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Showing metabocard for Nitrate (HMDB0002878)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-22 15:12:16 UTC
Update Date2020-10-09 21:10:40 UTC
HMDB IDHMDB0002878
Secondary Accession Numbers
  • HMDB0001853
  • HMDB01853
  • HMDB02878
Metabolite Identification
Common NameNitrate
DescriptionIn inorganic chemistry, a nitrate is a salt of nitric acid. In organic chemistry the esters of nitric acid and various alcohols are called nitrates. The nitrate ion is a polyatomic anion with the empirical formula NO3- and a molecular mass of 62.01 daltons; it consists of one central nitrogen atom surrounded by three identical oxygen atoms in a trigonal planar arrangement. The nitrate ion carries a negative one formal charge. Nitrates should not be confused with nitrites, the salts of nitrous acid. Organic compounds containing the nitro functional group (which has the same formula and structure as the nitrate ion save that one of the O2 atoms is replaced by the R group) are known as nitro compounds. Nitrate ions can be toxic. In particular, nitrate toxicosis in humans occurs through enterohepatic metabolism of nitrates to ammonia, with nitrite being an intermediate. Nitrites oxidize the iron atoms in hemoglobin from Ferrous Iron (2+) to Ferric Iron (3+), rendering it unable to carry oxygen. This condition is called methemoglobinemia and can lead to a lack of oxygen in tissues. Methemoglobinemia can be treated with methylene blue. -- Wikipedia .
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0002878 (Nitrate)

  Mrv1652306222023342D          

  4  3  0  0  0  0            999 V2000
    0.8250    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.2375   -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
  2  1  1  0  0  0  0
  3  1  2  0  0  0  0
  4  1  2  0  0  0  0
M  CHG  1   2  -1
M  END
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3D MOL for HMDB0002878 (Nitrate)

HMDB0002878
     RDKit          3D
Nitrate
  4  3  0  0  0  0  0  0  0  0999 V2000
   -0.5467    1.1635    0.0060 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0091    0.0296    0.0001 N   0  0  0  0  0  4  0  0  0  0  0  0
   -0.7880   -1.0875    0.0058 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.3438   -0.1057   -0.0120 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
M  CHG  3   2   1   3  -1   4  -1
M  END
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3D SDF for HMDB0002878 (Nitrate)

  Mrv1652306222023342D          

  4  3  0  0  0  0            999 V2000
    0.8250    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.2375   -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
  2  1  1  0  0  0  0
  3  1  2  0  0  0  0
  4  1  2  0  0  0  0
M  CHG  1   2  -1
M  END
> <DATABASE_ID>
HMDB0002878

> <DATABASE_NAME>
hmdb

> <SMILES>
[O-]N(=O)=O

> <INCHI_IDENTIFIER>
InChI=1S/NO3/c2-1(3)4/q-1

> <INCHI_KEY>
NHNBFGGVMKEFGY-UHFFFAOYSA-N

> <FORMULA>
NO3

> <MOLECULAR_WEIGHT>
62.0049

> <EXACT_MASS>
61.987817871

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
3.275441232355817

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
nitrate

> <JCHEM_LOGP>
0.8368003898615884

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_BASIC>
-9.93762264919614

> <JCHEM_POLAR_SURFACE_AREA>
66.2

> <JCHEM_REFRACTIVITY>
8.347100000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
nitrate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0002878 (Nitrate)

HMDB0002878
     RDKit          3D
Nitrate
  4  3  0  0  0  0  0  0  0  0999 V2000
   -0.5467    1.1635    0.0060 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0091    0.0296    0.0001 N   0  0  0  0  0  4  0  0  0  0  0  0
   -0.7880   -1.0875    0.0058 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.3438   -0.1057   -0.0120 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
M  CHG  3   2   1   3  -1   4  -1
M  END
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PDB for HMDB0002878 (Nitrate)

HEADER    PROTEIN                                 22-JUN-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-JUN-20         0                                  
HETATM    1  N   UNK     0       1.540   0.000   0.000  0.00  0.00           N+0
HETATM    2  O   UNK     0       2.310   1.334   0.000  0.00  0.00           O-1
HETATM    3  O   UNK     0       2.310  -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    3    4                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1                                                            
MASTER        0    0    0    0    0    0    0    0    4    0    6    0
END
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3D PDB for HMDB0002878 (Nitrate)

COMPND    HMDB0002878
HETATM    1  O1  UNL     1      -0.547   1.163   0.006  1.00  0.00           O  
HETATM    2  N1  UNL     1      -0.009   0.030   0.000  1.00  0.00           N1+
HETATM    3  O2  UNL     1      -0.788  -1.087   0.006  1.00  0.00           O1-
HETATM    4  O3  UNL     1       1.344  -0.106  -0.012  1.00  0.00           O1-
CONECT    1    2    2
CONECT    2    3    4
END
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SMILES for HMDB0002878 (Nitrate)

[O-]N(=O)=O
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INCHI for HMDB0002878 (Nitrate)

InChI=1S/NO3/c2-1(3)4/q-1
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View in JSmolView Stereo Labels
Synonyms
Chemical FormulaNO3
Average Molecular Weight62.0049
Monoisotopic Molecular Weight61.987817871
IUPAC Namenitrate
Traditional Namenitrate
CAS Registry Number14797-55-8
SMILES
[O-][N+]([O-])=O
InChI Identifier
InChI=1S/NO3/c2-1(3)4/q-1
InChI KeyNHNBFGGVMKEFGY-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of inorganic compounds known as non-metal nitrates. These are inorganic non-metallic compounds containing a nitrate as its largest oxoanion.
KingdomInorganic compounds
Super ClassHomogeneous non-metal compounds
ClassNon-metal oxoanionic compounds
Sub ClassNon-metal nitrates
Direct ParentNon-metal nitrates
Alternative Parents
Substituents
  • Non-metal nitrate
  • Inorganic oxide
Molecular FrameworkNot Available
External Descriptors
Ontology
Physiological effect
Health effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
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
logP0.84ChemAxon
pKa (Strongest Basic)-9.9ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area66.2 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity8.35 m³·mol⁻¹ChemAxon
Polarizability3.28 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Urine
Tissue Locations
  • Adipose Tissue
  • Bladder
  • Epidermis
  • Fibroblasts
  • Heart
  • Intestine
  • Kidney
  • Lung
  • Neuron
  • Pancreas
  • Platelet
  • Skeletal Muscle
  • Spleen
  • Testis
  • Thyroid Gland
Pathways
Normal Concentrations
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified27.4 +/- 8.2 uMChildren (1-13 years old)MaleDuchenne Muscular Dystrophy details
BloodDetected and Quantified129.0 (18.5-417.7) uMAdult (>18 years old)Both
Kidney disease		 details
Cerebrospinal Fluid (CSF)Detected and Quantified12.71 +/- 1.08 uMAdult (>18 years old)FemalePreeclampsia details
Cerebrospinal Fluid (CSF)Detected and Quantified102.0 +/- 33.0 uMAdult (>18 years old)Not SpecifiedAmyotrophic lateral sclerosis details
UrineDetected and Quantified230 +/- 126 umol/mmol creatinineChildren (1-13 years old)MaleDuchenne Muscular Dystrophy details
Associated Disorders and Diseases
Disease References
Kidney disease
  1. Galley HF, Le Cras AE, Yassen K, Grant IS, Webster NR: Circulating tetrahydrobiopterin concentrations in patients with septic shock. Br J Anaesth. 2001 Apr;86(4):578-80. [PubMed:11573638 ]
Duchenne Muscular Dystrophy
  1. Horster I, Weigt-Usinger K, Carmann C, Chobanyan-Jurgens K, Kohler C, Schara U, Kayacelebi AA, Beckmann B, Tsikas D, Lucke T: The L-arginine/NO pathway and homoarginine are altered in Duchenne muscular dystrophy and improved by glucocorticoids. Amino Acids. 2015 Sep;47(9):1853-63. doi: 10.1007/s00726-015-2018-x. Epub 2015 Jun 12. [PubMed:26066683 ]
Amyotrophic lateral sclerosis
  1. Boll MC, Alcaraz-Zubeldia M, Montes S, Murillo-Bonilla L, Rios C: Raised nitrate concentration and low SOD activity in the CSF of sporadic ALS patients. Neurochem Res. 2003 May;28(5):699-703. [PubMed:12716019 ]
Preeclampsia
  1. Celik O, Hascalik S, Turkoz Y, Hascalik M, Gokdeniz R: Cerebrospinal fluid nitric oxide level changes in preeclampsia. Eur J Obstet Gynecol Reprod Biol. 2003 Dec 10;111(2):141-5. [PubMed:14597241 ]
Associated OMIM IDs
  • 310200 (Duchenne Muscular Dystrophy)
  • 105400 (Amyotrophic lateral sclerosis)
DrugBank IDDBMET01481
Phenol Explorer Compound IDNot Available
FooDB IDFDB003811
KNApSAcK IDNot Available
Chemspider ID918
KEGG Compound IDC00244
BioCyc IDNITRATE
BiGG IDNot Available
Wikipedia LinkNitrate
METLIN ID3208
PubChem Compound943
PDB IDNot Available
ChEBI ID17632
Food Biomarker OntologyNot Available
VMH IDNO3
MarkerDB IDMDB00030005
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References