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
•
written
by
bioraghu.iisc •
1 answer
I would suggest the following way:
go here: http://nldb.hgc.jp/nldb/top
or here, that is about the same:
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.
Log in to answer this question.
-
Get data from KEGG Brite
written by sizeineb •
-
Drug/small molecule databases with SMILES and chemical properties?
written by TonyCN •
-
Is there any way to map ChEMBL compound IDs to KEGG Drug IDs?
written by Misha •
-
KEGG Pathway - A circle includes many compounds
written by zrongstudent •
-
metabolite mapping - from PDB ligand to KEGG
written by bioraghu.iisc •
-
Retriving compounds name from KEGG IDs
written by glady
-
List Of Naturally Occuring Metabolites/Compounds In Eukaryotes ?
written by Sudeep
-
Ligand Database For Compounds Present In Human Food
written by Flow
-
Kegg Data Download
written by Siva Kumar •
-
Mapping Bigg Metabolic Reaction Ids To Kegg Pathway Map Ids
written by Bernie •
