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Showing metabocard for Hydroxide (HMDB0001039)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2020-09-18 17:18:56 UTC
HMDB IDHMDB0001039
Secondary Accession Numbers
  • HMDB01039
Metabolite Identification
Common NameHydroxide
DescriptionHydroxide, also known as hydroxide ion, belongs to the class of inorganic compounds known as non-metal hydroxides. These are inorganic non-metallic compounds containing the hydroxide group as its largest oxoanion. Hydroxide exists in all living species, ranging from bacteria to plants to humans. Hydroxide has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make hydroxide a potential biomarker for the consumption of these foods. Hydroxide is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on Hydroxide.
Structure
Data?1600449536
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001039 (Hydroxide)

961
  Mrv0541 02231218532D          

  1  0  0  0  0  0            999 V2000
    2.4750    0.0000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
M  CHG  1   1  -1
M  END
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3D MOL for HMDB0001039 (Hydroxide)

HMDB0001039
     RDKit          3D
Hydroxide
  2  1  0  0  0  0  0  0  0  0999 V2000
    0.4956    0.0000    0.0000 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.4956    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
M  CHG  1   1  -1
M  END
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3D SDF for HMDB0001039 (Hydroxide)

961
  Mrv0541 02231218532D          

  1  0  0  0  0  0            999 V2000
    2.4750    0.0000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
M  CHG  1   1  -1
M  END
> <DATABASE_ID>
HMDB0001039

> <DATABASE_NAME>
hmdb

> <SMILES>
[OH-]

> <INCHI_IDENTIFIER>
InChI=1S/H2O/h1H2/p-1

> <INCHI_KEY>
XLYOFNOQVPJJNP-UHFFFAOYSA-M

> <FORMULA>
HO

> <MOLECULAR_WEIGHT>
17.0073

> <EXACT_MASS>
17.002739654

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
1.1909242651253518

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
hydroxide

> <JCHEM_LOGP>
-0.6519999999999999

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.7

> <JCHEM_PKA_STRONGEST_BASIC>
-1.7999999999999998

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
13.914900000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
hydroxide

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0001039 (Hydroxide)

HMDB0001039
     RDKit          3D
Hydroxide
  2  1  0  0  0  0  0  0  0  0999 V2000
    0.4956    0.0000    0.0000 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.4956    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
M  CHG  1   1  -1
M  END
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PDB for HMDB0001039 (Hydroxide)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 961                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0       4.620   0.000   0.000  0.00  0.00           O-1
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
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3D PDB for HMDB0001039 (Hydroxide)

COMPND    HMDB0001039
HETATM    1  O1  UNL     1       0.496   0.000   0.000  1.00  0.00           O1-
HETATM    2  H1  UNL     1      -0.496   0.000   0.000  1.00  0.00           H  
CONECT    1    2
END
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SMILES for HMDB0001039 (Hydroxide)

[OH-]
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INCHI for HMDB0001039 (Hydroxide)

InChI=1S/H2O/h1H2/p-1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
HYDROXIDE ionChEBI
OH(-)ChEBI
Hydroxyl ionMeSH
Hydridooxygenate(1-)HMDB
Hydrogen oxideHMDB
Hydroxide anionHMDB
Hydroxide ion(1-)HMDB
Hydroxide(1-)HMDB
HydroxyHMDB
Hydroxy anionHMDB
Hydroxy ionHMDB
HydroxylHMDB
Hydroxyl anionHMDB
Hydroxyl ion (OH1-)HMDB
Hydroxyl radicalHMDB
Hydroxyl radicalsHMDB
OHHMDB
OxidanideHMDB
Oxygen ion (O1-)HMDB
Water ion(1-)HMDB
Chemical FormulaHO
Average Molecular Weight17.0073
Monoisotopic Molecular Weight17.002739654
IUPAC Namehydroxide
Traditional Namehydroxide
CAS Registry Number14280-30-9
SMILES
[OH-]
InChI Identifier
InChI=1S/H2O/h1H2/p-1
InChI KeyXLYOFNOQVPJJNP-UHFFFAOYSA-M
Chemical Taxonomy
Description Belongs to the class of inorganic compounds known as non-metal hydroxides. These are inorganic non-metallic compounds containing the hydroxide group as its largest oxoanion.
KingdomInorganic compounds
Super ClassHomogeneous non-metal compounds
ClassNon-metal oxoanionic compounds
Sub ClassNon-metal hydroxides
Direct ParentNon-metal hydroxides
Alternative Parents
Substituents
  • Non-metal hydroxide
  • Inorganic hydride
  • Inorganic oxide
Molecular FrameworkNot Available
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Biological role
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
logP-0.65ChemAxon
pKa (Strongest Acidic)15.7ChemAxon
pKa (Strongest Basic)-1.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity13.91 m³·mol⁻¹ChemAxon
Polarizability1.19 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]+111.60930932474
DeepCCS[M-H]-109.84230932474
DeepCCS[M-2H]-145.06630932474
DeepCCS[M+Na]+118.42330932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 20227.7986 minutes33406817
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid276.8 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1014.8 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid439.4 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid185.0 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid359.2 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid215.6 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid331.3 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 Acid428.9 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)667.3 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid683.1 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid185.8 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid804.7 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid294.0 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid395.4 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate727.5 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA348.1 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water330.8 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Hydroxide[OH-]286.5Standard polar33892256
Hydroxide[OH-]171.3Standard non polar33892256
Hydroxide[OH-]97.0Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydroxide 10V, Positive-QTOFsplash10-014i-9000000000-8866e50c5f1c571c000d2016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydroxide 20V, Positive-QTOFsplash10-014i-9000000000-8866e50c5f1c571c000d2016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydroxide 40V, Positive-QTOFsplash10-014i-9000000000-8866e50c5f1c571c000d2016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydroxide 10V, Negative-QTOFsplash10-014i-9000000000-b337457efba80736ee4e2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydroxide 20V, Negative-QTOFsplash10-014i-9000000000-b337457efba80736ee4e2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydroxide 40V, Negative-QTOFsplash10-014i-9000000000-b337457efba80736ee4e2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydroxide 10V, Negative-QTOFsplash10-014i-9000000000-f607d1cf161edb4c90532021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydroxide 20V, Negative-QTOFsplash10-014i-9000000000-f607d1cf161edb4c90532021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydroxide 40V, Negative-QTOFsplash10-014i-9000000000-f607d1cf161edb4c90532021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Mitochondria
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 IDFDB022386
KNApSAcK IDC00025875
Chemspider ID936
KEGG Compound IDC01328
BioCyc IDOH
BiGG ID37371
Wikipedia LinkHydroxide
METLIN IDNot Available
PubChem Compound961
PDB IDNot Available
ChEBI ID16234
Food Biomarker OntologyNot Available
VMH IDOH1
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceRevzin, G. E.; Lavrent'eva, V. G.; Revzina, T. V.; Kashina, N. I. Preparation of hydroxides slightly soluble in water. U.S.S.R. (1967), CODEN: URXXAF SU 196735 19670531 CAN 68:4526 AN 1968:4526
Material Safety Data Sheet (MSDS)Download (PDF)
General ReferencesNot Available