Answers.Body: <p>Proving a negative is hard, but to my knowledge I do not know a database that has <em>all</em> the structure of <em>drug</em> bound protein. I can give some close matches.</p>
  
  <p>First a few terms to be on the same page. A <strong>ligand</strong> is something that binds, which can be physiological, such as a <strong>cofactor</strong> or <strong>substrate</strong>, or not (especially man-made), such as a <strong>drug</strong>, i.e. a compound that has a physiological effect, or a <strong>hit</strong>, a small fragment from a fragment screen that will not bind with nanomolar affinity. Generally, ligands are small molecules, but may include oligopeptides and oligonucleotides. In the case of crystal structures, you also have <strong>crystallisation additives</strong>, which are not ligands, but are hetatoms in PDBs. Also, the definition of drug may vary. <a href="https://www.drugbank.ca/" rel="nofollow noreferrer">drugbank.ca</a> has the following categories of drugs "approved", "experimental", "withdrawn" for pharmaceuticals, "illicit" for narcotics and "investigational" for probes and counts macromolecules as drugs.</p>
  
  <ul>
  <li><p><a href="https://www.rcsb.org/pdb/ligand/drugMapping.do" rel="nofollow noreferrer">RCSB PDB: drug mapping table</a> is a simple searchable table with ligands that are clinical drugs only —experimental compounds (=probes) will be absent.</p></li>
  <li><p><a href="https://www.bindingdb.org/bind/surflex_entry.jsp" rel="nofollow noreferrer">bindingdb.org</a> contains many table, including a '3D' one. This table contains all the PDBs with ligands and their affinities. This contains crystallisation additives and natural ligands. Peter Curran's repo for the HotSpots algorithm (first written by Chris Radoux) has a <a href="https://github.com/prcurran/hotspots/blob/master/hotspots/excluded_het_id.txt" rel="nofollow noreferrer">blacklist</a>, but you are bound to get stuff missed.</p></li>
  <li><p><a href="http://bindingmoad.org/" rel="nofollow noreferrer">bindingmoad.org</a> is a database with all the protein-ligand structures from PDB up until 2018, but it includes natural ligands, like cofactors and substrates as above.</p></li>
  <li><p><a href="https://klifs.vu-compmedchem.nl/index.php" rel="nofollow noreferrer">https://klifs.vu-compmedchem.nl</a> a well curated database of kinases, which has a lot of members and many ligands, but is not at all diverse. As a result it is a clean dataset often used as a testbed for novel methodologies.</p></li>
  <li><p>I mentioned in the comments the <a href="https://www.thesgc.org/tep" rel="nofollow noreferrer">SGC Target Enabling Packages</a> as a small subset of proteins with many hits each. But I realise that there is not a handy PDB list and the targets are not drugs, but probes.</p></li>
  </ul>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-08T15:26:30.383Z
Answers.LastActivityDate: 2020-03-05T08:17:13.430Z
Answers.LastEditDate: 2020-03-05T08:17:13.430Z
Answers.UserDisplayName: Matteo Ferla
Body: <p>I am looking for a way to download all pdb files that detail a protein-drug complex.</p>
  
  <p>While I could download the entirety of the pdb and search manually (or maybe write a script to discard all proteins that do not have an HETATM entry that details a non-water, non-salt molecule), that sounds effort intensive and error prone.</p>
  
  <p>It seems reasonable that this subset already exist, but I was not able to find it.</p>
  
  <p>Does such a list/database exists?  </p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-02-03T09:30:10.917Z
Comments.Text: Albeit only a small fraction, the SGC has Target Enabling Packages which are few dozen sets of crystal structures each with several hits, i.e. non-natural targets, but not necessarily with nanomolar affinity but generally obeying Lipinski's rules (drug-like). For some times of analysis this wider but shorter set many be a better set than a messier set with only one target each...
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-02-03T09:31:15.307Z
Comments.Text: Also, if you do end up looking manually, in this [blog post](https://blog.matteoferla.com/2019/11/go-away-glycerol.html) is a list of crystallisation ligands, like glycerol, to blacklist.
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-02-06T19:04:36.773Z
Comments.Text: Above I mention a small but diverse dataset with many ligands each. An alternative is [KLIFS](https://klifs.vu-compmedchem.nl/index.php), which has only kinases, which is curated, has a lot of members and many ligands, but is not at all diverse. As a result it is a clean dataset often used as a testbed for novel methodologies. However, it represents only one family.
Comments.UserDisplayName: Matteo Ferla
Tags: <pdb><interactions>
Title: Looking for a way to download all pdb files that detail a protein-drug complex
ThreadText: # Looking for a way to download all pdb files that detail a protein-drug complex
  
  (Asked by: username_0 on 2020-02-01)
  
  I am looking for a way to download all pdb files that detail a protein-drug complex.
  
  While I could download the entirety of the pdb and search manually (or maybe write a script to discard all proteins that do not have an HETATM entry that details a non-water, non-salt molecule), that sounds effort intensive and error prone.
  
  It seems reasonable that this subset already exist, but I was not able to find it.
  
  Does such a list/database exists?
  
  **Tags:** pdb, interactions
  
  > **Comments:**
  > **username_1**: Albeit only a small fraction, the SGC has Target Enabling Packages which are few dozen sets of crystal structures each with several hits, i.e. non-natural targets, but not necessarily with nanomolar affinity but generally obeying Lipinski's rules (drug-like). For some times of analysis this wider but shorter set many be a better set than a messier set with only one target each...  
  > **username_1**: Also, if you do end up looking manually, in this [blog post](https://blog.username_1.com/2019/11/go-away-glycerol.html) is a list of crystallisation ligands, like glycerol, to blacklist.  
  > **username_1**: Above I mention a small but diverse dataset with many ligands each. An alternative is [KLIFS](https://klifs.vu-compmedchem.nl/index.php), which has only kinases, which is curated, has a lot of members and many ligands, but is not at all diverse. As a result it is a clean dataset often used as a testbed for novel methodologies. However, it represents only one family.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-02-08. Score: 2
  
  Proving a negative is hard, but to my knowledge I do not know a database that has *all* the structure of *drug* bound protein. I can give some close matches.
  
  First a few terms to be on the same page. A **ligand** is something that binds, which can be physiological, such as a **cofactor** or **substrate**, or not (especially man-made), such as a **drug**, i.e. a compound that has a physiological effect, or a **hit**, a small fragment from a fragment screen that will not bind with nanomolar affinity. Generally, ligands are small molecules, but may include oligopeptides and oligonucleotides. In the case of crystal structures, you also have **crystallisation additives**, which are not ligands, but are hetatoms in PDBs. Also, the definition of drug may vary. [drugbank.ca](https://www.drugbank.ca/) has the following categories of drugs "approved", "experimental", "withdrawn" for pharmaceuticals, "illicit" for narcotics and "investigational" for probes and counts macromolecules as drugs.
  
  * [RCSB PDB: drug mapping table](https://www.rcsb.org/pdb/ligand/drugMapping.do) is a simple searchable table with ligands that are clinical drugs only —experimental compounds (=probes) will be absent.
  * [bindingdb.org](https://www.bindingdb.org/bind/surflex_entry.jsp) contains many table, including a '3D' one. This table contains all the PDBs with ligands and their affinities. This contains crystallisation additives and natural ligands. Peter Curran's repo for the HotSpots algorithm (first written by Chris Radoux) has a [blacklist](https://github.com/prcurran/hotspots/blob/master/hotspots/excluded_het_id.txt), but you are bound to get stuff missed.
  * [bindingmoad.org](http://bindingmoad.org/) is a database with all the protein-ligand structures from PDB up until 2018, but it includes natural ligands, like cofactors and substrates as above.
  * [https://klifs.vu-compmedchem.nl](https://klifs.vu-compmedchem.nl/index.php) a well curated database of kinases, which has a lot of members and many ligands, but is not at all diverse. As a result it is a clean dataset often used as a testbed for novel methodologies.
  * I mentioned in the comments the [SGC Target Enabling Packages](https://www.thesgc.org/tep) as a small subset of proteins with many hits each. But I realise that there is not a handy PDB list and the targets are not drugs, but probes.
  
  
  ---
  
  