generally accepted accounting principles, or U.S. GAAP, for interim financial information and with the instructions of the Securities and Exchange Commission, or SEC, on Form 10-Q 10-01 Regulation S-X. 10-K Use of Estimates The preparation of the accompanying unaudited consolidated financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts (including assets, liabilities, revenues and expenses) and related disclosures. Estimates have been prepared on the basis of the most current and best available information. However, actual results could differ from those estimates. Risk and Uncertainties The Company’s future results of operations involve a number of risks and uncertainties. Factors that could affect the Company’s future operating results and cause actual results to vary materially from expectations include, but are not limited to, uncertainty of results of clinical trials and reaching milestones, uncertainty of regulatory approval of the Company’s product candidates, uncertainty of market acceptance of the Company’s products if approved for sale, competition from substitute products and larger companies, securing and protecting proprietary technology, strategic relationships and dependence on key individuals. Products developed by the Company require clearances from international and domestic regulatory agencies prior to commercial sales in such jurisdictions. There can be no assurance that the products will receive the necessary clearances. If the Company was denied clearance, clearance was delayed or the Company was unable to maintain clearance, it could have a materially adverse impact on the Company. As of September 30, 2018, the Company had an accumulated deficit of $194.5 million and expects to incur substantial operating losses for the next several years. The Company believes that its existing cash and cash equivalents and cash inflow from operations will be sufficient to meet its anticipated cash needs for at least the next 12 months including all necessary activities leading up to and including potential commercial launch of PF708 in the United States as early as the fourth quarter of 2019, subject to FDA acceptance, approval of the new drug application and other factors. Cash and Cash Equivalents The Company considers all highly liquid investments that are readily convertible into cash and have an original maturity of 90 days or less at the time of purchase to be cash equivalents. Cash amounts that are restricted as to withdrawal or usage are presented as restricted cash. In January 2017, the Company entered into a Borrower’s Pledge Agreement, which required $0.2 million in restricted cash to be provided as security for its commercial credit card arrangement with one of the Company’s banks. Concentrations Financial instruments that potentially subject the Company to concentrations of credit risk consist primarily of cash, cash equivalents, investments and accounts and unbilled receivables. The Company has established guidelines intended to limit its exposure to credit risk by placing investments with high credit quality financial institutions, diversifying its investment portfolio and placing investments with maturities that help maintain safety and liquidity. All cash and cash equivalents were held at three major financial institutions as of September 30, 2018 and December 31, 2017. For the Company’s cash position of $68.0 million as of September 30, 2018, which included restricted cash of $0.2 million, the Company has exposure to credit loss for amounts in excess of insured limits in the event of non-performance by anticipate non-performance. Additional credit risk is related to the Company’s concentration of receivables. As of September 30, 2018 and December 31, 2017, receivables were concentrated among three customers representing 99% and 89% of total net receivables, respectively. No allowance for doubtful accounts was recorded at September 30, 2018 or December 31, 2017. For the three months ended September 30, 2018 and 2017, revenue was concentrated among two customers and/or collaboration partners representing 89% and two customers and/or collaborative partners representing 94% of total revenues, respectively. Revenue from two customers and/or collaboration partners represented 87% and 91% of total revenue for the nine months ended September 30, 2018 and 2017, respectively. A portion of revenue is earned from sales outside the United States. Non-U.S. non-U.S. Three Months Ended September 30, Nine Months Ended September 30, (in thousands) 2018 2017 2018 2017 US revenue $ 1,371 $ 2,190 $ 3,877 $ 4,453 Non-US 2,199 2,834 7,629 6,418 Total revenue $ 3,570 $ 5,024 $ 11,506 $ 10,871 During the three and nine months ended September 30, 2018 and 2017, Ireland accounted for more than 10% of the Company’s revenue. Revenue The Company’s revenue is related to the monetization of its protein production platform through collaboration agreements, service agreements, license agreements, government contracts and sales of CRM197, which may provide for various types of payments, including upfront payments, funding of research and development, milestone payments, intellectual property access fees and licensing fees. The Company’s revenue generating agreements also include potential revenues for achieving milestones and for product royalties. The specifics of the Company’s significant agreements are detailed in Note 7—Significant Research and Development Agreements. The Company considers a variety of factors in determining the appropriate method of accounting for its collaboration agreements, including whether multiple deliverables can be separated and accounted for individually as separate units of accounting. Where there are multiple deliverables within a collaboration agreement that cannot be separated and therefore are combined into a single unit of accounting, revenues are deferred and recognized using the relevant guidance over the estimated period of performance. To the extent an arrangement contains a contingent deliverable, the Company will recognize the allocated consideration once the deliverable has been fulfilled. If the deliverables can be separated, the Company applies the relevant revenue recognition guidance to each individual deliverable. The specific methodology for the recognition of the underlying revenue is determined on a case-by-case basis Upfront, nonrefundable licensing payments are assessed to determine whether or not the licensee is able to obtain standalone value from the license. Where the license does not have standalone value, non-refundable license Nonrefundable payments for research funding are generally recognized as revenue over the period the underlying research activities are performed. Revenue under service agreements are recorded as services are performed. These agreements do not require development achievement as a performance obligation and provide for payment when services are rendered. All such revenue is nonrefundable. Upfront, nonrefundable payments for license fees, exclusivity and feasibility services received in excess of amounts earned are classified as deferred revenue and recognized as income over the contract term or period of performance based on the nature of the related agreement. The Company recognizes revenue for its cost-plus fixed fee government contracts in accordance with the authoritative guidance for revenue recognition including the authoritative guidance specific to federal government contractors. Reimbursable costs under the Company’s government contracts primarily include direct labor, materials, subcontracts, accountable property and indirect costs. In addition, the Company receives a fixed fee under its government contracts, which is unconditionally earned as allowable costs are incurred and is not contingent on success factors. Reimbursable costs under the Company’s government contracts, including the fixed fee, are generally recognized as revenue in the period the reimbursable costs are incurred and become billable. The Company assesses milestone payments on an individual basis and recognizes revenue from nonrefundable milestone payments when the earnings process is complete and the payment is reasonably assured. Nonrefundable milestone payments related to arrangements under which the Company has continuing performance obligations are recognized as revenue upon achievement of the associated milestone, provided that (i) the milestone event is substantive and its achievability was not reasonably assured at the inception of the agreement, and (ii) the amount of the milestone payment is reasonable in relation to the effort expended or the risk associated with the milestone event. For the nine months ended September 30, 2018, $1.3 million in revenue was recognized in connection with the Merck and Jazz collaborations, with no revenue recognized for the quarter. For the three and nine months ended September 30, 2017, $1.0 million in revenue was recognized in connection with the achievement of development milestones associated with the Jazz collaboration. The Company’s reagent protein products are primarily comprised of internally developed reagent protein products. Revenues for reagent product sales are reflected net of attributable sales tax. The Company generally offers a 30-day Revenue under arrangements where the Company outsources the cost of fulfillment to third parties is evaluated as to whether the related amounts should be recorded gross or net. The Company records amounts collected from the customer as revenue, and the amounts paid to suppliers as cost of revenue when it holds all or substantially all of the risks and benefits related to the product or service. For transactions where the Company does not hold all or substantially all the risk, the Company uses net reporting and therefore records the transaction as if the end-user made Recently Adopted Accounting Pronouncements In November 2016, the Financial Accounting Standards Board (FASB) issued Accounting Standards Update (ASU) 2016-18, Statement of Cash Flows (Topic 230): Restricted Cash beginning-of-period end-of-period the beginning-of-period and end-of-period total 2016-18 In May 2017, the FASB issued ASU 2017-09, Compensation – Stock Compensation (Topic 718), Scope of Modification Accounting ASU 2017-09 was Recently Issued Accounting Pronouncements Not Yet Adopted In May 2014, the FASB issued ASU No. 2014-09, Revenue from Contracts with Customers (Topic 606) In February 2016, the FASB issued ASU No. 2016-02, Leases (Topic 842) 2018-10, Codification Improvements to Topic 842, Leases 2018-11, Leases (Topic 842): Targeted Improvements right-of-use In January 2017, the FASB issued ASU No. 2017-04, Intangibles – Goodwill and Other (Topic 350): Simplifying the Test for Goodwill Impairment current two-step quantitative In June 2018, the FASB issued ASU No. 2018-07, Compensation-Stock Compensation (Topic 718), In August 2018, the FASB issued ASU No. 2018-15, Intangibles—Goodwill and Other-Internal-Use 350-40): internal-use ASU 2018-15 is |