DB00399 : zoledronate

Approved drug zoledronate ... 3 targets DB00399

Generic name: zoledronate PDB Het Group: ZOL
16 structures in PDB
Brand name(s): aclasta, reclast, zometa, zometa concentrate.
Formula: C5H10N2O7P2
IUPAC Formula: [1-Hydroxy-2-(1h-Imidazol-1-Yl)-1-Phosphonoethyl]phosphonic acid
PDB name: Zoledronic acid

There are 3 target proteins defined in DrugBank for this drug.
2 of these target proteins have one or more structures in the PDB.
There are 10 PDB structures of the drug molecule bound to its target protein.
There are 6 PDB structures containing the drug molecule bound to a protein that is not specified as a target.
KEGG drug
Ligand Expo


Target proteins

DrugBank drug Target 1:   UniProt id: P14324 (FPPS_HUMAN)  -  Farnesyl pyrophosphate synthetase
UniProt id: P14324    418 a.a.  
1. 4p0v A   346 a.a. 346   X-ray 2.40 Å
  2. 4p0w A   346 a.a. 346   X-ray 2.41 Å
  3. 2f8z F   346 a.a. 346   X-ray 2.60 Å
  4. 3n45 F   343 a.a. 343   X-ray 1.88 Å
  5. 2f9k F   343 a.a. 343   X-ray 2.06 Å
   more ...
The PDB contains 10 entries of zoledronate bound to this target protein and 47 entries of this target protein in all (click on orange, plus icon for list).
DrugBank drug Target 2:   UniProt id: O95749 (GGPPS_HUMAN)  -  Geranylgeranyl pyrophosphate synthetase
UniProt id: O95749    299 a.a.  
1. 2fvi A,B,C,D,...     285 a.a. 285   X-ray 2.70 Å
  2. 2q80 A,B,C,D,...     285 a.a. 285   X-ray 2.70 Å
There are no PDB entries containing zoledronate 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 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  PfamB domain  Secondary structure  Bound drug molecule


Other proteins with zoledronate bound in the PDB

There are 4 "non-target" proteins in the PDB containing the zoledronate 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: Q12051 ()  -  Geranylgeranyl pyrophosphate synthase OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=BTS1 PE=1 SV=1
UniProt id: Q12051    335 a.a.  
2e91 A,B   296 a.a. 294   X-ray 2.14 Å
The PDB contains 1 entry of zoledronate bound to this protein
Protein 2:   UniProt id: Q5CR09 ()  -  Putative farnesyl pyrophosphate synthase (Fragment) OS=Cryptosporidium parvum (strain Iowa II) GN=cgd4_2550 PE=1 SV=1
UniProt id: Q5CR09    383 a.a.  
1. 2her A,B   335 a.a. 335   X-ray 2.37 Å
  2. 2q58 A,B   335 a.a. 335   X-ray 2.37 Å
The PDB contains 2 entries of zoledronate bound to this protein
Protein 3:   UniProt id: Q95WL3 ()  -  Farnesyl pyrophosphate synthase (Fragment) OS=Trypanosoma cruzi PE=1 SV=1
UniProt id: Q95WL3    361 a.a.  
3iba A   362 a.a. 361   X-ray 2.40 Å
The PDB contains 1 entry of zoledronate bound to this protein
Protein 4:   Crystal structure of plasmodium vivax geranylgeranylpyrophos synthase pvx_092040 with zoledronate and ipp bound
  No Pfam domain assignments available for this protein.
1. 3ez3 A,B,C,D   358 a.a. 358   X-ray 2.30 Å
  2. 3ldw A,B,C,D   358 a.a. 358   X-ray 2.47 Å

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
STRAP multiple alignment viewer
LIGPLOT diagrams
Press button below for LIGPLOT diagrams of drug-protein interactions in all selected structures above.