compound cid

Understanding "Compound CID"

1. Definition and Context

• What is a Compound CID?
  The term "Compound CID" typically refers to a Compound Identifier (CID) in databases like PubChem, a free chemistry database maintained by the National Institutes of Health (NIH). A CID is a unique numeric identifier assigned to a specific chemical compound, enabling standardized reference across scientific literature and databases.
• Purpose of CIDs
  CIDs facilitate efficient searching, sharing, and analysis of chemical data. They avoid ambiguity caused by naming variations (e.g., common names vs. IUPAC names) and ensure consistency in research and applications.

2. PubChem CID: Structure and Usage

• PubChem Database
  PubChem is a comprehensive resource for chemical information, including structures, properties, and biological activities. Each compound in PubChem is assigned a CID, which acts as its primary key in the database.
• How to Find a CID
  1. Search by Name: Enter the compound’s name (e.g., "aspirin") in PubChem’s search bar.
  2. Search by Structure: Draw or upload a chemical structure to retrieve its CID.
  3. Search by Formula: Use the molecular formula (e.g., "C9H8O4" for aspirin) to locate the CID.
• Example: The CID for aspirin (acetylsalicylic acid) is 2244, which can be accessed via PubChem’s CID page.

3. CID vs. Other Identifiers

• CID vs. CAS Number
  • CID: Unique to PubChem; numeric and database-specific.
  • CAS Number: Assigned by the Chemical Abstracts Service; alphanumeric and globally recognized (e.g., aspirin’s CAS number is 50-78-2).
• CID vs. InChI/SMILES
  • InChI (International Chemical Identifier): A text-based string encoding molecular structure (e.g., aspirin’s InChI is InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)).
  • SMILES: A simplified molecular notation (e.g., aspirin’s SMILES is CC(=O)Oc1ccccc1C(=O)O).
  • CID complements these by providing a direct link to PubChem’s curated data.

4. Applications of Compound CIDs

• Scientific Research
  CIDs enable researchers to quickly access data on compound properties, toxicity, and interactions. For example, a study on drug metabolism might reference CIDs to compare multiple compounds.
• Drug Discovery
  Pharmacologists use CIDs to screen databases for compounds with desired properties, such as binding affinity to a target protein.
• Chemical Education
  Students and educators rely on CIDs to verify compound information and explore related structures in interactive tools like PubChem’s 3D viewer.

5. How to Cite Compound CIDs

• Proper Citation Format
  When referencing a CID in academic work, include the database name and CID number. For example:

  Aspirin (PubChem CID: 2244) is a widely used analgesic.

• Linking to PubChem
  Always provide the URL to the compound’s PubChem page (e.g., https://pubchem.ncbi.nlm.nih.gov/compound/2244) for transparency and reproducibility.

6. Common Issues and Troubleshooting

• CID Not Found?
  • Verify the spelling of the compound name.
  • Check if the compound has alternative names or synonyms.
  • Ensure the structure is drawn correctly (if using a structure-based search).
• Multiple CIDs for One Compound?
  This may occur due to tautomers, isotopes, or stereoisomers. PubChem groups related compounds under a single "Isomeric SMILES" entry but assigns distinct CIDs to each form.

7. Advanced Tools for CID Exploration

• PubChem API
  Developers can programmatically retrieve CID data using PubChem’s RESTful API. For example, fetching data for CID 2244:

  https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/2244/JSON
  

• Chemical Structure Drawing Software
  Tools like ChemDraw or MarvinSketch can generate structures for CID searches, aiding in complex compound identification.

Summary

A Compound CID is a critical tool in chemistry and pharmacology, providing a standardized way to reference and access data on specific compounds. By understanding how to locate, use, and cite CIDs, researchers and students can enhance the accuracy and efficiency of their work.