Transforming Complement Therapeutics June 2018

Forward Looking Statements This presentation contains "forward-looking statements" within the meaning of the Private Securities Litigation Reform Act of 1995, including, but not limited to, statements regarding the safety, efficacy, regulatory and clinical progress and therapeutic potential of our product candidates, including RA101495 SC, our market opportunities, and management’s estimates about the potential size and characteristics for the patient populations that our product candidates are targeting. All such forward-looking statements are based on management's current expectations of future events and are subject to a number of risks and uncertainties that could cause actual results to differ materially and adversely from those set forth in or implied by such forward-looking statements. These risks and uncertainties include the risks that Ra Pharma’s product candidates, including RA101495 SC, will not successfully be developed or commercialized; the risk that topline results as of February 7, 2018 from the Company’s global Phase 2 clinical program evaluating RA101495 SC for the treatment of PNH may not be indicative of final study results; as well as the other factors discussed in the “Risk Factors” section in Ra Pharma’s most recently filed Annual Report on Form 10-K, as well as other risks detailed in Ra Pharma’s subsequent filings with the Securities and Exchange Commission. There can be no assurance that the actual results or developments anticipated by Ra Pharma will be realized or, even if substantially realized, that they will have the expected consequences to, or effects on, Ra Pharma. All information in this presentation is as of June 7, 2018, and Ra Pharma undertakes no duty to update this information unless required by law. 2

3 Transforming Complement Therapeutics Focused on rare hematologic, renal, and neurologic indications RA101495 SC: Convenient, self-administered, subcutaneous C5 inhibitor Phase 2 studies in paroxysmal nocturnal hemoglobinuria (PNH) completed Phase 2 study in generalized myasthenia gravis (gMG) ongoing Phase 1b PK study in renally impaired patients ongoing; Enrollment complete Portfolio of C5 inhibitors in pre-clinical development Extended release formulation of RA101495 SC First-in-class oral small molecule C5 inhibitor Powerful proprietary drug discovery engine Trillion member, highly diverse, synthetic macrocyclic peptide libraries Diversity and specificity of mAbs with the pharmacologic advantages of small molecules Collaboration with Merck for an oral peptide targeting a large CV market opportunity

Activated by non-self cells Activated by antibody-antigen complexes Activated by pathogen surfaces C5a C3 C1q – C1r – C1s C7, C8, C9 C5b6 Membrane attack complex (MAC) Binds C5 eculizumab RA101495 SC Binds C5 & C5b Proinflammatory cytokine Lectin Pathway Classical Pathway Alternative Pathway C5 C5b C6 Factor D, Factor B 4 Opportunities in Complement Inhibition aHUS: hemolytic anemia, thrombocytopenia, and renal failure PNH: rupture of RBC gMG: destruction of neuromuscular junction LN: inflammation of kidney glomerulus Multiple Indications

5 Pipeline Programs DISCOVERY/ RA101495 SC (PNH) Oral Macrocyclic Peptide (Cardiovascular target with a large market opportunity) Orphan Renal Diseases (SC) Ocular/Autoimmune/CNS diseases PRECLINICAL PHASE 1 PHASE 2 C5 Inhibition Franchise RA101495 SC (gMG) Oral Small Molecule Inhibitor RA101495 SC Extended Release (XR) Partnered Program (Non-Complement target) Factor D Inhibition Other Complement Inhibitors RA101495 SC (renal; aHUS/LN) PHASE 3

RA101495 SC – Positioned for Success Large mAb (140 kDa) Last Line Long Infusion (~1 hr) High Volume IV (90-120 mL) Exclusive Small Peptide (3 kDa) Earlier use Brief Injection (5-8 sec.) Convenient SC (~0.5 mL) Accessible Today RA101495 SC Rising Expectations for Complement Inhibition 6

7 RA101495 SC – Building a Pipeline within a Product Expanded Market Opportunities Through Convenient Complement Control gMG Ph2 Ph1 Development Potential 1st line option to target complement-mediated damage earlier Potential 1st line option to treat all naïve and most switch patients Potential 1st line option to urgently treat acute or progressive TMA PNH Ph2 ANCA Vasculitis Lupus Nephritis NMO TMA HELLP Potential Future Indications aHUS

8 Paroxysmal Nocturnal Hemoglobinuria (PNH) – Rare, Life-threatening, C5-Mediated Disease1 Estimated 1.3 per million per year newly diagnosed patients2 1. Kanakura Y. Int J Hematol. 2013; 98:406–416. 2. Hill A. Blood. 2006; 108:985. 3. Soliris® [package insert]. Alexion Pharmaceuticals Inc; revised 1/2017. 4. Houlton S. Prescriber. 2018 Jan; 23-27. Frequency ~ 8,000 to 10,000 people in North America and Europe ~1,000 to 2,000 in Japan2 Cause Spontaneous mutations in the PIG-A gene in red blood cells (RBCs) cause PNH1 Natural History Early diagnosis and intervention is critical Variability of PNH delays diagnosis, often up to 10 years3 35% of PNH patients die within 5 years of diagnosis1,3 Median survival after diagnosis is 10 years1,3 Treatment Expensive and exclusive Anti-complement C5 monoclonal antibody [eculizumab (Soliris®); Alexion]3 Biweekly IV infusion3 ; Approximate annual cost $600,0004 Consequences Serious and progressive Life-threatening complications in PNH include thromboses, renal insufficiency, and other organ damage Complement-mediated hemolysis underlies progressive morbidities and mortality in PNH1 PIG-A mutation results in surface complement deposition and activation due to loss of complement regulators (CD59, CD55) C3b, a fragment of complement C3, is deposited on RBC surface Convertases containing C3b activate C5 leading to MAC formation C5 activation and assembly of the membrane attack complex (MAC) Destruction of RBC C3b MAC RBC Lysis

9 RA101495 SC PNH Phase 2 – Study Design Extension Study Cohort B (switch) n=16 D1 Cohort A (naïve) n=10 W6 W12 W2 Inadequate Responders (LDH > 1.5 x ULN) n=3 Review of safety & efficacy Evaluation period for primary efficacy endpoint (change in LDH from baseline to mean of W6-12) Loading dose: 0.3mg/kg SC on Day 1 Starting dose: 0.1mg/kg SC once daily for the first 2 weeks Up-titration: from the week 2 visit onwards, if LDH is  1.5xULN, the dose is increased to 0.3mg/kg SC once daily

10 RA101495 SC in Treatment Naïve PNH – Rapid, Robust, Sustained Reduction of LDH References: 1.Hillmen et al. N Engl J Med 2006. 2.U.S. FDA/CDER. (2007) BLA 125166 Pharmacometrics Review Eculizumab/Soliris **Weekly eculizumab loading period *Not a head-to-head comparison. **Relative overdosing of eculizumab during weekly loading period coincides with relative underdosing of RA101495 during dose-titration ** Comparable LDH Reduction to Eculizumab1,2 Dose Dependence of Complement Inhibition 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 0 500 1000 1500 2000 2500 Weeks 1.5X ULN L D H ( U / L ) RA101495 RA101495 N = 10 10 10 10 10 10 10 9 9 7 Eculizumab (N=41)

11 RA101495 SC in Treatment Naïve PNH – Treatment Satisfaction and Transfusion Improvements At final study visit (W12) 50% of treatment naïve, transfusion-dependent patients have been transfusion-free while on RA101495 SC Treatment Satisfaction Score Mean (SE), n=19 Improvements in Transfusion Dependence

12 RA101495 SC in Eculizumab Switch – Success in Defined Sub-Population Robust LDH Control in Transfusion-Independent Patients Reticulocyte Count at Time of Switching is an Important Predictor of Switch Success 0 500 1000 1500 Week L D H ( U / L ) 1 2 3 4 6 8 10 12 Baseline 16 20 24 1.5x ULN Transfusion Dependent Transfusion Independent Week Baseline * 1 2 3 4 6 8 10 12 16 20 24 Transfusion Dependent, n 11 11 11 11 10 9 7 6 4 2 1 1 Transfusion Independent, n 5 5 5 5 5 5 4 4 4 2 2 2

13 RA101495 SC Phase 2 PNH Program – Safety and Tolerability Cumulative RA101495 SC exposure: Over 700 patient-weeks No dosing interruptions, down-titrations, or discontinuations due to tolerability No meningococcal infections observed No thromboembolic events observed ~100% compliance with once daily subcutaneous self-administration at home observed (monitored remotely by smartphone) Majority of adverse events observed deemed unrelated to study drug Most common related adverse event observed has been headache 9 mild (grade 1) ISRs among 5 subjects out of >5,000 self-administered injections

14 PNH Opportunity – Potential 1st Line Option to Treat All Naïve and Most Switch Patients Not Yet Diagnosed: ~60% Newly Diagnosed Per Year: ~10% 40% With EVH (transfusion dependent) 60% Without EVH (transfusion independent and reticulocyte <2xULN) On Treatment: ~30% Prevalence: ~15.9 per million References: 1. Hill A. Blood. 2006; 108:985. 2. Schrezenmeier H. Haematologica. doi: 10.3324/haematol.2013.093161. 3. Risitano AM. Blood. 2009; 113:4049-100. RA101495 SC Opportunity

15 RA101495 SC – Building a Pipeline within a Product aHUS gMG Ph2 Ph1 Development Potential 1st line option to target complement-mediated damage earlier Potential 1st line option to treat all naïve and most switch patients Potential 1st line option to urgently treat acute or progressive TMA PNH Ph2 ANCA Vasculitis Lupus Nephritis NMO TMA HELLP Potential Future Indications Expanded Market Opportunities Through Convenient Complement Control

16 Generalized Myasthenia Gravis (gMG) – Rare, Debilitating, C5-Mediated Disease1 References: 1. Howard JF. Lancet Neurol. 2017;16(12):976-986. 2. Myasthenia Gravis Foundation of America and Howard JF. Reviewed 2015. Available at http://www.myasthenia.org/HealthProfessionals/ 3. Conti-Fine BM. J Clin Invest. 2006; 116(11):2843-2855. 4. Spillane J, et al. BMJ. 2013; 346:36-39. 5. Wang et al. BMC Neurology. 2017;17:77-83. 6. Renton AE, et al. JAMA Neurol. 2015 Apr;72(4):396-404. 7. Heatwole C, et al. J Clin Neuromuscul Dis. 2011; 13(2): 85–94. 8. Soliris® [package insert]. Alexion Pharmaceuticals Inc; revised 1/2017. 9. Prime Therapeutics. AMCP 2018, April 23-26, Boston. Frequency ~ 60,000 people in the US alone2 Cause Antibodies block signals from nerves to muscles and complement activation destroys the neuromuscular junction3 Natural History A rare disease, often overlooked3 Commonly misdiagnosed; diagnosis can be delayed >5 years4 ~80% of patients progress to generalized muscle weakness5; ~20% experience crisis6 Treatment Sporadic, expensive, and often non-specific Cholinesterase inhibitors, corticosteroids, immunosuppressants, thymectomy Intravenous immunoglobulin (IVIg) and plasma exchange; Annual costs are ~$100,0007 Eculizumab (Soliris®; Alexion), approved for gMG in 20178; Annual costs are ~$700,0009 Consequences Serious and progressive Systemic weakness significantly impacting quality of life1,2 Autoantibodies and complement-mediated destruction of the neuromuscular junction cause pathology in gMG1,2 Signal blocked Signal proceeds Myasthenia Gravis Normal Acetylcholine (Ach) Nerve cell Acetylcholine receptor (AChR) Muscle cell Autoantibody that binds to AChr Complement-mediated MAC assembly Muscle contracts Destruction of membrane

17 RA101495 SC in gMG – Opportunity to Target Complement-Mediated Damage Earlier Thymectomy Steroids Acetylcholinesterase Inhibitor MG Diagnosis Immunosuppressive Therapies IVIg/PLEX (Crises or Chronic) Refractory Soliris (eculizumab) IV RA101495 SC Opportunity IVIg = intravenous immunoglobulin PLEX = plasmapheresis

18 RA101495 SC in gMG – Phase 2 Design Design: Randomized, double-blind placebo-controlled multicenter study, 12-week treatment period followed by a long term extension (LTE) study Patient Population: Generalized MG (Myasthenia Gravis Foundation of America class II-IVa) AChR-antibody positive Quantitative Myasthenia Gravis (QMG) score of  12 No requirement to have failed multiple prior therapies Stable doses of corticosteroids and/or immunosuppressants

19 RA101495 SC in gMG – Phase 2 Design N=36 Screening and Washout 1:1:1 Randomization 0.3 mg/kg SC Longterm Extension (Active Drug) 0.1 mg/kg SC Placebo Anticipated initial data read-out 1H19 Study Period Long Term Extension 19 Patients Dosed as of June 5, 2018 Primary Efficacy Endpoint: Change in QMG score from baseline to week 12 Secondary Endpoints include: Myasthenia Gravis Activities of Daily Living (MG-ADL), Myasthenia Gravis Quality of Life (MG-QOL15r), Myasthenia Gravis Composite (MGC)

20 gMG Opportunity – Potential 1st Line Option to Treat Complement-Mediated Damage Earlier Controlled: ~40% Uncontrolled: ~40% Last Line: ~20% Patients adequately managed on steroids or Pyridostigmine Patients lacking control despite treatments, including steroids and multiple ISTs. Patients reverting to IVIg or plasmapheresis after trying earlier line treatments Prevalence: ~200 per million References: 1. IQVIA market research sufficiency counts, May 4, 2018 2. IQVIA market research sufficiency counts, May 17, 2018. 3. Market research, May 2018. RA101495 SC Opportunity

21 RA101495 SC – Building a Pipeline within a Product gMG Ph2 Ph1 Development Potential 1st line option to target complement-mediated damage earlier Potential 1st line option to treat all naïve and most switch patients Potential 1st line option to urgently treat acute or progressive TMA PNH Ph2 ANCA Vasculitis Lupus Nephritis NMO TMA HELLP Potential Future Indications Expanded Market Opportunities Through Convenient Complement Control aHUS

22 Atypical Hemolytic Uremic Syndrome (aHUS) – Rare, Life-threatening, C5-Mediated Disease Historically, despite management, within 3 years of diagnosis 79% of patients required dialysis, had permanent kidney damage, or died.3 References: 1. Loirat C. Orphanet J Rare Dis. 2011; 6: 60. 2. Hosler GA. Arch Pathol Lab Med. 2003;127:834-839. 3. Noris M. N Engl J Med. 2009;361:1676-1687. 4. Nester CM. Hematology Am Soc Hematol Educ Program. 2012;2012:617-25. 5. Noris M. Clin J Am Soc Nephrol. 2010;5:1844-1859. 6. Kaplan BS. Intractable & Rare Diseases Research. 2014; 3(2):34-45. 7. Soliris® [package insert]. Alexion Pharmaceuticals Inc; revised 1/2017. Frequency ~ 2 cases per million worldwide1 Cause Uncontrolled fluid phase activation of complement that results in formation of blood clots in small blood vessels throughout the body2,3 Diagnosis Ultra rare, frequently not recognized2-4 In 70% of patients, aHUS onset was associated with a triggering event, such as infection4,5 ~60% are children (<18 years of age) Treatment Expensive and often imperfect Plasma infusion or exchange, dialysis, kidney transplant6 Eculizumab (Soliris®; Alexion) is the first FDA-approved treatment for aHUS7 Consequences Severe and life-threatening Kidney failure, stroke, heart attacks, seizures and high blood pressure8 Chronic, uncontrolled fluid phase complement activation leads to thrombotic microangiopathy (TMA) causing permanent tissue damage5,6 Endothelial cell injury, tissue damage and organ failure Platelet activation and formation of TMA lesions Activation of the immune system Continual fluid phase complement activation TMA Activated leukocytes

23 Phase 1b PK Study in Renal Indications Multi-center, Open-label Trial Data Expected Mid-2018 Enrollment Recently Completed 8 patients with severe renal impairment 8 healthy control subjects with normal renal function Each patient receives a single, SC dose of 0.3 mg/kg of RA101495 SC Trial will compare the PK profile in patients with renal impairment with subjects with normal renal function

24 Orally-Available, Small Molecule Inhibitors of C5 Serum + HCl Serum* Serum + HCl + Eculizumab Serum + HCl + Compound A Compound A concentration Type III Type I+II SM Inhibits Complement Mediated Hemolysis of Human PNH Type III Erythrocytes in a Dose-Dependent Manner Podium presentation at EHA 23 (Stockholm) Alonso Ricardo, Ph.D. Sunday, June 17, 8:15-8:30 CEST Room A8; Abstract Code: 3854 Molecules bind to novel, cryptic site on C5 and prevent cleavage into C5a and C5b Block C5 activation by classical/lectin pathway and alternative pathway convertases Exhibit desirable drug-like properties (solubility, polar surface area, CLogP, etc.) High potency and oral availability, favorable DMPK properties, and no adverse safety signals to date

25 Transforming Complement Therapeutics Focused on rare hematologic, renal, and neurologic indications RA101495 SC: Convenient, self-administered, subcutaneous C5 inhibitor Phase 2 studies in paroxysmal nocturnal hemoglobinuria (PNH) completed Phase 2 study in generalized myasthenia gravis (gMG) ongoing Phase 1b PK study in renally impaired patients ongoing; Enrollment complete Portfolio of C5 inhibitors in pre-clinical development Extended release formulation of RA101495 SC First-in-class oral small molecule C5 inhibitor Powerful proprietary drug discovery engine Trillion member, highly diverse, synthetic macrocyclic peptide libraries Diversity and specificity of mAbs with the pharmacologic advantages of small molecules Collaboration with Merck for an oral peptide targeting a large CV market opportunity