Structure guide · 10/7/2026
The same formula does not mean the same molecule
Distinguish connectivity, stereochemistry, salt forms and alternative SMILES representations.
Read the two structures
Preserve sertraline’s source stereochemical annotations and compare its ring connections with fluoxetine. These molecules are not presented as a matched stereoisomer pair. Rotating a drawing is different from changing molecular stereochemistry; use the complete source representation for identity checks.
| Observation | Sertraline | Fluoxetine |
|---|---|---|
| Fluorine atoms | 0 | 3 |
| Chlorine atoms | 2 | 0 |
Connect the structural observations with the fingerprint result
Fluoxetine has three fluorine atoms and no chlorine; sertraline has no fluorine and two chlorines. Fluoxetine’s fluorines cluster around one carbon, while sertraline’s chlorines attach to an aromatic ring. A broad “halogen-containing” category hides different local environments. [Sertraline] · [Fluoxetine]
Eight shared set bits across a union of 62 give 0.129. The molecules can be compared within an antidepressant class, but that grouping does not establish close structural proximity under this fingerprint.
Halogen counts alone cannot establish brain exposure or individual treatment response. These are observations of selected structural representations; exposure and response require separate measurements and clinical context.
Calculated structural similarity: 0.129 · Morgan radius 2 / 2048 bits · Tanimoto
Calculation: 8 / (34 + 36 − 8) = 8 / 62 ≈ 0.129. Set-bit counts are not counts of unique atoms or functional groups.
Query definitions and reproducibility
- Fluorine atoms:
[F] - Chlorine atoms:
[Cl]
RDKit 2025.03.4 · Matches with identical atom sets are counted once. Colours mark atoms and bonds matching selected queries, not a proven shared scaffold or synthesis route.
- Read elemental composition from the formulas.
- Trace ring and substituent connections in each drawing.
- Compare your observations with the fingerprint score calculated under identical settings.
- Check stereochemistry and the complete InChIKey in the source records.
The score is fingerprint overlap, not a percentage of efficacy or safety. RDKit
Structure-source check: 2026-10-08 / 2026-10-08 · Editorial update and calculation check: 2026-10-16
Download source structures, queries and bit counts for this comparison (JSON)
Composition is not connectivity
A molecular formula counts elements without fully describing their bond connections. Isomers may share a formula while having different connectivity or stereochemistry. Read the source drawing and SMILES alongside the formula instead of treating the formula as a complete identity test.
Alternative strings can describe one structure
A SMILES string can start at a different atom or use different ring numbers and still encode the same structure. Normalization with a chemical toolkit is useful, but the input stereochemical information must be preserved. A text difference is not automatically a molecular difference.
Read stereochemistry in the source
Look for the source’s stereochemical annotations rather than judging only a rotated drawing. Compare the full InChIKey and isomeric structure representation. The example structures below illustrate the reading workflow; they are not claimed to be a matched pair of stereoisomers.
A similarity of one still needs context
A default Morgan fingerprint can fail to distinguish some stereochemical differences, and hashed features can collide. A score of one is equality in the selected fingerprint representation, not independent proof of complete molecular identity. Document the settings and preserve the original source record.
Sources and review
Editorial update: 10/12/2026 · Structure-source check: 2026-10-08. Calculations and cited experiments are separate evidence.
Related compounds
Editorial responsibility and corrections
Operated and edited by the independent StructureMoa project. Explanations use AI assistance; structural identity and similarity are checked against source records and calculation tests. Molecular data and clinical or regulatory evidence have separate review scopes.
- Source structures
- PubChem · CID / SMILES / InChIKey
- Calculations and automated checks
- RDKit · Morgan / SMARTS
- Disclosed specialist review
- No separate external specialist review is disclosed. Passing automated tests is not specialist review of clinical claims.
For a correction, include the page URL, molecule name or CID, the field in question and a supporting source. Corrections are checked against sources, and the affected editorial update date is changed when a correction is published. [email protected]