Drug · CDK4/6 inhibitor · CDK4/6 inhibitor · Sourced compound
Palbociclib structure · mechanism
PubChem CID 5330286. Molecular formula C24H29N7O2. Independently assigned structure; reviewed 2026-10-08. Family grouping is editorial and does not establish shared activity.
Palbociclib 2D structure
- Role
- Drug
- Mechanism class
- CDK4/6 inhibitor
- Aliases
- ibrance
- InChIKey
AHJRHEGDXFFMBM-UHFFFAOYSA-N
- Structure checked
- 2026-10-08
- Molecular formula
- C24H29N7O2
- Structure source
- PubChem
- PubChem CID
- 5330286
- InChI Key
- AHJRHEGDXFFMBM-UHFFFAOYSA-N
Read the two structures
Separate nitrogen-labelled rings from side chains in palbociclib and ribociclib, and trace their attachments. Compare connections between rings and external substituents together rather than judging a single ring. This gives context for shared and different fingerprint features.
| Observation | Palbociclib | Ribociclib |
|---|---|---|
| C(=O)–N connections | 1 | 1 |
| Aromatic nitrogen atoms | 4 | 4 |
Connect the structural observations with the fingerprint result
Each molecule has one selected C(=O)–N connection and four aromatic nitrogen matches. These two counts alone can hide differences. Ring arrangement and substituent attachment positions must still be compared independently. [Palbociclib] · [Ribociclib]
The fingerprints share 46 set bits across a union of 76, giving 0.605. This is greater overlap than in several other example pairs here, but not molecular identity. Equal selected motif counts can coexist with different local environments across the complete fingerprint.
Aromatic nitrogen count is not total nitrogen count. It includes atoms matching [n] and excludes aliphatic amine nitrogens. Keeping the query definition fixed makes the numbers comparable.
Calculated structural similarity: 0.605 · Morgan radius 2 / 2048 bits · Tanimoto
Calculation: 46 / (62 + 60 − 46) = 46 / 76 ≈ 0.605. Set-bit counts are not counts of unique atoms or functional groups.
Query definitions and reproducibility
- C(=O)–N connections:
[#6](=[#8])[#7] - Aromatic nitrogen atoms:
[n]
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)
StructureMoa editorial · source review 2026-10-08
Molecular identity
Palbociclib: independently retrieved PubChem CID 5330286, formula C24H29N7O2.
How to compare
Separate nitrogen-labelled rings from side chains in palbociclib and ribociclib, and trace their attachments. Compare connections between rings and external substituents together rather than judging a single ring. This gives context for shared and different fingerprint features.
Interpretation limits
The Morgan/Tanimoto score measures fingerprint overlap. It does not establish efficacy, safety, clinical superiority or full stereochemical identity.
SMILES
CC1=C(C(=O)N(C2=NC(=NC=C12)NC3=NC=C(C=C3)N4CCNCC4)C5CCCC5)C(=O)CTags
Related compounds
External IDs · BioMoa
StructureMoa is a chemical-structure exploration tool. Structural similarity, clustering, and SAR relationships are intended for research exploration and do not establish shared potency, selectivity, safety, efficacy, or clinical performance.
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]