Structure guide · 10/7/2026
What does a Tanimoto similarity of 0.8 mean?
A worked example of fingerprint overlap, its calculation settings and its limits.
Read the two structures
Locate ring nitrogens in gefitinib and erlotinib, then compare the substituents outside the rings. Check halogen labels and side-chain differences using both formula and drawing. A shared local motif does not establish identity of the whole molecule.
| Observation | Gefitinib | Erlotinib |
|---|---|---|
| Carbon triple bond C≡C | 0 | 1 |
| Fluorine atoms | 1 | 0 |
| Chlorine atoms | 1 | 0 |
Connect the structural observations with the fingerprint result
Gefitinib has one highlighted fluorine and one chlorine. Erlotinib has neither of these query matches and instead has one carbon triple-bond C≡C match. Read the coloured regions with the counts to distinguish the selected substituents concretely. [Gefitinib] · [Erlotinib]
There are 31 shared set bits across a union of 76, giving 0.408. The selected substituents differ while other encoded environments overlap. This is a whole-structure fingerprint calculation, not a score comparing only halogens and the triple bond.
Visual resemblance is a useful observation, but this calculation neither computes a maximum common substructure nor establishes an identical scaffold. Fingerprint overlap and a shared-scaffold claim require different evidence.
Calculated structural similarity: 0.408 · Morgan radius 2 / 2048 bits · Tanimoto
Calculation: 31 / (60 + 47 − 31) = 31 / 76 ≈ 0.408. Set-bit counts are not counts of unique atoms or functional groups.
Query definitions and reproducibility
- Carbon triple bond C≡C:
C#C - 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)
From atom environments to a fingerprint
Morgan fingerprints expand the environment around each atom and encode structural features in a fixed-length vector. StructureMoa uses radius 2 and 2048 bits. These settings must stay constant when comparing scores. Salts, protonation, stereochemical settings and fingerprint type can change the result.
Calculate a small example
Suppose fingerprint A has 70 set bits, fingerprint B has 60 and they share 40. The union contains 70 + 60 − 40 = 90 bits. Tanimoto is 40 / 90, approximately 0.444. It is neither 40 / 70 nor the percentage of atoms that the molecules share.
What the score leaves out
A value of 0.8 means overlap in this fingerprint representation. It does not mean 80% identical potency, selectivity or safety. Fixed-length bit vectors can have collisions. The default comparison does not independently establish stereochemical identity; check the source SMILES and complete InChIKey as well.
Read the picture before the ranking
Inspect the two structures below before looking at their computed score. Locate repeated ring motifs and then different substituents. The score summarizes encoded local environments rather than proving a common synthesis route. The graph displays edges at 0.2 for readability; an absent edge does not demonstrate absent biological activity.
Sources and review
Editorial update: 10/12/2026 · Structure-source check: 2026-10-08. Calculations and cited experiments are separate evidence.
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]