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DB00560 : tigecycline

Approved drug tigecycline ... 6 targets DB00560

Generic name: tigecycline PDB Het Group: T1C
 
5 structures in PDB
Brand name(s): tygacil.
Formula: C29H39N5O8
IUPAC Formula: (4s,4as,5ar,12as)-9-[2-(Tert-Butylamino)acetamido]-4,7-Bis(dimethylamino)-3,10,12,12a-Tetrahydroxy-
1,11-Dioxo-1,4,4a,5,5a,6,11,12a-Octahydrotetracene-2-Carboxamide
PDB name: Tigecycline

6
There are 6 target proteins defined in DrugBank for this drug.
 5 
5 of these target proteins have one or more structures in the PDB.
 3 
There are 3 PDB structures containing the drug molecule bound to a protein that is not specified as a target.
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Information  
Pharmacology
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Target proteins

DrugBank drug Target 1:   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)
DrugBank drug Target 2:   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 tigecycline bound to this target protein, although there are 105 entries of the target protein (click the orange, plus icon for a list).
DrugBank drug Target 3:   UniProt id: P0A7S3 (RS12_ECOLI)  -  30S ribosomal protein S12
UniProt id: P0A7S3    123 a.a.  
1. 4tp8 L     123 a.a. 123   X-ray 2.80 Å
  2. 4tpa L     123 a.a. 123   X-ray 2.80 Å
  3. 4tpc L     123 a.a. 123   X-ray 2.80 Å
  4. 4tpe L     123 a.a. 123   X-ray 2.80 Å
  5. 4kiy L     123 a.a. 123   X-ray 2.90 Å
   more ...
There are no PDB entries containing tigecycline bound to this target protein, although there are 109 entries of the target protein (click the orange, plus icon for a list).
DrugBank drug Target 4:   UniProt id: P0A7S9 (RS13_ECOLI)  -  30S ribosomal protein S13
UniProt id: P0A7S9    117 a.a.  
1. 3j00 M     117 a.a. 117   Not given  
  2. 3j0u P     117 a.a. 117   Not given  
  3. 3j0v P     117 a.a. 117   Not given  
  4. 3j0x P     117 a.a. 117   Not given  
  5. 3j0z P     117 a.a. 117   Not given  
   more ...
There are no PDB entries containing tigecycline bound to this target protein, although there are 104 entries of the target protein (click the orange, plus icon for a list).
DrugBank drug Target 5:   UniProt id: P0AG59 (RS14_ECOLI)  -  30S ribosomal protein S14
UniProt id: P0AG59    100 a.a.  
1. 3j00 N     100 a.a. 100   Not given  
  2. 3j0u Q     100 a.a. 100   Not given  
  3. 3j0v Q     100 a.a. 100   Not given  
  4. 3j0x Q     100 a.a. 100   Not given  
  5. 3j0z Q     100 a.a. 100   Not given  
   more ...
There are no PDB entries containing tigecycline bound to this target protein, although there are 104 entries of the target protein (click the orange, plus icon for a list).
DrugBank drug Target 6:   UniProt id: P0A7U3 (RS19_ECOLI)  -  30S ribosomal protein S19
UniProt id: P0A7U3    91 a.a.  
1. 3j00 S     91 a.a. 91   Not given  
  2. 3j0u V     91 a.a. 91   Not given  
  3. 3j0v V     91 a.a. 91   Not given  
  4. 3j0x V     91 a.a. 91   Not given  
  5. 3j0z V     91 a.a. 91   Not given  
   more ...
There are no PDB entries containing tigecycline bound to this target protein, although there are 104 entries of the target protein (click the orange, plus icon for a list).

Key:    PfamA domain  Secondary structure  Bound drug molecule

 

Other proteins with tigecycline bound in the PDB

There are 2 "non-target" proteins in the PDB containing the tigecycline 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: P0ACT4 ()  -  Tetracycline repressor protein class D OS=Escherichia coli GN=tetR PE=1 SV=2
UniProt id: P0ACT4    217 a.a.  
4abz A   196 a.a. 195   X-ray 1.89 Å
The PDB contains 1 entry of tigecycline bound to this protein
Protein 2:   UniProt id: Q93L51 ()  -  TetX2 protein OS=Bacteroides thetaiotaomicron GN=tetX2 PE=1 SV=1
UniProt id: Q93L51    387 a.a.  
1. 4a6n A,B,C,D   368 a.a. 367   X-ray 2.30 Å
  2. 3v3o A,B,C,D   368 a.a. 365   X-ray 2.90 Å
The PDB contains 2 entries of tigecycline 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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