spacer
spacer

Search 

DB01045 : rifampin

Approved drug rifampin ... 3 targets DB01045

Generic name: rifampin PDB Het Group: RFP
 
7 structures in PDB
Brand name(s): archidyn, rifadin, rifadine, rifagen, rifaldin, rifaprodin, rifoldin, rifoldine, riforal, rimactan, rimactane, rimactin, rimazid, rofact, tubocin.
Formula: C43H58N4O12
IUPAC Formula: (7s,11s,12r,13s,14r,15r,16r,17s,18s)-2,15,17,27,29-Pentahydroxy-11-Methoxy-3,7,12,14,16,18,22-
Heptamethyl-26-[(E)-N-(4-Methylpiperazin-1-Yl)carboximidoyl]-6,23-Dioxo-8,30-Dioxa-24-
Azatetracyclo[23.3.1.1^{4,7}.0^{5,28}]triaconta-1,3,5(28),9,19,21,25(29),26-Octaen-13-Yl acetate
PDB name: Rifampicin

3
There are 3 target proteins defined in DrugBank for this drug.
 3 
3 of these target proteins have one or more structures in the PDB.
 2 
There are 2 PDB structures of the drug molecule bound to its target protein.
 3 
There are 3 PDB structures containing the drug molecule bound to a protein that is not specified as a target.
Links  
DrugBank
RxList
ChEBI
KEGG drug
PubChem
MSDChem
Ligand Expo
HIC-Up
Information  
Pharmacology
Indication
Action

 

Target proteins

DrugBank drug Target 1:   UniProt id: P0A8V2 (RPOB_ECOLI)  -  DNA-directed RNA polymerase beta chain
UniProt id: P0A8V2    1341 a.a.  
4kmu C,H   1335 a.a. 1335   X-ray 3.85 Å
The PDB contains 1 entry of rifampin bound to this target protein and 13 entries of this target protein in all (click on orange, plus icon for list).
DrugBank drug Target 2:   UniProt id: P0A8T7 (RPOC_ECOLI)  -  DNA-directed RNA polymerase subunit beta'
UniProt id: P0A8T7    1406 a.a.  
1. 3iyd D     1368 a.a. 1368   Not given  
  2. 3lu0 D     1364 a.a. 1364   Not given  
  3. 4kn7 D,I     1160 a.a. 1160   X-ray 3.69 Å
  4. 4igc D,I     1160 a.a. 1160   X-ray 3.70 Å
  5. 4kmu D,I     1160 a.a. 1160   X-ray 3.85 Å
   more ...
There are no PDB entries containing rifampin bound to this target protein, although there are 13 entries of the target protein (click the orange, plus icon for a list).
DrugBank drug Target 3:   UniProt id: O75469 (NR1I2_HUMAN)  -  Nuclear receptor subfamily 1 group I member 2
UniProt id: O75469    433 a.a.  
1skx A   242 a.a. 242   X-ray 2.80 Å
The PDB contains 1 entry of rifampin bound to this target protein and 11 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 rifampin bound in the PDB

There are 2 "non-target" proteins in the PDB containing the rifampin molecule bound. That is, the UniProt code for the proteins is missing or does not match any of the drug targets listed above.

Protein 1:   UniProt id: A0QRS5 ()  -  Rifampin ADP-ribosyl transferase OS=Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) GN=MSMEG_1221 PE=1 SV=1
UniProt id: A0QRS5    141 a.a.  
2hw2 A   138 a.a. 136   X-ray 1.45 Å
The PDB contains 1 entry of rifampin bound to this protein
Protein 2:   UniProt id: Q9KWU7 ()  -  DNA-directed RNA polymerase subunit beta OS=Thermus aquaticus GN=rpoB PE=1 SV=1
UniProt id: Q9KWU7    1118 a.a.  
1. 1ynn C   1114 a.a. 1113   X-ray 3.30 Å
  2. 1i6v C   1113 a.a. 1111   X-ray 3.30 Å
The PDB contains 2 entries of rifampin 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.

 

Structure selection

Use the checkboxes above to select the structure(s) of interest, and then press the required button below to view:
View 3D structure
Select preferred viewer and click on 3D struct button
AstexViewer™@MSD-EBI
RasMol
STRAP multiple alignment viewer
LIGPLOT diagrams
Press button below for LIGPLOT diagrams of drug-protein interactions in all selected structures above.

  spacer

spacer