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Showing metabocard for beta-Gentiobiose (HMDB0341292)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2022-09-09 20:13:26 UTC
Update Date2022-09-22 18:34:46 UTC
HMDB IDHMDB0341292
Secondary Accession NumbersNone
Metabolite Identification
Common Namebeta-Gentiobiose
Descriptionbeta-D-Glcp-(1->6)-beta-D-Glcp, also known as b-D-GLC-(1->6)-b-D-GLC or beta-gentiobiose, belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond. beta-D-Glcp-(1->6)-beta-D-Glcp is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
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MOLSDFPDBSMILESInChI

MOL for HMDB0341292 (beta-Gentiobiose)


  Mrv1652309272006272D          

 23 24  0  0  0  0            999 V2000
 9998.8937 9998.8296    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.6084 9999.2415    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.037110000.0673    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.4700 9999.2415    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.0371 9996.7641    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.4700 9997.5899    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.463410001.3061    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.748310001.7190    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.4634 9998.0038    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9996.0330 9998.8296    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9996.033010000.4803    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.463410000.4796    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9996.749010000.0671    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9996.7490 9999.2421    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9997.4634 9998.8297    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9998.1778 9999.2421    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9998.177810000.0671    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.0385 9999.2414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10000.3241 9998.8289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10000.3241 9998.0039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.0385 9997.5915    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10001.7530 9998.0039    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10001.7530 9998.8289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  7  8  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 18 19  1  0  0  0  0
 18 23  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 12 17  1  0  0  0  0
 16 17  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 16  1  1  1  0  0  0
 12  7  1  1  0  0  0
 13 11  1  6  0  0  0
 14 10  1  1  0  0  0
 15  9  1  6  0  0  0
 19  2  1  6  0  0  0
 18  3  1  1  0  0  0
 23  4  1  6  0  0  0
 22  6  1  1  0  0  0
 21  5  1  6  0  0  0
M  END
Download

3D MOL for HMDB0341292 (beta-Gentiobiose)

Download
3D SDF for HMDB0341292 (beta-Gentiobiose)

  Mrv1652309272006272D          

 23 24  0  0  0  0            999 V2000
 9998.8937 9998.8296    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.6084 9999.2415    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.037110000.0673    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.4700 9999.2415    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.0371 9996.7641    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.4700 9997.5899    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.463410001.3061    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.748310001.7190    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.4634 9998.0038    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9996.0330 9998.8296    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9996.033010000.4803    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.463410000.4796    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9996.749010000.0671    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9996.7490 9999.2421    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9997.4634 9998.8297    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9998.1778 9999.2421    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9998.177810000.0671    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.0385 9999.2414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10000.3241 9998.8289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10000.3241 9998.0039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.0385 9997.5915    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10001.7530 9998.0039    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10001.7530 9998.8289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  7  8  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 18 19  1  0  0  0  0
 18 23  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 12 17  1  0  0  0  0
 16 17  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 16  1  1  1  0  0  0
 12  7  1  1  0  0  0
 13 11  1  6  0  0  0
 14 10  1  1  0  0  0
 15  9  1  6  0  0  0
 19  2  1  6  0  0  0
 18  3  1  1  0  0  0
 23  4  1  6  0  0  0
 22  6  1  1  0  0  0
 21  5  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0341292

> <DATABASE_NAME>
hmdb

> <SMILES>
OC[C@H]1O[C@@H](OC[C@H]2O[C@@H](O)[C@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C12H22O11/c13-1-3-5(14)8(17)10(19)12(23-3)21-2-4-6(15)7(16)9(18)11(20)22-4/h3-20H,1-2H2/t3-,4-,5-,6-,7+,8+,9-,10-,11-,12-/m1/s1

> <INCHI_KEY>
DLRVVLDZNNYCBX-LIZSDCNHSA-N

> <FORMULA>
C12H22O11

> <MOLECULAR_WEIGHT>
342.297

> <EXACT_MASS>
342.116211528

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
45

> <JCHEM_AVERAGE_POLARIZABILITY>
31.51626803420827

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5S,6R)-6-({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxane-2,3,4,5-tetrol

> <ALOGPS_LOGP>
-3.00

> <JCHEM_LOGP>
-4.703374863666666

> <ALOGPS_LOGS>
0.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.133081366054801

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.248198780146973

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981083422322401

> <JCHEM_POLAR_SURFACE_AREA>
189.52999999999997

> <JCHEM_REFRACTIVITY>
68.33670000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.11e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
gentiobiose

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for HMDB0341292 (beta-Gentiobiose)
Download
PDB for HMDB0341292 (beta-Gentiobiose)
HEADER    PROTEIN                                 27-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-SEP-20         0                                  
HETATM    1  O   UNK     0    8664.6028664.482   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0    8665.9368665.251   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0    8668.6038666.792   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0    8671.2778665.251   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8668.6038660.626   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8671.2778662.168   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0    8661.9328669.105   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0    8660.5978669.875   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0    8661.9328662.940   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0    8659.2628664.482   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0    8659.2628667.563   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0    8661.9328667.562   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0    8660.5988666.792   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0    8660.5988665.252   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8661.9328664.482   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8663.2658665.252   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0    8663.2658666.792   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0    8668.6058665.251   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0    8667.2728664.481   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0    8667.2728662.941   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0    8668.6058662.171   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0    8669.9398662.941   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0    8669.9398664.481   0.000  0.00  0.00           C+0
CONECT    1    2   16                                                       
CONECT    2    1   19                                                       
CONECT    3   18                                                            
CONECT    4   23                                                            
CONECT    5   21                                                            
CONECT    6   22                                                            
CONECT    7    8   12                                                       
CONECT    8    7                                                            
CONECT    9   15                                                            
CONECT   10   14                                                            
CONECT   11   13                                                            
CONECT   12   13   17    7                                                  
CONECT   13   12   14   11                                                  
CONECT   14   13   15   10                                                  
CONECT   15   14   16    9                                                  
CONECT   16   15   17    1                                                  
CONECT   17   12   16                                                       
CONECT   18   19   23    3                                                  
CONECT   19   18   20    2                                                  
CONECT   20   19   21                                                       
CONECT   21   22   20    5                                                  
CONECT   22   21   23    6                                                  
CONECT   23   18   22    4                                                  
MASTER        0    0    0    0    0    0    0    0   23    0   48    0
END

Download
3D PDB for HMDB0341292 (beta-Gentiobiose)
Download
SMILES for HMDB0341292 (beta-Gentiobiose)
OC[C@H]1O[C@@H](OC[C@H]2O[C@@H](O)[C@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@@H](O)[C@@H]1O
Download
INCHI for HMDB0341292 (beta-Gentiobiose)
InChI=1S/C12H22O11/c13-1-3-5(14)8(17)10(19)12(23-3)21-2-4-6(15)7(16)9(18)11(20)22-4/h3-20H,1-2H2/t3-,4-,5-,6-,7+,8+,9-,10-,11-,12-/m1/s1
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
6-O-beta-D-Glucopyranosyl-beta-D-glucopyranoseChEBI
beta-D-GLC-(1->6)-beta-D-GLCChEBI
beta-D-Glucosyl-(1->6)-beta-D-glucoseChEBI
beta-GentiobioseChEBI
GLCB1-6GLCBChEBI
Glcbeta1-6glcbetaChEBI
6-O-b-D-Glucopyranosyl-b-D-glucopyranoseGenerator
6-O-Β-D-glucopyranosyl-β-D-glucopyranoseGenerator
b-D-GLC-(1->6)-b-D-GLCGenerator
Β-D-GLC-(1->6)-β-D-GLCGenerator
b-D-Glucosyl-(1->6)-b-D-glucoseGenerator
Β-D-glucosyl-(1->6)-β-D-glucoseGenerator
b-GentiobioseGenerator
Β-gentiobioseGenerator
b-D-GLCP-(1->6)-b-D-GLCPGenerator
Β-D-GLCP-(1->6)-β-D-GLCPGenerator
AmygdaloseMeSH
D-GentiobioseMeSH
6-O-beta-D-Glucopyranosyl-D-glucosePhytoBank
6-O-β-D-Glucopyranosyl-D-glucosePhytoBank
6-(beta-D-Glucosido)-D-glucosePhytoBank
6-(β-D-Glucosido)-D-glucosePhytoBank
6-O-beta-D-glucopyranosyl-D-glucopyranosePhytoBank
6-O-β-D-glucopyranosyl-D-glucopyranosePhytoBank
beta-D-Glc-(1->6)-D-GlcPhytoBank
β-D-Glc-(1→6)-D-GlcPhytoBank
beta-D-Glcp-(1->6)-D-GlcpPhytoBank
β-D-Glcp-(1→6)-D-GlcpPhytoBank
beta-D-glucopyranosyl-(1->6)-D-glucosePhytoBank
β-D-glucopyranosyl-(1→6)-D-glucosePhytoBank
beta-D-glucosyl-(1->6)-D-glucosePhytoBank
β-D-glucosyl-(1→6)-D-glucosePhytoBank
D-Glc(beta1->6)D-GlcPhytoBank
D-Glc(β1→6)D-GlcPhytoBank
beta-D-Glc-(1→6)-D-GlcPhytoBank
beta-D-Glcp-(1→6)-D-GlcpPhytoBank
beta-D-glucopyranosyl-(1→6)-D-glucosePhytoBank
beta-D-glucosyl-(1→6)-D-glucosePhytoBank
D-Glc(beta1→6)D-GlcPhytoBank
Chemical FormulaC12H22O11
Average Molecular Weight342.297
Monoisotopic Molecular Weight342.116211528
IUPAC Name(2R,3R,4S,5S,6R)-6-({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxane-2,3,4,5-tetrol
Traditional Namegentiobiose
CAS Registry NumberNot Available
SMILES
OC[C@H]1O[C@@H](OC[C@H]2O[C@@H](O)[C@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C12H22O11/c13-1-3-5(14)8(17)10(19)12(23-3)21-2-4-6(15)7(16)9(18)11(20)22-4/h3-20H,1-2H2/t3-,4-,5-,6-,7+,8+,9-,10-,11-,12-/m1/s1
InChI KeyDLRVVLDZNNYCBX-LIZSDCNHSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbohydrates and carbohydrate conjugates  
Direct ParentO-glycosyl compounds  
Alternative Parents
Substituents
  • O-glycosyl compound
    • 

  • Disaccharide
    • 

  • Oxane
    • 

  • Secondary alcohol
    • 

  • Hemiacetal
    • 

  • Oxacycle
    • 

  • Organoheterocyclic compound
    • 

  • Polyol
    • 

  • Acetal
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • Alcohol
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Not AvailableNot 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
logP-3ALOGPS
logP-4.7ChemAxon
logS0.17ALOGPS
pKa (Strongest Acidic)11.25ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count11ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area189.53 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity68.34 m³·mol⁻¹ChemAxon
Polarizability31.52 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties
Predicted Kovats Retention Indices
Not Available
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
    • 

  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation  details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation  details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID390156  
KEGG Compound IDC08240  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound441422  
PDB IDNot Available
ChEBI ID71422  
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. Simon-Manso Y, Marupaka R, Yan X, Liang Y, Telu KH, Mirokhin Y, Stein SE: Mass Spectrometry Fingerprints of Small-Molecule Metabolites in Biofluids: Building a Spectral Library of Recurrent Spectra for Urine Analysis. Anal Chem. 2019 Sep 17;91(18):12021-12029. doi: 10.1021/acs.analchem.9b02977. Epub 2019 Aug 30. [PubMed:31424920  ]