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Showing metabocard for Molybdate (HMDB0012260)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (1) Show 1 proteinXML
enzymes (1) Show 1 protein
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2009-04-06 16:21:55 UTC
Update Date2020-09-15 19:34:27 UTC
HMDB IDHMDB0012260
Secondary Accession Numbers
  • HMDB12260
Metabolite Identification
Common NameMolybdate
DescriptionMolybdate, also known as molybdic acid, belongs to the class of inorganic compounds known as miscellaneous molybdates. These are inorganic compounds in which the largest metallic oxoanion is molybdate, to which either no atom or a non metal atom is bonded. Molybdate exists in all living organisms, ranging from bacteria to humans. Molybdate is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review very few articles have been published on Molybdate.
Structure
Data?1600198467
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0012260 (Molybdate)


  Mrv1652309042000352D          

  5  4  0  0  0  0            999 V2000
    0.8250   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 Mo  0  2  0  0  0  0  0  0  0  0  0  0
    0.8250    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.0000    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  1  0  0  0  0
  2  4  2  0  0  0  0
  2  5  2  0  0  0  0
M  CHG  1   2   2
M  END
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3D MOL for HMDB0012260 (Molybdate)

HMDB0012260
     RDKit          3D
Molybdate
  7  6  0  0  0  0  0  0  0  0999 V2000
   -0.4667    1.5530   -1.4596 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1681    0.3362   -0.3361 Mo  0  0  0  0  0  6  0  0  0  0  0  0
    0.4513    1.5316    1.5892 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3289   -0.7801   -0.4422 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6579   -0.5516    0.6348 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9688   -1.0855    0.2242 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7924   -1.0037   -0.2102 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  2  0
  2  4  1  0
  2  5  1  0
  4  6  1  0
  5  7  1  0
M  CHG  1   2   2
M  END
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3D SDF for HMDB0012260 (Molybdate)


  Mrv1652309042000352D          

  5  4  0  0  0  0            999 V2000
    0.8250   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 Mo  0  2  0  0  0  0  0  0  0  0  0  0
    0.8250    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.0000    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  1  0  0  0  0
  2  4  2  0  0  0  0
  2  5  2  0  0  0  0
M  CHG  1   2   2
M  END
> <DATABASE_ID>
HMDB0012260

> <DATABASE_NAME>
hmdb

> <SMILES>
O[Mo++](O)(=O)=O

> <INCHI_IDENTIFIER>
InChI=1S/Mo.2H2O.2O/h;2*1H2;;/q+4;;;;/p-2

> <INCHI_KEY>
KAZXQXRLRUTACQ-UHFFFAOYSA-L

> <FORMULA>
H2MoO4

> <MOLECULAR_WEIGHT>
161.96

> <EXACT_MASS>
163.899616

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
6.510685281089675

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
dihydroxydioxomolybdenumbis(ylium)

> <JCHEM_LOGP>
-1.7751999999999997

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
3.301029995663981

> <JCHEM_PKA_STRONGEST_ACIDIC>
-2.3010299956639804

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
8.015

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
dihydroxydioxomolybdenumbis(ylium)

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0012260 (Molybdate)

HMDB0012260
     RDKit          3D
Molybdate
  7  6  0  0  0  0  0  0  0  0999 V2000
   -0.4667    1.5530   -1.4596 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1681    0.3362   -0.3361 Mo  0  0  0  0  0  6  0  0  0  0  0  0
    0.4513    1.5316    1.5892 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3289   -0.7801   -0.4422 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6579   -0.5516    0.6348 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9688   -1.0855    0.2242 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7924   -1.0037   -0.2102 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  2  0
  2  4  1  0
  2  5  1  0
  4  6  1  0
  5  7  1  0
M  CHG  1   2   2
M  END
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PDB for HMDB0012260 (Molybdate)

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  O   UNK     0       1.540  -1.540   0.000  0.00  0.00           O+0
HETATM    2 Mo   UNK     0       1.540   0.000   0.000  0.00  0.00          Mo+2
HETATM    3  O   UNK     0       1.540   1.540   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       3.080   0.000   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4    5                                             
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    2                                                            
MASTER        0    0    0    0    0    0    0    0    5    0    8    0
END
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3D PDB for HMDB0012260 (Molybdate)

COMPND    HMDB0012260
HETATM    1  O1  UNL     1      -0.467   1.553  -1.460  1.00  0.00           O  
HETATM    2 MO1  UNL     1       0.168   0.336  -0.336  1.00  0.00          MO2+
HETATM    3  O2  UNL     1       0.451   1.532   1.589  1.00  0.00           O  
HETATM    4  O3  UNL     1       1.329  -0.780  -0.442  1.00  0.00           O  
HETATM    5  O4  UNL     1      -1.658  -0.552   0.635  1.00  0.00           O  
HETATM    6  H1  UNL     1       1.969  -1.085   0.224  1.00  0.00           H  
HETATM    7  H2  UNL     1      -1.792  -1.004  -0.210  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    3    4    5
CONECT    4    6
CONECT    5    7
END
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SMILES for HMDB0012260 (Molybdate)

O[Mo++](O)(=O)=O
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INCHI for HMDB0012260 (Molybdate)

InChI=1S/Mo.2H2O.2O/h;2*1H2;;/q+4;;;;/p-2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Molybdic acidGenerator
Chemical FormulaH2MoO4
Average Molecular Weight161.96
Monoisotopic Molecular Weight163.899616
IUPAC Namedihydroxydioxomolybdenumbis(ylium)
Traditional Namedihydroxydioxomolybdenumbis(ylium)
CAS Registry NumberNot Available
SMILES
O[Mo++](O)(=O)=O
InChI Identifier
InChI=1S/Mo.2H2O.2O/h;2*1H2;;/q+4;;;;/p-2
InChI KeyKAZXQXRLRUTACQ-UHFFFAOYSA-L
Chemical Taxonomy
Description Belongs to the class of inorganic compounds known as miscellaneous molybdates. These are inorganic compounds in which the largest metallic oxoanion is molybdate, to which either no atom or a non metal atom is bonded.
KingdomInorganic compounds
Super ClassMixed metal/non-metal compounds
ClassMiscellaneous mixed metal/non-metals
Sub ClassMiscellaneous metallic oxoanionic compounds
Direct ParentMiscellaneous molybdates
Alternative Parents
Substituents
  • Molybdate
  • Inorganic oxide
  • Inorganic salt
Molecular FrameworkNot Available
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Source
Process
Naturally occurring process
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
logP-1.8ChemAxon
pKa (Strongest Acidic)-2.3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area74.6 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity8.02 m³·mol⁻¹ChemAxon
Polarizability6.51 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
AllCCS[M+H]+123.332859911
AllCCS[M+H-H2O]+119.332859911
AllCCS[M+NH4]+127.032859911
AllCCS[M+Na]+128.132859911
AllCCS[M-H]-154.032859911
AllCCS[M+Na-2H]-159.632859911
AllCCS[M+HCOO]-165.732859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid201.2 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1500.9 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid506.7 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid199.1 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid386.9 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid227.7 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid437.1 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 Acid564.1 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)590.3 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid903.9 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid339.1 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1100.0 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid356.7 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid418.4 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate897.7 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA406.8 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water377.5 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra
Biological Properties
Cellular LocationsNot Available
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 IDFDB028899
KNApSAcK IDNot Available
Chemspider ID74188
KEGG Compound IDC06232
BioCyc IDCPD-3
BiGG IDNot Available
Wikipedia LinkMolybdate
METLIN IDNot Available
PubChem Compound82208
PDB IDNot Available
ChEBI ID25371
Food Biomarker OntologyNot Available
VMH IDMOBD
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Gephyrin
General function:
Involved in Mo-molybdopterin cofactor biosynthetic process
Specific function:
Microtubule-associated protein involved in membrane protein-cytoskeleton interactions. It is thought to anchor the inhibitory glycine receptor (GLYR) to subsynaptic microtubules (By similarity). Catalyzes two steps in the biosynthesis of the molybdenum cofactor. In the first step, molybdopterin is adenylated. Subsequently, molybdate is inserted into adenylated molybdopterin and AMP is released.
Gene Name:
GPHN
Uniprot ID:
Q9NQX3
Molecular weight:
79747.635
Reactions
Adenylyl-molybdopterin + Molybdate → Molybdopterin + Adenosine monophosphatedetails