LigandBox
2020/06/11Web Site: http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en
FTP Site: ftp://ftp.biosciencedbc.jp/archive/ligandbox/
The 'ready-to-dock' database of small chemical compounds, for virtual drug screening on computer docking studies.
README Content
1. Database Component
- README
- Compounds of Namiki (Single Conformer)
- Compounds of Namiki
- Compounds of PDB (Single Conformer)
- Compounds of PDB
2. Data Description
2.1 README
| Data name | README |
|---|---|
| Description of data contents | HTML file to describe "LigandBox" data. |
| File | README_e.html (English) |
2.2 Compounds of Namiki (Single Conformer)
| Data name | Compounds of Namiki (Single Conformer) |
|---|---|
| Description of data contents | Extracted single conformer data from each compound provided by Namiki Shoji Co.,Ltd. (Oct. 2017). They are assembled on a file in Mol2 format. Comments in Mol2 format are extracted to another CSV file. They can be searched in simple search. |
| File | ligandbox_namiki.zip (CSV format) (495 MB)
Namiki_Single.mol2.gz (Mol2 format) (6GB) |
Data items are the following:
| Data item | Description |
|---|---|
| LIGANDBOX_ID | ID in LigandBox |
| SINGLE | "ture" if the entry is extacted as single conformer, else "false". |
| SOURCE | Source of this compound |
| SOURCE_ID | ID in the source |
| MOLECULAR_FORMULA | Molecular formula |
| MOLECULAR_WEIGHT | Molecular weight |
| MOLECULAR_CHARGE | Molecular charge |
| NUM_OF_DONOR | Number of hydrogen bond donors |
| NUM_OF_ACCEPTOR | Number of hydrogen bond acceptors |
| NUM_OF_CHIRAL_ATOMS | Number of chiral atoms |
| TPSA | Topological Polar Surface Area |
| HOMO | Highest Occupied Molecular Orbital energy |
| LUMO | Lowest Unoccupied Molecular Orbital energy |
| LOGP | Partition coefficient |
| LOGS | Solubility |
| INCHI | InChI |
| INCHI_KEY | InChIKey |
| MOL2_FILE | URL of mol2 file for the entry |
2.3 Compounds of Namiki
| Data name | Compounds of Namiki |
|---|---|
| Description of data contents | Compounds provided by Namiki Shoji Co.,Ltd. (Oct. 2017). All conformers are included in it. They are assembled on a file in Mol2 format. Comments in Mol2 format are extracted to another CSV file. They can be searched in simple search. |
| File | ligandbox_namiki.zip (CSV format) (495MB)
Namiki_Multiple.mol2.gz (Mol2 format) (8.8GB) |
Data items are the following:
| Data item | Description |
|---|---|
| LIGANDBOX_ID | ID in LigandBox |
| SINGLE | "TRUE" if the entry is extacted as single conformer, else "FALSE". |
| SOURCE | Source of this compound |
| SOURCE_ID | ID in the source |
| MOLECULAR_FORMULA | Molecular formula |
| MOLECULAR_WEIGHT | Molecular weight |
| MOLECULAR_CHARGE | Molecular charge |
| NUM_OF_DONOR | Number of hydrogen bond donors |
| NUM_OF_ACCEPTOR | Number of hydrogen bond acceptors |
| NUM_OF_CHIRAL_ATOMS | Number of chiral atoms |
| TPSA | Topological Polar Surface Area |
| HOMO | Highest Occupied Molecular Orbital energy |
| LUMO | Lowest Unoccupied Molecular Orbital energy |
| LOGP | Partition coefficient |
| LOGS | Solubility |
| INCHI | InChI |
| INCHI_KEY | InChIKey |
| MOL2_FILE | URL of mol2 file for the entry |
2.4 Compounds of PDB (Single Conformer)
| Data name | Compounds of PDB (Single Conformer) |
|---|---|
| Description of data contents | Extracted single conformer data from each compound in PDB. They are assembled on a file in Mol2 format. Comments in Mol2 format are extracted to another CSV file. They can be searched in simple search. |
| File | ligandbox_pdb.zip (CSV format) (3.9 MB)
PDB_Single.mol2.gz (Mol2 format) (31MB) |
Data items are the following:
| Data item | Description |
|---|---|
| LIGANDBOX_ID | ID in LigandBox |
| SINGLE | "true" if the entry is extacted as single conformer, else "false". |
| SOURCE | Source of this compound |
| IDNUMBER | ID in the source |
| MOLECULAR_FORMULA | Molecular formula |
| MOLECULAR_WEIGHT | Molecular weight |
| MOLECULAR_CHARGE | Molecular charge |
| NUM_OF_DONOR | Number of hydrogen bond donors |
| NUM_OF_ACCEPTOR | Number of hydrogen bond acceptors |
| NUM_OF_CHIRAL_ATOMS | Number of chiral atoms |
| TPSA | Topological Polar Surface Area |
| HOMO | Highest Occupied Molecular Orbital energy |
| LUMO | Lowest Unoccupied Molecular Orbital energy |
| LOGP | Partition coefficient |
| LOGS | Solubility |
| INCHI | InChI |
| INCHI_KEY | InChIKey |
| MOL2_FILE | URL of mol2 file for the entry |
2.5 Compounds of PDB
| Data name | Compounds of PDB |
|---|---|
| Description of data contents | Compounds in PDB. All conformers are included in it. They are assembled on a file in Mol2 format. Comments in Mol2 format are extracted to another CSV file. They can be searched in simple search. |
| File | ligandbox_pdb.zip (CSV format) (3.9MB)
PDB_Multiple.mol2.gz (Mol2 format) (102MB) |
Data items are the following:
| Data item | Description |
|---|---|
| LIGANDBOX_ID | ID in LigandBox |
| SINGLE | "TRUE" if the entry is extacted as single conformer, else "FALSE". |
| SOURCE | Source of this compound |
| IDNUMBER | ID in the source |
| MOLECULAR_FORMULA | Molecular formula |
| MOLECULAR_WEIGHT | Molecular weight |
| MOLECULAR_CHARGE | Molecular charge |
| NUM_OF_DONOR | Number of hydrogen bond donors |
| NUM_OF_ACCEPTOR | Number of hydrogen bond acceptors |
| NUM_OF_CHIRAL_ATOMS | Number of chiral atoms |
| TPSA | Topological Polar Surface Area |
| HOMO | Highest Occupied Molecular Orbital energy |
| LUMO | Lowest Unoccupied Molecular Orbital energy |
| LOGP | Partition coefficient |
| LOGS | Solubility |
| INCHI | InChI |
| INCHI_KEY | InChIKey |
| MOL2_FILE | URL of mol2 file for the entry |
3. License
You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.
The license for this database is specified in the Creative Commons Attribution-Share Alike 4.0 International.
If you use data from this database, please be sure attribute this database as follows: "LigandBox © Technology Research Association for Next generation natural products chemistry licensed under CC Attribution-Share Alike 4.0 International".
The summary of the Creative Commons Attribution-Share Alike 4.0 International is found here.
With regard to this database, you are licensed to:
- freely access part or whole of this database, and acquire data;
- freely redistribute part or whole of the data from this database; and
- freely create and distribute database and other adapted materials based on part or whole of the data from this database,
under the license, as long as you comply with the following conditions:
- You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any adapted material.
- You must distribute any adapted material based on part or whole of the data from this database under CC Attribution-Share Alike 4.0 (or later), or CC Attribution-Share Alike Compatible License (the list is here).
- You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.
https://www.mypresto5.jp/en/contact/
About Providing Links to This Database
You can freely provide links to all contents in this database. But, contents might be changed without notice.
4. Update History
| Date | Update contents |
|---|---|
| 2020/06/11 | Archive version V8 Released. The following data are updated. |
| 2020/03/26 | Simple search tables of single and multiple conformer are integrated. URL of mol2 files are changed. |
| 2020/03/16 | LigandBox English archive site is opened. |
5. Literature
Kawabata,T., Sugihara, Y., Fukunishi, Y., Nakamura, H.LigandBox : a database for 3D structures of chemical compounds.
BIOPHYSICS,9,113-121.
PMID: 27493549