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Showing metabocard for (2R*,3R*)-1,2,3-Butanetriol (HMDB0034778)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2012-09-11 19:42:02 UTC
Update Date2022-03-07 02:54:14 UTC
HMDB IDHMDB0034778
Secondary Accession Numbers
  • HMDB34778
Metabolite Identification
Common Name(2R*,3R*)-1,2,3-Butanetriol
Description(2R*,3R*)-1,2,3-Butanetriol, also known as 1,2,3-trihydroxybutane, belongs to the class of organic compounds known as secondary alcohols. Secondary alcohols are compounds containing a secondary alcohol functional group, with the general structure HOC(R)(R') (R,R'=alkyl, aryl) (2R*,3R*)-1,2,3-Butanetriol has been detected, but not quantified in, herbs and spices. This could make (2R*,3R*)-1,2,3-butanetriol a potential biomarker for the consumption of these foods. Based on a literature review a small amount of articles have been published on (2R*,3R*)-1,2,3-Butanetriol.
Structure
Data?1563862617
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0034778 ((2R*,3R*)-1,2,3-Butanetriol)


  Mrv0541 02241209282D          

  7  6  0  0  0  0            999 V2000
    1.0697   -1.0690    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3743   -0.6417    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3743    0.1599    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3483    0.5873    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3483    1.0690    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8016    0.5615    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0697    0.1871    0.0000 C   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
  3  4  1  0  0  0  0
  3  6  1  0  0  0  0
  4  5  1  0  0  0  0
  4  7  1  0  0  0  0
M  END
Download

3D MOL for HMDB0034778 ((2R*,3R*)-1,2,3-Butanetriol)

HMDB0243859
     RDKit          3D
1-Deoxy-D-erythritol
 17 16  0  0  0  0  0  0  0  0999 V2000
    1.7323    0.4698   -0.2582 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9009   -0.6312    0.3672 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0160   -0.5254    1.7276 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4917   -0.6366   -0.1676 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4181   -0.7492   -1.5525 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3149    0.5616    0.1843 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5894    0.3647   -0.3666 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2799    1.4552   -0.0462 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7241    0.4517    0.2699 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8987    0.3010   -1.3400 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3780   -1.5858    0.0586 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6797    0.2840    2.1317 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0406   -1.5343    0.1884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4455    0.1161   -2.0190 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9343    1.5004   -0.3121 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4671    0.7190    1.2484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9079   -0.5611   -0.1139 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
  4 13  1  0
  5 14  1  0
  6 15  1  0
  6 16  1  0
  7 17  1  0
M  END
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3D SDF for HMDB0034778 ((2R*,3R*)-1,2,3-Butanetriol)


  Mrv0541 02241209282D          

  7  6  0  0  0  0            999 V2000
    1.0697   -1.0690    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3743   -0.6417    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3743    0.1599    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3483    0.5873    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3483    1.0690    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8016    0.5615    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0697    0.1871    0.0000 C   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
  3  4  1  0  0  0  0
  3  6  1  0  0  0  0
  4  5  1  0  0  0  0
  4  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0034778

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(O)C(O)CO

> <INCHI_IDENTIFIER>
InChI=1S/C4H10O3/c1-3(6)4(7)2-5/h3-7H,2H2,1H3

> <INCHI_KEY>
YAXKTBLXMTYWDQ-UHFFFAOYSA-N

> <FORMULA>
C4H10O3

> <MOLECULAR_WEIGHT>
106.1204

> <EXACT_MASS>
106.062994186

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
10.7900574015348

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
butane-1,2,3-triol

> <ALOGPS_LOGP>
-1.75

> <JCHEM_LOGP>
-1.4224389979999998

> <ALOGPS_LOGS>
0.97

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.060910413712342

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.38427309510853

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9717943057235576

> <JCHEM_POLAR_SURFACE_AREA>
60.69

> <JCHEM_REFRACTIVITY>
24.9349

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.96e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1,2,3-trihydroxybutane

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0034778 ((2R*,3R*)-1,2,3-Butanetriol)

HMDB0243859
     RDKit          3D
1-Deoxy-D-erythritol
 17 16  0  0  0  0  0  0  0  0999 V2000
    1.7323    0.4698   -0.2582 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9009   -0.6312    0.3672 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0160   -0.5254    1.7276 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4917   -0.6366   -0.1676 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4181   -0.7492   -1.5525 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3149    0.5616    0.1843 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5894    0.3647   -0.3666 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2799    1.4552   -0.0462 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7241    0.4517    0.2699 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8987    0.3010   -1.3400 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3780   -1.5858    0.0586 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6797    0.2840    2.1317 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0406   -1.5343    0.1884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4455    0.1161   -2.0190 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9343    1.5004   -0.3121 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4671    0.7190    1.2484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9079   -0.5611   -0.1139 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
  4 13  1  0
  5 14  1  0
  6 15  1  0
  6 16  1  0
  7 17  1  0
M  END
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PDB for HMDB0034778 ((2R*,3R*)-1,2,3-Butanetriol)

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  O   UNK     0       1.997  -1.996   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       0.699  -1.198   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.699   0.298   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.650   1.096   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -0.650   1.996   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       1.496   1.048   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -1.997   0.349   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    6                                                  
CONECT    4    3    5    7                                                  
CONECT    5    4                                                            
CONECT    6    3                                                            
CONECT    7    4                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for HMDB0034778 ((2R*,3R*)-1,2,3-Butanetriol)

COMPND    HMDB0243859
HETATM    1  C1  UNL     1       1.732   0.470  -0.258  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.901  -0.631   0.367  1.00  0.00           C  
HETATM    3  O1  UNL     1       1.016  -0.525   1.728  1.00  0.00           O  
HETATM    4  C3  UNL     1      -0.492  -0.637  -0.168  1.00  0.00           C  
HETATM    5  O2  UNL     1      -0.418  -0.749  -1.552  1.00  0.00           O  
HETATM    6  C4  UNL     1      -1.315   0.562   0.184  1.00  0.00           C  
HETATM    7  O3  UNL     1      -2.589   0.365  -0.367  1.00  0.00           O  
HETATM    8  H1  UNL     1       1.280   1.455  -0.046  1.00  0.00           H  
HETATM    9  H2  UNL     1       2.724   0.452   0.270  1.00  0.00           H  
HETATM   10  H3  UNL     1       1.899   0.301  -1.340  1.00  0.00           H  
HETATM   11  H4  UNL     1       1.378  -1.586   0.059  1.00  0.00           H  
HETATM   12  H5  UNL     1       0.680   0.284   2.132  1.00  0.00           H  
HETATM   13  H6  UNL     1      -1.041  -1.534   0.188  1.00  0.00           H  
HETATM   14  H7  UNL     1      -0.445   0.116  -2.019  1.00  0.00           H  
HETATM   15  H8  UNL     1      -0.934   1.500  -0.312  1.00  0.00           H  
HETATM   16  H9  UNL     1      -1.467   0.719   1.248  1.00  0.00           H  
HETATM   17  H10 UNL     1      -2.908  -0.561  -0.114  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3    4   11
CONECT    3   12
CONECT    4    5    6   13
CONECT    5   14
CONECT    6    7   15   16
CONECT    7   17
END
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SMILES for HMDB0034778 ((2R*,3R*)-1,2,3-Butanetriol)

CC(O)C(O)CO
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INCHI for HMDB0034778 ((2R*,3R*)-1,2,3-Butanetriol)

InChI=1S/C4H10O3/c1-3(6)4(7)2-5/h3-7H,2H2,1H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
1,2,3-TrihydroxybutaneChEBI
Chemical FormulaC4H10O3
Average Molecular Weight106.1204
Monoisotopic Molecular Weight106.062994186
IUPAC Namebutane-1,2,3-triol
Traditional Name1,2,3-trihydroxybutane
CAS Registry NumberNot Available
SMILES
CC(O)C(O)CO
InChI Identifier
InChI=1S/C4H10O3/c1-3(6)4(7)2-5/h3-7H,2H2,1H3
InChI KeyYAXKTBLXMTYWDQ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as secondary alcohols. Secondary alcohols are compounds containing a secondary alcohol functional group, with the general structure HOC(R)(R') (R,R'=alkyl, aryl).
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassAlcohols and polyols
Direct ParentSecondary alcohols
Alternative Parents
Substituents
  • Secondary alcohol
  • Polyol
  • Hydrocarbon derivative
  • Primary alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
Role
Biological role
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
Water Solubility996 g/LALOGPS
logP-1.8ALOGPS
logP-1.4ChemAxon
logS0.97ALOGPS
pKa (Strongest Acidic)13.38ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area60.69 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity24.93 m³·mol⁻¹ChemAxon
Polarizability10.79 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
DarkChem[M+H]+121.55531661259
DarkChem[M-H]-115.00131661259
DeepCCS[M+H]+123.50930932474
DeepCCS[M-H]-121.16230932474
DeepCCS[M-2H]-157.27530932474
DeepCCS[M+Na]+131.80730932474
AllCCS[M+H]+128.532859911
AllCCS[M+H-H2O]+124.232859911
AllCCS[M+NH4]+132.532859911
AllCCS[M+Na]+133.732859911
AllCCS[M-H]-124.032859911
AllCCS[M+Na-2H]-127.932859911
AllCCS[M+HCOO]-132.232859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. 1.06 minutes32390414
Predicted by Siyang on May 30, 20229.2285 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.65 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid255.6 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
(2R*,3R*)-1,2,3-ButanetriolCC(O)C(O)CO2158.5Standard polar33892256
(2R*,3R*)-1,2,3-ButanetriolCC(O)C(O)CO996.3Standard non polar33892256
(2R*,3R*)-1,2,3-ButanetriolCC(O)C(O)CO1020.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
(2R*,3R*)-1,2,3-Butanetriol,1TMS,isomer #1CC(O[Si](C)(C)C)C(O)CO1139.5Semi standard non polar33892256
(2R*,3R*)-1,2,3-Butanetriol,1TMS,isomer #2CC(O)C(CO)O[Si](C)(C)C1102.8Semi standard non polar33892256
(2R*,3R*)-1,2,3-Butanetriol,1TMS,isomer #3CC(O)C(O)CO[Si](C)(C)C1123.4Semi standard non polar33892256
(2R*,3R*)-1,2,3-Butanetriol,2TMS,isomer #1CC(O[Si](C)(C)C)C(CO)O[Si](C)(C)C1207.7Semi standard non polar33892256
(2R*,3R*)-1,2,3-Butanetriol,2TMS,isomer #2CC(O[Si](C)(C)C)C(O)CO[Si](C)(C)C1212.2Semi standard non polar33892256
(2R*,3R*)-1,2,3-Butanetriol,2TMS,isomer #3CC(O)C(CO[Si](C)(C)C)O[Si](C)(C)C1212.2Semi standard non polar33892256
(2R*,3R*)-1,2,3-Butanetriol,3TMS,isomer #1CC(O[Si](C)(C)C)C(CO[Si](C)(C)C)O[Si](C)(C)C1300.5Semi standard non polar33892256
(2R*,3R*)-1,2,3-Butanetriol,1TBDMS,isomer #1CC(O[Si](C)(C)C(C)(C)C)C(O)CO1365.9Semi standard non polar33892256
(2R*,3R*)-1,2,3-Butanetriol,1TBDMS,isomer #2CC(O)C(CO)O[Si](C)(C)C(C)(C)C1345.8Semi standard non polar33892256
(2R*,3R*)-1,2,3-Butanetriol,1TBDMS,isomer #3CC(O)C(O)CO[Si](C)(C)C(C)(C)C1341.9Semi standard non polar33892256
(2R*,3R*)-1,2,3-Butanetriol,2TBDMS,isomer #1CC(O[Si](C)(C)C(C)(C)C)C(CO)O[Si](C)(C)C(C)(C)C1638.1Semi standard non polar33892256
(2R*,3R*)-1,2,3-Butanetriol,2TBDMS,isomer #2CC(O[Si](C)(C)C(C)(C)C)C(O)CO[Si](C)(C)C(C)(C)C1637.0Semi standard non polar33892256
(2R*,3R*)-1,2,3-Butanetriol,2TBDMS,isomer #3CC(O)C(CO[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C1637.0Semi standard non polar33892256
(2R*,3R*)-1,2,3-Butanetriol,3TBDMS,isomer #1CC(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C1905.1Semi standard non polar33892256
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen Locations
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothBladder cancer details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB013331
KNApSAcK IDNot Available
Chemspider ID19304
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound20497
PDB IDNot Available
ChEBI ID131388
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. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .