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DB00254 : doxycycline

Approved drug doxycycline ... 3 targets DB00254

Generic name: doxycycline PDB Het Group: DXT
 
2 structures in PDB
Brand name(s): alti-doxycycline, apo-doxy, atridox, doryx, doxy 100, doxy-caps, doxy-lemmon, doxychel, doxychel hyclate, doxycin, doxylin, doxytec, jenacyclin, monodox, novo-doxylin, nu-doxycycline, oracea, periostat, supracyclin, vibra-tabs, vibramycin.
Formula: C22H24N2O8
IUPAC Formula: (4s,4ar,5s,5ar,6r,12as)-4-(Dimethylamino)-3,5,10,12,12a-Pentahydroxy-6-Methyl-1,11-Dioxo-
1,4,4a,5,5a,6,11,12a-Octahydrotetracene-2-Carboxamide
PDB name: (4s,4ar,5s,5ar,6r,12as)-4-(Dimethylamino)-3,5,10,12,12a-Pentahydroxy-6-Methyl-1,11-Dioxo-
1,4,4a,5,5a,6,11,12a-Octahydrotetracene-2-Carboxamide

3
There are 3 target proteins defined in DrugBank for this drug.
 2 
2 of these target proteins have one or more structures in the PDB.
 2 
There are 2 PDB structures containing the drug molecule bound to a protein that is not specified as a target.
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Target proteins

DrugBank drug Target 1:   UniProt id: P0A7X3 (RS9_ECOLI)  -  30S ribosomal protein S9
UniProt id: P0A7X3    129 a.a.  
1. 3j00 I     129 a.a. 129   Not given  
  2. 3j0u L     129 a.a. 129   Not given  
  3. 3j0v L     129 a.a. 129   Not given  
  4. 3j0x L     129 a.a. 129   Not given  
  5. 3j0z L     129 a.a. 129   Not given  
   more ...
There are no PDB entries containing doxycycline bound to this target protein, although there are 103 entries of the target protein (click the orange, plus icon for a list).
DrugBank drug Target 2:   UniProt id: P0A7V8 (RS4_ECOLI)  -  30S ribosomal protein S4
UniProt id: P0A7V8    205 a.a.  
1. 4tp8 D     205 a.a. 205   X-ray 2.80 Å
  2. 4tpa D     205 a.a. 205   X-ray 2.80 Å
  3. 4tpc D     205 a.a. 205   X-ray 2.80 Å
  4. 4tpe D     205 a.a. 205   X-ray 2.80 Å
  5. 4kiy D     205 a.a. 205   X-ray 2.90 Å
   more ...
There are no PDB entries containing doxycycline bound to this target protein, although there are 102 entries of the target protein (click the orange, plus icon for a list).
DrugBank drug Target 3:   Bacterial outer membrane
  No Pfam domain assignments available for this protein.
 
There are no structures of the target protein in the PDB (click icon on left for list of closest matches)

Key:    PfamA domain  Secondary structure  Bound drug molecule

 

Other proteins with doxycycline bound in the PDB

There is 1 "non-target" protein in the PDB containing the doxycycline molecule bound. That is, the UniProt code for the protein is missing or does not match any of the drug targets listed above.

Protein 1:   UniProt id: P0ACT4 ()  -  Tetracycline repressor protein class D OS=Escherichia coli GN=tetR PE=1 SV=2
UniProt id: P0ACT4    217 a.a.  
1. 2o7o A   207 a.a. 206   X-ray 1.89 Å
  2. 2xrl A   207 a.a. 205   X-ray 1.85 Å
The PDB contains 2 entries of doxycycline bound to this protein

Key:    PfamA domain  Secondary structure  Bound drug molecule

The black crosses on the secondary structure diagrams indicate where the PDB and UniProt sequences differ.

Where there is more than one PDB model for a given UniProt sequence, the models are ordered by: 1. decreasing order of similarity to the UniProt sequence, 2. X-ray structures (in order of increasing resolution), NMR structures, and theoretical models. Clicking on any PDB code take you to the corresponding PDBsum page.

 

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