natural ligands in PDB

Question

[bioraghu.iisc]

Dear all

Is there any database available that has only natural ligands in PDB? I came across - NLDB -natural ligand db, but there seems to be no option for download, neither is there a list of all natural ligands used.

Also databases like KEGG Reaction (compounds) have a problem of mapping the KEGG IDs to PDBIDs and much of the information is lost.

Could you pls. suggest any downloadable natural ligand DB

Answer 1

[natasha.sernova]

I would suggest the following way:

go here: http://nldb.hgc.jp/nldb/top

or here, that is about the same:

http://nldb.hgc.jp/

Insert your ligand-name into an empty line

You will have some output, and a chance to download.

I've used ATP just to try:

I got: 581 reactions found with KEGG-links.

To have a structure, you need to insert this ligand PDB-id, I suppose.

Later I saw this link:

https://www3.rcsb.org/ligand/ATP

Here you will have a structure and several codes on the left. This pdb structures should be possible to be downloaded,

This one, for example:

http://www.rcsb.org/pdb/explore/explore.do?structureId=1A49

I've also used PDB-site

http://www.rcsb.org/pdb/home/home.do

and inserted 'natural ligand' into the empty line in the upper right corner:

I've got 51 structures, since it has no additional information.