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Showing metabocard for Ground limestone (HMDB0303230)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 00:22:03 UTC
Update Date2021-09-24 00:22:03 UTC
HMDB IDHMDB0303230
Secondary Accession NumbersNone
Metabolite Identification
Common NameGround limestone
DescriptionCalcium carbonate, also known as CACO3 or carbonate de calcium, belongs to the class of organic compounds known as organic carbonic acids. Organic carbonic acids are compounds comprising the carbonic acid functional group. Calcium carbonate is a drug which is used for relief of heartburn and acid indigestion. may also be used as a nutritional supplement or to treat hypocalcemia. . Based on a literature review a significant number of articles have been published on Calcium carbonate.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0303230 (Ground limestone)


  Mrv0541 02241215312D          

  5  3  0  0  0  0            999 V2000
   -1.3621   -0.9905    0.0000 Ca  0  2  0  0  0  0  0  0  0  0  0  0
   -0.0409    0.9905    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.3621    0.9905    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.6189    0.5777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6189   -0.2473    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  4  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
M  CHG  3   1   2   2  -1   3  -1
M  END
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3D MOL for HMDB0303230 (Ground limestone)

HMDB0303230
     RDKit          3D
Ground limestone
  5  3  0  0  0  0  0  0  0  0999 V2000
   -0.4766    1.1749    0.1783 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0106    0.0261    0.0040 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8578   -1.0553   -0.0720 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.3450   -0.1456   -0.1102 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Ca  0  0  0  0  0 15  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
M  CHG  3   3  -1   4  -1   5   2
M  END
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3D SDF for HMDB0303230 (Ground limestone)


  Mrv0541 02241215312D          

  5  3  0  0  0  0            999 V2000
   -1.3621   -0.9905    0.0000 Ca  0  2  0  0  0  0  0  0  0  0  0  0
   -0.0409    0.9905    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.3621    0.9905    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.6189    0.5777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6189   -0.2473    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  4  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
M  CHG  3   1   2   2  -1   3  -1
M  END
> <DATABASE_ID>
HMDB0303230

> <DATABASE_NAME>
hmdb

> <SMILES>
[Ca++].[O-]C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/CH2O3.Ca/c2-1(3)4;/h(H2,2,3,4);/q;+2/p-2

> <INCHI_KEY>
VTYYLEPIZMXCLO-UHFFFAOYSA-L

> <FORMULA>
CCaO3

> <MOLECULAR_WEIGHT>
100.087

> <EXACT_MASS>
99.947335021

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
3.515525686064488

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
calcium carbonate

> <ALOGPS_LOGP>
0.47

> <JCHEM_LOGP>
0.25005136566666664

> <ALOGPS_LOGS>
-0.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
10.638414228618219

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.052541895520343

> <JCHEM_POLAR_SURFACE_AREA>
63.19

> <JCHEM_REFRACTIVITY>
31.172400000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.28e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
calcium carbonate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0303230 (Ground limestone)

HMDB0303230
     RDKit          3D
Ground limestone
  5  3  0  0  0  0  0  0  0  0999 V2000
   -0.4766    1.1749    0.1783 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0106    0.0261    0.0040 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8578   -1.0553   -0.0720 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.3450   -0.1456   -0.1102 O   0  0  0  0  0  1  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Ca  0  0  0  0  0 15  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
M  CHG  3   3  -1   4  -1   5   2
M  END
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PDB for HMDB0303230 (Ground limestone)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1 Ca   UNK     0      -2.543  -1.849   0.000  0.00  0.00          Ca+2
HETATM    2  O   UNK     0      -0.076   1.849   0.000  0.00  0.00           O-1
HETATM    3  O   UNK     0       2.543   1.849   0.000  0.00  0.00           O-1
HETATM    4  C   UNK     0       1.155   1.078   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.155  -0.462   0.000  0.00  0.00           O+0
CONECT    2    4                                                            
CONECT    3    4                                                            
CONECT    4    2    3    5                                                  
CONECT    5    4                                                            
MASTER        0    0    0    0    0    0    0    0    5    0    6    0
END
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3D PDB for HMDB0303230 (Ground limestone)

COMPND    HMDB0303230
HETATM    1  O1  UNL     1      -0.477   1.175   0.178  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.011   0.026   0.004  1.00  0.00           C  
HETATM    3  O2  UNL     1      -0.858  -1.055  -0.072  1.00  0.00           O1-
HETATM    4  O3  UNL     1       1.345  -0.146  -0.110  1.00  0.00           O1-
HETATM    5 CA1  UNL     1       0.000   0.000   0.000  1.00  0.00          CA2+
CONECT    1    2    2
CONECT    2    3    4
END
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SMILES for HMDB0303230 (Ground limestone)

[Ca++].[O-]C([O-])=O
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INCHI for HMDB0303230 (Ground limestone)

InChI=1S/CH2O3.Ca/c2-1(3)4;/h(H2,2,3,4);/q;+2/p-2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
CaCO3ChEBI
Calcium carbonate (1:1)ChEBI
CalciumcarbonatChEBI
Carbonate de calciumChEBI
Carbonato de calcioChEBI
Carbonic acid calcium salt (1:1)ChEBI
e 170ChEBI
KalziumkarbonatChEBI
Kohlensaurer kalkChEBI
Precipitated calcium carbonateChEBI
Calcium carbonate, precipitatedKegg
Cal-supKegg
Calcium carbonic acid (1:1)Generator
Carbonic acid de calciumGenerator
Carbonate calcium salt (1:1)Generator
Precipitated calcium carbonic acidGenerator
Calcium carbonic acid, precipitatedGenerator
Calcium carbonic acidGenerator
CalciteMeSH
VateriteMeSH
AragoniteMeSH
Calcium milkMeSH
ChalkMeSH
LimestoneMeSH
Carbonate, calciumMeSH
MarbleMeSH
Milk OF calciumMeSH
Chemical FormulaCCaO3
Average Molecular Weight100.087
Monoisotopic Molecular Weight99.947335021
IUPAC Namecalcium carbonate
Traditional Namecalcium carbonate
CAS Registry NumberNot Available
SMILES
[Ca++].[O-]C([O-])=O
InChI Identifier
InChI=1S/CH2O3.Ca/c2-1(3)4;/h(H2,2,3,4);/q;+2/p-2
InChI KeyVTYYLEPIZMXCLO-UHFFFAOYSA-L
Chemical Taxonomy
Description Belongs to the class of organic compounds known as organic carbonic acids. Organic carbonic acids are compounds comprising the carbonic acid functional group.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassOrganic carbonic acids and derivatives
Sub ClassOrganic carbonic acids
Direct ParentOrganic carbonic acids
Alternative Parents
Substituents
  • Carbonate salt
  • Carbonic acid
  • Organic calcium salt
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organic salt
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect
Organoleptic effect
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
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
logP0.47ALOGPS
logP0.25ChemAxon
logS-0.08ALOGPS
pKa (Strongest Acidic)6.05ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area63.19 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity31.17 m³·mol⁻¹ChemAxon
Polarizability3.52 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]+114.5432859911
AllCCS[M+H-H2O]+110.86332859911
AllCCS[M+Na]+118.95932859911
AllCCS[M+NH4]+117.9732859911
AllCCS[M-H]-67.58332859911
AllCCS[M+Na-2H]-73.732859911
AllCCS[M+HCOO]-80.39332859911
DeepCCS[M+H]+109.51230932474
DeepCCS[M-H]-107.48530932474
DeepCCS[M-2H]-143.26930932474
DeepCCS[M+Na]+117.70430932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1429.0 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid584.5 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid243.2 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid459.8 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid296.6 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid450.8 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 Acid604.5 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)666.5 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid939.3 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid342.9 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1099.4 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid368.8 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid554.2 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate895.2 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA503.3 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water342.5 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Ground limestone GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9000000000-155f3b1435b7efbb0e7b2017-08-28Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ground limestone 10V, Positive-QTOFsplash10-0udi-0900000000-763a74cbb19205ba5b1f2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ground limestone 20V, Positive-QTOFsplash10-0udi-0900000000-763a74cbb19205ba5b1f2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ground limestone 40V, Positive-QTOFsplash10-0udi-0900000000-763a74cbb19205ba5b1f2019-02-22Wishart LabView Spectrum
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 IDDB06724
Phenol Explorer Compound IDNot Available
FooDB IDFDB009528
KNApSAcK IDNot Available
Chemspider ID9708
KEGG Compound IDC08129
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkCalcium_carbonate
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID3311
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1098041
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available