Melanotan 2

Covalent structure (atoms, bonds, charges and stereochemistry): PubChem CID 92432, cross-checked against the FDA Global Substance Registration System record for MELANOTAN II. The 3D coordinates are a computed conformer (RDKit ETKDG distance-geometry embedding followed by MMFF94 force-field minimisation), not an experimental structure.

All 143 atoms, including 69 hydrogens, are generated from the PubChem structure with explicit hydrogens added; the protonation state is exactly the PubChem record's (neutral, no formal charges). 148 conformers were embedded with RDKit 2025.09.2 ETKDGv3 (fixed random seed) and each was minimised with the MMFF94 force field. The lowest-energy conformer without atomic clashes and every amide bond trans (8 checked) was kept (MMFF94 -108.09 kcal/mol); it is the best of 148 sampled conformers, not a proven global minimum, and not a solution or crystal structure. The model was then re-centred and rotated to its principal axes. No atom position is experimental, so every atom has PDB occupancy 0.00. Formula, mass, bond graph, stereocentres and InChIKey were re-derived from the published coordinate file and agree with PubChem. Ring closures were re-checked in the written file: macrocycle of 23 atoms; the configuration of every amino-acid alpha carbon was re-derived from the coordinates. The stereochemistry was also confirmed by assembling the molecule residue by residue from the stated sequence, with every D and L residue written explicitly, and matching its InChIKey to the modelled structure's. Modelled as the neutral free peptide (guanidine, imidazole and indole un-ionised), which is the form the formula and mass describe; salts such as the acetate are not modelled. The ring is a lactam from the Asp side-chain carboxyl to the Lys side-chain amine. The model is one computed shape of a flexible cyclic peptide, not evidence of the shape it adopts in solution or in the body.

7 defined stereocentres, each matching PubChem; CIP labels re-derived from the published coordinates agree with the source structure. Amino-acid alpha carbons re-derived from the published coordinates: 6 L, 1 D. Checked explicitly in the coordinates: Nle1 alpha carbon L; Asp2 alpha carbon L; His3 alpha carbon L; D-Phe4 alpha carbon D; Arg5 alpha carbon L; Trp6 alpha carbon L; Lys7 alpha carbon L.