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

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (1) Show 1 proteinXML
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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
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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
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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
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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

$$$$
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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
Predicted Chromatographic Properties
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 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
  3. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [PubMed:10592235 ]