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Showing metabocard for Ammonium (HMDB0041827)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2012-09-13 11:41:19 UTC
Update Date2020-10-09 21:09:43 UTC
HMDB IDHMDB0041827
Secondary Accession Numbers
  • HMDB41827
Metabolite Identification
Common NameAmmonium
DescriptionAmmonium is an important source of nitrogen for many plant species, especially those growing on hypoxic soils. However, it is also toxic to most crop species and is rarely applied as a sole nitrogen source. The ammonium (more obscurely: aminium) cation is a positively charged polyatomic cation with the chemical formula NH4+. It is formed by the protonation of ammonia (NH3). Ammonium is also a general name for positively charged or protonated substituted amines and quaternary ammonium cations (NR4+), where one or more hydrogen atoms are replaced by organic radical groups (indicated by R). Ammonium is found to be associated with N-acetylglutamate synthetase deficiency, which is an inborn error of metabolism.
Structure
Data?1563863706
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0041827 (Ammonium)


  Mrv1652309042000392D          

  1  0  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
M  CHG  1   1   1
M  END
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3D MOL for HMDB0041827 (Ammonium)

HMDB0041827
     RDKit          3D
Ammonium
  5  4  0  0  0  0  0  0  0  0999 V2000
    0.0026    0.0171   -0.0115 N   0  0  0  0  0  4  0  0  0  0  0  0
   -0.5990    0.1502    0.8239 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3721   -0.8042   -0.5433 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0162    0.8836   -0.5823 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9523   -0.2467    0.3131 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  1  3  1  0
  1  4  1  0
  1  5  1  0
M  CHG  1   1   1
M  END
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3D SDF for HMDB0041827 (Ammonium)


  Mrv1652309042000392D          

  1  0  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
M  CHG  1   1   1
M  END
> <DATABASE_ID>
HMDB0041827

> <DATABASE_NAME>
hmdb

> <SMILES>
[NH4+]

> <INCHI_IDENTIFIER>
InChI=1S/H3N/h1H3/p+1

> <INCHI_KEY>
QGZKDVFQNNGYKY-UHFFFAOYSA-O

> <FORMULA>
H4N

> <MOLECULAR_WEIGHT>
18.0385

> <EXACT_MASS>
18.034374133

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
2.380178155685953

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
azanium

> <JCHEM_LOGP>
-0.9779999999999999

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
8.861981369487705

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
16.3149

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
azanium

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0041827 (Ammonium)

HMDB0041827
     RDKit          3D
Ammonium
  5  4  0  0  0  0  0  0  0  0999 V2000
    0.0026    0.0171   -0.0115 N   0  0  0  0  0  4  0  0  0  0  0  0
   -0.5990    0.1502    0.8239 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3721   -0.8042   -0.5433 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0162    0.8836   -0.5823 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9523   -0.2467    0.3131 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  1  3  1  0
  1  4  1  0
  1  5  1  0
M  CHG  1   1   1
M  END
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PDB for HMDB0041827 (Ammonium)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+1
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
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3D PDB for HMDB0041827 (Ammonium)

COMPND    HMDB0041827
HETATM    1  N1  UNL     1       0.003   0.017  -0.011  1.00  0.00           N1+
HETATM    2  H1  UNL     1      -0.599   0.150   0.824  1.00  0.00           H  
HETATM    3  H2  UNL     1      -0.372  -0.804  -0.543  1.00  0.00           H  
HETATM    4  H3  UNL     1       0.016   0.884  -0.582  1.00  0.00           H  
HETATM    5  H4  UNL     1       0.952  -0.247   0.313  1.00  0.00           H  
CONECT    1    2    3    4    5
END
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SMILES for HMDB0041827 (Ammonium)

[NH4+]
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INCHI for HMDB0041827 (Ammonium)

InChI=1S/H3N/h1H3/p+1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
[NH4](+)ChEBI
Ammonium cationChEBI
Ammonium ionChEBI
Ammonium(1+)ChEBI
NH4+ChEBI
NH4(+)ChEBI
Ammonia ionKegg
Ammonium chlorideHMDB
AzaniumHMDB
[NH4]+HMDB
Ammonium compoundsHMDB
Chemical FormulaH4N
Average Molecular Weight18.0385
Monoisotopic Molecular Weight18.034374133
IUPAC Nameazanium
Traditional Nameazanium
CAS Registry Number14798-03-9
SMILES
[NH4+]
InChI Identifier
InChI=1S/H3N/h1H3/p+1
InChI KeyQGZKDVFQNNGYKY-UHFFFAOYSA-O
Chemical Taxonomy
Description Belongs to the class of inorganic compounds known as homogeneous other non-metal compounds. These are inorganic non-metallic compounds in which the largest atom belongs to the class of 'other non-metals'.
KingdomInorganic compounds
Super ClassHomogeneous non-metal compounds
ClassHomogeneous other non-metal compounds
Sub ClassNot Available
Direct ParentHomogeneous other non-metal compounds
Alternative ParentsNot Available
Substituents
  • Homogeneous other non metal
Molecular FrameworkNot Available
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility10.2 mg/mL at 20 °CNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-0.98ChemAxon
pKa (Strongest Basic)8.86ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity16.31 m³·mol⁻¹ChemAxon
Polarizability2.38 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+110.07530932474
DeepCCS[M-H]-108.34330932474
DeepCCS[M-2H]-143.56130932474
DeepCCS[M+Na]+116.87630932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 20227.48 minutes33406817
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid310.9 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid497.2 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid346.5 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid123.2 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid276.0 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid152.3 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid236.5 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 Acid259.3 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)694.8 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid521.7 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid56.6 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid575.0 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid218.9 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid318.2 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate623.4 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA374.2 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water289.1 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Ammonium[NH4+]352.9Standard polar33892256
Ammonium[NH4+]175.0Standard non polar33892256
Ammonium[NH4+]131.7Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ammonium 10V, Positive-QTOFsplash10-014i-9000000000-865a280eac64792eb43e2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ammonium 20V, Positive-QTOFsplash10-014i-9000000000-865a280eac64792eb43e2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ammonium 40V, Positive-QTOFsplash10-014i-9000000000-865a280eac64792eb43e2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ammonium 10V, Negative-QTOFsplash10-014i-9000000000-b764e01bee53b44bf4492015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ammonium 20V, Negative-QTOFsplash10-014i-9000000000-b764e01bee53b44bf4492015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ammonium 40V, Negative-QTOFsplash10-014i-9000000000-b764e01bee53b44bf4492015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ammonium 10V, Positive-QTOFsplash10-014i-9000000000-4d3180e05bafd704562f2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ammonium 20V, Positive-QTOFsplash10-014i-9000000000-4d3180e05bafd704562f2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ammonium 40V, Positive-QTOFsplash10-014i-9000000000-4d3180e05bafd704562f2021-09-22Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Sweat
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified<40 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified22-55 uMInfant (0-1 year old)Not SpecifiedNormal details
SweatDetected and Quantified21630-114850 uMAdult (60 years old)Male
Normal		 details
SweatDetected and Quantified< 10 uMAdult (40 years old)Male
Normal		 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified78 uMAdult (>18 years old)Male
N-Acetylglutamate synthetase deficiency		 details
BloodDetected and Quantified86 uMInfant (0-1 year old)MaleCoenzyme Q10 deficiency, primary, 1 details
Associated Disorders and Diseases
Disease References
N-acetylglutamate synthetase deficiency
  1. Hinnie J, Colombo JP, Wermuth B, Dryburgh FJ: N-Acetylglutamate synthetase deficiency responding to carbamylglutamate. J Inherit Metab Dis. 1997 Nov;20(6):839-40. [PubMed:9427158 ]
Coenzyme Q10 deficiency, primary, 1
  1. Diomedi-Camassei F, Di Giandomenico S, Santorelli FM, Caridi G, Piemonte F, Montini G, Ghiggeri GM, Murer L, Barisoni L, Pastore A, Muda AO, Valente ML, Bertini E, Emma F: COQ2 nephropathy: a newly described inherited mitochondriopathy with primary renal involvement. J Am Soc Nephrol. 2007 Oct;18(10):2773-80. doi: 10.1681/ASN.2006080833. Epub 2007 Sep 12. [PubMed:17855635 ]
Associated OMIM IDs
  • 608300 (N-acetylglutamate synthetase deficiency)
  • 607426 (Coenzyme Q10 deficiency, primary, 1)
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB030676
KNApSAcK IDNot Available
Chemspider ID218
KEGG Compound IDC01342
BioCyc IDAMMONIUM
BiGG IDNot Available
Wikipedia LinkAmmonium
METLIN IDNot Available
PubChem Compound16741146
PDB IDNH4
ChEBI ID28938
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDMDB00029853
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available