PubChem Compound Search

Overview

PubChem (NCBI) is the largest freely available chemical database — 110M+ compounds, 280M+ substances, and millions of bioassay records. Its PUG-REST JSON API is the canonical programmatic surface, and every example here uses it directly via plain requests. The Python pubchempy wrapper is not required; the PUG-REST URL grammar is small enough that direct calls are more transparent, easier to retry/cache, and avoid sandbox dependency issues (the library is not in TOOL_STATUS.md).

The URL pattern is fixed and predictable:

https://pubchem.ncbi.nlm.nih.gov/rest/pug/<input>/<operation>/<output>

• <input> = compound/{name,cid,smiles,inchikey,formula}/<value>
• <operation> = cids, property/<list>, synonyms, description, assaysummary, JSON (full record), SDF, PNG
• <output> = JSON, CSV, TXT, SDF, PNG

For long-running operations (similarity, substructure, formula) the API returns HTTP 202 + {"Waiting": {"ListKey": "..."}}; poll compound/listkey/{key}/cids/JSON until it returns IdentifierList. The skill handles this pattern in Module 4.

When to Use

• Looking up a compound by name, SMILES, InChIKey, or formula to get its PubChem CID
• Retrieving molecular properties (molecular weight, XLogP, TPSA, H-bond donor/acceptor counts, rotatable bonds, formula, IUPAC name) for one or many CIDs in a single request
• Finding structurally similar compounds via Tanimoto similarity (async ListKey poll)
• Searching for compounds containing a substructure / pharmacophore motif
• Fetching every synonym / trade name / CAS number for a CID
• Pulling assay summary tables (active/inactive screening results) for a compound
• Converting between identifier formats (name ↔ CID ↔ SMILES ↔ InChI ↔ InChIKey) in one API call
• Downloading 2D SDF or PNG structures for figures or downstream RDKit work
• For local cheminformatics (fingerprints, descriptors, 3D conformers, scaffold extraction) use rdkit
• For deeper bioactivity / target-binding data (IC50, Ki against specific targets) use chembl-database-bioactivity

Prerequisites

• Python packages: requests, pandas — both already in standard environments
• No API key required — PubChem is fully public
• Rate limits: max 5 requests/second and 400 requests/minute per IP. Throttle with time.sleep(0.25) in loops; return code 503 means you tripped the limit.

If you are inside a pixi/conda environment that already provides requests and pandas, skip the install and invoke scripts with pixi run python ....

pip install requests pandas

Quick Start

import requests

BASE = "https://pubchem.ncbi.nlm.nih.gov/rest/pug"

# name → CID
cid = requests.get(f"{BASE}/compound/name/aspirin/cids/JSON").json()["IdentifierList"]["CID"][0]

# CID → properties (single call, many fields)
r = requests.get(
    f"{BASE}/compound/cid/{cid}/property/"
    "MolecularWeight,XLogP,TPSA,HBondDonorCount,HBondAcceptorCount,SMILES,IUPACName/JSON")
p = r.json()["PropertyTable"]["Properties"][0]
print(f"CID {cid} — {p['IUPACName']}")
print(f"  MW={p['MolecularWeight']}  XLogP={p['XLogP']}  TPSA={p['TPSA']}")
print(f"  HBD={p['HBondDonorCount']}  HBA={p['HBondAcceptorCount']}")
print(f"  SMILES={p['SMILES']}")

Core API

Module 1: Identifier lookup

Resolve any external identifier to a PubChem CID via /compound/{namespace}/{value}/cids/JSON. Namespaces: name, cid, smiles, inchikey, inchi, formula.

import requests
from urllib.parse import quote

BASE = "https://pubchem.ncbi.nlm.nih.gov/rest/pug"

# By name (returns all matching CIDs as a list)
cids = requests.get(f"{BASE}/compound/name/caffeine/cids/JSON").json()["IdentifierList"]["CID"]
print(f"caffeine CIDs: {cids}")

# By canonical SMILES (URL-encode!)
smi = quote("CC(=O)OC1=CC=CC=C1C(=O)O", safe="")
cid = requests.get(f"{BASE}/compound/smiles/{smi}/cids/JSON").json()["IdentifierList"]["CID"][0]
print(f"aspirin SMILES → CID {cid}")

# By InChIKey (exact match, fastest if you already have one)
ikey = "BSYNRYMUTXBXSQ-UHFFFAOYSA-N"
cid = requests.get(f"{BASE}/compound/inchikey/{ikey}/cids/JSON").json()["IdentifierList"]["CID"][0]
print(f"InChIKey → CID {cid}")

Module 2: Property retrieval

/compound/cid/{cid_or_csv}/property/<csv-list>/JSON returns all requested properties in one round trip. CIDs and property names are both CSV-joinable — batch up to ~200 CIDs and many properties at once.

import requests

BASE = "https://pubchem.ncbi.nlm.nih.gov/rest/pug"

# Full property set for a single compound (ibuprofen CID 3672)
url = (f"{BASE}/compound/cid/3672/property/"
       "MolecularWeight,XLogP,TPSA,HBondDonorCount,HBondAcceptorCount,"
       "RotatableBondCount,SMILES,InChIKey,IUPACName,MolecularFormula/JSON")
p = requests.get(url).json()["PropertyTable"]["Properties"][0]
print(f"{p['IUPACName']}  formula={p['MolecularFormula']}")
print(f"  MW={p['MolecularWeight']} XLogP={p['XLogP']} TPSA={p['TPSA']}")
print(f"  HBD={p['HBondDonorCount']} HBA={p['HBondAcceptorCount']} RotB={p['RotatableBondCount']}")

import requests, pandas as pd

# Batch: 4 CIDs, 3 properties — one request, one round trip
cids = "2244,3672,2157,2662"   # aspirin, ibuprofen, naproxen, celecoxib
r = requests.get(
    f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/{cids}/property/"
    "MolecularWeight,XLogP,TPSA/JSON")
df = pd.DataFrame(r.json()["PropertyTable"]["Properties"])
print(df.to_string(index=False))

Module 3: Synonyms and description

Synonyms (trade names, CAS numbers, alternative spellings) and curated descriptions live at /compound/{ns}/{value}/{synonyms|description}/JSON.

import requests

BASE = "https://pubchem.ncbi.nlm.nih.gov/rest/pug"

# Full synonym list (aspirin has ~700)
info = requests.get(f"{BASE}/compound/cid/2244/synonyms/JSON").json()["InformationList"]["Information"][0]
print(f"aspirin synonyms: {len(info['Synonym'])}")
for s in info["Synonym"][:8]:
    print(f"  {s}")

import requests

# Curated descriptions (NCBI MeSH, CAMEO, etc.)
r = requests.get("https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/aspirin/description/JSON")
for item in r.json()["InformationList"]["Information"]:
    if "Description" in item:
        print(f"[{item.get('DescriptionSourceName','?')}]")
        print(f"  {item['Description'][:200]}…")
        print()

Module 4: Similarity & substructure search (async ListKey pattern)

Structure searches return HTTP 202 + {"Waiting": {"ListKey": "..."}}. Poll /compound/listkey/{key}/cids/JSON every ~2s until it returns IdentifierList. Wrap this in a helper since it's used everywhere.

import requests, time
from urllib.parse import quote

BASE = "https://pubchem.ncbi.nlm.nih.gov/rest/pug"

def poll_listkey(listkey, max_polls=10, interval=2.0):
    """Block until PubChem finishes async search; return CID list."""
    for _ in range(max_polls):
        time.sleep(interval)
        j = requests.get(f"{BASE}/compound/listkey/{listkey}/cids/JSON", timeout=20).json()
        if "IdentifierList" in j:
            return j["IdentifierList"]["CID"]
    raise TimeoutError(f"ListKey {listkey} did not complete")

# Tanimoto similarity (90% threshold, max 20 hits) — starting from aspirin SMILES
smi = quote("CC(=O)OC1=CC=CC=C1C(=O)O", safe="")
init = requests.get(
    f"{BASE}/compound/similarity/smiles/{smi}/JSON?Threshold=90&MaxRecords=20").json()
cids = poll_listkey(init["Waiting"]["ListKey"]) if "Waiting" in init \
       else init["IdentifierList"]["CID"]
print(f"aspirin @90% similarity: {len(cids)} hits, sample={cids[:5]}")

import requests
from urllib.parse import quote

BASE = "https://pubchem.ncbi.nlm.nih.gov/rest/pug"

# Substructure search — all compounds containing a sulfonamide group
smi = quote("S(=O)(=O)N", safe="")
init = requests.get(
    f"{BASE}/compound/substructure/smiles/{smi}/JSON?MaxRecords=20").json()
cids = poll_listkey(init["Waiting"]["ListKey"]) if "Waiting" in init \
       else init["IdentifierList"]["CID"]
print(f"sulfonamide-containing CIDs: {len(cids)}, sample={cids[:5]}")

Module 5: Assay summary (bioactivity data)

/compound/cid/{cid}/assaysummary/JSON returns a Table of every PubChem BioAssay the compound appears in (assay AID, target, outcome, micromolar activity if available).

import requests, pandas as pd

BASE = "https://pubchem.ncbi.nlm.nih.gov/rest/pug"

r = requests.get(f"{BASE}/compound/cid/2244/assaysummary/JSON", timeout=30)
rows = r.json().get("Table", {}).get("Row", [])
cols = r.json().get("Table", {}).get("Columns", {}).get("Column", [])
print(f"aspirin appears in {len(rows)} bioassays")

# First few columns + rows as a DataFrame
df = pd.DataFrame([row["Cell"] for row in rows[:5]], columns=cols)
print(df.iloc[:, :6].to_string(index=False))

Module 6: Structure file download (SDF / PNG)

/compound/cid/{cid}/SDF returns 2D MOL/SDF; /compound/cid/{cid}/PNG returns a structure image (use ?image_size=large for higher resolution).

import requests

BASE = "https://pubchem.ncbi.nlm.nih.gov/rest/pug"
cid = 2519   # caffeine

# 2D SDF for downstream RDKit / OpenBabel
sdf = requests.get(f"{BASE}/compound/cid/{cid}/SDF", timeout=15).text
with open("caffeine.sdf", "w") as f:
    f.write(sdf)
print(f"caffeine.sdf: {len(sdf)} chars, ends with M  END={'M  END' in sdf}")

# PNG structure image
png = requests.get(f"{BASE}/compound/cid/{cid}/PNG?image_size=large", timeout=15).content
with open("caffeine.png", "wb") as f:
    f.write(png)
print(f"caffeine.png: {len(png)} bytes")

Key Concepts

Async ListKey pattern

Similarity, substructure, and formula searches are asynchronous — the API kicks off a background job and returns HTTP 202 with {"Waiting": {"ListKey": "<id>"}}. Poll /compound/listkey/{id}/cids/JSON every ~2 seconds until the response contains IdentifierList. Most searches finish in 5–15s; tighten polling for tiny searches, loosen for very large ones. Use the poll_listkey helper from Module 4 everywhere.

A small fraction of fast searches return IdentifierList directly on the first call (no Waiting field); check for both possibilities.

Property name reference

CSV-join any subset in a single /property/<csv>/JSON URL. Note that MolecularWeight returns as a string; cast to float before arithmetic.

Response envelope shapes

• cids/JSON → {"IdentifierList": {"CID": [int, ...]}}
• property/.../JSON → {"PropertyTable": {"Properties": [{...}, ...]}} (one dict per CID, in input order)
• synonyms/JSON → {"InformationList": {"Information": [{"CID": int, "Synonym": [str, ...]}]}}
• description/JSON → {"InformationList": {"Information": [{"CID": int, "Description": str, "DescriptionSourceName": str, ...}, ...]}}
• assaysummary/JSON → {"Table": {"Columns": {"Column": [...]}, "Row": [{"Cell": [...]}, ...]}}
• async-init (similarity, substructure, formula) → 202 with {"Waiting": {"ListKey": "..."}}
• listkey poll → {"IdentifierList": {"CID": [...]}} when ready

Common Workflows

Workflow 1: Property comparison across a drug panel

Goal: side-by-side physicochemical comparison of a small molecule set.

import requests, pandas as pd, time
from urllib.parse import quote

BASE = "https://pubchem.ncbi.nlm.nih.gov/rest/pug"

drugs = ["aspirin", "ibuprofen", "naproxen", "celecoxib"]

# Resolve names → CIDs in a loop (rate-limited)
cids = []
for d in drugs:
    cid = requests.get(f"{BASE}/compound/name/{quote(d)}/cids/JSON",
                       timeout=15).json()["IdentifierList"]["CID"][0]
    cids.append(cid)
    time.sleep(0.25)

# Single batched property pull
cid_csv = ",".join(str(c) for c in cids)
r = requests.get(
    f"{BASE}/compound/cid/{cid_csv}/property/"
    "MolecularWeight,XLogP,TPSA,HBondDonorCount,HBondAcceptorCount/JSON")
df = pd.DataFrame(r.json()["PropertyTable"]["Properties"])
df["Name"] = drugs
df = df[["Name", "CID", "MolecularWeight", "XLogP", "TPSA",
         "HBondDonorCount", "HBondAcceptorCount"]]
print(df.to_string(index=False))

Workflow 2: Lead compound → similar analogs → properties

Goal: starting from a kinase inhibitor (gefitinib), find 85%-similar analogs and pull their properties.

import requests, time
from urllib.parse import quote

BASE = "https://pubchem.ncbi.nlm.nih.gov/rest/pug"

def poll_listkey(listkey, max_polls=10, interval=2.0):
    for _ in range(max_polls):
        time.sleep(interval)
        j = requests.get(f"{BASE}/compound/listkey/{listkey}/cids/JSON",
                         timeout=20).json()
        if "IdentifierList" in j:
            return j["IdentifierList"]["CID"]
    raise TimeoutError("listkey timeout")

# 1. lead → CID → canonical SMILES
ref_cid = requests.get(
    f"{BASE}/compound/name/gefitinib/cids/JSON").json()["IdentifierList"]["CID"][0]
ref_smi = requests.get(
    f"{BASE}/compound/cid/{ref_cid}/property/SMILES/JSON"
    ).json()["PropertyTable"]["Properties"][0]["SMILES"]
print(f"gefitinib CID={ref_cid}  SMILES={ref_smi}")

# 2. similarity search
smi_q = quote(ref_smi, safe="")
init = requests.get(
    f"{BASE}/compound/similarity/smiles/{smi_q}/JSON?Threshold=85&MaxRecords=15"
    ).json()
sim_cids = poll_listkey(init["Waiting"]["ListKey"]) if "Waiting" in init \
           else init["IdentifierList"]["CID"]
print(f"  {len(sim_cids)} analogs @85% Tanimoto")

# 3. batch-pull properties for top 5 analogs
cid_csv = ",".join(str(c) for c in sim_cids[:5])
r = requests.get(
    f"{BASE}/compound/cid/{cid_csv}/property/"
    "MolecularWeight,XLogP,TPSA,RotatableBondCount/JSON")
for row in r.json()["PropertyTable"]["Properties"]:
    print(f"  CID {row['CID']}: MW={row['MolecularWeight']} XLogP={row['XLogP']}")

Workflow 3: Pharmacophore screen via substructure → bioactivity check

Goal: find compounds with a sulfonamide motif and check which have bioactivity records.

import requests, time
from urllib.parse import quote

BASE = "https://pubchem.ncbi.nlm.nih.gov/rest/pug"

def poll_listkey(listkey, max_polls=10, interval=2.0):
    for _ in range(max_polls):
        time.sleep(interval)
        j = requests.get(f"{BASE}/compound/listkey/{listkey}/cids/JSON",
                         timeout=20).json()
        if "IdentifierList" in j:
            return j["IdentifierList"]["CID"]
    raise TimeoutError("listkey timeout")

smi = quote("S(=O)(=O)N", safe="")
init = requests.get(
    f"{BASE}/compound/substructure/smiles/{smi}/JSON?MaxRecords=10").json()
cids = poll_listkey(init["Waiting"]["ListKey"]) if "Waiting" in init \
       else init["IdentifierList"]["CID"]
print(f"sulfonamide CIDs: {cids}")

# Bioactivity row counts for the first few hits
for cid in cids[:3]:
    rows = requests.get(f"{BASE}/compound/cid/{cid}/assaysummary/JSON",
                        timeout=30).json().get("Table", {}).get("Row", [])
    print(f"  CID {cid}: {len(rows)} assay rows")
    time.sleep(0.3)

Key Parameters

Best Practices

1. Always go through `cids/JSON` first when starting from a name or external identifier. The name→CID resolution and the CID→property lookup are separate calls; doing both at once via name → property works but throws away the canonical CID list that downstream queries need.

1. Batch properties, never loop them. compound/cid/2244,3672,2157,.../property/MolecularWeight,XLogP,.../JSON accepts up to ~200 CIDs and any number of properties — one round trip instead of N. Looping get_compounds per name is the most common rate-limit trap.

1. URL-encode every SMILES. Use urllib.parse.quote(smiles, safe=""). Bare SMILES with =, #, (, ), [, ] will sometimes work but breaks unpredictably on +, /, \, or query-string-looking substrings.

1. Treat similarity/substructure/formula as async. Branch on "Waiting" in response and poll listkey rather than re-issuing the search. Re-issuing creates a new ListKey and wastes the server's job slot.

1. Throttle ≤ 5 req/sec, ≤ 400/min. Insert time.sleep(0.25) in any tight loop. HTTP 503 means you tripped the limit — wait 10s and reduce concurrency.

1. Cast `MolecularWeight` to `float`. It's returned as a string ("180.16") for full decimal fidelity. Comparing strings against numeric thresholds is a silent bug.

1. For 100+ CIDs use POST. GET URLs over ~2000 chars get truncated by some HTTP proxies. PubChem also accepts POST with cid in the form body: requests.post(f"{BASE}/compound/cid/property/MolecularWeight/JSON", data={"cid": cid_csv}).

1. 2025 SMILES property rename. PubChem renamed two SMILES properties in the 2025 PUG-REST schema: old IsomericSMILES (with stereo) → SMILES, and old CanonicalSMILES (connectivity only, no stereo) → ConnectivitySMILES. The URL path still accepts the legacy names as input (e.g. /property/CanonicalSMILES/JSON returns 200), but the response JSON is keyed with the new names. So a request succeeds and only the parse step breaks with KeyError. Use SMILES / ConnectivitySMILES in new code and read those keys.

Common Recipes

Recipe 1 — Lipinski's Rule of Five check

import requests
from urllib.parse import quote

BASE = "https://pubchem.ncbi.nlm.nih.gov/rest/pug"

def check_lipinski(name):
    cid = requests.get(f"{BASE}/compound/name/{quote(name)}/cids/JSON"
                       ).json()["IdentifierList"]["CID"][0]
    p = requests.get(
        f"{BASE}/compound/cid/{cid}/property/"
        "MolecularWeight,XLogP,HBondDonorCount,HBondAcceptorCount/JSON"
        ).json()["PropertyTable"]["Properties"][0]
    mw, xlogp = float(p["MolecularWeight"]), p.get("XLogP", 0) or 0
    hbd, hba  = p["HBondDonorCount"], p["HBondAcceptorCount"]
    rules = {"MW ≤ 500": mw <= 500, "XLogP ≤ 5": xlogp <= 5,
             "HBD ≤ 5": hbd <= 5,   "HBA ≤ 10": hba <= 10}
    v = sum(1 for ok in rules.values() if not ok)
    return rules, v

rules, v = check_lipinski("metformin")
print(f"violations: {v}/4 ({'PASS' if v <= 1 else 'FAIL'})")
for r, ok in rules.items(): print(f"  {'✓' if ok else '✗'} {r}")

Recipe 2 — Pull every synonym / trade name

import requests

r = requests.get("https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/aspirin/synonyms/JSON")
syns = r.json()["InformationList"]["Information"][0]["Synonym"]
print(f"{len(syns)} synonyms")
for s in syns[:10]:
    print(f"  {s}")

Recipe 3 — Download a structure PNG

import requests

cid = 2519   # caffeine
png = requests.get(
    f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/{cid}/PNG?image_size=large"
    ).content
with open("caffeine.png", "wb") as f:
    f.write(png)
print(f"wrote caffeine.png ({len(png)} bytes)")

Recipe 4 — Robust session with retry / 429 handling

import requests
from requests.adapters import HTTPAdapter
from urllib3.util.retry import Retry

s = requests.Session()
s.headers.update({"Accept": "application/json"})
s.mount("https://", HTTPAdapter(max_retries=Retry(
    total=4, backoff_factor=1.0,
    status_forcelist=[429, 500, 502, 503, 504],
    allowed_methods=["GET", "POST"])))

r = s.get(
    "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/property/MolecularWeight/JSON",
    timeout=15)
r.raise_for_status()
print(r.json()["PropertyTable"]["Properties"][0]["MolecularWeight"])

Expected Outputs

• CID lookup (/.../cids/JSON): {"IdentifierList": {"CID": [...]}} — list of integer CIDs, ordered by relevance for name searches.
• Properties (/.../property/.../JSON): {"PropertyTable": {"Properties": [{"CID": ..., "MolecularWeight": "180.16", ...}, ...]}}. One row per CID in input order; MolecularWeight is a string.
• Synonyms: {"InformationList": {"Information": [{"CID": 2244, "Synonym": ["aspirin", "ACETYLSALICYLIC ACID", "50-78-2", ...]}]}}.
• Async search init: HTTP 202 with {"Waiting": {"ListKey": "12345..."}}. Poll /compound/listkey/{key}/cids/JSON until it returns IdentifierList.
• Assay summary: {"Table": {"Columns": {"Column": [...col names...]}, "Row": [{"Cell": [...]}, ...]}}.
• SDF: plain text starting with the CID header line; ends with M END followed by SDF property blocks.
• PNG: binary image/png, ~2–4 KB at default size, ~10–20 KB at image_size=large.

Troubleshooting

Related Skills

• chembl-database-bioactivity — IC50 / Ki / Kd target-binding data, deeper than PubChem's assay summaries
• rdkit-cheminformatics — local SMILES/MOL manipulation, fingerprints, descriptors, scaffold extraction
• pdb-database — protein structures co-crystallized with the small molecules found via PubChem CIDs

References

• PubChem PUG-REST documentation — Full URL grammar reference
• PUG-REST tutorial with worked examples — Step-by-step API walk-through
• PubChem property table — Authoritative list of /property/<name> values and their semantics
• PubChem main site — Web interface for spot-checks
• Kim et al. (2023) Nucleic Acids Res — PubChem 2023 update