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How to get an experimental ligand structure from the PDB?

Asked by [ Admin ] , Edited by Noel O'Boyle [ Admin ]

Given a PDB code, what is the simplest way to get an SDF file with the experimental coordinates of a particular ligand?

My current procedure is to go to the PDB Ligand Expo, and use the “Search for instances of chemical components by 3-letter ID code” at the bottom with “PDB entry codes + coordinates files” chosen. This requires me to specify the 3-letter ID code, which I need to have obtained from the web page for the PDB file.

On the search results page, I can simply click on the SDF file for the particular PDB file in which I am interested to download the experimental coordinates.

Is there an easier way? For example, it does not seem to be possible to go directly from the website for a particular PDB entry.

(I would also be interested in the same question applied to a handling a large number of PDB codes at the same time.)

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1 answer

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matteo floris [ Editor ]

I think it is faster to write a tool with Python and Pybel.

First, you should download this dictionary (Tabulation of PDB entries containing each chemical component);

in this way you can get the full list of ligands associated to PDB entries.
Then, the best is to download the SDF file with all the ligands and use the dictionary for the mapping PDB identifier –> list of associated ligands.


NN comments
chem-bla-ics
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Matteo, what is the license for this data? Can Noel reuse and redistribute it?

baoilleach
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Hi Mattero, does the SDF file just have one structure per ligand even where the ligand is in different PDB entries?

matteo floris
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Hi Noel, we have not unique ligands but unique combinations of PDB entry – ligand – PDB entry chain… let me show two examples: the first is the ligand ZU3, for which we have the coordinates in all the PDB where this ligand is present:

2zu3ZU31A501B 2zu4ZU31A501B

the second example, the ligand ZZC, that is present in the SDF file for the same PDB entry but in 2 different chains (A and B):

2wodZZC1A401D 2wodZZC1B401F

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