MiMeDB: Showing metabocard for D-Xylotriose (MMDBc0057112)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-10-17 17:53:43 UTC

Update Date

2022-10-17 17:53:43 UTC

Metabolite ID

MMDBc0057112

Metabolite Identification

Common Name

D-Xylotriose

Description

xylotriose, also known as (xyl)3 or xylosaccharide, belongs to the class of organic compounds known as oligosaccharides. These are carbohydrates made up of 3 to 10 monosaccharide units linked to each other through glycosidic bonds. Based on a literature review a significant number of articles have been published on xylotriose.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652310172219532D          

 28 30  0  0  1  0            999 V2000
    3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -5.3625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5724   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -6.6000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2868   -7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -7.8375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -7.4250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.4302   -7.8375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -8.6625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.1447   -9.0750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -9.9000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302  -10.3125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302  -11.1375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -9.9000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.0013  -10.3125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -9.0750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.0013   -8.6625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -6.6000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.4302   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -6.1875    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.0013   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.9500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  1  0  0  0
  7  6  1  1  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  6  0  0  0
 12 11  1  6  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
 15 17  1  0  0  0  0
 17 18  1  6  0  0  0
 17 19  1  0  0  0  0
 12 19  1  0  0  0  0
 19 20  1  1  0  0  0
 10 21  1  0  0  0  0
 21 22  1  1  0  0  0
 21 23  1  0  0  0  0
  7 23  1  0  0  0  0
 23 24  1  6  0  0  0
  5 25  1  0  0  0  0
 25 26  1  6  0  0  0
 25 27  1  0  0  0  0
  2 27  1  0  0  0  0
 27 28  1  1  0  0  0
M  END


  Mrv1652310172219532D          

 28 30  0  0  1  0            999 V2000
    3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -5.3625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5724   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -6.6000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2868   -7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -7.8375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -7.4250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.4302   -7.8375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -8.6625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.1447   -9.0750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -9.9000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302  -10.3125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302  -11.1375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -9.9000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.0013  -10.3125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -9.0750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.0013   -8.6625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -6.6000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.4302   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -6.1875    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.0013   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.9500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  1  0  0  0
  7  6  1  1  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  6  0  0  0
 12 11  1  6  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
 15 17  1  0  0  0  0
 17 18  1  6  0  0  0
 17 19  1  0  0  0  0
 12 19  1  0  0  0  0
 19 20  1  1  0  0  0
 10 21  1  0  0  0  0
 21 22  1  1  0  0  0
 21 23  1  0  0  0  0
  7 23  1  0  0  0  0
 23 24  1  6  0  0  0
  5 25  1  0  0  0  0
 25 26  1  6  0  0  0
 25 27  1  0  0  0  0
  2 27  1  0  0  0  0
 27 28  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0057112

> <DATABASE_NAME>
MIME

> <SMILES>
O[C@@H]1CO[C@@H](O[C@@H]2CO[C@@H](O[C@@H]3COC(O)[C@H](O)[C@H]3O)[C@H](O)[C@H]2O)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C15H26O13/c16-4-1-25-14(11(21)7(4)17)28-6-3-26-15(12(22)9(6)19)27-5-2-24-13(23)10(20)8(5)18/h4-23H,1-3H2/t4-,5-,6-,7+,8+,9+,10-,11-,12-,13?,14+,15+/m1/s1

> <INCHI_KEY>
JCSJTDYCNQHPRJ-FDVJSPBESA-N

> <FORMULA>
C15H26O13

> <MOLECULAR_WEIGHT>
414.36

> <EXACT_MASS>
414.137340897

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
54

> <JCHEM_AVERAGE_POLARIZABILITY>
39.197953885141814

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4S,5R)-2-{[(3R,4R,5R,6S)-4,5-dihydroxy-6-{[(3R,4R,5R)-4,5,6-trihydroxyoxan-3-yl]oxy}oxan-3-yl]oxy}oxane-3,4,5-triol

> <ALOGPS_LOGP>
-2.77

> <JCHEM_LOGP>
-4.583205683333333

> <ALOGPS_LOGS>
0.13

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.979278842027233

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.226041154430973

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5265806595271325

> <JCHEM_POLAR_SURFACE_AREA>
207.98999999999998

> <JCHEM_REFRACTIVITY>
82.86249999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.56e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
xylotriose

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-OCT-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-OCT-22         0                                  
HETATM    1  O   UNK     0       6.668  -5.390   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       8.002  -9.240   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       6.668 -10.010   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       6.668 -11.550   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       8.002 -12.320   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.002 -13.860   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       9.336 -14.630   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      10.669 -13.860   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      12.003 -14.630   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      12.003 -16.170   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      13.337 -16.940   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      13.337 -18.480   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      12.003 -19.250   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      12.003 -20.790   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      10.669 -18.480   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       9.336 -19.250   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      10.669 -16.940   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       9.336 -16.170   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      10.669 -12.320   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      12.003 -11.550   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       9.336 -11.550   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       9.336 -10.010   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       5.335  -9.240   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       4.001 -10.010   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   27                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   25                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   23                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   21                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   19                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   12   20                                                  
CONECT   20   19                                                            
CONECT   21   10   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21    7   24                                                  
CONECT   24   23                                                            
CONECT   25    5   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25    2   28                                                  
CONECT   28   27                                                            
MASTER        0    0    0    0    0    0    0    0   28    0   60    0
END

Synonyms

Value	Source
(Xyl)3	ChEBI
beta-D-Xyl-(1->4)-beta-D-xyl-(1->4)-D-xyl	ChEBI
beta-D-Xylosyl-(1->4)-beta-D-xylosyl-(1->4)-D-xylose	ChEBI
D-Xylotriose	ChEBI
Xylosaccharide	ChEBI
b-D-Xyl-(1->4)-b-D-xyl-(1->4)-D-xyl	Generator
Β-D-xyl-(1->4)-β-D-xyl-(1->4)-D-xyl	Generator
b-D-Xylosyl-(1->4)-b-D-xylosyl-(1->4)-D-xylose	Generator
Β-D-xylosyl-(1->4)-β-D-xylosyl-(1->4)-D-xylose	Generator

Molecular Formula

C₁₅H₂₆O₁₃

Average Mass

414.36

Monoisotopic Mass

414.137340897

IUPAC Name

(2S,3R,4S,5R)-2-{[(3R,4R,5R,6S)-4,5-dihydroxy-6-{[(3R,4R,5R)-4,5,6-trihydroxyoxan-3-yl]oxy}oxan-3-yl]oxy}oxane-3,4,5-triol

Traditional Name

xylotriose

CAS Registry Number

Not Available

SMILES

O[C@@H]1CO[C@@H](O[C@@H]2CO[C@@H](O[C@@H]3COC(O)[C@H](O)[C@H]3O)[C@H](O)[C@H]2O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C15H26O13/c16-4-1-25-14(11(21)7(4)17)28-6-3-26-15(12(22)9(6)19)27-5-2-24-13(23)10(20)8(5)18/h4-23H,1-3H2/t4-,5-,6-,7+,8+,9+,10-,11-,12-,13?,14+,15+/m1/s1

InChI Key

JCSJTDYCNQHPRJ-FDVJSPBESA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as oligosaccharides. These are carbohydrates made up of 3 to 10 monosaccharide units linked to each other through glycosidic bonds.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Oligosaccharides

Alternative Parents

Substituents

Oligosaccharide
O-glycosyl compound
Glycosyl compound
Oxane
Secondary alcohol
Hemiacetal
Oxacycle
Organoheterocyclic compound
Polyol
Acetal
Hydrocarbon derivative
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

trisaccharide (CHEBI:62783 )

Functional Ontology

Not Available

Physical Properties

State

Not Available

Predicted Properties

Property	Value	Source
Water Solubility	556 g/L	ALOGPS
logP	-2.8	ALOGPS
logP	-4.6	ChemAxon
logS	0.13	ALOGPS
pKa (Strongest Acidic)	11.23	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	207.99 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	82.86 m³·mol⁻¹	ChemAxon
Polarizability	39.2 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

8377351

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10201852

PDB ID

Not Available

ChEBI ID

62783

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for D-Xylotriose (MMDBc0057112)

MOL for #<Metabolite:0x00007fecf44d4520>

3D MOL for #<Metabolite:0x00007fecf44d4520>

3D SDF for #<Metabolite:0x00007fecf44d4520>

3D-SDF for #<Metabolite:0x00007fecf44d4520>

PDB for #<Metabolite:0x00007fecf44d4520>

3D PDB for #<Metabolite:0x00007fecf44d4520>

SMILES for #<Metabolite:0x00007fecf44d4520>

INCHI for #<Metabolite:0x00007fecf44d4520>

Structure for #<Metabolite:0x00007fecf44d4520>

3D Structure for #<Metabolite:0x00007fecf44d4520>