Hmdb loader

Showing metabocard for Niobium (HMDB0061921)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2014-10-09 16:46:22 UTC
Update Date2019-07-23 07:17:27 UTC
HMDB IDHMDB0061921
Secondary Accession Numbers
  • HMDB61921
Metabolite Identification
Common NameNiobium
DescriptionNiobium, formerly columbium, is a chemical element with symbol Nb (formerly Cb) and atomic number 41. It is a soft, grey, ductile transition metal, which is often found in the pyrochlore mineral, the main commercial source for niobium, and columbite. The name comes from Greek mythology: Niobe, daughter of Tantalus.
Structure
Data?1563866247
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0061921 (Niobium)


  Mrv0541 10091412522D          

  1  0  0  0  0  0            999 V2000
   -0.3571    0.6696    0.0000 Nb  0  0  0  0  0  0  0  0  0  0  0  0
M  CHG  1   1   5
M  END
Download

3D MOL for HMDB0061921 (Niobium)

HMDB0061921
     RDKit          3D
Niobium
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Nb  0  0  0  0  0 15  0  0  0  0  0  0
M  CHG  1   1   5
M  END
Download

3D SDF for HMDB0061921 (Niobium)


  Mrv0541 10091412522D          

  1  0  0  0  0  0            999 V2000
   -0.3571    0.6696    0.0000 Nb  0  0  0  0  0  0  0  0  0  0  0  0
M  CHG  1   1   5
M  END
> <DATABASE_ID>
HMDB0061921

> <DATABASE_NAME>
hmdb

> <SMILES>
[Nb+5]

> <INCHI_IDENTIFIER>
InChI=1S/Nb/q+5

> <INCHI_KEY>
QUWPZPLTANKXAM-UHFFFAOYSA-N

> <FORMULA>
Nb

> <MOLECULAR_WEIGHT>
92.9036

> <EXACT_MASS>
92.903634644

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
1.7784

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
5

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
niobium(5+) ion

> <JCHEM_LOGP>
0.0

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
5

> <JCHEM_PKA>
3.55

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.09

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
0.0

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
niobium(5+) ion

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0061921 (Niobium)

HMDB0061921
     RDKit          3D
Niobium
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Nb  0  0  0  0  0 15  0  0  0  0  0  0
M  CHG  1   1   5
M  END
Download

PDB for HMDB0061921 (Niobium)

HEADER    PROTEIN                                 09-OCT-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-OCT-14         0                                  
HETATM    1 Nb   UNK     0      -0.667   1.250   0.000  0.00  0.00          Nb+5
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
Download

3D PDB for HMDB0061921 (Niobium)

COMPND    HMDB0061921
HETATM    1 NB1  UNL     1       0.000   0.000   0.000  1.00  0.00          NB5+
END
Download

SMILES for HMDB0061921 (Niobium)

[Nb+5]
Download

INCHI for HMDB0061921 (Niobium)

InChI=1S/Nb/q+5
Download
View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaNb
Average Molecular Weight92.9036
Monoisotopic Molecular Weight92.903634644
IUPAC Nameniobium(5+) ion
Traditional Nameniobium(5+) ion
CAS Registry Number7440-03-1
SMILES
[Nb+5]
InChI Identifier
InChI=1S/Nb/q+5
InChI KeyQUWPZPLTANKXAM-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of inorganic compounds known as homogeneous transition metal compounds. These are inorganic compounds containing only metal atoms,with the largest atom being a transition metal atom.
KingdomInorganic compounds
Super ClassHomogeneous metal compounds
ClassHomogeneous transition metal compounds
Sub ClassNot Available
Direct ParentHomogeneous transition metal compounds
Alternative ParentsNot Available
Substituents
  • Homogeneous transition metal
Molecular FrameworkNot Available
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point2477 °CNot Available
Boiling Point4744 °CNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP0ChemAxon
pKa (Strongest Acidic)3.09ChemAxon
Physiological Charge5ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity0 m³·mol⁻¹ChemAxon
Polarizability1.78 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
AllCCS[M+H]+124.232859911
AllCCS[M+H-H2O]+120.532859911
AllCCS[M+NH4]+127.632859911
AllCCS[M+Na]+128.532859911
AllCCS[M-H]-141.832859911
AllCCS[M+Na-2H]-153.432859911
AllCCS[M+HCOO]-166.232859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid905.7 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid426.1 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid193.9 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid352.4 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid211.7 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid318.0 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 Acid408.4 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)632.7 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid654.0 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid177.5 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid747.3 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid288.3 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid376.9 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate689.1 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA369.7 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water304.1 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Niobium[Nb+5]690.9Standard polar33892256
Niobium[Nb+5]229.8Standard non polar33892256
Niobium[Nb+5]52.0Semi standard non polar33892256
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Saliva
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.00043-0.00500 uMAdult (>18 years old)Both
Normal		 details
SalivaDetected and Quantified0.008 +/- 0.006 uMAdult (>18 years old)BothNormal
    • Zerihun T. Dame, ...
 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNiobium
METLIN IDNot Available
PubChem Compound3863468
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available