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Showing metabocard for Rubidium (HMDB0001327)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-08-16 13:16:24 UTC
Update Date2022-03-07 02:49:09 UTC
HMDB IDHMDB0001327
Secondary Accession Numbers
  • HMDB01327
Metabolite Identification
Common NameRubidium
DescriptionRubidium is a soft, silvery-white metallic element of the alkali metal group, present in traces amounts in human tissues and fluids. Rb-87, a naturally occurring isotope, is (slightly) radioactive. Rubidium is very soft and highly reactive, with properties similar to other elements in group 1, like rapid oxidation in air. Rubidium, particularly 87Rb, in the form of vapor, is one of the most commonly-used atomic species employed for laser cooling and Bose-Einstein condensation. Its desirable features for this application include the ready availability of inexpensive diode laser light at the relevant wavelength, and the moderate temperatures required to obtain substantial vapor pressures. Physiologically, it exists as an ion in the body. It has been found slightly increased in neoplastic human breast tissues obtained from patients at the time of mastectomy, compared to normal tissue. (PMID: 6488192 , 15820728 , 7324778 , 9630429 , 577330 ).
Structure
Data?1582752192
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001327 (Rubidium)


  Mrv0541 02231219032D          

  1  0  0  0  0  0            999 V2000
   27.8173  -18.1466    0.0000 Rb  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 HMDB0001327 (Rubidium)

HMDB0001327
     RDKit          3D
Rubidium
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Rb  0  0  0  0  0 15  0  0  0  0  0  0
M  CHG  1   1   1
M  END
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3D SDF for HMDB0001327 (Rubidium)


  Mrv0541 02231219032D          

  1  0  0  0  0  0            999 V2000
   27.8173  -18.1466    0.0000 Rb  0  3  0  0  0  0  0  0  0  0  0  0
M  CHG  1   1   1
M  END
> <DATABASE_ID>
HMDB0001327

> <DATABASE_NAME>
hmdb

> <SMILES>
[Rb+]

> <INCHI_IDENTIFIER>
InChI=1S/Rb/q+1

> <INCHI_KEY>
NCCSSGKUIKYAJD-UHFFFAOYSA-N

> <FORMULA>
Rb

> <MOLECULAR_WEIGHT>
85.4678

> <EXACT_MASS>
84.911789341

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
1.7784

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
rubidium(1+) ion

> <JCHEM_LOGP>
0

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
0

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
rubidium(1+) ion

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0001327 (Rubidium)

HMDB0001327
     RDKit          3D
Rubidium
  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Rb  0  0  0  0  0 15  0  0  0  0  0  0
M  CHG  1   1   1
M  END
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PDB for HMDB0001327 (Rubidium)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1 Rb   UNK     0      51.926 -33.874   0.000  0.00  0.00          Rb+1
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
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3D PDB for HMDB0001327 (Rubidium)

COMPND    HMDB0001327
HETATM    1 RB1  UNL     1       0.000   0.000   0.000  1.00  0.00          RB1+
END
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SMILES for HMDB0001327 (Rubidium)

[Rb+]
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INCHI for HMDB0001327 (Rubidium)

InChI=1S/Rb/q+1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
RB(+)ChEBI
Rb+ChEBI
RUBIDIUM ionChEBI
Rubidium(1+)Kegg
Rubidium +HMDB
RubidiumHMDB
Chemical FormulaRb
Average Molecular Weight85.4678
Monoisotopic Molecular Weight84.911789341
IUPAC Namerubidium(1+) ion
Traditional Namerubidium(1+) ion
CAS Registry Number7440-17-7
SMILES
[Rb+]
InChI Identifier
InChI=1S/Rb/q+1
InChI KeyNCCSSGKUIKYAJD-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of inorganic compounds known as homogeneous alkali metal compounds. These are inorganic compounds containing only metal atoms,with the largest atom being a alkali metal atom.
KingdomInorganic compounds
Super ClassHomogeneous metal compounds
ClassHomogeneous alkali metal compounds
Sub ClassNot Available
Direct ParentHomogeneous alkali metal compounds
Alternative ParentsNot Available
Substituents
  • Homogeneous alkali metal
Molecular FrameworkNot Available
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point39 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP0ChemAxon
Physiological Charge1ChemAxon
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]+124.44532859911
AllCCS[M-H]-147.77132859911
AllCCS[M+H]+124.432859911
AllCCS[M+H-H2O]+120.732859911
AllCCS[M+NH4]+127.932859911
AllCCS[M+Na]+128.932859911
AllCCS[M-H]-147.832859911
AllCCS[M+Na-2H]-159.532859911
AllCCS[M+HCOO]-172.332859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid282.0 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid894.5 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid426.2 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid193.2 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid352.1 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid206.2 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid315.0 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 Acid370.3 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)594.6 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid649.6 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid170.4 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid743.2 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid287.9 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid377.7 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate685.9 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA367.6 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water300.7 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Rubidium[Rb+]700.3Standard polar33892256
Rubidium[Rb+]211.3Standard non polar33892256
Rubidium[Rb+]65.5Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Rubidium 10V, Positive-QTOFsplash10-001i-9000000000-ddf16821b4f8d12eb7572017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Rubidium 20V, Positive-QTOFsplash10-001i-9000000000-ddf16821b4f8d12eb7572017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Rubidium 40V, Positive-QTOFsplash10-001i-9000000000-ddf16821b4f8d12eb7572017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Rubidium 10V, Positive-QTOFsplash10-001i-9000000000-8be68b59717be150de6f2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Rubidium 20V, Positive-QTOFsplash10-001i-9000000000-8be68b59717be150de6f2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Rubidium 40V, Positive-QTOFsplash10-001i-9000000000-8be68b59717be150de6f2021-09-22Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Saliva
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot Available
Normal
      Not Available
 details
BloodDetected and Quantified1.17-3.18 uMAdult (>18 years old)BothNormal details
Cerebrospinal Fluid (CSF)Detected and Quantified0.499 +/- 0.097 uMAdult (>18 years old)Not SpecifiedNormal details
SalivaDetected and Quantified8.047 +/- 3.15 uMAdult (>18 years old)BothNormal
    • Zerihun T. Dame, ...
 details
SalivaDetected and Quantified0.751 +/- 0.143 uMAdult (>18 years old)Male
Normal		 details
SalivaDetected and Quantified0.808 +/- 0.233 uMAdult (>18 years old)Male
Normal		 details
SalivaDetected and Quantified0.808 +/- 0.233 uMAdult (>18 years old)Male
Normal		 details
SalivaDetected and Quantified0.736 +/- 0.157 uMAdult (>18 years old)Male
Normal		 details
UrineDetected and Quantified1.84 +/- 0.46 umol/mmol creatinineAdult (>18 years old)BothNormal
    • Geigy Scientific ...
    • West Cadwell, N.J...
    • Basel, Switzerlan...
 details
UrineDetected and Quantified1.354 (0.187-3.673) umol/mmol creatinineAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB003783
KNApSAcK IDNot Available
Chemspider ID94865
KEGG Compound IDC17061
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkRubidium
METLIN IDNot Available
PubChem Compound105153
PDB IDNot Available
ChEBI ID49847
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 References
  1. Rizk SL, Sky-Peck HH: Comparison between concentrations of trace elements in normal and neoplastic human breast tissue. Cancer Res. 1984 Nov;44(11):5390-4. [PubMed:6488192 ]
  2. Barany E, Bergdahl IA, Bratteby LE, Lundh T, Samuelson G, Skerfving S, Oskarsson A: Iron status influences trace element levels in human blood and serum. Environ Res. 2005 Jun;98(2):215-23. [PubMed:15820728 ]
  3. Meurling S, Plantin LO: The concentrations of trace elements in blood from healthy newborn infants. Acta Chir Scand. 1981;147(6):481-5. [PubMed:7324778 ]
  4. Cornett CR, Ehmann WD, Wekstein DR, Markesbery WR: Trace elements in Alzheimer's disease pituitary glands. Biol Trace Elem Res. 1998 Apr-May;62(1-2):107-14. [PubMed:9630429 ]
  5. Hagenfeldt K, Landgren BM, Plantin LO, Diczfalusy E: Trace elements in the human endometrium and decidua. A multielement analysis. Acta Endocrinol (Copenh). 1977 Jun;85(2):406-14. [PubMed:577330 ]