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DB01051 : novobiocin

Approved drug novobiocin ... 1 target DB01051

Generic name: novobiocin PDB Het Group: NOV
 
6 structures in PDB
Brand name(s): albamix, albamycin, cardelmycin, cathocin, cathomycin, inamycin, novo-r, robiocina, sirbiocina, spheromycin, stilbiocina, streptonivicin.
Formula: C31H36N2O11
IUPAC Formula: (3r,4s,5r,6r)-5-Hydroxy-6-[(4-Hydroxy-3-{[4-Hydroxy-3-(3-Methylbut-2-En-1-Yl)benzene]amido}-8-
Methyl-2-Oxo-2h-Chromen-7-Yl)oxy]-3-Methoxy-2,2-Dimethyloxan-4-Yl carbamate
PDB name: Novobiocin

1
There is 1 target protein defined in DrugBank for this drug.
 1 
The target protein has one or more structures in the PDB.
 1 
There is 1 PDB structure of the drug molecule bound to its target protein.
 5 
There are 5 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: P0A0K8 (GYRB_STAAU)  -  DNA gyrase subunit B
UniProt id: P0A0K8    643 a.a.  
4uro A,B,C,D   187 a.a. 186   X-ray 2.59 Å
The PDB contains 1 entry of novobiocin bound to this target protein and 8 entries of this target protein in all (click on orange, plus icon for list).

Key:    PfamA domain  Secondary structure  Bound drug molecule

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

 

Other proteins with novobiocin bound in the PDB

There are 5 "non-target" proteins in the PDB containing the novobiocin molecule bound. That is, the UniProt code for the proteins is missing or does not match the drug target above.

Protein 1:   UniProt id: P0AES6 ()  -  DNA gyrase subunit B OS=Escherichia coli (strain K12) GN=gyrB PE=1 SV=2
UniProt id: P0AES6    803 a.a.  
1aj6 A   194 a.a. 193   X-ray 2.30 Å
The PDB contains 1 entry of novobiocin bound to this protein
Protein 2:   UniProt id: P20083 ()  -  DNA topoisomerase 4 subunit B OS=Escherichia coli (strain K12) GN=parE PE=1 SV=3
UniProt id: P20083    629 a.a.  
1s14 A   168 a.a. 168   X-ray 2.00 Å
The PDB contains 1 entry of novobiocin bound to this protein
Protein 3:   UniProt id: Q5GYJ8 ()  -  DNA topoisomerase 4 subunit B OS=Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85) GN=parE PE=1 SV=1
UniProt id: Q5GYJ8    672 a.a.  
3lps A   347 a.a. 347   X-ray 2.29 Å
The PDB contains 1 entry of novobiocin bound to this protein
Protein 4:   UniProt id: Q9LCX5 ()  -  DNA gyrase subunit B OS=Thermus thermophilus GN=gyrB PE=1 SV=1
UniProt id: Q9LCX5    633 a.a.  
1kij A,B   384 a.a. 384   X-ray 2.30 Å
The PDB contains 1 entry of novobiocin bound to this protein
Protein 5:   UniProt id: X5EN43 ()  -  DNA topoisomerase 4 subunit B OS=Staphylococcus aureus GN=parE PE=1 SV=1
  No Pfam domain assignments available for this protein.
4urn A,C   188 a.a. 188   X-ray 2.30 Å
The PDB contains 1 entry of novobiocin 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.

 

Structure selection

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