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DB02546 : vorinostat

Approved drug vorinostat ... 6 targets DB02546

Generic name: vorinostat PDB Het Group: SHH
 
9 structures in PDB
Brand name(s): saha, zolinza.
Formula: C14H20N2O3
IUPAC Formula: N-Hydroxy-N'-Phenyloctanediamide
PDB name: Octanedioic acid hydroxyamide phenylamide

6
There are 6 target proteins defined in DrugBank for this drug.
 6 
6 of these target proteins have one or more structures in the PDB.
 5 
There are 5 PDB structures of the drug molecule bound to its target protein.
 4 
There are 4 PDB structures containing the drug molecule bound to a protein that is not specified as a target.
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Pharmacology
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Target proteins

DrugBank drug Target 1:   UniProt id: Q13547 (HDAC1_HUMAN)  -  Histone deacetylase 1
  No Pfam domain assignments available for this protein.
1. 4bkx B     369 a.a. 369   X-ray 3.00 Å
  2. 1tyi A     327 a.a. 327   Theor. model
There are no PDB entries containing vorinostat bound to this target protein, although there are 2 entries of the target protein (click the orange, plus icon for a list).
DrugBank drug Target 2:   UniProt id: Q92769 (HDAC2_HUMAN)  -  Histone deacetylase 2
UniProt id: Q92769    487 a.a.  
4lxz A,B,C   368 a.a. 368   X-ray 1.85 Å
The PDB contains 1 entry of vorinostat bound to this target protein and 3 entries of this target protein in all (click on orange, plus icon for list).
DrugBank drug Target 3:   UniProt id: O15379 (HDAC3_HUMAN)  -  Histone deacetylase 3
UniProt id: O15379    427 a.a.  
4a69 A,B     369 a.a. 369   X-ray 2.06 Å
There are no PDB entries containing vorinostat bound to this target protein, although there is 1 entry of the target protein in the PDB (see above).
DrugBank drug Target 4:   UniProt id: Q9UBN7 (HDAC6_HUMAN)  -  Histone deacetylase 6
UniProt id: Q9UBN7    1214 a.a.  
1. 3c5k A     108 a.a. 107   X-ray 1.55 Å
  2. 3phd A,B     102 a.a. 102   X-ray 3.00 Å
  3. 3gv4 A     99 a.a. 99   X-ray 1.72 Å
There are no PDB entries containing vorinostat bound to this target protein, although there are 3 entries of the target protein (click the orange, plus icon for a list).
DrugBank drug Target 5:   UniProt id: Q9BY41 (HDAC8_HUMAN)  -  Histone deacetylase 8
UniProt id: Q9BY41    376 a.a.  
1. 4qa0 A,B   371 a.a. 363   X-ray 2.24 Å
  2. 1t69 A   358 a.a. 358   X-ray 2.91 Å
  3. 4qa2 A,B   356 a.a. 354   X-ray 2.38 Å
The PDB contains 3 entries of vorinostat bound to this target protein and 29 entries of this target protein in all (click on orange, plus icon for list).
DrugBank drug Target 6:   UniProt id: O67135 (O67135_AQUAE)  -  Acetoin utilization protein
UniProt id: O67135    374 a.a.  
1c3s A   372 a.a. 368   X-ray 2.50 Å
The PDB contains 1 entry of vorinostat bound to this target protein and 3 entries of this target protein in all (click on orange, plus icon for list).

Key:    PfamA domain  PfamB 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 vorinostat bound in the PDB

There are 4 "non-target" proteins in the PDB containing the vorinostat 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: A5H660 ()  -  Histone deacetylase 8 OS=Schistosoma mansoni GN=HDAC8 PE=1 SV=1
UniProt id: A5H660    439 a.a.  
4bz6 A,B,C,D   397 a.a. 397   X-ray 2.00 Å
The PDB contains 1 entry of vorinostat bound to this protein
Protein 2:   UniProt id: Q70I53 ()  -  Histone deacetylase-like amidohydrolase OS=Alcaligenes sp. (strain DSM 11172) GN=hdaH PE=1 SV=3
UniProt id: Q70I53    368 a.a.  
1zz1 A,B,C,D   367 a.a. 366   X-ray 1.57 Å
The PDB contains 1 entry of vorinostat bound to this protein
Protein 3:   UniProt id: Q8WUI4 ()  -  Histone deacetylase 7 OS=Homo sapiens GN=HDAC7 PE=1 SV=2
UniProt id: Q8WUI4    951 a.a.  
1. 2pqo A,B   386 a.a. 386   X-ray 2.00 Å
  2. 3c0z C   359 a.a. 359   X-ray 2.10 Å
The PDB contains 2 entries of vorinostat bound to this protein
Protein 4:   Crystal structure of catalytic domain of human histone deacetylase hdac7 in complex with saha
  No Pfam domain assignments available for this protein.
3c0z A,B   383 a.a. 383   X-ray 2.10 Å

Key:    PfamA domain  PfamB 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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