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Showing metabocard for Clodronate (HMDB0014858)

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enzymes (4) Show 4 proteins
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:50 UTC
Update Date2022-03-07 02:51:46 UTC
HMDB IDHMDB0014858
Secondary Accession Numbers
  • HMDB14858
Metabolite Identification
Common NameClodronate
DescriptionClodronate is only found in individuals that have used or taken this drug. It is a diphosphonate which affects calcium metabolism. It inhibits bone resorption and soft tissue calcification. [PubChem]The bisphosphonate group binds strongly to the bone mineral, hydroxyapatite. This explains the specific pharmacological action of these compounds on mineralized tissues, especially bone. The exact mechanism of action of clodronate is not known, however it is known that it does not inhibit protein isoprenylation but can be metabolized intracellularly to a β-γ-methylene (AppCp-type) analog of ATP (AppCCl2p), which is cytotoxic to macrophages in vitro. Inhibition of the ADP/ATP translocase by the metabolite AppCCl2p is a likely route by which clodronate causes osteoclast apoptosis and inhibits bone resorption. Recently, the slime mold Dictyostelium discoideum was shown to take up bisphosphonates by pinocytosis. In these cells, clodronate, but not other pharmacologically active bisphosphonates, was incorporated into adenine nucleotides, which could potentially explain why this bisphosphonate sometimes seems to act differently than the other bisphosphonates. Clodronate, like all biphosphonates, also binds protein-tyrosine-phosphatase.
Structure
Data?1582753229
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0014858 (Clodronate)

720
  Mrv0541 02231214572D          

 11 10  0  0  0  0            999 V2000
    2.8760    0.5977    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    3.7010   -0.8312    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    4.0031    0.2958    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.5741   -0.5292    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    4.7175    0.7083    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5906    1.0102    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8596   -0.9418    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1615    0.1852    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4156   -0.4187    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9866   -1.2437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2885   -0.1167    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 11  1  0  0  0  0
  2 11  1  0  0  0  0
  3  5  1  0  0  0  0
  3  6  1  0  0  0  0
  3  9  2  0  0  0  0
  3 11  1  0  0  0  0
  4  7  1  0  0  0  0
  4  8  1  0  0  0  0
  4 10  2  0  0  0  0
  4 11  1  0  0  0  0
M  END
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3D MOL for HMDB0014858 (Clodronate)

HMDB0014858
     RDKit          3D
Clodronate
 15 14  0  0  0  0  0  0  0  0999 V2000
    1.8378   -2.0458   -0.2130 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4232   -0.5903   -0.0021 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.7346    0.3507   -0.5736 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2598   -0.2500    1.6336 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0100   -0.1686   -0.9738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2513   -1.4568   -2.1981 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.2221    1.3681   -1.8705 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -1.5273   -0.0313   -0.0402 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.6765   -0.0902   -1.0535 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6763    1.4697    0.7381 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7242   -1.2556    1.0998 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4618    1.2997   -0.4761 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0829    0.1721    2.0175 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8095    2.2024    0.0988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3471   -0.9739    1.8130 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  2  5  1  0
  5  6  1  0
  5  7  1  0
  5  8  1  0
  8  9  2  0
  8 10  1  0
  8 11  1  0
  3 12  1  0
  4 13  1  0
 10 14  1  0
 11 15  1  0
M  END
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3D SDF for HMDB0014858 (Clodronate)

720
  Mrv0541 02231214572D          

 11 10  0  0  0  0            999 V2000
    2.8760    0.5977    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    3.7010   -0.8312    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    4.0031    0.2958    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.5741   -0.5292    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    4.7175    0.7083    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5906    1.0102    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8596   -0.9418    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1615    0.1852    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4156   -0.4187    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9866   -1.2437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2885   -0.1167    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 11  1  0  0  0  0
  2 11  1  0  0  0  0
  3  5  1  0  0  0  0
  3  6  1  0  0  0  0
  3  9  2  0  0  0  0
  3 11  1  0  0  0  0
  4  7  1  0  0  0  0
  4  8  1  0  0  0  0
  4 10  2  0  0  0  0
  4 11  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0014858

> <DATABASE_NAME>
hmdb

> <SMILES>
OP(O)(=O)C(Cl)(Cl)P(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/CH4Cl2O6P2/c2-1(3,10(4,5)6)11(7,8)9/h(H2,4,5,6)(H2,7,8,9)

> <INCHI_KEY>
ACSIXWWBWUQEHA-UHFFFAOYSA-N

> <FORMULA>
CH4Cl2O6P2

> <MOLECULAR_WEIGHT>
244.892

> <EXACT_MASS>
243.886016298

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
15.295152638978966

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[dichloro(phosphono)methyl]phosphonic acid

> <ALOGPS_LOGP>
0.16

> <JCHEM_LOGP>
-0.06669455533333335

> <ALOGPS_LOGS>
-1.52

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
1.3807016226800877

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.6193091569714033

> <JCHEM_POLAR_SURFACE_AREA>
115.06

> <JCHEM_REFRACTIVITY>
38.2136

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.47e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
clodronate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0014858 (Clodronate)

HMDB0014858
     RDKit          3D
Clodronate
 15 14  0  0  0  0  0  0  0  0999 V2000
    1.8378   -2.0458   -0.2130 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4232   -0.5903   -0.0021 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.7346    0.3507   -0.5736 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2598   -0.2500    1.6336 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0100   -0.1686   -0.9738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2513   -1.4568   -2.1981 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.2221    1.3681   -1.8705 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -1.5273   -0.0313   -0.0402 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.6765   -0.0902   -1.0535 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6763    1.4697    0.7381 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7242   -1.2556    1.0998 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4618    1.2997   -0.4761 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0829    0.1721    2.0175 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8095    2.2024    0.0988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3471   -0.9739    1.8130 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  2  5  1  0
  5  6  1  0
  5  7  1  0
  5  8  1  0
  8  9  2  0
  8 10  1  0
  8 11  1  0
  3 12  1  0
  4 13  1  0
 10 14  1  0
 11 15  1  0
M  END
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PDB for HMDB0014858 (Clodronate)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 720                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1 Cl   UNK     0       5.369   1.116   0.000  0.00  0.00          Cl+0
HETATM    2 Cl   UNK     0       6.909  -1.552   0.000  0.00  0.00          Cl+0
HETATM    3  P   UNK     0       7.472   0.552   0.000  0.00  0.00           P+0
HETATM    4  P   UNK     0       4.805  -0.988   0.000  0.00  0.00           P+0
HETATM    5  O   UNK     0       8.806   1.322   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       6.702   1.886   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       3.471  -1.758   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       4.035   0.346   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       8.242  -0.782   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       5.575  -2.322   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       6.139  -0.218   0.000  0.00  0.00           C+0
CONECT    1   11                                                            
CONECT    2   11                                                            
CONECT    3    5    6    9   11                                             
CONECT    4    7    8   10   11                                             
CONECT    5    3                                                            
CONECT    6    3                                                            
CONECT    7    4                                                            
CONECT    8    4                                                            
CONECT    9    3                                                            
CONECT   10    4                                                            
CONECT   11    1    2    3    4                                             
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for HMDB0014858 (Clodronate)

COMPND    HMDB0014858
HETATM    1  O1  UNL     1       1.838  -2.046  -0.213  1.00  0.00           O  
HETATM    2  P1  UNL     1       1.423  -0.590  -0.002  1.00  0.00           P  
HETATM    3  O2  UNL     1       2.735   0.351  -0.574  1.00  0.00           O  
HETATM    4  O3  UNL     1       1.260  -0.250   1.634  1.00  0.00           O  
HETATM    5  C1  UNL     1      -0.010  -0.169  -0.974  1.00  0.00           C  
HETATM    6 CL1  UNL     1      -0.251  -1.457  -2.198  1.00  0.00          CL  
HETATM    7 CL2  UNL     1       0.222   1.368  -1.870  1.00  0.00          CL  
HETATM    8  P2  UNL     1      -1.527  -0.031  -0.040  1.00  0.00           P  
HETATM    9  O4  UNL     1      -2.677  -0.090  -1.053  1.00  0.00           O  
HETATM   10  O5  UNL     1      -1.676   1.470   0.738  1.00  0.00           O  
HETATM   11  O6  UNL     1      -1.724  -1.256   1.100  1.00  0.00           O  
HETATM   12  H1  UNL     1       2.462   1.300  -0.476  1.00  0.00           H  
HETATM   13  H2  UNL     1       2.083   0.172   2.018  1.00  0.00           H  
HETATM   14  H3  UNL     1      -1.809   2.202   0.099  1.00  0.00           H  
HETATM   15  H4  UNL     1      -2.347  -0.974   1.813  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4    5
CONECT    3   12
CONECT    4   13
CONECT    5    6    7    8
CONECT    8    9    9   10   11
CONECT   10   14
CONECT   11   15
END
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SMILES for HMDB0014858 (Clodronate)

OP(O)(=O)C(Cl)(Cl)P(O)(O)=O
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INCHI for HMDB0014858 (Clodronate)

InChI=1S/CH4Cl2O6P2/c2-1(3,10(4,5)6)11(7,8)9/h(H2,4,5,6)(H2,7,8,9)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
(Dichloro-phosphono-methyl)-phosphonic acidChEBI
(Dichloromethylene)bisphosphonic acidChEBI
(Dichloromethylene)diphosphonic acidChEBI
Acide clodroniqueChEBI
Acido clodronicoChEBI
Acidum clodronicumChEBI
ClodronsaeureChEBI
Dichloromethylene-1,1-bisphosphonic acidChEBI
Dichloromethylene-1,1-diphosphonic acidChEBI
Dichloromethylidene diphosphonateChEBI
(Dichloro-phosphono-methyl)-phosphonateGenerator
(Dichloromethylene)bisphosphonateGenerator
(Dichloromethylene)diphosphonateGenerator
Dichloromethylene-1,1-bisphosphonateGenerator
Dichloromethylene-1,1-diphosphonateGenerator
Dichloromethylidene diphosphonic acidGenerator
Clodronic acidGenerator
Acid, dichloromethanediphosphonicHMDB
BonefosHMDB
Clodronate disodiumHMDB
DichloromethanediphosphonateHMDB
Dichloromethylene diphosphonateHMDB
Acid, clodronicHMDB
Dichloromethane diphosphonateHMDB
Dichloromethylene biphosphonateHMDB
Diphosphonate, dichloromethaneHMDB
Biphosphonate, dichloromethyleneHMDB
Diphosphonate, dichloromethyleneHMDB
Disodium, clodronateHMDB
Sodium, clodronateHMDB
CL2MDPHMDB
Clodronate sodiumHMDB
Dichloromethanediphosphonic acidHMDB
DichloromethylenebisphosphonateHMDB
ClodronateChEBI
Chemical FormulaCH4Cl2O6P2
Average Molecular Weight244.892
Monoisotopic Molecular Weight243.886016298
IUPAC Name[dichloro(phosphono)methyl]phosphonic acid
Traditional Nameclodronate
CAS Registry Number10596-23-3
SMILES
OP(O)(=O)C(Cl)(Cl)P(O)(O)=O
InChI Identifier
InChI=1S/CH4Cl2O6P2/c2-1(3,10(4,5)6)11(7,8)9/h(H2,4,5,6)(H2,7,8,9)
InChI KeyACSIXWWBWUQEHA-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
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organophosphorus compound
  • Organochloride
  • Organohalogen compound
  • Alkyl halide
  • Alkyl chloride
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
Role
Industrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point250 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility7.47 g/LNot Available
LogP-2.4Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility7.47 g/LALOGPS
logP0.16ALOGPS
logP-0.067ChemAxon
logS-1.5ALOGPS
pKa (Strongest Acidic)0.62ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area115.06 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity38.21 m³·mol⁻¹ChemAxon
Polarizability15.3 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+119.40230932474
DeepCCS[M-H]-115.81930932474
DeepCCS[M-2H]-153.59730932474
DeepCCS[M+Na]+129.10930932474
AllCCS[M+H]+145.332859911
AllCCS[M+H-H2O]+142.032859911
AllCCS[M+NH4]+148.332859911
AllCCS[M+Na]+149.132859911
AllCCS[M-H]-134.632859911
AllCCS[M+Na-2H]-136.732859911
AllCCS[M+HCOO]-139.032859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.1.72 minutes32390414
Predicted by Siyang on May 30, 20228.849 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20226.27 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid491.7 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid471.1 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid360.6 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid48.2 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid252.1 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid137.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid279.0 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid233.1 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)900.6 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid590.5 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid38.7 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid626.9 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid227.0 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid372.0 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate885.2 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA629.1 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water504.7 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
ClodronateOP(O)(=O)C(Cl)(Cl)P(O)(O)=O3121.5Standard polar33892256
ClodronateOP(O)(=O)C(Cl)(Cl)P(O)(O)=O1668.9Standard non polar33892256
ClodronateOP(O)(=O)C(Cl)(Cl)P(O)(O)=O1848.7Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Clodronate,1TMS,isomer #1C[Si](C)(C)OP(=O)(O)C(Cl)(Cl)P(=O)(O)O1918.3Semi standard non polar33892256
Clodronate,1TMS,isomer #1C[Si](C)(C)OP(=O)(O)C(Cl)(Cl)P(=O)(O)O1647.9Standard non polar33892256
Clodronate,1TMS,isomer #1C[Si](C)(C)OP(=O)(O)C(Cl)(Cl)P(=O)(O)O2402.0Standard polar33892256
Clodronate,2TMS,isomer #1C[Si](C)(C)OP(=O)(O[Si](C)(C)C)C(Cl)(Cl)P(=O)(O)O1937.6Semi standard non polar33892256
Clodronate,2TMS,isomer #1C[Si](C)(C)OP(=O)(O[Si](C)(C)C)C(Cl)(Cl)P(=O)(O)O1790.2Standard non polar33892256
Clodronate,2TMS,isomer #1C[Si](C)(C)OP(=O)(O[Si](C)(C)C)C(Cl)(Cl)P(=O)(O)O2066.7Standard polar33892256
Clodronate,2TMS,isomer #2C[Si](C)(C)OP(=O)(O)C(Cl)(Cl)P(=O)(O)O[Si](C)(C)C1945.5Semi standard non polar33892256
Clodronate,2TMS,isomer #2C[Si](C)(C)OP(=O)(O)C(Cl)(Cl)P(=O)(O)O[Si](C)(C)C1768.9Standard non polar33892256
Clodronate,2TMS,isomer #2C[Si](C)(C)OP(=O)(O)C(Cl)(Cl)P(=O)(O)O[Si](C)(C)C2090.1Standard polar33892256
Clodronate,3TMS,isomer #1C[Si](C)(C)OP(=O)(O)C(Cl)(Cl)P(=O)(O[Si](C)(C)C)O[Si](C)(C)C1943.2Semi standard non polar33892256
Clodronate,3TMS,isomer #1C[Si](C)(C)OP(=O)(O)C(Cl)(Cl)P(=O)(O[Si](C)(C)C)O[Si](C)(C)C1850.1Standard non polar33892256
Clodronate,3TMS,isomer #1C[Si](C)(C)OP(=O)(O)C(Cl)(Cl)P(=O)(O[Si](C)(C)C)O[Si](C)(C)C1961.0Standard polar33892256
Clodronate,4TMS,isomer #1C[Si](C)(C)OP(=O)(O[Si](C)(C)C)C(Cl)(Cl)P(=O)(O[Si](C)(C)C)O[Si](C)(C)C1943.9Semi standard non polar33892256
Clodronate,4TMS,isomer #1C[Si](C)(C)OP(=O)(O[Si](C)(C)C)C(Cl)(Cl)P(=O)(O[Si](C)(C)C)O[Si](C)(C)C1939.7Standard non polar33892256
Clodronate,4TMS,isomer #1C[Si](C)(C)OP(=O)(O[Si](C)(C)C)C(Cl)(Cl)P(=O)(O[Si](C)(C)C)O[Si](C)(C)C1871.2Standard polar33892256
Clodronate,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OP(=O)(O)C(Cl)(Cl)P(=O)(O)O2193.2Semi standard non polar33892256
Clodronate,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OP(=O)(O)C(Cl)(Cl)P(=O)(O)O1872.6Standard non polar33892256
Clodronate,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OP(=O)(O)C(Cl)(Cl)P(=O)(O)O2539.1Standard polar33892256
Clodronate,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OP(=O)(O[Si](C)(C)C(C)(C)C)C(Cl)(Cl)P(=O)(O)O2412.3Semi standard non polar33892256
Clodronate,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OP(=O)(O[Si](C)(C)C(C)(C)C)C(Cl)(Cl)P(=O)(O)O2174.6Standard non polar33892256
Clodronate,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OP(=O)(O[Si](C)(C)C(C)(C)C)C(Cl)(Cl)P(=O)(O)O2344.6Standard polar33892256
Clodronate,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OP(=O)(O)C(Cl)(Cl)P(=O)(O)O[Si](C)(C)C(C)(C)C2418.6Semi standard non polar33892256
Clodronate,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OP(=O)(O)C(Cl)(Cl)P(=O)(O)O[Si](C)(C)C(C)(C)C2160.2Standard non polar33892256
Clodronate,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OP(=O)(O)C(Cl)(Cl)P(=O)(O)O[Si](C)(C)C(C)(C)C2380.8Standard polar33892256
Clodronate,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OP(=O)(O)C(Cl)(Cl)P(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2576.3Semi standard non polar33892256
Clodronate,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OP(=O)(O)C(Cl)(Cl)P(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2368.8Standard non polar33892256
Clodronate,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OP(=O)(O)C(Cl)(Cl)P(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2337.3Standard polar33892256
Clodronate,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OP(=O)(O[Si](C)(C)C(C)(C)C)C(Cl)(Cl)P(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2726.4Semi standard non polar33892256
Clodronate,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OP(=O)(O[Si](C)(C)C(C)(C)C)C(Cl)(Cl)P(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2562.9Standard non polar33892256
Clodronate,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OP(=O)(O[Si](C)(C)C(C)(C)C)C(Cl)(Cl)P(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2326.1Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Clodronate GC-MS (Non-derivatized) - 70eV, Positivesplash10-001i-9040000000-af3c2e18902e147f8d422017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Clodronate 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 - Clodronate 10V, Positive-QTOFsplash10-0006-1190000000-c4ab9891e7e58566d92f2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Clodronate 20V, Positive-QTOFsplash10-03ed-3940000000-c29d8ff76855c0aaef6c2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Clodronate 40V, Positive-QTOFsplash10-001i-9000000000-01a0eea1cf84ed37407a2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Clodronate 10V, Negative-QTOFsplash10-03dl-0950000000-1845236a124e15b5c59b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Clodronate 20V, Negative-QTOFsplash10-006x-1390000000-3ae475737e6b4b8c76642016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Clodronate 40V, Negative-QTOFsplash10-004i-9000000000-974168c5223d898e9a792016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Clodronate 10V, Positive-QTOFsplash10-000x-6090000000-8989f8d7643382de70bc2021-10-11Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Clodronate 20V, Positive-QTOFsplash10-03di-2900000000-95542c15d3d7df8beff22021-10-11Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Clodronate 40V, Positive-QTOFsplash10-03ea-4900000000-e088c1d2fe760f01f20d2021-10-11Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Clodronate 10V, Negative-QTOFsplash10-00dl-0090000000-125baa903034088b47b62021-10-11Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Clodronate 20V, Negative-QTOFsplash10-00fr-6590000000-8d753c1dbb524b991ddf2021-10-11Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Clodronate 40V, Negative-QTOFsplash10-00di-1090000000-29462d306ece6e9df24d2021-10-11Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Membrane
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00720 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00720 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 IDDB00720
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID23731
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkClodronic acid
METLIN IDNot Available
PubChem Compound25419
PDB IDNot Available
ChEBI ID110423
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 ReferencesNot Available

Enzymes

Enzyme Details
1. Prostaglandin G/H synthase 2
General function:
Involved in peroxidase activity
Specific function:
Mediates the formation of prostaglandins from arachidonate. May have a role as a major mediator of inflammation and/or a role for prostanoid signaling in activity-dependent plasticity.
Gene Name:
PTGS2
Uniprot ID:
P35354
Molecular weight:
68995.625
References
  1. Liu L, Igarashi K, Kanzaki H, Chiba M, Shinoda H, Mitani H: Clodronate inhibits PGE(2) production in compressed periodontal ligament cells. J Dent Res. 2006 Aug;85(8):757-60. [PubMed:16861295 ]
Enzyme Details
2. ADP/ATP translocase 1
General function:
Involved in transporter activity
Specific function:
Catalyzes the exchange of ADP and ATP across the mitochondrial inner membrane
Gene Name:
SLC25A4
Uniprot ID:
P12235
Molecular weight:
33064.3
References
  1. Lehenkari PP, Kellinsalmi M, Napankangas JP, Ylitalo KV, Monkkonen J, Rogers MJ, Azhayev A, Vaananen HK, Hassinen IE: Further insight into mechanism of action of clodronate: inhibition of mitochondrial ADP/ATP translocase by a nonhydrolyzable, adenine-containing metabolite. Mol Pharmacol. 2002 May;61(5):1255-62. [PubMed:11961144 ]
  2. Chen X, Ji ZL, Chen YZ: TTD: Therapeutic Target Database. Nucleic Acids Res. 2002 Jan 1;30(1):412-5. [PubMed:11752352 ]
Enzyme Details
3. ADP/ATP translocase 2
General function:
Involved in transporter activity
Specific function:
Catalyzes the exchange of ADP and ATP across the mitochondrial inner membrane
Gene Name:
SLC25A5
Uniprot ID:
P05141
Molecular weight:
32895.0
References
  1. Lehenkari PP, Kellinsalmi M, Napankangas JP, Ylitalo KV, Monkkonen J, Rogers MJ, Azhayev A, Vaananen HK, Hassinen IE: Further insight into mechanism of action of clodronate: inhibition of mitochondrial ADP/ATP translocase by a nonhydrolyzable, adenine-containing metabolite. Mol Pharmacol. 2002 May;61(5):1255-62. [PubMed:11961144 ]
Enzyme Details
4. ADP/ATP translocase 3
General function:
Involved in transporter activity
Specific function:
Catalyzes the exchange of ADP and ATP across the mitochondrial inner membrane. May participate in the formation of the permeability transition pore complex (PTPC) responsible for the release of mitochondrial products that triggers apoptosis
Gene Name:
SLC25A6
Uniprot ID:
P12236
Molecular weight:
32866.0
References
  1. Lehenkari PP, Kellinsalmi M, Napankangas JP, Ylitalo KV, Monkkonen J, Rogers MJ, Azhayev A, Vaananen HK, Hassinen IE: Further insight into mechanism of action of clodronate: inhibition of mitochondrial ADP/ATP translocase by a nonhydrolyzable, adenine-containing metabolite. Mol Pharmacol. 2002 May;61(5):1255-62. [PubMed:11961144 ]