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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:49 UTC
Update Date2020-02-26 21:39:38 UTC
HMDB IDHMDB0014427
Secondary Accession Numbers
  • HMDB14427
Metabolite Identification
Common NamePamidronate
DescriptionPamidronate is only found in individuals that have used or taken this drug.Pamidronate, marketed as pamidronate disodium pentahydrate under the brand name Aredia, is a bisphosphonate. [Wikipedia ]The mechanism of action of pamidronate is inhibition of bone resorption. Pamidronate adsorbs to calcium phosphate (hydroxyapatite) crystals in bone and may directly block dissolution of this mineral component of bone. In vitro studies also suggest that inhibition of osteoclast activity contributes to inhibition of bone resorption. Pamidronate also targets farnesyl pyrophosphate (FPP) synthase. Nitrogen-containing bisphosphonates (such as pamidronate, alendronate, risedronate, ibandronate and zoledronate) appear to act as analogues of isoprenoid diphosphate lipids, thereby inhibiting FPP synthase, an enzyme in the mevalonate pathway. Inhibition of this enzyme in osteoclasts prevents the biosynthesis of isoprenoid lipids (FPP and GGPP) that are essential for the post-translational farnesylation and geranylgeranylation of small GTPase signalling proteins. This activity inhibits osteoclast activity and reduces bone resorption and turnover. In postmenopausal women, it reduces the elevated rate of bone turnover, leading to, on average, a net gain in bone mass.
Structure
Data?1582753178
Synonyms
ValueSource
Pamidronic acidKegg
RibodroatKegg
Pamidronate disodiumHMDB
(3-Amino-1-hydroxypropylidene)-1,1-biphosphonateHMDB
Novartis brand OF pamidronate disodium saltHMDB
Amino-1-hydroxypropane-1,1-diphosphonateHMDB
Pamidronate calciumHMDB
(3-Amino-1-hydroxypropylidene)-1,1-bisphosphonateHMDB
ArediaHMDB
1-Hydroxy-3-aminopropane-1,1-diphosphonic acidHMDB
AmidronateHMDB
Aminohydroxypropylidene diphosphonateHMDB
Pamidronate monosodiumHMDB
AHPrBPHMDB
APDHMDB
AminopropanehydroxydiphosphonateHMDB
1 Hydroxy 3 aminopropane 1,1 diphosphonic acidHMDB
Amino 1 hydroxypropane 1,1 diphosphonateHMDB
Chemical FormulaC3H11NO7P2
Average Molecular Weight235.0695
Monoisotopic Molecular Weight235.001074735
IUPAC Name(3-amino-1-hydroxy-1-phosphonopropyl)phosphonic acid
Traditional Namepamidronate
CAS Registry Number40391-99-9
SMILES
NCCC(O)(P(O)(O)=O)P(O)(O)=O
InChI Identifier
InChI=1S/C3H11NO7P2/c4-2-1-3(5,12(6,7)8)13(9,10)11/h5H,1-2,4H2,(H2,6,7,8)(H2,9,10,11)
InChI KeyWRUUGTRCQOWXEG-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as bisphosphonates. These are organic compounds containing two phosphonate groups linked together through a carbon atoms.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassOrganic phosphonic acids and derivatives
Sub ClassBisphosphonates
Direct ParentBisphosphonates
Alternative Parents
Substituents
  • Bisphosphonate
  • Organophosphonic acid
  • 1,3-aminoalcohol
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary amine
  • Organophosphorus compound
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Amine
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Disposition

Biological location

Source

Route of exposure

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility15.8 g/LNot Available
LogP-4.7Not Available
Experimental Spectral PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility15.8 g/LALOGPS
logP10(-1.4) g/LALOGPS
logP10(-4.5) g/LChemAxon
logS10(-1.2) g/LALOGPS
pKa (Strongest Acidic)0.67ChemAxon
pKa (Strongest Basic)9.86ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area161.31 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity42.62 m³·mol⁻¹ChemAxon
Polarizability17.34 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Spectral Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+151.40331661259
DarkChem[M-H]-144.6931661259

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Pamidronate,1TMS,#1C[Si](C)(C)OC(CCN)(P(=O)(O)O)P(=O)(O)O2259.4Semi standard non polarhttps://arxiv.org/abs/1905.12712
Pamidronate,1TMS,#2C[Si](C)(C)OP(=O)(O)C(O)(CCN)P(=O)(O)O2226.9Semi standard non polarhttps://arxiv.org/abs/1905.12712
Pamidronate,1TMS,#3C[Si](C)(C)NCCC(O)(P(=O)(O)O)P(=O)(O)O2288.6Semi standard non polarhttps://arxiv.org/abs/1905.12712
Pamidronate,1TBDMS,#1CC(C)(C)[Si](C)(C)OC(CCN)(P(=O)(O)O)P(=O)(O)O2500.2Semi standard non polarhttps://arxiv.org/abs/1905.12712
Pamidronate,1TBDMS,#2CC(C)(C)[Si](C)(C)OP(=O)(O)C(O)(CCN)P(=O)(O)O2463.0Semi standard non polarhttps://arxiv.org/abs/1905.12712
Pamidronate,1TBDMS,#3CC(C)(C)[Si](C)(C)NCCC(O)(P(=O)(O)O)P(=O)(O)O2552.3Semi standard non polarhttps://arxiv.org/abs/1905.12712
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Pamidronate GC-MS (Non-derivatized) - 70eV, Positivesplash10-001i-9010000000-c609aeb84dc854acef5e2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pamidronate GC-MS (1 TMS) - 70eV, Positivesplash10-0fl0-9530000000-3dcc66dec182929ad44c2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Pamidronate GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pamidronate 10V, Positive-QTOFsplash10-00kr-0590000000-70afb6f8f6bd4fa8dc0c2016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pamidronate 20V, Positive-QTOFsplash10-0f80-4900000000-d984e8b630279adf91172016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pamidronate 40V, Positive-QTOFsplash10-00lr-9220000000-23665351b55d845211712016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pamidronate 10V, Negative-QTOFsplash10-0f89-2590000000-b548987abea1368137052016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pamidronate 20V, Negative-QTOFsplash10-0uyi-5940000000-2fa45eefdeb643c061942016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pamidronate 40V, Negative-QTOFsplash10-003r-9000000000-57907eeacb268739b1252016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pamidronate 10V, Positive-QTOFsplash10-001r-9070000000-60834fd1c274bf3a378e2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pamidronate 20V, Positive-QTOFsplash10-000i-0690000000-46aca5e6c3a2ca2b76cf2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pamidronate 40V, Positive-QTOFsplash10-00di-9200000000-4a70bd6f6de42e1622e12021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pamidronate 10V, Negative-QTOFsplash10-00lr-0090000000-2ee377abd33f38d7b1d92021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pamidronate 20V, Negative-QTOFsplash10-01q9-9020000000-13ae78878ab3e85dd77f2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Pamidronate 40V, Negative-QTOFsplash10-03di-9000000000-818b4c1881e12ac6419e2021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00282 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00282 details
Abnormal Concentrations
Not Available
Predicted Concentrations
BiospecimenValueOriginal ageOriginal sexOriginal conditionComments
Blood0.000 uMAdult (>18 years old)BothNormalPredicted based on drug qualities
Blood0.000 umol/mmol creatinineAdult (>18 years old)BothNormalPredicted based on drug qualities
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB00282
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID4512
KEGG Compound IDC07395
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPamidronic acid
METLIN IDNot Available
PubChem Compound4674
PDB ID210
ChEBI ID160401
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Zarychanski R, Elphee E, Walton P, Johnston J: Osteonecrosis of the jaw associated with pamidronate therapy. Am J Hematol. 2006 Jan;81(1):73-5. [PubMed:16369966 ]

Enzymes

General function:
Involved in isoprenoid biosynthetic process
Specific function:
Key enzyme in isoprenoid biosynthesis which catalyzes the formation of farnesyl diphosphate (FPP), a precursor for several classes of essential metabolites including sterols, dolichols, carotenoids, and ubiquinones. FPP also serves as substrate for protein farnesylation and geranylgeranylation. Catalyzes the sequential condensation of isopentenyl pyrophosphate with the allylic pyrophosphates, dimethylallyl pyrophosphate, and then with the resultant geranylpyrophosphate to the ultimate product farnesyl pyrophosphate.
Gene Name:
FDPS
Uniprot ID:
P14324
Molecular weight:
48275.03
References
  1. Chen X, Ji ZL, Chen YZ: TTD: Therapeutic Target Database. Nucleic Acids Res. 2002 Jan 1;30(1):412-5. [PubMed:11752352 ]
  2. Bergstrom JD, Bostedor RG, Masarachia PJ, Reszka AA, Rodan G: Alendronate is a specific, nanomolar inhibitor of farnesyl diphosphate synthase. Arch Biochem Biophys. 2000 Jan 1;373(1):231-41. [PubMed:10620343 ]
  3. Dunford JE, Thompson K, Coxon FP, Luckman SP, Hahn FM, Poulter CD, Ebetino FH, Rogers MJ: Structure-activity relationships for inhibition of farnesyl diphosphate synthase in vitro and inhibition of bone resorption in vivo by nitrogen-containing bisphosphonates. J Pharmacol Exp Ther. 2001 Feb;296(2):235-42. [PubMed:11160603 ]
  4. Notarnicola M, Messa C, Cavallini A, Bifulco M, Tecce MF, Eletto D, Di Leo A, Montemurro S, Laezza C, Caruso MG: Higher farnesyl diphosphate synthase activity in human colorectal cancer inhibition of cellular apoptosis. Oncology. 2004;67(5-6):351-8. [PubMed:15713990 ]
  5. Riebeling C, Forsea AM, Raisova M, Orfanos CE, Geilen CC: The bisphosphonate pamidronate induces apoptosis in human melanoma cells in vitro. Br J Cancer. 2002 Jul 29;87(3):366-71. [PubMed:12177810 ]
  6. Zhang PL, Lun M, Siegelmann-Danieli N, Blasick TM, Brown RE: Pamidronate resistance and associated low ras levels in breast cancer cells: a role for combinatorial therapy. Ann Clin Lab Sci. 2004 Summer;34(3):263-70. [PubMed:15487700 ]