io.github.cyanheads/pubchem-mcp-server
REMOTE · PUBCHEM.CASEYJHAND.COM · 2 COMPONENTS · SCANNED SEP 20
Search PubChem compounds, properties, safety data, bioactivity, and cross-references.
Available components
How this component scores in each security and reliability category. Every signal is checked automatically against the live server, and we only credit what we can confirm. How we score → Why this is hard to score →
Endpoint Security66
- The endpoint's TLS certificate is valid, in date, and uses a strong key. View diagnostics → Pass
- Authorisation not fully verified: no authorisation is required to call this server, and 10 tool(s) never declared a destructiveHint. The MCP spec treats an absent hint as destructive by default, so we cannot call this surface safe. See how to fix → View diagnostics → Unverified
- HTTPS is enforced; there's no plaintext access path. View diagnostics → Pass
- The HSTS (Strict-Transport-Security) header is present. View diagnostics → Pass
- DNSSEC is configured correctly; the domain's records validate against the full chain to the root. View diagnostics → Pass
Transport & Reachability100
- Verified streamable-http transport via a live MCP handshake. View diagnostics → Pass
Schema Quality & AI Usability63
- AI-judged instruction clarity (excellent).Pass
- Context-footprint check failed: tool/resource definitions use about 3369 tokens (~336/item across 10 items; 10 tools + 0 resources), over budget; trim descriptions and params. See how to fix → Fail
- Usage-examples check failed: none of the tools include examples. See how to fix → Fail
Stability & Change Management100
- No destabilizing schema changes in the last 30 days.Pass
Tool Coverage100
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 100% of tool parameters carry a description.Pass
- Structured output schemas are declared (100% of tools); any adoption earns full credit.Pass
Tool Safety100
- No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.Pass
- We read all 10 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 11 captured unit(s) of tool text and found none that tries to manipulate the model reading it.Pass
Capabilities100
- Implements a current MCP spec version (2026-07-28).Pass
How do I install the io.github.cyanheads/pubchem-mcp-server server?
io.github.cyanheads/pubchem-mcp-server is a hosted endpoint at https://pubchem.caseyjhand.com/mcp, so there is nothing to install locally. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.
remote · pubchem.caseyjhand.com
claude mcp add --transport http cyanheads-pubchem-mcp-server 'https://pubchem.caseyjhand.com/mcp'
{
"mcpServers": {
"cyanheads-pubchem-mcp-server": {
"url": "https://pubchem.caseyjhand.com/mcp"
}
}
} {
"servers": {
"cyanheads-pubchem-mcp-server": {
"type": "http",
"url": "https://pubchem.caseyjhand.com/mcp"
}
}
} [mcp_servers.cyanheads-pubchem-mcp-server] url = "https://pubchem.caseyjhand.com/mcp"
{
"$schema": "https://opencode.ai/config.json",
"mcp": {
"cyanheads-pubchem-mcp-server": {
"type": "remote",
"url": "https://pubchem.caseyjhand.com/mcp",
"enabled": true
}
}
} openclaw mcp add cyanheads-pubchem-mcp-server --url 'https://pubchem.caseyjhand.com/mcp' --transport streamable-http
mcp_servers:
cyanheads-pubchem-mcp-server:
url: "https://pubchem.caseyjhand.com/mcp" {
"McpServers": {
"cyanheads-pubchem-mcp-server": {
"Transport": "http",
"Url": "https://pubchem.caseyjhand.com/mcp"
}
}
} assistant mcp add cyanheads-pubchem-mcp-server -t streamable-http -u 'https://pubchem.caseyjhand.com/mcp'
{
"mcpServers": {
"cyanheads-pubchem-mcp-server": {
"type": "http",
"url": "https://pubchem.caseyjhand.com/mcp"
}
}
} The mcpServers block is a cross-client convention. Remote transports vary, so check your client's docs.
Every change we have recorded for this component, newest first. Security-relevant changes are always shown. ▲ marks a change for the better, ▼ a change for the worse; unmarked changes are neutral.
- 19 Sept 26 0
- Server version: 0.6.2 → 0.6.3 functional
- 13 Sept 26 0
- Server version: 0.6.1 → 0.6.2 functional
- 9 Sept 26 +1
- Stability: 0.97 → pass security
- 7 Sept 26 −1
- Stability: pass → 0.93 functional
- 27 Aug 26 +3
- Stability: fail → pass ▲ security
- 26 Aug 26 +1
- We updated how we score, so this day's move reflects our rubric, not a change to the server See what changed → functional
- 24 Aug 26 +1
No change was recorded against any check on this day. Stability & Change Management went from 73 to 77.
- 22 Aug 26 75
- MCP protocol: Implements a current MCP spec version (2026-07-28). functional
- MCP protocol version: 2025-11-25 → 2026-07-28 functional
- Server version: 0.6.0 → 0.6.1 functional
Diagnostic detail from the automated scan of this channel: what the scanner observed at each step, so you can see exactly where a check passed or failed. It is informational only and never changes the trust score.
Captured 20 Sept 2026 · Probed https://pubchem.caseyjhand.com/mcp
TLS valid
Negotiated TLS 1.3 with TLS_AES_128_GCM_SHA256 .
| Subject | Issuer | Valid from | Valid until | Key | Signature | Serial |
|---|---|---|---|---|---|---|
| CN=caseyjhand.com | CN=WE1,O=Google Trust Services,C=US | 4 Sept 2026 | 3 Dec 2026 | ECDSA 256 | ECDSA-SHA256 | a6985204ed51ae050e7738aa6be668e9 |
| SANs: caseyjhand.com, *.caseyjhand.com | ||||||
| CN=WE1,O=Google Trust Services,C=US (CA) | CN=GTS Root R4,O=Google Trust Services LLC,C=US | 13 Dec 2023 | 20 Feb 2029 | ECDSA 256 | ECDSA-SHA384 | 7ff31977972c224a76155d13b6d685e3 |
| CN=GTS Root R4,O=Google Trust Services LLC,C=US (CA) | CN=GlobalSign Root CA,OU=Root CA,O=GlobalSign nv-sa,C=BE | 15 Nov 2023 | 28 Jan 2028 | ECDSA 384 | SHA256-RSA | 7fe530bf331343bedd821610493d8a1b |
Background: What to check on a remote MCP endpoint →
DNSSEC secure
Validation of pubchem.caseyjhand.com. — Secure
| Zone | DS | Keys | Algorithms | Outcome |
|---|---|---|---|---|
| . | trust_anchor | 20326, 38696 | 8, 8 | Verified |
| com. | present | 19718 | 13 | Verified |
| caseyjhand.com. | present | 2371 | 13 | Verified |
| pubchem.caseyjhand.com. | Verified address RRset verified with the apex keys |
Authentication No authorisation required
The endpoint answered without asking for a token. Anyone who knows the URL can reach it.
| Result | No authorisation required |
|---|---|
| HTTP status | 200 |
| Header | Value |
|---|---|
| strict-transport-security | max-age=63072000; includeSubDomains; preload |
| x-content-type-options | nosniff |
Background: How OAuth 2.1 works in the 2026 MCP spec →
Transports 2 probes
| Transport | URL | Outcome | Status | Location |
|---|---|---|---|---|
| streamable-http | https://pubchem.caseyjhand.com/mcp | Verified | 200 | |
| http (plaintext) | http://pubchem.caseyjhand.com/mcp | HTTPS enforced | 301 | https://pubchem.caseyjhand.com/mcp |
The tools this component advertises to a client, with an estimated token cost for each. Expand a tool to see its parameters and schema. The per-tool counts are indicative and are not scored directly; the schema's total context footprint is one signal in Schema Quality & AI Usability. A tool's description is untrusted text the model reads on every call, which is what makes this list a security surface and not just an inventory: how tool poisoning works →
pubchem_get_bioactivity Get Bioactivity ~360
Get a compound's bioactivity profile: which assays tested it, activity outcomes (Active/Inactive/Inconclusive), target identifiers (NCBI Gene ID, UniProt/GenBank accession), and quantitative values (IC50, EC50, Ki, etc.). Filter by outcome and/or a specific molecular target (NCBI Gene ID or protein accession) to focus the profile — e.g. "is this compound active against target T?".
| Name | Type | Req | Description |
|---|---|---|---|
| cid | integer | yes | PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds. |
| maxResults | integer | – | Max assay results to return per page (1-100). Well-studied compounds have thousands of records; use offset to reach the ones past this page. Default: 20. |
| offset | integer | – | Zero-based index of the first assay to return, applied after the outcome and target filters. Pass the nextOffset from a previous call to read the following page. Default: 0. |
| outcomeFilter | string | – | Filter by activity outcome. "active" shows only assays where the compound showed activity — most useful for understanding biological profile. Default: "all". |
| targetAccession | string | – | Filter to assays against this target protein accession (UniProt/GenBank), e.g. "P35354". Obtain accessions from pubchem_search_assays or the targetAccession field of an unfiltered result here. |
| targetGeneId | integer | – | Filter to assays against this NCBI Gene ID. Obtain Gene IDs from pubchem_search_assays or the targetGeneId field of an unfiltered result here. Combine with outcomeFilter="active" to answer "is this c… |
| Name | Type | Req | Description |
|---|---|---|---|
| activeCount | number | – | Assays with "Active" outcome. |
| cap | number | – | The maxResults cap that was applied. |
| cid | number | – | PubChem Compound ID. |
| error | object | – | Present when the call failed. Absent on success. |
| filteredCount | number | – | Exact number of assays matching the outcome and target filters, across all pages. |
| inactiveCount | number | – | Assays with "Inactive" outcome. |
| nextOffset | number | – | Offset to pass on the next call to continue past this page. Omitted when no further assays match. |
| notice | string | – | Recovery guidance when the filter yields no results or the compound has no bioactivity data. |
| offset | number | – | Zero-based index of the first assay returned. |
| outcomeFilter | string | – | Outcome filter applied: active, inactive, or all. |
| results | array | – | Assay results matching the filter. |
| returnedCount | number | – | Assays returned on this page. |
| shown | number | – | Assays returned on this page. |
| targetFilter | string | – | Target filter applied (gene ID and/or protein accession), when set. |
| totalAssays | number | – | Total unique assays for this compound. |
| truncated | boolean | – | True when matching assays remain past this page. |
No examples provided.
pubchem_get_compound_3d_structure Get Compound 3D Structure ~361
Get a compound's default 3D conformer — atomic coordinates and bonds — for one CID. format="json" (default) returns atoms and bonds parsed into structured fields; format="sdf" returns the raw V2000 SDF text for passthrough to docking, rendering, or conformer tools. Optionally lists alternate conformer IDs. Not every compound has computed 3D coordinates (large molecules, mixtures, and some salts do not).
| Name | Type | Req | Description |
|---|---|---|---|
| cid | integer | yes | PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds. |
| format | string | – | Output format. "json" (default) returns parsed atoms and bonds. "sdf" returns the raw V2000 SDF text for passthrough to other tools. |
| includeAlternateConformerIds | boolean | – | List the IDs of additional computed conformers beyond the default. Slower than the default response. Default: false. |
| includeRawSdf | boolean | – | For format="sdf", return the complete raw V2000 SDF even when it exceeds the safe line cap. Default false: an SDF longer than 500 lines is line-capped with disclosure. No effect when format="json". |
| maxAtoms | integer | – | Cap the atoms returned in the format="json" preview. atomCount always reports the full total; omitted rows are disclosed via the truncated/shownAtoms enrichment. Defaults to the first 200 atoms. |
| maxBonds | integer | – | Cap the bonds returned in the format="json" preview. bondCount always reports the full total; omitted rows are disclosed via the truncated/shownBonds enrichment. Defaults to the first 200 bonds. |
| Name | Type | Req | Description |
|---|---|---|---|
| alternateConformerIds | array | – | Conformer IDs beyond the default. Present when includeAlternateConformerIds is set and alternates exist. |
| atomCap | number | – | The atom cap applied (explicit maxAtoms or the safe default), when the atom list was capped. |
| atomCount | number | – | Number of atoms in the conformer. |
| atoms | array | – | Parsed atoms. Populated when format="json". |
| bondCap | number | – | The bond cap applied (explicit maxBonds or the safe default), when the bond list was capped. |
| bondCount | number | – | Number of bonds in the conformer. |
| bonds | array | – | Parsed bonds. Populated when format="json". |
| cid | number | – | PubChem Compound ID. |
| conformerId | string | – | Default (primary) conformer ID. Present when includeAlternateConformerIds is set. |
| error | object | – | Present when the call failed. Absent on success. |
| notice | string | – | Guidance naming which lists were capped and how to widen them. |
| sdf | string | – | Raw V2000 SDF text. Populated when format="sdf". |
| shownAtoms | number | – | Atoms returned after the cap, when fewer than atomCount. Raise maxAtoms for more. |
| shownBonds | number | – | Bonds returned after the cap, when fewer than bondCount. Raise maxBonds for more. |
| shownSdfLines | number | – | SDF lines returned when format="sdf" and the raw text was line-capped. Set includeRawSdf for the full record. |
| truncated | boolean | – | True when the atom list, bond list, or raw SDF was capped below its total. atomCount/bondCount always report the full totals. |
No examples provided.
pubchem_get_compound_details Get Compound Details ~656
Get detailed compound information by CID. Returns physicochemical properties (molecular weight, SMILES, InChIKey, XLogP, TPSA, etc.), optionally with a textual description (pharmacology, mechanism, therapeutic use), known synonyms, drug-likeness assessment (Lipinski/Veber rules), and/or pharmacological classification (FDA classes, MeSH classes, ATC codes). Accepts up to 100 CIDs per call.
| Name | Type | Req | Description |
|---|---|---|---|
| cids | array | yes | PubChem Compound IDs to fetch (1-100). Resolve from names/SMILES with pubchem_search_compounds. |
| descriptionOffset | integer | – | Zero-based index of the first description to return within each compound's description list. The same offset is applied to every compound in the batch. Pass the nextDescriptionOffset from a previous… |
| includeClassification | boolean | – | Include pharmacological classification: FDA Established Pharmacologic Classes, mechanisms of action, MeSH classes, and ATC codes. Fetched only for the first 10 CIDs in the batch; remaining CIDs retur… |
| includeDescription | boolean | – | Include textual descriptions (pharmacology, mechanism, therapeutic use) attributed by source. Well-studied compounds have many overlapping summaries — paged via descriptionOffset/maxDescriptions. Fet… |
| includeDrugLikeness | boolean | – | Compute drug-likeness assessment: Lipinski Rule of Five (MW, XLogP, HBD, HBA) and Veber rules (TPSA, rotatable bonds). Computed from the returned properties, so it adds no latency. |
| includeSynonyms | boolean | – | Fetch known names and synonyms (trade names, systematic names, registry numbers), paged via synonymOffset/maxSynonyms. Fetched for every found CID in the batch. Slower for large CID lists. |
| maxDescriptions | integer | – | Max number of distinct description entries per compound per page (1-20). PubChem returns near-duplicate summaries from many depositors; duplicates are collapsed before this cap applies. Default: 3. |
| maxSynonyms | integer | – | Max synonyms returned per compound per page (1-100). PubChem lists hundreds for common drugs; use synonymOffset to reach the ones past this page. Default: 20. |
| properties | array | – | Properties to retrieve. Defaults to a core set: MolecularFormula, MolecularWeight, IUPACName, CanonicalSMILES, IsomericSMILES, InChIKey, XLogP, TPSA, HBondDonorCount, HBondAcceptorCount, RotatableBon… |
| synonymOffset | integer | – | Zero-based index of the first synonym to return within each compound's synonym list. The same offset is applied to every compound in the batch. Pass the nextSynonymOffset from a previous call to read… |
| Name | Type | Req | Description |
|---|---|---|---|
| compounds | array | – | Compound detail records. |
| descriptionOffset | number | – | Zero-based index of the first description returned within each compound's list. Present when includeDescription is true. |
| enrichedCids | array | – | CIDs whose descriptions and classification were fetched. Present only when the batch exceeded the per-call fan-out limit and other CIDs were skipped. |
| error | object | – | Present when the call failed. Absent on success. |
| nextDescriptionOffset | number | – | descriptionOffset to pass on the next call to continue past this page. Omitted when no compound in the batch has further descriptions. |
| nextSynonymOffset | number | – | synonymOffset to pass on the next call to continue past this page. Omitted when no compound in the batch has further synonyms. |
| notice | string | – | Recovery guidance covering the skipped CIDs, an offset that runs past every compound, and pages that remain. Absent when nothing was skipped or truncated. |
| skippedCids | array | – | CIDs found in PubChem whose descriptions and classification were NOT fetched because the batch exceeded the per-call fan-out limit. Their absence from a record means "not requested", not "PubChem has… |
| synonymOffset | number | – | Zero-based index of the first synonym returned within each compound's list. Present when includeSynonyms is true. |
| truncated | boolean | – | True when this response is not the whole picture: a compound has further synonyms or descriptions past this page, or CIDs were skipped by the per-call fan-out limit. Per-compound totals are in compou… |
No examples provided.
pubchem_get_compound_image Get Compound Image ~84
Fetch a 2D structure diagram (PNG image) for a compound by CID.
| Name | Type | Req | Description |
|---|---|---|---|
| cid | integer | yes | PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds. |
| size | string | – | Image size: "small" (100x100) or "large" (300x300). Default: "large". |
| Name | Type | Req | Description |
|---|---|---|---|
| cid | number | – | PubChem Compound ID. |
| error | object | – | Present when the call failed. Absent on success. |
| height | number | – | Image height in pixels. |
| imageBase64 | string | – | Base64-encoded PNG image data. |
| mimeType | string | – | MIME type — always "image/png". |
| width | number | – | Image width in pixels. |
No examples provided.
pubchem_get_compound_interactions Get Compound Interactions ~278
Get a compound's interaction data: drug-drug interactions (DrugBank), drug-food interactions, and chemical-target interactions (binding/activity from BindingDB, ChEMBL, and others). Each entry carries its originating source. Results are paged per kind, with the source-record total and the next offset reported for each. Richest for approved drugs; many compounds have no deposited interaction records.
| Name | Type | Req | Description |
|---|---|---|---|
| cid | integer | yes | PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds. |
| kinds | array | – | Interaction kinds to fetch. "drug-drug" (interactions with other drugs), "drug-food" (dietary interactions), "target" (binding/activity against molecular targets). Default: ["drug-drug"]. |
| maxEntries | integer | – | Max entries per kind per page (1-50). Well-studied drugs have a long tail of interactions; use offset to reach the ones past this page. Default: 10. |
| offset | integer | – | Zero-based start position within each requested kind, counted in source records rather than returned entries. The same offset applies to every kind in the call, and the kinds advance at different rat… |
| Name | Type | Req | Description |
|---|---|---|---|
| cid | number | – | PubChem Compound ID. |
| entries | array | – | Interaction entries across the requested kinds. |
| error | object | – | Present when the call failed. Absent on success. |
| failedKinds | string | – | Interaction kinds that could not be retrieved (comma-separated). The returned entries cover the kinds that succeeded; retry to re-attempt the failed ones. |
| nextOffset | number | – | Offset to pass on the next call, reported when exactly one requested kind has records remaining. Omitted when none do, and when several do — those advance to different positions, so read paging[].nex… |
| notice | string | – | Guidance when a kind failed, when no interaction data was found, when the offset runs past every requested kind, or when further pages remain. Absent when this page is complete and every kind resolve… |
| offset | number | – | Zero-based start position read within each requested kind. |
| paging | array | – | Per-kind page position, one entry per requested kind that was retrieved. A kind listed in failedKinds is absent — its position is unknown, not exhausted. |
| requestedKinds | string | – | Interaction kinds requested (comma-separated). |
| returnedCount | number | – | Total interaction entries returned across all kinds. |
| truncated | boolean | – | True when at least one requested kind has source records remaining past this page. Which kinds, and how many records each holds, is in paging[].truncated / paging[].totalRecords. |
No examples provided.
pubchem_get_compound_safety Get Compound Safety ~108
Get GHS (Globally Harmonized System) hazard classification and safety data for one or more compounds by CID. Returns signal word, pictograms, hazard statements (H-codes), and precautionary statements (P-codes) per compound. Data sourced from PubChem depositors — source attribution included.
| Name | Type | Req | Description |
|---|---|---|---|
| cids | array | yes | PubChem Compound IDs to fetch safety data for (1-25). Resolve from names/SMILES with pubchem_search_compounds. |
| Name | Type | Req | Description |
|---|---|---|---|
| error | object | – | Present when the call failed. Absent on success. |
| notice | string | – | Recovery guidance when one or more CIDs returned no GHS data, listing the unrecognized CIDs to verify separately from the CIDs that exist but carry no deposited classification. |
| requestedCount | number | – | CIDs requested. |
| results | array | – | Safety results, one per requested CID (input order preserved). |
| withDataCount | number | – | CIDs with GHS safety data available. |
No examples provided.
pubchem_get_compound_xrefs Get Compound Cross-References ~260
Get external database cross-references for a compound: PubMed citations, patent IDs, gene/protein associations, registry numbers, and taxonomy IDs. Results are paged per type — capped at maxPerType with the total count reported; reach the IDs past a page with offset.
| Name | Type | Req | Description |
|---|---|---|---|
| cid | integer | yes | PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds. |
| maxPerType | integer | – | Max IDs to return per xref type per page (1-500). A compound may have thousands of PubMed references; use offset to reach the ones past this page. Total count always reported. Default: 50. |
| offset | integer | – | Zero-based index of the first ID to return within each xref type. The same offset is applied to every requested type. Pass the nextOffset from a previous call to read the following page. Default: 0. |
| xrefTypes | array | yes | Cross-reference types to retrieve. String IDs: RegistryID (DSSTox/EPA registry numbers), RN (CAS numbers), PatentID. Numeric IDs: PubMedID, GeneID (NCBI Gene), ProteinGI (legacy NCBI Protein GI), Tax… |
| Name | Type | Req | Description |
|---|---|---|---|
| cid | number | – | PubChem Compound ID. |
| error | object | – | Present when the call failed. Absent on success. |
| nextOffset | number | – | Offset to pass on the next call to continue past this page. Omitted when no requested type has further IDs. |
| notice | string | – | Recovery guidance when every requested xref type returned zero IDs, when the offset runs past every type, or when further pages remain. Absent when this page is complete and non-empty. |
| offset | number | – | Zero-based index of the first ID returned within each type. |
| truncated | boolean | – | True when at least one requested type has IDs remaining past this page. Which types, and how many IDs each holds in total, is in xrefs[].truncated / xrefs[].totalAvailable. |
| xrefs | array | – | Cross-references grouped by type. |
No examples provided.
pubchem_get_summary Get Entity Summary ~148
Get descriptive summaries for PubChem entities by ID. Supports assays (AID), genes (Gene ID), proteins (UniProt accession), and taxonomy (Tax ID). Up to 10 per call.
| Name | Type | Req | Description |
|---|---|---|---|
| entityType | string | yes | Entity type. Determines ID format and returned fields. |
| identifiers | array | yes | Entity identifiers (1-10). Type depends on entityType: - assay: AID (number), e.g. [1000] - gene: Gene ID (number), e.g. [1956] - protein: UniProt accession (string), e.g. ["P00533"] - taxonomy: Tax… |
| Name | Type | Req | Description |
|---|---|---|---|
| entityType | string | – | Entity type queried. |
| error | object | – | Present when the call failed. Absent on success. |
| foundCount | number | – | Identifiers resolved to a summary. |
| notice | string | – | Recovery guidance when one or more identifiers were not found. |
| requestedCount | number | – | Identifiers requested. |
| summaries | array | – | Summary results. |
No examples provided.
pubchem_search_assays Search Assays ~253
Find PubChem bioassays associated with a biological target. Search by gene symbol (e.g. "EGFR"), protein name, NCBI Gene ID, or UniProt accession. Returns a page of assay IDs (AIDs) — page past maxResults with offset — which can be explored further with pubchem_get_summary.
| Name | Type | Req | Description |
|---|---|---|---|
| maxResults | integer | – | Max AIDs to return per page (1-200). Popular targets may have thousands of assays; use offset to reach the ones past this page. Default: 50. |
| offset | integer | – | Zero-based index of the first AID to return. Pass the nextOffset from a previous call to read the following page. Default: 0. |
| targetQuery | string | yes | Target identifier. Examples: "EGFR" (genesymbol), "Epidermal growth factor receptor" (proteinname), "1956" (geneid), "P00533" (proteinaccession). |
| targetType | string | yes | Target identifier type. "genesymbol" and "proteinname" accept text names. "geneid" accepts NCBI Gene IDs. "proteinaccession" accepts UniProt accessions. |
| Name | Type | Req | Description |
|---|---|---|---|
| aids | array | – | PubChem Assay IDs. |
| cap | number | – | The maxResults cap that was applied. |
| error | object | – | Present when the call failed. Absent on success. |
| nextOffset | number | – | Offset to pass on the next call to continue past this page. Omitted when no further AIDs match. |
| notice | string | – | Recovery guidance when no assays matched, when the offset runs past the result set, or when further pages remain. Absent when this page is complete and non-empty. |
| offset | number | – | Zero-based index of the first AID returned. |
| shown | number | – | AIDs returned on this page. |
| targetQuery | string | – | Target identifier searched. |
| targetType | string | – | Target identifier type used: genesymbol, proteinname, geneid, or proteinaccession. |
| totalFound | number | – | Total AIDs found for this target, across all pages. |
| truncated | boolean | – | True when matching AIDs remain past this page. |
No examples provided.
pubchem_search_compounds Search Compounds ~625
Search PubChem for chemical compounds by identifier (name, SMILES, or InChIKey, batched up to 25), molecular formula in Hill notation, substructure or superstructure containment, or 2D Tanimoto similarity. Returns a page of CIDs — reach matches past maxResults with offset. Optionally hydrate results with properties to avoid a follow-up pubchem_get_compound_details call.
| Name | Type | Req | Description |
|---|---|---|---|
| allowOtherElements | boolean | – | Formula search only. When true, includes compounds with additional elements beyond the formula. |
| formula | string | – | Required for formula search. Molecular formula in Hill notation (e.g. "C6H12O6", "CaH2O2"). |
| identifierType | string | – | Required for identifier search. Type of chemical identifier: "name", "smiles", or "inchikey". |
| identifiers | array | – | Required for identifier search. Array of identifiers to resolve (1-25). Examples: ["aspirin", "ibuprofen"] for name, ["CC(=O)OC1=CC=CC=C1C(=O)O"] for SMILES, ["BSYNRYMUTXBXSQ-UHFFFAOYSA-N"] for inchi… |
| maxResults | integer | – | Maximum CIDs to return per page (1-200). Use offset to reach matches past this page. Default: 20. |
| offset | integer | – | Zero-based index of the first CID to return. Pass the nextOffset from a previous call to read the following page. Identifier lookups resolve every match up front, so paging them is free; formula, sub… |
| properties | array | – | Optional: fetch these properties for each result, avoiding a follow-up details call. E.g. ["MolecularFormula", "MolecularWeight", "CanonicalSMILES"]. |
| query | string | – | Required for substructure/superstructure/similarity searches. A SMILES string (e.g. "CC(=O)O") or PubChem CID as a string (e.g. "2244"). |
| queryType | string | – | Required for structure/similarity searches. Format of the query: "smiles" or "cid". |
| searchType | string | yes | Search strategy. "identifier": name/SMILES/InChIKey lookup. "formula": molecular formula. "substructure": find compounds containing the query as a substructure. "superstructure": find compounds that… |
| threshold | number | – | Similarity search only. Minimum Tanimoto similarity (70-100). 90+ for close analogs, 70-80 for scaffold hops. Default: 90. |
| Name | Type | Req | Description |
|---|---|---|---|
| cap | number | – | The maxResults cap that was applied. |
| error | object | – | Present when the call failed. Absent on success. |
| nextOffset | number | – | Offset to pass on the next call to continue past this page. Omitted when no further matches remain. |
| notice | string | – | Recovery guidance when no compounds matched, when the offset runs past the matches observed, when identifiers failed to resolve, or when further pages remain. Absent when this page is complete and ev… |
| offset | number | – | Zero-based index of the first CID returned. |
| results | array | – | Matching compounds. |
| searchType | string | – | Search strategy used: identifier, formula, substructure, superstructure, or similarity. |
| shown | number | – | CIDs returned on this page. |
| totalFound | number | – | Exact number of matching CIDs across all pages. Omitted when a formula, substructure, superstructure, or similarity search saturated the records it requested — PubChem returns no match count for thos… |
| totalFoundAtLeast | number | – | Lower bound on matching CIDs, reported in place of totalFound when the exact count is unavailable. At least this many match, and the true total may be higher; page further with offset to observe more. |
| truncated | boolean | – | True when matching CIDs remain past this page. |
| unresolvedIdentifiers | array | – | Identifier-mode only: input identifiers that resolved to no CID. Omitted when every identifier resolved and for non-identifier searches. |
No examples provided.
What is the io.github.cyanheads/pubchem-mcp-server server?
io.github.cyanheads/pubchem-mcp-server is listed in the public MCP registry as io.github.cyanheads/pubchem-mcp-server. Search PubChem compounds, properties, safety data, bioactivity, and cross-references. This page covers its hosted endpoint (https://pubchem.caseyjhand.com/mcp).
Is the io.github.cyanheads/pubchem-mcp-server server safe to use?
io.github.cyanheads/pubchem-mcp-server scores 80 out of 100 on VerifyMCP. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.
What tools does the io.github.cyanheads/pubchem-mcp-server server expose?
io.github.cyanheads/pubchem-mcp-server exposes 10 tools: pubchem_search_compounds, pubchem_get_compound_details, pubchem_get_compound_image, pubchem_get_compound_3d_structure, pubchem_get_compound_xrefs, and 5 more. Their descriptions and schemas cost roughly 3,133 tokens of context every time the server is loaded.
Does the io.github.cyanheads/pubchem-mcp-server server require authentication?
No. We connected to io.github.cyanheads/pubchem-mcp-server without credentials and it answered, so anything it exposes is reachable by anyone who knows the address.
Is the io.github.cyanheads/pubchem-mcp-server server still maintained?
io.github.cyanheads/pubchem-mcp-server is still listed as active in the MCP registry. We last reached this channel on 20 September 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.