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 ® ® ® Product Candidates and Collaborations The following table summarizes certain information about the Company’s lead product candidates: Product Candidate Branded Reference Drug Program Indication Proposed Therapeutic Equivalent PF708 – Teriparatide Forteo Licensed in Mainland China, Hong Kong, Singapore, Malaysia & Thailand; Wholly-Owned Rest of World Osteoporosis Novel Vaccines Px563L/RPA563 – rPA based anthrax vaccines N/A U.S. Government Funded Anthrax post-exposure prophylaxis The following table summarizes certain information about the Company’s lead collaboration: Collaboration Partner Products Indication Jazz Pharmaceuticals Ireland Limited Multiple Hematology/Oncology Products Various PF708 is being developed as a therapeutic equivalent candidate to Forteo, marketed by Eli Lilly and Company. The Company completed enrollment in its Study PF708-301 in in mid-February 2018. parameters. Top-line immunogenicity On April 18, 2018, the Company and China NT Pharma Group Company Limited (NT Pharma) entered into a Development and License Agreement (the NT Pharma Agreement), pursuant to which Pfenex granted an exclusive license to NT Pharma to commercialize PF708 in Mainland China, Hong Kong, Singapore, Malaysia and Thailand and a non-exclusive The Company is also developing Px563L/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 . In July 2016, Pfenex and Jazz announced an agreement under which Pfenex 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. 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, Pfenex decided to pause its development activities for PF582 and PF529 and focus the Company’s efforts and resources elsewhere in its product portfolio. While the Company is seeking a new collaboration partner for the development and commercialization of PF582 and PF529, there are no assurances that it will find a new collaboration partner or that the terms and timing of any such arrangements would be acceptable to us. 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 collaboration agreements, service agreements, government contracts and reagent protein product sales 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. On March 15, 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. The Sales Agreement provides that William Blair will be entitled to compensation for its services that will equal 3.0% of the gross sales price per share of all shares sold through William Blair under the Sales Agreement. The Sales Agreement shall automatically terminate upon the issuance and sale of placement shares equaling sales proceeds of $20.0 million and may be terminated earlier by either the Company or William Blair upon five days’ notice. The Company has no obligation to sell any shares under the Sales Agreement, and may at any time suspend solicitation and offers under the Sales Agreement. As of March 31, 2018, the Company had not sold any shares under the Sales Agreement. 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 March 31, 2018, the Company had an accumulated deficit of $172.7 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. Although the Company believes it has sufficient cash resources to fund all necessary activities leading up to and including submission of an NDA for PF708 to the FDA (assuming positive results from Study PF708-301), Cash and Cash Equivalents The Company considers all highly liquid investments that are readily convertible into cash and have an original maturity of six months 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 March 31, 2018 and December 31, 2017. For the Company’s cash position of $47.3 million as of March 31, 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 March 31, 2018 and December 31, 2017, receivables were concentrated among two and three customers representing 84% and 89% of total net receivables, respectively. No allowance for doubtful accounts was recorded at March 31, 2018 or December 31, 2017. Revenue from two customers and/or collaboration partners represented 90% and 88% of total revenue for the three months ended March 31, 2018 and 2017, respectively. A portion of revenue is earned from sales outside the United States. Non-U.S. revenue and non-U.S. sources Three Months Ended March 31, 2018 2017 (in thousands) US Revenue $ 1,594 $ 1,057 Non-US 2,152 1,761 $ 3,746 $ 2,818 During the three months ended March 31, 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 reagent protein products, 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. 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 three months ended March 31, 2018 and 2017, no 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 return policy. The Company recognizes reagent product revenue from product sales when it is realized or realizable and earned. As of March 31, 2018, the Company has had minimal product returns related to reagent protein product sales. Therefore, no reserve for warranty and return rights was recorded as of March 31, 2018 and December 31, 2017, respectively. 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 FASB issued ASU 2016-18, Statement 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 ASU 2017-09 was Recently Issued Accounting Pronouncements Not Yet Adopted In May 2014, the Financial Accounting Standards Board (FASB) issued Accounting Standards Update (ASU) No. 2014-09 Revenue In February 2016, the FASB issued ASU No. 2016-02 Leases In January 2017, the FASB issued ASU No. 2017-04, Intangibles current two-step quantitative |