pubchem-mcp-server

Get Compound Interactions

pubchem_get_compound_interactions

Read-onlyIdempotent

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.

Input Schema

TableJSON Schema

Name	Required	Description
`cid`	Yes	PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.
`kinds`	No	Interaction kinds to fetch. "drug-drug" (interactions with other drugs), "drug-food" (dietary interactions), "target" (binding/activity against molecular targets). Default: ["drug-drug"].
`offset`	No	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 rates — when paging past the first page, request one kind per call and pass that kind's nextOffset. Default: 0.
`maxEntries`	No	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.

Output Schema

TableJSON Schema

Name	Required	Description
`cid`	No	PubChem Compound ID.
`error`	No	Present when the call failed. Absent on success.
`notice`	No	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 resolved.
`offset`	No	Zero-based start position read within each requested kind.
`paging`	No	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.
`entries`	No	Interaction entries across the requested kinds.
`truncated`	No	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.
`nextOffset`	No	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[].nextOffset instead.
`failedKinds`	No	Interaction kinds that could not be retrieved (comma-separated). The returned entries cover the kinds that succeeded; retry to re-attempt the failed ones.
`returnedCount`	No	Total interaction entries returned across all kinds.
`requestedKinds`	No	Interaction kinds requested (comma-separated).

Schema Changelog

Changes observed during successful MCP inspections.

Changed2 schema fields changedSep 25, 2026
- removedInput schema / properties / cid / exclusiveMinimum
```
Removed value: -0
```
- addedInput schema / properties / cid / minimum
```
Added value: +1
```

Changed7 schema fields changedAug 21, 2026

changedInput schema / $schema

Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"

addedInput schema / additionalProperties
```
Added value: +false
```

changedOutput schema / $schema

Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"

addedOutput schema / anyOf

Added value: +[
+  {
+    "not": {
+      "required": [
+        "error"
+      ]
+    },
+    "required": [
+      "cid",
+      "entries",
+      "paging",
+      "requestedKinds",
+      "returnedCount",
+      "truncated",
+      "offset"
+    ]
+  },
+  {
+    "required": [
+      "error"
+    ]
+  }
+]

addedOutput schema / properties / error

Added value: +{
+  "additionalProperties": {},
+  "description": "Present when the call failed. Absent on success.",
+  "properties": {
+    "code": {
+      "description": "JSON-RPC error code for this failure.",
+      "maximum": 9007199254740991,
+      "minimum": -9007199254740991,
+      "type": "integer"
+    },
+    "data": {
+      "additionalProperties": {},
+      "properties": {
+        "reason": {
+          "description": "Machine-readable failure mode.",
+          "type": "string"
+        },
+        "recovery": {
+          "additionalProperties": {},
+          "description": "Actionable next step for the caller.",
+          "properties": {
+            "hint": {
+              "type": "string"
+            }
+          },
+          "required": [
+            "hint"
+          ],
+          "type": "object"
+        },
+        "retryable": {
+          "description": "Whether retrying may succeed.",
+          "type": "boolean"
+        }
+      },
+      "type": "object"
+    },
+    "message": {
+      "description": "Human-readable description of what went wrong.",
+      "type": "string"
+    }
+  },
+  "required": [
+    "code",
+    "message"
+  ],
+  "type": "object"
+}

addedOutput schema / properties / truncated

Added value: +{
+  "description": "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.",
+  "type": "boolean"
+}

removedOutput schema / required

Removed value: -[
-  "cid",
-  "entries",
-  "paging",
-  "requestedKinds",
-  "returnedCount",
-  "offset"
-]

Changed7 schema fields changedJul 28, 2026

changedInput schema / properties / maxEntries / description

Previous value: -"Max entries per kind (1-50). Well-studied drugs have a long tail of interactions. Default: 10."New value: +"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."

addedInput schema / properties / offset

Added value: +{
+  "default": 0,
+  "description": "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 rates — when paging past the first page, request one kind per call and pass that kind's nextOffset. Default: 0.",
+  "maximum": 2147483646,
+  "minimum": 0,
+  "type": "integer"
+}

addedOutput schema / properties / nextOffset

Added value: +{
+  "description": "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[].nextOffset instead.",
+  "type": "number"
+}

changedOutput schema / properties / notice / description

Previous value: -"Guidance when no interaction data was found for the requested kinds."New value: +"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 resolved."

addedOutput schema / properties / offset

Added value: +{
+  "description": "Zero-based start position read within each requested kind.",
+  "type": "number"
+}

addedOutput schema / properties / paging

Added value: +{
+  "description": "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.",
+  "items": {
+    "additionalProperties": false,
+    "description": "Page position for one interaction kind.",
+    "properties": {
+      "kind": {
+        "description": "Interaction category this page covers.",
+        "enum": [
+          "drug-drug",
+          "drug-food",
+          "target"
+        ],
+        "type": "string"
+      },
+      "nextOffset": {
+        "description": "Offset to pass on the next call to continue this kind past the current page. Omitted when no records remain.",
+        "type": "number"
+      },
+      "returnedCount": {
+        "description": "Interaction entries returned for this kind.",
+        "type": "number"
+      },
+      "totalRecords": {
+        "description": "Source records available for this kind, across all pages. Entries are derived from these records and can be fewer: a \"target\" record naming no molecular target and a \"drug-drug\" record carrying no statement both yield nothing, and duplicate measurements collapse within a page. Pages divide the records, not the entries, so a duplicate split across two pages is reported on both.",
+        "type": "number"
+      },
+      "truncated": {
+        "description": "True when source records remain for this kind past the current page.",
+        "type": "boolean"
+      }
+    },
+    "required": [
+      "kind",
+      "returnedCount",
+      "totalRecords",
+      "truncated"
+    ],
+    "type": "object"
+  },
+  "type": "array"
+}

changedOutput schema / required

Previous value: -[
-  "cid",
-  "entries",
-  "requestedKinds",
-  "returnedCount"
-]New value: +[
+  "cid",
+  "entries",
+  "paging",
+  "requestedKinds",
+  "returnedCount",
+  "offset"
+]

Changed1 schema field changedJul 28, 2026

removedOutput schema / properties / entries / items / properties / severity

Removed value: -{
-  "description": "Raw severity as the source reports it — not normalized across sources, and frequently unset (most sources embed severity in the statement text).",
-  "type": "string"
-}

AddedJun 2, 2026

TDQS

A4.3/5.0

Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations declare readOnlyHint, openWorldHint, and idempotentHint, but the description adds valuable context beyond these: results are paged per kind with source-record totals and nextOffset, and that richness varies by drug type. It also discloses that many compounds lack records, which is open-world behavior. This enriches the annotation-driven understanding without contradiction.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is concise, spanning three sentences that each earn their place: the first explains what is fetched, the second explains paging behavior, and the third sets expectations on data richness. It is front-loaded with purpose, and the paging detail is critical for correct usage. No fluff or redundant repetition of schema details.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the complexity of paging logic and multiple interaction kinds, the description fully covers necessary operational details: paging per kind, nextOffset semantics, and the recommendation for one kind per call. The output schema exists, so return format is not needed in the description. The description also notes the open-world nature (many compounds have no records), which is essential context for agents. All critical information is covered.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so the description does not need to explain parameters, but it enhances understanding of the `offset` and `maxEntries` interplay by noting that kinds advance at different rates and advising one kind per call when paging. The description of `kinds` in the schema aligns with the description's list of interactions concatenated with sourcesressor. This adds a layer of nuance not present in the schema, though baseline is 3 due to high coverage.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly identifies the tool as fetching compound interaction data, listing specific interaction types (drug-drug, drug-food, chemical-target) and their sources. It distinguishes itself from siblings like pubchem_get_bioactivity, which focuses on bioactivity data, and pubchem_get_compound_details, which covers general details. The specificity of 'interaction data' with enumerated kinds and source mentions leaves no ambiguity about purpose.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description provides clear context for when to use this tool (to retrieve interaction data) and notes that it is richest for approved drugs, implying alternatives for other cases. It does not explicitly warn against using it for bioactivity assays, but the direct reference to interaction data and the enumerations in the schema differentiate it from siblings like pubchem_get_bioactivity. The mention that many compounds have no deposited records guides expectation setting, which is useful for decision-making.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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