SS-31 is a synthetic tetrapeptide consisting of four amino acid residues arranged in a defined sequence: D-Arg-Dmt-Lys-Phe-NH₂. Also known as elamipretide or MTP-131, it has a molecular formula of C₃₂H₄₉N₉O₅ and a molecular weight of approximately 639.8 g/mol.
Unlike peptides composed entirely of standard L-amino acids, SS-31 contains a D-arginine residue and a modified tyrosine residue known as 2,6-dimethyltyrosine (Dmt). The peptide also has a C-terminal amide modification.
These features distinguish SS-31 from other synthetic peptides and make its chemical identification more specific than simply counting its amino acid residues.
Researchers examining SS-31 peptide structure must consider its sequence, stereochemistry, molecular mass, terminal modifications, and chemical form.
This article explains the structural characteristics of SS-31, how its molecular properties are documented, and which analytical techniques can help verify its identity.
What Is the Chemical Structure of SS-31?
SS-31 belongs to the Szeto-Schiller family of synthetic aromatic-cationic peptides.
The peptide contains four residues connected through peptide bonds.
Its chemical structure can be described by the sequence:
H-D-Arg-Dmt-Lys-Phe-NH₂
This notation identifies the residues and terminal groups making up the molecule.
The four residues are:
- D-Arginine (D-Arg)
- 2,6-Dimethyl-L-tyrosine (Dmt)
- L-Lysine (Lys)
- L-Phenylalaninamide (Phe-NH₂)
The sequence contains a combination of charged and aromatic side chains.
D-Arginine and lysine contribute basic functional groups, while dimethyltyrosine and phenylalanine contain aromatic rings.
These characteristics are relevant when studying the peptide’s chemical properties and interactions with other molecules.
SS-31 is also known as elamipretide, the established nonproprietary name associated with the same parent peptide structure.
Researchers can review the SS-31 10mg research compound at Orion Peptides for compound-specific information and available analytical documentation.
SS-31 Amino Acid Sequence Explained
The amino acid sequence defines the order in which residues are connected within a peptide.
For SS-31, that sequence is:
D-Arg-Dmt-Lys-Phe-NH₂
Although SS-31 contains only four amino acid residues, two of them require special attention when documenting its structure.
D-Arginine: The First Residue
The first residue in SS-31 is D-arginine.
Arginine is a basic amino acid containing a guanidino functional group.
Most amino acids incorporated into proteins by ordinary biological translation have the L-configuration.
However, SS-31 contains the D-enantiomer of arginine.
D-arginine and L-arginine have the same molecular formula but different three-dimensional arrangements around their chiral carbon centers.
This stereochemical difference is an essential part of SS-31’s identity.
An analytical method that confirms molecular mass alone cannot necessarily distinguish these two configurations.
2,6-Dimethyltyrosine: The Second Residue
The second residue is 2,6-dimethyl-L-tyrosine, commonly abbreviated as Dmt.
Dmt is a modified derivative of tyrosine containing two methyl groups attached to its aromatic ring.
These substitutions distinguish it from conventional tyrosine.
The dimethyl modification changes the residue’s molecular composition and contributes to the overall chemical properties of SS-31.
Because Dmt is not one of the standard protein-building amino acids, its identity should be represented explicitly in peptide sequence documentation.
Lysine: The Third Residue
The third residue is L-lysine.
Lysine contains a side chain terminating in an amino group.
Under many aqueous conditions, this group is positively charged.
The lysine residue contributes to the peptide’s basic chemical characteristics.
Like the other residues, its position within the sequence is part of the defined SS-31 structure.
Phenylalaninamide: The Fourth Residue
The fourth residue is L-phenylalanine with a modified C-terminus.
Phenylalanine contains an aromatic benzyl side chain.
In SS-31, the terminal carboxyl group is converted into a primary amide.
This modification is represented by –NH₂ at the end of the peptide sequence.
C-terminal amidation changes the peptide’s terminal chemical group and must be considered when calculating molecular formula and mass.
Why Does SS-31 Contain Modified Amino Acid Residues?
SS-31 is not simply a chain of four unmodified amino acids.
Its defining structure includes a D-amino acid, a methylated aromatic residue, and a terminal amide.
These modifications are important because chemical structure depends on more than the names of individual amino acids.
Stereochemical Modification
The D-arginine residue has a different spatial configuration from L-arginine.
Stereochemistry is important in peptide characterization because two compounds can share the same formula and molecular weight while having different three-dimensional structures.
Aromatic Ring Modification
The dimethyltyrosine residue contains two additional methyl substitutions on its aromatic ring compared with unmodified tyrosine.
These substituents contribute to the molecular formula of SS-31.
C-Terminal Amidation
The phenylalanine residue at the end of the peptide contains a carboxamide rather than a free carboxylic acid.
This terminal modification distinguishes SS-31 from a hypothetical peptide with the same residue order but an unmodified carboxyl terminus.
The exact sequence and chemical modifications should therefore be verified together.
SS-31 Molecular Formula and Molecular Weight
The parent molecular formula of SS-31 is:
C₃₂H₄₉N₉O₅
This represents:
- 32 carbon atoms
- 49 hydrogen atoms
- 9 nitrogen atoms
- 5 oxygen atoms
Its average molecular weight is approximately 639.8 g/mol.
The corresponding monoisotopic mass is approximately 639.3857 Da.
SS-31 Chemical Properties Table
| Property | Value |
|---|---|
| Compound name | SS-31 |
| Alternative name | Elamipretide |
| Research code | MTP-131 |
| Peptide family | Szeto-Schiller |
| Number of residues | 4 |
| Sequence | D-Arg-Dmt-Lys-Phe-NH₂ |
| Molecular formula | C₃₂H₄₉N₉O₅ |
| Average molecular weight | 639.8 g/mol |
| Monoisotopic mass | 639.3857 Da |
| CAS number | 736992-21-5 |
| PubChem CID | 11764719 |
| C-terminal group | Primary amide |
| Chemical classification | Synthetic tetrapeptide |
These molecular values describe the parent elamipretide structure.
They should not automatically be used as the complete formula or mass of a salt preparation containing additional counterions.
The PubChem Elamipretide record provides further chemical identifiers and structural information.
Why Are Average Molecular Weight and Monoisotopic Mass Different?
Average molecular weight and monoisotopic mass describe related but different properties.
Average molecular weight is calculated using the weighted average atomic masses of the elements.
Monoisotopic mass is calculated using the masses of specific isotopes, generally the most abundant stable isotopes.
For SS-31:
- Average molecular weight: approximately 639.8 g/mol
- Monoisotopic mass: approximately 639.3857 Da
The values are numerically close but are not interchangeable in every analytical context.
For example, high-resolution mass spectrometry commonly involves monoisotopic mass calculations and the expected mass-to-charge ratios of particular ions.
Researchers must therefore determine which mass convention is used in a laboratory report.
Does SS-31 Have a Free Amino Terminus and an Amidated Carboxyl Terminus?
Yes. The parent SS-31 structure contains a free N-terminal amino group and a C-terminal primary amide.
The sequence may be represented as:
H-D-Arg-Dmt-Lys-Phe-NH₂
The initial H indicates the unprotected N-terminal amino group.
The final NH₂ indicates the C-terminal amide.
These terminal groups are part of the defined chemical structure.
A peptide with the same four amino acids but a different terminal modification would not be chemically identical to the standard SS-31 parent structure.
Why Does Peptide Stereochemistry Matter?
Stereochemistry refers to the three-dimensional arrangement of atoms within a molecule.
Many amino acids are chiral, meaning they can exist as mirror-image configurations.
SS-31 includes D-arginine, while its other chiral amino acid residues have the designated L-configurations.
These distinctions help establish the correct peptide identity.
Can Mass Spectrometry Distinguish D-Arginine From L-Arginine?
Not through molecular mass alone.
D-arginine and L-arginine are enantiomers and therefore have identical elemental formulas and molecular masses.
Their different configurations may require specialized stereoselective methods or other suitable analytical evidence.
This means that a mass-spectrometry result matching the expected SS-31 mass is useful supporting evidence but does not independently establish every stereochemical detail.
SS-31 Free Peptide vs. Salt Forms
A frequently overlooked distinction in peptide research is the difference between the parent peptide and a supplied salt preparation.
Peptides containing basic functional groups may be isolated or supplied in association with counterions.
For example, elamipretide has been described in different salt forms in scientific and pharmaceutical contexts.
The molecular formula C₃₂H₄₉N₉O₅ refers to the parent elamipretide structure.
It does not automatically account for additional hydrochloride, acetate, trifluoroacetate, or other counterions.
Why Does the Salt Form Matter?
A salt form can affect the total mass of supplied material.
For example, the mass of a peptide salt includes both the peptide component and associated counterions.
As a result, the total sample mass should not automatically be treated as equivalent to the net mass of parent peptide.
The chemical form should be established using the relevant supplier specifications and analytical documentation.
Does a Different Counterion Change the Peptide Sequence?
Not necessarily.
Salt formation does not ordinarily change the covalent amino acid sequence of the peptide.
However, it can change the overall chemical composition of the isolated material.
This is why researchers must distinguish molecular sequence verification from formulation and counterion identification.
How Is SS-31 Peptide Identity Verified in a Laboratory?
Accurate peptide identification may involve several complementary analytical methods.
No single technique necessarily establishes every aspect of peptide structure and composition.
High-Performance Liquid Chromatography
High-Performance Liquid Chromatography (HPLC) can be used to separate components in a peptide sample.
Suitable chromatographic methods can provide information about purity and related substances.
However, a high HPLC purity result does not automatically establish the correct peptide sequence or stereochemistry.
Mass Spectrometry
Mass spectrometry measures ions based on mass-to-charge ratio.
For SS-31, mass spectrometry can provide evidence consistent with the expected molecular mass.
The parent peptide’s monoisotopic mass is approximately 639.3857 Da.
The observed instrument signal depends on the ion formed, charge state, and analytical conditions.
Tandem Mass Spectrometry
Tandem mass spectrometry, also known as MS/MS, can provide additional structural information through fragmentation.
Peptide fragments may help establish aspects of the amino acid sequence.
However, interpretation can be more complex when nonstandard residues or stereochemical distinctions are involved.
Nuclear Magnetic Resonance Spectroscopy
Nuclear Magnetic Resonance (NMR) spectroscopy can provide structural information about organic molecules.
When appropriate, NMR data can support the characterization of specific chemical groups and molecular environments.
Stereochemical Analysis
Specialized methods may be required to verify the stereochemical configuration of particular residues.
Mass matching or conventional purity testing should not automatically be considered proof of complete stereochemical identity.
SS-31 Peptide vs. Other Mitochondrial Research Peptides
SS-31 is often discussed alongside other peptides associated with mitochondrial research.
One example is MOTS-C.
However, the two compounds have different chemical identities.
SS-31 contains four residues, while MOTS-C contains sixteen.
SS-31 is a synthetically designed Szeto-Schiller peptide, whereas MOTS-C is classified as a mitochondrial-derived peptide based on its genomic origin.
Their molecular formulas and weights also differ substantially.
For a detailed chemical comparison, read SS-31 vs. MOTS-C: Differences in Peptide Structure, Sequence, and Molecular Properties.
Editorial note: The link above opens Orion’s existing MOTS-C guide. Once the dedicated SS-31 vs. MOTS-C comparison article is published, replace this link with that article’s actual URL.
SS-31 10mg and 5mg: Chemical Identity vs. Declared Quantity
Orion Peptides lists SS-31 in different declared research quantities.
The existing listings include:
The 5mg and 10mg designations refer to listed quantities, not different amino acid sequences.
If both preparations contain the same parent elamipretide structure, their reference molecular formula and parent molecular weight are identical.
However, researchers should not assume that different batches or compounds have identical counterion contents, net peptide percentages, or analytical results.
Each preparation should be evaluated using its own batch-specific documentation.
Orion Peptides supplies these materials strictly for laboratory research and analytical purposes.
Why Is a Certificate of Analysis Important for SS-31 Research Materials?
A Certificate of Analysis, commonly abbreviated COA, provides analytical information about a particular compound batch.
Depending on the testing performed, a COA may report:
- Peptide identity
- Batch or lot number
- Chromatographic purity
- Mass-spectrometry results
- Testing date
- Net peptide content
- Additional tested characteristics
Researchers should understand that these measurements describe different properties.
Purity Is Not the Same as Net Peptide Content
Chromatographic purity generally refers to the relative proportion of detected components under a specified analytical method.
Net peptide content refers to the amount or fraction of actual peptide material within the preparation.
A sample with high chromatographic purity may still contain counterions, water, or other components that affect the net peptide fraction.
Therefore, purity claims should be interpreted according to the actual analytical report.
Confirming Chemical Identity
The reference molecular formula and sequence are useful starting points for identification.
However, a complete assessment may require consideration of peptide sequence, mass spectrometry, stereochemistry, and chemical form.
Researchers can visit Orion Peptides’ SS-31 10mg compound page for available compound information and analytical documentation.
Frequently Asked Questions
What is the SS-31 peptide sequence?
The sequence is D-Arg-Dmt-Lys-Phe-NH₂, where Dmt represents 2,6-dimethyl-L-tyrosine.
How many amino acids are in SS-31?
SS-31 contains four amino acid residues and is classified as a tetrapeptide.
What is the molecular weight of SS-31?
The average molecular weight of the parent elamipretide structure is approximately 639.8 g/mol.
What is the molecular formula of SS-31?
The parent molecular formula is C₃₂H₄₉N₉O₅.
What is SS-31’s CAS number?
The CAS number associated with parent elamipretide is 736992-21-5.
Is SS-31 the same as elamipretide?
Yes. SS-31 is a research designation associated with the peptide known as elamipretide. However, a research preparation should not automatically be considered equivalent to an approved pharmaceutical formulation.
What does Dmt mean in SS-31?
Dmt stands for 2,6-dimethyltyrosine, a modified aromatic amino acid residue.
Does SS-31 contain D-amino acids?
Yes. The first residue is D-arginine.
Is SS-31 a tetrapeptide?
Yes. A tetrapeptide contains four amino acid residues joined through peptide bonds.
Is SS-31 C-terminally amidated?
Yes. Its sequence ends in a primary amide, represented by Phe-NH₂.
Does SS-31 contain disulfide bonds?
No. Its standard sequence contains no cysteine residues and therefore does not contain cysteine-based disulfide bonds.
Are SS-31 5mg and SS-31 10mg chemically different?
The quantity designations alone do not indicate a different peptide structure. Researchers should compare the actual chemical form and batch-specific analytical specifications.
How can SS-31 identity be confirmed?
Appropriate analytical methods may include chromatography, mass spectrometry, fragmentation analysis, and other techniques selected according to the required identity characteristics.
Conclusion
SS-31 peptide structure is defined by its four-residue sequence, modified amino acid chemistry, stereochemistry, and C-terminal amidation.
The peptide contains D-arginine, 2,6-dimethyltyrosine, lysine, and phenylalaninamide.
Its parent molecular formula is C₃₂H₄₉N₉O₅, with an average molecular weight of approximately 639.8 g/mol.
These chemical properties distinguish SS-31 from conventional peptides composed entirely of standard L-amino acids.
However, molecular weight and sequence alone do not necessarily establish the complete composition of a supplied research preparation.
Salt form, counterion composition, purity, and batch-specific characteristics also matter.
For additional research information, explore Orion Peptides’ SS-31 10mg listing, SS-31 5mg listing, and SS-31 mitochondrial research overview.
Scientific References
- National Center for Biotechnology Information. PubChem Compound Summary: Elamipretide, CID 11764719. Molecular formula, sequence, molecular weight, stereochemistry, and chemical identifiers.
- National Center for Biotechnology Information. PubChem SS-31 Chemical Structure Record. Molecular structure and standardized chemical nomenclature.
- National Institute on Drug Abuse. Research Resources: Drug Supply Program Peptide Catalog. Historical research-material entry identifying SS-31 and its sequence, including a trifluoroacetate salt formulation.
- International Union of Pure and Applied Chemistry. Nomenclature and Symbolism for Amino Acids and Peptides. Chemical nomenclature conventions for peptides, residues, and structural modifications.
- National Center for Biotechnology Information. PubChem Database. Reference database for molecular formulas, chemical structures, and identifiers.
Research Use Only (RUO) Disclaimer
All compounds offered by Orion Peptides, including SS-31 10mg and SS-31 5mg, are intended strictly for laboratory research, chemical analysis, and scientific investigation.
These compounds are not intended for human or veterinary consumption, clinical administration, diagnosis, treatment, cure, or prevention of disease.
This article is provided for scientific and educational purposes only. Descriptions of chemical structures, peptide sequences, analytical methods, and molecular properties do not establish the safety, efficacy, or suitability of Orion Peptides research materials for clinical use.
Researchers should verify compound identity, supplied chemical form, and batch-specific analytical information before laboratory use and comply with applicable safety protocols and regulations.
