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Showing metabocard for Peroxynitrite (HMDB0002179)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-22 14:17:40 UTC
Update Date2023-02-21 17:16:14 UTC
HMDB IDHMDB0002179
Secondary Accession Numbers
  • HMDB02179
Metabolite Identification
Common NamePeroxynitrite
DescriptionPeroxynitrite is a potent oxidant synthesized by the cell during its normal metabolism. The peroxynitrite anion (ONOO-) is a reactive species produced in the reaction between the superoxide anion (O2*-) and nitric oxide (*NO). Peroxynitrite (ONOO-) is a strong oxidation and nitration agent, which damages DNA, proteins and other cellular structures. ONOO- is involved in several pathological conditions such as inflammation, arteriosclerosis, and neurodegenerative and cardiovascular disorders. ONOO- inhibits different steps of blood platelet activation and causes the depletion of platelet thiols. (PMID 15647782 ).
Structure
Data?1676999774
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0002179 (Peroxynitrite)


  Mrv1652305171807312D          

  4  3  0  0  0  0            999 V2000
    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 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  4  1  1  0  0  0  0
M  END
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3D MOL for HMDB0002179 (Peroxynitrite)

HMDB0002179
     RDKit          3D
Peroxynitrite
  5  4  0  0  0  0  0  0  0  0999 V2000
    1.6798    0.6132   -0.1843 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1012   -0.4371    0.2091 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1039   -0.6947   -0.4164 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9549    0.3395   -0.5579 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7222    0.1791    0.0526 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
M  END
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3D SDF for HMDB0002179 (Peroxynitrite)


  Mrv1652305171807312D          

  4  3  0  0  0  0            999 V2000
    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 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  4  1  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0002179

> <DATABASE_NAME>
hmdb

> <SMILES>
OON=O

> <INCHI_IDENTIFIER>
InChI=1S/HNO3/c2-1-4-3/h3H

> <INCHI_KEY>
CMFNMSMUKZHDEY-UHFFFAOYSA-N

> <FORMULA>
HNO3

> <MOLECULAR_WEIGHT>
63.012

> <EXACT_MASS>
62.995642896

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
3.643044709466887

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
hydroxy nitrite

> <JCHEM_LOGP>
0.31724056766666664

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.552998912617396

> <JCHEM_PKA_STRONGEST_BASIC>
-5.5323808596145705

> <JCHEM_POLAR_SURFACE_AREA>
58.89

> <JCHEM_REFRACTIVITY>
10.0719

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
peroxynitrous acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0002179 (Peroxynitrite)

HMDB0002179
     RDKit          3D
Peroxynitrite
  5  4  0  0  0  0  0  0  0  0999 V2000
    1.6798    0.6132   -0.1843 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1012   -0.4371    0.2091 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1039   -0.6947   -0.4164 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9549    0.3395   -0.5579 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7222    0.1791    0.0526 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
M  END
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PDB for HMDB0002179 (Peroxynitrite)

HEADER    PROTEIN                                 17-MAY-18   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-MAY-18         0                                  
HETATM    1  O   UNK     0       1.540   0.000   0.000  0.00  0.00           O+0
HETATM    2  N   UNK     0       2.310  -1.334   0.000  0.00  0.00           N+0
HETATM    3  O   UNK     0       3.850  -1.334   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2    4                                                       
CONECT    2    1    3                                                       
CONECT    3    2                                                            
CONECT    4    1                                                            
MASTER        0    0    0    0    0    0    0    0    4    0    6    0
END
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3D PDB for HMDB0002179 (Peroxynitrite)

COMPND    HMDB0002179
HETATM    1  O1  UNL     1       1.680   0.613  -0.184  1.00  0.00           O  
HETATM    2  N1  UNL     1       1.101  -0.437   0.209  1.00  0.00           N  
HETATM    3  O2  UNL     1      -0.104  -0.695  -0.416  1.00  0.00           O  
HETATM    4  O3  UNL     1      -0.955   0.339  -0.558  1.00  0.00           O  
HETATM    5  H1  UNL     1      -1.722   0.179   0.053  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3
CONECT    3    4
CONECT    4    5
END
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SMILES for HMDB0002179 (Peroxynitrite)

OON=O
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INCHI for HMDB0002179 (Peroxynitrite)

InChI=1S/HNO3/c2-1-4-3/h3H
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View in JSmolView Stereo Labels
Synonyms
ValueSource
[NO(OOH)]ChEBI
HNO(O2)ChEBI
[No(oo)](-)HMDB
PeroxonitriteHMDB
(-)OxoperoxonitrateHMDB
(1-)OxidoperoxidonitrateHMDB
AzoperoxoiteHMDB
PernitriteHMDB
PeroxynitrateHMDB
Peroxynitrosyl (NO3)HMDB
Acid, peroxynitrousHMDB
PeroxynitritesHMDB
PeroxonitritesHMDB
Peroxynitrous acidsHMDB
Peroxynitrous acidHMDB
Peroxynitrous acid, potassium saltHMDB
Acids, peroxynitrousHMDB
PeroxynitriteMeSH
Chemical FormulaHNO3
Average Molecular Weight63.012
Monoisotopic Molecular Weight62.995642896
IUPAC Namehydroxy nitrite
Traditional Nameperoxynitrous acid
CAS Registry Number19059-14-4
SMILES
OON=O
InChI Identifier
InChI=1S/HNO3/c2-1-4-3/h3H
InChI KeyCMFNMSMUKZHDEY-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of inorganic compounds known as non-metal peroxynitrites. These are inorganic non-metallic compounds containing a peroxynitrite as its largest oxoanion.
KingdomInorganic compounds
Super ClassHomogeneous non-metal compounds
ClassNon-metal oxoanionic compounds
Sub ClassNon-metal peroxynitrites
Direct ParentNon-metal peroxynitrites
Alternative Parents
Substituents
  • Non-metal peroxynitrite
  • Inorganic nitrite
  • Inorganic oxide
Molecular FrameworkNot Available
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
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
logP0.32ChemAxon
pKa (Strongest Acidic)6.55ChemAxon
pKa (Strongest Basic)-5.5ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area58.89 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity10.07 m³·mol⁻¹ChemAxon
Polarizability3.64 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
DarkChem[M+H]+108.81831661259
DarkChem[M-H]-100.70431661259
DeepCCS[M+H]+115.07230932474
DeepCCS[M-H]-113.2630932474
DeepCCS[M-2H]-148.64830932474
DeepCCS[M+Na]+122.57330932474
AllCCS[M+H]+121.132859911
AllCCS[M+H-H2O]+116.632859911
AllCCS[M+NH4]+125.332859911
AllCCS[M+Na]+126.532859911
AllCCS[M-H]-125.732859911
AllCCS[M+Na-2H]-132.532859911
AllCCS[M+HCOO]-139.932859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 20228.5164 minutes33406817
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid242.7 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid960.8 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid416.2 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid162.4 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid329.4 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid154.3 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid321.7 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 Acid424.3 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)582.7 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid666.0 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid160.3 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid848.7 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid279.9 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid381.3 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate749.4 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA351.9 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water327.9 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
PeroxynitriteOON=O1191.4Standard polar33892256
PeroxynitriteOON=O734.9Standard non polar33892256
PeroxynitriteOON=O667.8Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Peroxynitrite 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 - Peroxynitrite 10V, Positive-QTOFsplash10-03di-9000000000-443746556ab5ddacacad2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Peroxynitrite 20V, Positive-QTOFsplash10-03di-9000000000-9a031d53f6433a211bcb2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Peroxynitrite 40V, Positive-QTOFsplash10-002b-9000000000-be87841dd4947fc1cd642019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Peroxynitrite 10V, Negative-QTOFsplash10-03di-9000000000-9914f528ef3fe70f2c162019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Peroxynitrite 20V, Negative-QTOFsplash10-03di-9000000000-3d79816b8d0b30ca57102019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Peroxynitrite 40V, Negative-QTOFsplash10-03di-9000000000-587cdf7700b936c20a052019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Peroxynitrite 10V, Positive-QTOFsplash10-03di-9000000000-253295f4073d2376f7cd2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Peroxynitrite 20V, Positive-QTOFsplash10-03di-9000000000-db88b76918368d52a7972021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Peroxynitrite 40V, Positive-QTOFsplash10-03dj-9000000000-3d568fcf3dff4beeabf02021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Peroxynitrite 10V, Negative-QTOFsplash10-03di-9000000000-8c9248f9c4b7a86e34592021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Peroxynitrite 20V, Negative-QTOFsplash10-03di-9000000000-8c9248f9c4b7a86e34592021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Peroxynitrite 40V, Negative-QTOFsplash10-03di-9000000000-8c9248f9c4b7a86e34592021-09-22Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-03FELIX labView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Cerebrospinal Fluid (CSF)
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
Cerebrospinal Fluid (CSF)Detected and Quantified0.17 +/- 0.01 uMAdult (>18 years old)Not SpecifiedNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
Cerebrospinal Fluid (CSF)Detected and Quantified0.28 +/- 0.02 uMAdult (>18 years old)Not SpecifiedMultiple sclerosis details
Cerebrospinal Fluid (CSF)Detected and Quantified0.20 +/- 0.03 uMAdult (>18 years old)Not Specified
Multiple sclerosis		 details
Associated Disorders and Diseases
Disease References
Multiple sclerosis
  1. Calabrese V, Scapagnini G, Ravagna A, Bella R, Butterfield DA, Calvani M, Pennisi G, Giuffrida Stella AM: Disruption of thiol homeostasis and nitrosative stress in the cerebrospinal fluid of patients with active multiple sclerosis: evidence for a protective role of acetylcarnitine. Neurochem Res. 2003 Sep;28(9):1321-8. [PubMed:12938853 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022889
KNApSAcK IDNot Available
Chemspider ID109951
KEGG Compound IDC16845
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPeroxynitrite
METLIN IDNot Available
PubChem Compound123349
PDB IDNot Available
ChEBI ID25942
Food Biomarker OntologyNot Available
VMH IDCE5643
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNiles, Jacquin C.; Wishnok, John S.; Tannenbaum, Steven R. A novel nitration product formed during the reaction of peroxynitrite with 2',3',5'-tri-O-acetyl-7,8-dihydro-8-oxoguanosine: N-nitro-N'-[1-(2,3,5-tri-O-acetyl-beta-D-erythro-pentofuranosyl)- 2, 4-dioxoimidazolidin-5-ylidene]guanidine. Chem Res Toxicol. 2000 May;13(5):390-6.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Calabrese V, Scapagnini G, Ravagna A, Bella R, Butterfield DA, Calvani M, Pennisi G, Giuffrida Stella AM: Disruption of thiol homeostasis and nitrosative stress in the cerebrospinal fluid of patients with active multiple sclerosis: evidence for a protective role of acetylcarnitine. Neurochem Res. 2003 Sep;28(9):1321-8. [PubMed:12938853 ]
  2. Calabrese V, Scapagnini G, Ravagna A, Bella R, Foresti R, Bates TE, Giuffrida Stella AM, Pennisi G: Nitric oxide synthase is present in the cerebrospinal fluid of patients with active multiple sclerosis and is associated with increases in cerebrospinal fluid protein nitrotyrosine and S-nitrosothiols and with changes in glutathione levels. J Neurosci Res. 2002 Nov 15;70(4):580-7. [PubMed:12404512 ]
  3. Olas B, Nowak P, Wachowicz B: Resveratrol protects against peroxynitrite-induced thiol oxidation in blood platelets. Cell Mol Biol Lett. 2004;9(4A):577-87. [PubMed:15647782 ]