Ligand Expo Downloads

Ligand Expo will be retired in 2025.
Users should transition to RCSB PDB and wwPDB services.
Please contact info@rcsb.org to receive announcements about this transition.

Chemical Component Dictionaries

Please transition to accessing these data at wwPDB

• mmCIF format dictionary (text | gzip) | Alternate download site http://www.wwpdb.org/data/ccd
• mmCIF format variants dictionary (text | gzip) | Alternate download site http://www.wwpdb.org/data/ccd
• SDF/MOL format file of dictionary ideal geometries (gzip) | Alternate download site http://www.wwpdb.org/data/ccd
• Legacy PDBML format dictionary (tar.gz)
• Legacy PDBML format variants dictionary (tar.gz)

SMILES/InChI data files:

Please transition to accessing these data at wwPDB

• SMILES (OpenEye with stereo) (tab delimited text) | Alternate download site http://www.wwpdb.org/data/ccd
• SMILES (OpenEye) (tab delimited text) | Alternate download site http://www.wwpdb.org/data/ccd
• SMILES (CACTVS with stereo) (tab delimited text) | Alternate download site http://www.wwpdb.org/data/ccd
• SMILES (CACTVS) (tab delimited text) | Alternate download site http://www.wwpdb.org/data/ccd
• InChI (tab delimited text) | Alternate download site http://www.wwpdb.org/data/ccd
• InChIKey (tab delimited text) | Alternate download site http://www.wwpdb.org/data/ccd

Chemical component coordinate data files:

Please transition to accessing these data at RCSB.org

• First, use RCSB PDB Search API https://search.rcsb.org/#search-api to find all PDB entries with a specific ligand.
  Example: Find all PDB entries with ligand ATP
• Next, use RCSB ModelServer API https://models.rcsb.org/#/General/ligand to retrieve atomic coordinates of the specific ligands in a PDB entry, in mmCIF/SDF/MOL format.
  Example: To retrive mmCIF coordinates of ligand ATP in PDB entry 9ash, run the following command. Change encoding to SDF/MOL for output in another format.
  curl -X 'GET' 'https://models.rcsb.org/v1/9ash/ligand?label_comp_id=ATP&encoding=cif&copy_all_categories=false&download=true' -H 'accept: text/plain'
• Experimental coordinates for non-polymer molecules and non-standard amino acids and nucleotides are bundled in legacy single data files (SDF and mmCIF) or tar file bundles (PDB and PDBML/XML)¹
  (SDF/MOL (gz) (>60MB) | mmCIF (gz) (>120MB) | PDBML/XML (tar.gz) (>290MB) | PDB (tar.gz) (>185MB) | SDF/MOL (tar.gz) (>95MB) )

PDB and chemical component identifier correspondences

Please transition to accessing these data at RCSB.org

• Use RCSB PDB Search API https://search.rcsb.org/#search-api.
  Example: Find all PDB entries with ligand ATP
• Legacy tabulation of PDB entries containing each chemical component. (tab delimited text)

Chemical component counting statistics

• Use RCSB PDB Search API https://search.rcsb.org/#search-api.
  Example: Find all PDB entries with ligand ATP
• Legacy tabulation of the number of PDB entries containing each chemical component. (tab delimited text)
• Legacy tabulation of the number of PDB entries containing each chemical component (including name and formula). (tab delimited text)

Downloading experimental coordinates for a particular chemical component¹:

Please transition to accessing these data at RCSB.org

Since all chemical component dictionary entries follow a specific naming convention, you can easily skip searching and download the coordinates by entering the correct URL. The URL template is:

• http://ligand-expo.rcsb.org/files/<HASH>/<CC_ID>/<FORMAT>/

  where:

  <HASH>

  is the first character of the component identifier code,

  <CC_ID>

  is the 3-letter-code component identifier,

  <FORMAT>

  is one of icif, isdf, ipdb, ixml, or ccif for mmCIF, SDF/MOL, PDB, PDBML/XML, or mmCIF definition formats, respectively.

  For example, all experimental coordinate files in SDF/MOL format for ATP can be found in the URL:

  http://ligand-expo.rcsb.org/files/A/ATP/isdf/

• Use RCSB ModelServer API https://models.rcsb.org/#/General/ligand to retrieve atomic coordinates of the specific ligands in a PDB entry, in mmCIF/SDF/MOL format.
  Example: To retrive mmCIF coordinates of ligand ATP in PDB entry 9ash, run the following command. Change encoding to SDF/MOL for output in another format.
  curl -X 'GET' 'https://models.rcsb.org/v1/9ash/ligand?label_comp_id=ATP&encoding=cif&copy_all_categories=false&download=true' -H 'accept: text/plain'

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[1] Notes of files names: to uniquely identity experimental coordinate files the following underscore delimited coding scheme has been used:

PDB ID _ Component ID _ Model No. _ Chain ID _ Residue No. _ mmCIF Sequence No. _ mmCIF Asym ID _ Disorder Flag _

For example, the file name: 1pk8_ATP_1_B_801__R_D_.icif

Identifier	Value
PDB ID	1PK8
Component/residue code	ATP
Model number	1 (default)
Chain ID	B
Residue number	801
mmCIF sequence number	not applicable
mmCIF Asym ID	R
Disorder Flag	D (modeled with disorder)

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