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Showing metabocard for diphosphate (HMDB0304340)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 09:02:24 UTC
Update Date2021-09-24 09:02:24 UTC
HMDB IDHMDB0304340
Secondary Accession NumbersNone
Metabolite Identification
Common Namediphosphate
DescriptionPyrophosphate, also known as diphosphoric acid or ppi, is a member of the class of compounds known as non-metal pyrophosphates. Non-metal pyrophosphates are inorganic non-metallic compoundscontaining a pyrophosphate as its largest oxoanion. Pyrophosphate can be found in a number of food items such as bitter gourd, babassu palm, groundcherry, and black crowberry, which makes pyrophosphate a potential biomarker for the consumption of these food products. Pyrophosphate can be found primarily in blood, saliva, and urine, as well as throughout most human tissues. Pyrophosphate exists in all living organisms, ranging from bacteria to humans. In humans, pyrophosphate is involved in several metabolic pathways, some of which include cardiolipin biosynthesis CL(18:0/16:1(9Z)/16:1(9Z)/16:0), cardiolipin biosynthesis cl(i-13:0/a-17:0/i-18:0/a-17:0), cardiolipin biosynthesis cl(i-12:0/i-16:0/a-15:0/a-25:0), and cardiolipin biosynthesis cl(a-13:0/i-24:0/i-22:0/i-14:0). Pyrophosphate is also involved in several metabolic disorders, some of which include hyperinsulinism-hyperammonemia syndrome, methionine adenosyltransferase deficiency, mevalonic aciduria, and g(m2)-gangliosidosis: variant B, tay-sachs disease. Pyrophosphate is a non-carcinogenic (not listed by IARC) potentially toxic compound. In chemistry, a pyrophosphate is a phosphorus oxyanion. Compounds such as salts and esters are also called pyrophosphates. The group is also called diphosphate or dipolyphosphate, although this should not be confused with phosphates. As a food additive, diphosphates are known as E450. A number of hydrogen pyrophosphates also exist, such as Na2H2P2O7, as well as the normal pyrophosphates .
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304340 (diphosphate)


  Mrv1652305221920492D          

  9  8  0  0  0  0            999 V2000
    1.6500   -1.4289    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.9520   -0.3020    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.5230   -1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  8  1  1  0  0  0  0
  8  2  1  0  0  0  0
  8  3  2  0  0  0  0
  8  7  1  0  0  0  0
  9  4  1  0  0  0  0
  9  5  1  0  0  0  0
  9  6  2  0  0  0  0
  9  7  1  0  0  0  0
M  CHG  4   1  -1   2  -1   4  -1   5  -1
M  END
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3D MOL for HMDB0304340 (diphosphate)

HMDB0304340
     RDKit          3D
diphosphate
  9  8  0  0  0  0  0  0  0  0999 V2000
   -2.2340    1.4753    0.0688 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4100    0.1989    0.0860 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.2907   -0.9009    1.0526 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.1845   -0.4152   -1.4751 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.0565    0.5688    0.8258 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3756   -0.0992    0.0603 P   0  0  0  0  0  5  0  0  0  0  0  0
    1.0277   -1.3607   -0.7072 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0246    1.0139   -1.0512 O   0  0  0  0  0  1  0  0  0  0  0  0
    2.6349   -0.4810    1.1400 O   0  0  0  0  0  1  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
  6  7  2  0
  6  8  1  0
  6  9  1  0
M  CHG  4   3  -1   4  -1   8  -1   9  -1
M  END
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3D SDF for HMDB0304340 (diphosphate)


  Mrv1652305221920492D          

  9  8  0  0  0  0            999 V2000
    1.6500   -1.4289    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.9520   -0.3020    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.5230   -1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  8  1  1  0  0  0  0
  8  2  1  0  0  0  0
  8  3  2  0  0  0  0
  8  7  1  0  0  0  0
  9  4  1  0  0  0  0
  9  5  1  0  0  0  0
  9  6  2  0  0  0  0
  9  7  1  0  0  0  0
M  CHG  4   1  -1   2  -1   4  -1   5  -1
M  END
> <DATABASE_ID>
HMDB0304340

> <DATABASE_NAME>
hmdb

> <SMILES>
[O-]P([O-])(=O)OP([O-])([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)/p-4

> <INCHI_KEY>
XPPKVPWEQAFLFU-UHFFFAOYSA-J

> <FORMULA>
O7P2

> <MOLECULAR_WEIGHT>
173.9433

> <EXACT_MASS>
173.911925378

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
9.06291107638218

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-4

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(phosphonooxy)phosphonate

> <JCHEM_LOGP>
-1.4419023016666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.060391741362254

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7026764435673858

> <JCHEM_POLAR_SURFACE_AREA>
135.61

> <JCHEM_REFRACTIVITY>
21.038000000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
phosphonooxyphosphonate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0304340 (diphosphate)

HMDB0304340
     RDKit          3D
diphosphate
  9  8  0  0  0  0  0  0  0  0999 V2000
   -2.2340    1.4753    0.0688 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4100    0.1989    0.0860 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.2907   -0.9009    1.0526 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.1845   -0.4152   -1.4751 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.0565    0.5688    0.8258 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3756   -0.0992    0.0603 P   0  0  0  0  0  5  0  0  0  0  0  0
    1.0277   -1.3607   -0.7072 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0246    1.0139   -1.0512 O   0  0  0  0  0  1  0  0  0  0  0  0
    2.6349   -0.4810    1.1400 O   0  0  0  0  0  1  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
  6  7  2  0
  6  8  1  0
  6  9  1  0
M  CHG  4   3  -1   4  -1   8  -1   9  -1
M  END
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PDB for HMDB0304340 (diphosphate)

HEADER    PROTEIN                                 22-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-MAY-19         0                                  
HETATM    1  O   UNK     0       3.080  -2.667   0.000  0.00  0.00           O-1
HETATM    2  O   UNK     0       3.644  -0.564   0.000  0.00  0.00           O-1
HETATM    3  O   UNK     0       0.976  -2.104   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      -1.540   0.000   0.000  0.00  0.00           O-1
HETATM    5  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O-1
HETATM    6  O   UNK     0       0.000  -1.540   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       1.540   0.000   0.000  0.00  0.00           O+0
HETATM    8  P   UNK     0       2.310  -1.334   0.000  0.00  0.00           P+0
HETATM    9  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
CONECT    1    8                                                            
CONECT    2    8                                                            
CONECT    3    8                                                            
CONECT    4    9                                                            
CONECT    5    9                                                            
CONECT    6    9                                                            
CONECT    7    8    9                                                       
CONECT    8    1    2    3    7                                             
CONECT    9    4    5    6    7                                             
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for HMDB0304340 (diphosphate)

COMPND    HMDB0304340
HETATM    1  O1  UNL     1      -2.234   1.475   0.069  1.00  0.00           O  
HETATM    2  P1  UNL     1      -1.410   0.199   0.086  1.00  0.00           P  
HETATM    3  O2  UNL     1      -2.291  -0.901   1.053  1.00  0.00           O1-
HETATM    4  O3  UNL     1      -1.185  -0.415  -1.475  1.00  0.00           O1-
HETATM    5  O4  UNL     1       0.056   0.569   0.826  1.00  0.00           O  
HETATM    6  P2  UNL     1       1.376  -0.099   0.060  1.00  0.00           P  
HETATM    7  O5  UNL     1       1.028  -1.361  -0.707  1.00  0.00           O  
HETATM    8  O6  UNL     1       2.025   1.014  -1.051  1.00  0.00           O1-
HETATM    9  O7  UNL     1       2.635  -0.481   1.140  1.00  0.00           O1-
CONECT    1    2    2
CONECT    2    3    4    5
CONECT    5    6
CONECT    6    7    7    8    9
END
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SMILES for HMDB0304340 (diphosphate)

[O-]P([O-])(=O)OP([O-])([O-])=O
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INCHI for HMDB0304340 (diphosphate)

InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)/p-4
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View in JSmolView Stereo Labels
Synonyms
ValueSource
[O3POPO3](4-)ChEBI
DiphosphatChEBI
DIphosphATEChEBI
P2O7(4-)ChEBI
PPiChEBI
PyrophosphatChEBI
PyrophosphateChEBI
Pyrophosphate ionChEBI
DIphosphoric acidGenerator
Pyrophosphoric acidGenerator
Pyrophosphoric acid ionGenerator
Diphosphoric acid(4-)Generator
(4-)Diphosphoric acid ionHMDB
(P2O74-)DiphosphateHMDB
PyrometaphosphateHMDB
Pyrophosphate tetraanionHMDB
Pyrophosphate(4-) ionHMDB
Chemical FormulaO7P2
Average Molecular Weight173.9433
Monoisotopic Molecular Weight173.911925378
IUPAC Name(phosphonooxy)phosphonate
Traditional Namephosphonooxyphosphonate
CAS Registry NumberNot Available
SMILES
[O-]P([O-])(=O)OP([O-])([O-])=O
InChI Identifier
InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)/p-4
InChI KeyXPPKVPWEQAFLFU-UHFFFAOYSA-J
Chemical Taxonomy
Description Belongs to the class of inorganic compounds known as non-metal pyrophosphates. These are inorganic non-metallic compounds containing a pyrophosphate as its largest oxoanion.
KingdomInorganic compounds
Super ClassHomogeneous non-metal compounds
ClassNon-metal oxoanionic compounds
Sub ClassNon-metal pyrophosphates
Direct ParentNon-metal pyrophosphates
Alternative Parents
Substituents
  • Non-metal pyrophosphate
  • Inorganic oxide
Molecular FrameworkNot Available
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-1.4ChemAxon
pKa (Strongest Acidic)1.7ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area135.61 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity21.04 m³·mol⁻¹ChemAxon
Polarizability9.06 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
AllCCS[M+H]+137.23932859911
AllCCS[M+H-H2O]+133.22832859911
AllCCS[M+Na]+142.0532859911
AllCCS[M+NH4]+140.97432859911
AllCCS[M-H]-109.80532859911
AllCCS[M+Na-2H]-112.18332859911
AllCCS[M+HCOO]-114.81432859911
DeepCCS[M+H]+114.65730932474
DeepCCS[M-H]-111.33530932474
DeepCCS[M-2H]-148.39930932474
DeepCCS[M+Na]+123.26630932474

Predicted Kovats Retention Indices

Not Available
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - diphosphate GC-MS (4 TMS)splash10-0udi-0320900000-0abbcb28a43d7e24fe812014-06-16HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - diphosphate GC-MS (Non-derivatized)splash10-0udi-0320900000-0abbcb28a43d7e24fe812017-09-12HMDB team, MONA, MassBankView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - diphosphate Quattro_QQQ 10V, Positive-QTOF (Annotated)splash10-004j-5900000000-6633d5123eb37c2662472012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - diphosphate Quattro_QQQ 25V, Positive-QTOF (Annotated)splash10-0002-9000000000-1274b83242b279e9dac72012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - diphosphate Quattro_QQQ 40V, Positive-QTOF (Annotated)splash10-001i-9000000000-69bc4c795fec87fef4b82012-07-24HMDB team, MONAView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB030832
KNApSAcK IDNot Available
Chemspider ID559142
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID18361
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