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Showing metabocard for (2R,3R)-2,3-Butanediol (HMDB0033007)

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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 Date2012-09-11 17:53:12 UTC
Update Date2023-02-21 17:22:59 UTC
HMDB IDHMDB0033007
Secondary Accession Numbers
  • HMDB33007
Metabolite Identification
Common Name(2R,3R)-2,3-Butanediol
Description(2R,3R)-2,3-Butanediol is found in cocoa and cocoa products. (2R,3R)-2,3-Butanediol is isolated from cocoa butter and roots of Ruta graveolens (rue).2,3-Butanediol is one of the constitutional isomers of butanediol. The 2R,3R stereoisomer of 2,3-butanediol is produced by a variety of microorganisms, in a process known as butanediol fermentation. It is found in cocoa butter and in the roots of Ruta graveolens. (Wikipedia).
Structure
Data?1677000178
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0033007 ((2R,3R)-2,3-Butanediol)


  Mrv0541 02241220092D          

  6  5  0  0  0  0            999 V2000
    0.3857    0.0019    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7864    0.7230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8027   -0.7399    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3904    0.0019    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8273    0.7017    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8041   -0.7092    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  4  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  1  0  0  0
  1  6  1  1  0  0  0
M  END
Download

3D MOL for HMDB0033007 ((2R,3R)-2,3-Butanediol)

HMDB0033007
     RDKit          3D
(2R,3R)-2,3-Butanediol
 16 15  0  0  0  0  0  0  0  0999 V2000
   -1.9219    0.5675   -0.1262 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6011    0.1234    0.4765 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6850   -1.1440    1.0488 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4996    0.1747   -0.5734 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8212   -0.0360    0.1235 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2920   -0.7150   -1.5914 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3596   -0.2156   -0.7815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6731    1.4767   -0.7444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6203    0.9127    0.6603 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3833    0.8292    1.3016 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0120   -1.2491    1.7450 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4953    1.1972   -1.0088 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3739   -0.8944   -0.3207 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6994   -0.2445    1.1939 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4937    0.8578   -0.0082 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5572   -1.6408   -1.3949 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
  1  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  1
  3 11  1  0
  4 12  1  6
  5 13  1  0
  5 14  1  0
  5 15  1  0
  6 16  1  0
M  END
Download

3D SDF for HMDB0033007 ((2R,3R)-2,3-Butanediol)


  Mrv0541 02241220092D          

  6  5  0  0  0  0            999 V2000
    0.3857    0.0019    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7864    0.7230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8027   -0.7399    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3904    0.0019    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8273    0.7017    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8041   -0.7092    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  4  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  1  0  0  0
  1  6  1  1  0  0  0
M  END
> <DATABASE_ID>
HMDB0033007

> <DATABASE_NAME>
hmdb

> <SMILES>
C[C@@H](O)[C@@H](C)O

> <INCHI_IDENTIFIER>
InChI=1S/C4H10O2/c1-3(5)4(2)6/h3-6H,1-2H3/t3-,4-/m1/s1

> <INCHI_KEY>
OWBTYPJTUOEWEK-QWWZWVQMSA-N

> <FORMULA>
C4H10O2

> <MOLECULAR_WEIGHT>
90.121

> <EXACT_MASS>
90.068079564

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
9.818183938702159

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R)-butane-2,3-diol

> <ALOGPS_LOGP>
-0.59

> <JCHEM_LOGP>
-0.37552903133333315

> <ALOGPS_LOGS>
0.83

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.678062098346835

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.224481598439645

> <JCHEM_PKA_STRONGEST_BASIC>
-3.006341228739074

> <JCHEM_POLAR_SURFACE_AREA>
40.46

> <JCHEM_REFRACTIVITY>
23.391199999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.03e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(R,R)-butane-2,3-diol

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0033007 ((2R,3R)-2,3-Butanediol)

HMDB0033007
     RDKit          3D
(2R,3R)-2,3-Butanediol
 16 15  0  0  0  0  0  0  0  0999 V2000
   -1.9219    0.5675   -0.1262 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6011    0.1234    0.4765 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6850   -1.1440    1.0488 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4996    0.1747   -0.5734 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8212   -0.0360    0.1235 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2920   -0.7150   -1.5914 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3596   -0.2156   -0.7815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6731    1.4767   -0.7444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6203    0.9127    0.6603 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3833    0.8292    1.3016 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0120   -1.2491    1.7450 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4953    1.1972   -1.0088 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3739   -0.8944   -0.3207 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6994   -0.2445    1.1939 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4937    0.8578   -0.0082 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5572   -1.6408   -1.3949 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
  1  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  1
  3 11  1  0
  4 12  1  6
  5 13  1  0
  5 14  1  0
  5 15  1  0
  6 16  1  0
M  END
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PDB for HMDB0033007 ((2R,3R)-2,3-Butanediol)

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  C   UNK     0       0.720   0.004   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.468   1.350   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.498  -1.381   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.729   0.004   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -1.544   1.310   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       1.501  -1.324   0.000  0.00  0.00           O+0
CONECT    1    2    4    6                                                  
CONECT    2    1                                                            
CONECT    3    4                                                            
CONECT    4    1    3    5                                                  
CONECT    5    4                                                            
CONECT    6    1                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   10    0
END
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3D PDB for HMDB0033007 ((2R,3R)-2,3-Butanediol)

COMPND    HMDB0033007
HETATM    1  C1  UNL     1      -1.922   0.567  -0.126  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.601   0.123   0.476  1.00  0.00           C  
HETATM    3  O1  UNL     1      -0.685  -1.144   1.049  1.00  0.00           O  
HETATM    4  C3  UNL     1       0.500   0.175  -0.573  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.821  -0.036   0.123  1.00  0.00           C  
HETATM    6  O2  UNL     1       0.292  -0.715  -1.591  1.00  0.00           O  
HETATM    7  H1  UNL     1      -2.360  -0.216  -0.781  1.00  0.00           H  
HETATM    8  H2  UNL     1      -1.673   1.477  -0.744  1.00  0.00           H  
HETATM    9  H3  UNL     1      -2.620   0.913   0.660  1.00  0.00           H  
HETATM   10  H4  UNL     1      -0.383   0.829   1.302  1.00  0.00           H  
HETATM   11  H5  UNL     1       0.012  -1.249   1.745  1.00  0.00           H  
HETATM   12  H6  UNL     1       0.495   1.197  -1.009  1.00  0.00           H  
HETATM   13  H7  UNL     1       2.374  -0.894  -0.321  1.00  0.00           H  
HETATM   14  H8  UNL     1       1.699  -0.244   1.194  1.00  0.00           H  
HETATM   15  H9  UNL     1       2.494   0.858  -0.008  1.00  0.00           H  
HETATM   16  H10 UNL     1       0.557  -1.641  -1.395  1.00  0.00           H  
CONECT    1    2    7    8    9
CONECT    2    3    4   10
CONECT    3   11
CONECT    4    5    6   12
CONECT    5   13   14   15
CONECT    6   16
END
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SMILES for HMDB0033007 ((2R,3R)-2,3-Butanediol)

C[C@@H](O)[C@@H](C)O
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INCHI for HMDB0033007 ((2R,3R)-2,3-Butanediol)

InChI=1S/C4H10O2/c1-3(5)4(2)6/h3-6H,1-2H3/t3-,4-/m1/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
(R,R)-(-)-Butane-2,3-diolChEBI
(R,R)-2,3-ButanediolChEBI
(R,R)-2,3-Butylene glycolChEBI
(-)-(2R,3R)-ButanediolHMDB
(-)-2,3-ButanediolHMDB
(2R,3R)-(-)-2,3-ButanediolHMDB
(2R,3R)-Butane-2,3-diolHMDB
L-(-)-2,3-ButanediolHMDB
levo-2,3-ButanediolHMDB
Chemical FormulaC4H10O2
Average Molecular Weight90.121
Monoisotopic Molecular Weight90.068079564
IUPAC Name(2R,3R)-butane-2,3-diol
Traditional Name(R,R)-butane-2,3-diol
CAS Registry Number24347-58-8
SMILES
C[C@@H](O)[C@@H](C)O
InChI Identifier
InChI=1S/C4H10O2/c1-3(5)4(2)6/h3-6H,1-2H3/t3-,4-/m1/s1
InChI KeyOWBTYPJTUOEWEK-QWWZWVQMSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 1,2-diols. These are polyols containing an alcohol group at two adjacent positions.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassAlcohols and polyols
Direct Parent1,2-diols
Alternative Parents
Substituents
  • Secondary alcohol
  • 1,2-diol
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Industrial applicationBiological role
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point19.7 °CNot Available
Boiling Point77.00 to 78.00 °C. @ 10.00 mm HgThe Good Scents Company Information System
Water Solubility759300 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP0.88Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility603 g/LALOGPS
logP-0.59ALOGPS
logP-0.38ChemAxon
logS0.83ALOGPS
pKa (Strongest Acidic)14.22ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area40.46 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity23.39 m³·mol⁻¹ChemAxon
Polarizability9.82 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]+117.95431661259
DarkChem[M-H]-114.71131661259
DeepCCS[M+H]+125.39430932474
DeepCCS[M-H]-122.84830932474
DeepCCS[M-2H]-158.87730932474
DeepCCS[M+Na]+133.6930932474
AllCCS[M+H]+126.332859911
AllCCS[M+H-H2O]+122.032859911
AllCCS[M+NH4]+130.432859911
AllCCS[M+Na]+131.632859911
AllCCS[M-H]-127.332859911
AllCCS[M+Na-2H]-132.032859911
AllCCS[M+HCOO]-137.132859911

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. 0.77 minutes32390414
Predicted by Siyang on May 30, 20229.0387 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.63 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid179.3 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid933.7 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid337.0 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid65.0 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid205.6 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid48.7 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid264.1 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 Acid257.7 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)122.0 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid602.3 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid137.2 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid749.1 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid193.2 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid254.4 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate478.4 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA319.0 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water170.0 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
(2R,3R)-2,3-ButanediolC[C@@H](O)[C@@H](C)O1549.7Standard polar33892256
(2R,3R)-2,3-ButanediolC[C@@H](O)[C@@H](C)O760.1Standard non polar33892256
(2R,3R)-2,3-ButanediolC[C@@H](O)[C@@H](C)O753.7Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
(2R,3R)-2,3-Butanediol,1TMS,isomer #1C[C@@H](O)[C@@H](C)O[Si](C)(C)C901.5Semi standard non polar33892256
(2R,3R)-2,3-Butanediol,2TMS,isomer #1C[C@@H](O[Si](C)(C)C)[C@@H](C)O[Si](C)(C)C1028.0Semi standard non polar33892256
(2R,3R)-2,3-Butanediol,1TBDMS,isomer #1C[C@@H](O)[C@@H](C)O[Si](C)(C)C(C)(C)C1123.9Semi standard non polar33892256
(2R,3R)-2,3-Butanediol,2TBDMS,isomer #1C[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H](C)O[Si](C)(C)C(C)(C)C1483.2Semi standard non polar33892256
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
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 IDFDB010997
KNApSAcK IDNot Available
Chemspider ID196452
KEGG Compound IDC03044
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound225936
PDB IDNot Available
ChEBI ID16982
Food Biomarker OntologyNot Available
VMH IDBTD_RR
MarkerDB IDNot Available
Good Scents IDrw1138431
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.. .

Enzymes

Enzyme Details
1. Ubiquitin-conjugating enzyme E2 D2
General function:
Involved in acid-amino acid ligase activity
Specific function:
Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-48'-linked polyubiquitination. Mediates the selective degradation of short-lived and abnormal proteins. Functions in the E6/E6-AP-induced ubiquitination of p53/TP53. Mediates ubiquitination of PEX5 and autoubiquitination of STUB1 and TRAF6. Involved in the signal-induced conjugation and subsequent degradation of NFKBIA, FBXW2-mediated GCM1 ubiquitination and degradation, MDM2-dependent degradation of p53/TP53 and the activation of MAVS in the mitochondria by DDX58/RIG-I in response to viral infection. Essential for viral activation of IRF3.
Gene Name:
UBE2D2
Uniprot ID:
P62837
Molecular weight:
16735.06
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
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