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Showing metabocard for Nitrogen (HMDB0001371)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-08-16 14:01:37 UTC
Update Date2023-02-21 17:15:38 UTC
HMDB IDHMDB0001371
Secondary Accession Numbers
  • HMDB01371
Metabolite Identification
Common NameNitrogen
DescriptionElemental nitrogen is a colorless, odorless, tasteless and mostly inert diatomic gas at standard conditions, constituting 78% by volume of Earth's atmosphere. Nitrogen occurs in all living organisms. It is a constituent element of amino acids and therefore of proteins and nucleic acids (DNA and RNA). Nitrogen is found in the chemical structure of almost all neurotransmitters and is a key component of alkaloids. Specific bacteria (e.g. Rhizobium trifolium) possess nitrogenase enzymes which can fix atmospheric nitrogen into a form (ammonium ion) which is chemically useful to higher organisms. Animals use nitrogen-containing amino acids from plant sources, as starting materials for all nitrogen-compound animal biochemistry, including the manufacture of proteins and nucleic acids. Animal metabolism of NO (nitric oxide) results in production of nitrite. Animal metabolism of nitrogen in proteins generally results in excretion of urea, while animal metabolism of nucleic acids results in excretion of urea and uric acid. The characteristic odor of animal flesh decay is caused by nitrogen-containing long-chain amines, such as putrescine and cadaverine. Decay of organisms and their waste products may produce small amounts of nitrate, but most decay eventually returns nitrogen content to the atmosphere, as molecular nitrogen. The circulation of nitrogen from the atmosphere through organics and then back to the atmosphere is commonly referred to as the nitrogen cycle. Nitrogen can be measured in urine with the Kjeldahl method or by spectrophotometric methods (enzymic tests). Total urinary nitrogen is calculated based on urea urinary nitrogen quantified with these methods.
Structure
Data?1676999738
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001371 (Nitrogen)

947
  Mrv0541 02231219052D          

  2  1  0  0  0  0            999 V2000
    1.6500    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0  0  0  0
M  END
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3D MOL for HMDB0001371 (Nitrogen)

HMDB0001371
     RDKit          3D
Nitrogen
  2  1  0  0  0  0  0  0  0  0999 V2000
    0.5629    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5629    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0
M  END
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3D SDF for HMDB0001371 (Nitrogen)

947
  Mrv0541 02231219052D          

  2  1  0  0  0  0            999 V2000
    1.6500    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0001371

> <DATABASE_NAME>
hmdb

> <SMILES>
N#N

> <INCHI_IDENTIFIER>
InChI=1S/N2/c1-2

> <INCHI_KEY>
IJGRMHOSHXDMSA-UHFFFAOYSA-N

> <FORMULA>
N2

> <MOLECULAR_WEIGHT>
28.0134

> <EXACT_MASS>
28.00614801

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
1.7660811281543802

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
diazyne

> <JCHEM_LOGP>
0.31153025599999995

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
47.58

> <JCHEM_REFRACTIVITY>
26.2298

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
nitrogen

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0001371 (Nitrogen)

HMDB0001371
     RDKit          3D
Nitrogen
  2  1  0  0  0  0  0  0  0  0999 V2000
    0.5629    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5629    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0
M  END
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PDB for HMDB0001371 (Nitrogen)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 947                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  N   UNK     0       3.080   0.000   0.000  0.00  0.00           N+0
HETATM    2  N   UNK     0       4.620   0.000   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1                                                            
MASTER        0    0    0    0    0    0    0    0    2    0    2    0
END
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3D PDB for HMDB0001371 (Nitrogen)

COMPND    HMDB0001371
HETATM    1  N1  UNL     1       0.563   0.000   0.000  1.00  0.00           N  
HETATM    2  N2  UNL     1      -0.563   0.000   0.000  1.00  0.00           N  
CONECT    1    2    2    2
END
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SMILES for HMDB0001371 (Nitrogen)

N#N
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INCHI for HMDB0001371 (Nitrogen)

InChI=1S/N2/c1-2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Molecular nitrogenChEBI
N2ChEBI
N#NChEBI
NitrogenChEBI
DinitrogenHMDB
Nitrogen gasHMDB
Chemical FormulaN2
Average Molecular Weight28.0134
Monoisotopic Molecular Weight28.00614801
IUPAC Namediazyne
Traditional Namenitrogen
CAS Registry Number7727-37-9
SMILES
N#N
InChI Identifier
InChI=1S/N2/c1-2
InChI KeyIJGRMHOSHXDMSA-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of inorganic compounds known as other non-metal nitrides. These are inorganic compounds of nitrogen where nitrogen has a formal oxidation state of -3, and the heaviest atom bonded to it belongs to the class of 'other non-metals'.
KingdomInorganic compounds
Super ClassHomogeneous non-metal compounds
ClassOther non-metal organides
Sub ClassOther non-metal nitrides
Direct ParentOther non-metal nitrides
Alternative Parents
Substituents
  • Other non-metal nitride
  • Inorganic nitride
Molecular FrameworkNot Available
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Industrial applicationBiological role
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-210.01 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility18.1 mg/mL at 21 °CNot Available
LogP0.67HANSCH,C ET AL. (1995)
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP0.31ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area47.58 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity26.23 m³·mol⁻¹ChemAxon
Polarizability1.77 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]+110.00830932474
DeepCCS[M-H]-108.27130932474
DeepCCS[M-2H]-143.43130932474
DeepCCS[M+Na]+116.75930932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 20228.271 minutes33406817
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid269.8 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid940.0 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid421.9 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid186.8 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid345.5 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid193.9 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid311.5 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 Acid399.1 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)571.8 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid656.0 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid172.3 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid767.3 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid279.1 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid365.0 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate686.9 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA356.1 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water294.8 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
NitrogenN#N1105.7Standard polar33892256
NitrogenN#N353.8Standard non polar33892256
NitrogenN#N412.4Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Nitrogen GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-9000000000-900558b878d696839ddd2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Nitrogen GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
MSMass Spectrum (Electron Ionization)splash10-004i-9000000000-6369f2c7b3a3b0e3772c2015-03-01Not AvailableView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nitrogen 10V, Positive-QTOFsplash10-004i-9000000000-096cae140ae566643e882015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nitrogen 20V, Positive-QTOFsplash10-004i-9000000000-096cae140ae566643e882015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nitrogen 40V, Positive-QTOFsplash10-004i-9000000000-096cae140ae566643e882015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nitrogen 10V, Negative-QTOFsplash10-004i-9000000000-6d8e7ecefdead45cc87d2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nitrogen 20V, Negative-QTOFsplash10-004i-9000000000-6d8e7ecefdead45cc87d2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nitrogen 40V, Negative-QTOFsplash10-004i-9000000000-6d8e7ecefdead45cc87d2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nitrogen 10V, Positive-QTOFsplash10-004i-9000000000-1fb6bb5f9fe3af7d141e2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nitrogen 20V, Positive-QTOFsplash10-004i-9000000000-1fb6bb5f9fe3af7d141e2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nitrogen 40V, Positive-QTOFsplash10-004i-9000000000-1fb6bb5f9fe3af7d141e2021-09-24Wishart 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+Na]+)2023-02-03FELIX labView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Urine
Tissue Locations
  • Epidermis
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected and Quantified161827.316 +/- 35697.202 umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified231793.832 +/- 43788.568 umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified30842.383 +/- 7615.403 umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified32106.667 +/- 15380 umol/mmol creatinineAdolescent (13-18 years old)BothNormal details
UrineDetected and Quantified35866.667 +/- 9333.333 umol/mmol creatinineChildren (1 - 13 years old)BothNormal details
UrineDetected and Quantified41866.667 +/- 11333.333 umol/mmol creatinineChildren (1 - 13 years old)BothNormal details
UrineDetected and Quantified23560.153 +/- 4521.646 umol/mmol creatinineAdult (>18 years old)FemaleNormal details
UrineDetected and Quantified27106.0754 +/- 5473.571 umol/mmol creatinineAdult (>18 years old)FemaleNormal details
UrineDetected and Quantified30461.612 +/- 4759.627 umol/mmol creatinineAdult (>18 years old)MaleNormal details
UrineDetected and Quantified35030.854 +/- 7853.384 umol/mmol creatinineAdult (>18 years old)MaleNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected and Quantified171346.570 +/- 38077.0155 umol/mmol creatinineAdult (>18 years old)FemalePregnancy details
Associated Disorders and Diseases
Disease References
Pregnancy
  1. Mikkelsen TB, Osler M, Olsen SF: Validity of protein, retinol, folic acid and n-3 fatty acid intakes estimated from the food-frequency questionnaire used in the Danish National Birth Cohort. Public Health Nutr. 2006 Sep;9(6):771-8. [PubMed:16925883 ]
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC00697
BioCyc IDNITROGEN-MOLECULE
BiGG IDNot Available
Wikipedia LinkNitrogen
METLIN IDNot Available
PubChem Compound947
PDB IDNot Available
ChEBI ID17997
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDMDB00029899
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Balafa C, Smith-Thomas L, Phillips J, Moustafa M, George E, Blount M, Nicol S, Westgate G, MacNeil S: Dopa oxidase activity in the hair, skin and ocular melanocytes is increased in the presence of stressed fibroblasts. Exp Dermatol. 2005 May;14(5):363-72. [PubMed:15854130 ]
  2. Konya C, Sanada H, Sugama J, Kitayama Y, Ishikawa S, Togashi H, Tamura S: Skin debris and micro-organisms on the periwound skin of pressure ulcers and the influence of periwound cleansing on microbial flora. Ostomy Wound Manage. 2005 Jan;51(1):50-9. [PubMed:15695835 ]