NP-MRD: Showing NP-Card for d-melibiose (NP0255047)

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Record Information

Version

2.0

Created at

2022-09-07 19:23:56 UTC

Updated at

2022-09-07 19:23:56 UTC

NP-MRD ID

NP0255047

Secondary Accession Numbers

None

Natural Product Identification

Common Name

d-melibiose

Description

d-melibiose is found in Arabidopsis thaliana, Daphnia pulex, Medicago sativa and Paris polyphylla. d-melibiose was first documented in 1957 (PMID: 13416199).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02231218182D          

 23 24  0  0  1  0            999 V2000
   -0.9016    0.3431    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.6208    0.7520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1898    0.7593    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9016   -0.4819    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3363    0.3431    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5220    1.1718    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6208   -0.8943    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1862   -0.8943    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3363   -0.4819    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0372    0.7520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2376    0.7593    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.6208   -1.7193    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0372   -0.8943    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6687    0.2226    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2376   -0.0620    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9457    1.1718    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9457   -0.4746    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5257   -0.4709    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6648    0.7630    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
    2.6648   -0.0620    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9457   -1.2996    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3841    1.1791    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3804   -0.4746    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  6  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  4  7  1  0  0  0  0
  4  8  1  6  0  0  0
  5  9  1  0  0  0  0
  5 10  1  1  0  0  0
 11  6  1  1  0  0  0
  7 12  1  1  0  0  0
  9 13  1  1  0  0  0
 10 14  1  0  0  0  0
 11 15  1  0  0  0  0
 11 16  1  0  0  0  0
 15 17  1  0  0  0  0
 15 18  1  6  0  0  0
 16 19  1  0  0  0  0
 17 20  1  0  0  0  0
 17 21  1  1  0  0  0
 19 22  1  4  0  0  0
 20 23  1  6  0  0  0
  7  9  1  0  0  0  0
 19 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0255047

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@H](OC[C@H]2OC(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-ABXHMFFYSA-N

> <FORMULA>
C12H22O11

> <MOLECULAR_WEIGHT>
342.2965

> <EXACT_MASS>
342.116211546

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_AVERAGE_POLARIZABILITY>
30.969712846476867

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4S,5S,6R)-6-({[(2S,3R,4S,5R,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>
68.3367

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.11e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-melibiose

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      -1.683   0.640   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -3.025   1.404   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      -0.354   1.417   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -1.683  -0.900   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -4.361   0.640   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.974   2.187   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.025  -1.669   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -0.348  -1.669   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -4.361  -0.900   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -5.669   1.404   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.310   1.417   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -3.025  -3.209   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -5.669  -1.669   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -6.848   0.416   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       2.310  -0.116   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       3.632   2.187   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       3.632  -0.886   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       0.981  -0.879   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       4.974   1.424   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.974  -0.116   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       3.632  -2.426   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       6.317   2.201   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       6.310  -0.886   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5                                                       
CONECT    3    1    6                                                       
CONECT    4    1    7    8                                                  
CONECT    5    2    9   10                                                  
CONECT    6    3   11                                                       
CONECT    7    4   12    9                                                  
CONECT    8    4                                                            
CONECT    9    5   13    7                                                  
CONECT   10    5   14                                                       
CONECT   11    6   15   16                                                  
CONECT   12    7                                                            
CONECT   13    9                                                            
CONECT   14   10                                                            
CONECT   15   11   17   18                                                  
CONECT   16   11   19                                                       
CONECT   17   15   20   21                                                  
CONECT   18   15                                                            
CONECT   19   16   22   20                                                  
CONECT   20   17   23   19                                                  
CONECT   21   17                                                            
CONECT   22   19                                                            
CONECT   23   20                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   48    0
END

View in JSmol

Synonyms

Value	Source
(Gal)1 (GLC)1	ChEBI
6-O-(alpha-D-Galactopyranosyl)-D-glucopyranose	ChEBI
6-O-alpha-D-Galactopyranosyl-D-glucopyranose	ChEBI
alpha-D-Gal-(1->6)-D-GLC	ChEBI
alpha-D-Galactosyl-(1->6)-D-glucose	ChEBI
alpha-D-Galp-(1->6)-D-GLCP	ChEBI
D-Melibiose	ChEBI
D-Mellibiose	ChEBI
Gal-alpha(1,6)GLC	ChEBI
6-O-(a-D-Galactopyranosyl)-D-glucopyranose	Generator
6-O-(α-D-galactopyranosyl)-D-glucopyranose	Generator
6-O-a-D-Galactopyranosyl-D-glucopyranose	Generator
6-O-α-D-galactopyranosyl-D-glucopyranose	Generator
a-D-Gal-(1->6)-D-GLC	Generator
α-D-gal-(1->6)-D-GLC	Generator
a-D-Galactosyl-(1->6)-D-glucose	Generator
α-D-galactosyl-(1->6)-D-glucose	Generator
a-D-Galp-(1->6)-D-GLCP	Generator
α-D-galp-(1->6)-D-GLCP	Generator
Gal-a(1,6)GLC	Generator
Gal-α(1,6)GLC	Generator
6-(a-D-galactosido)-D-Glucose	HMDB
6-(a-delta-galactosido)-delta-Glucose	HMDB
6-(D-galactosido)-D-Glucose	HMDB
6-(D-galactosido)-delta-Glucose	HMDB
6-O-a-D-Galactopyranosyl-D-glucose	HMDB
6-O-alpha-D-Galactopyranosyl-D-glucose	HMDB
6-O-alpha-delta-Galactopyranosyl-delta-glucose	HMDB
6-O-Hexopyranosylhexose	HMDB
alpha-D-Melibiose	HMDB
alpha-delta-Melibiose	HMDB
alpha-Melibiose	HMDB
D-(+)-Melibiose	HMDB
delta-(+)-Melibiose	HMDB
delta-Melibiose	HMDB
Mellibiose	HMDB

Chemical Formula

C₁₂H₂₂O₁₁

Average Mass

342.2965 Da

Monoisotopic Mass

342.11621 Da

IUPAC Name

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

Traditional Name

D-melibiose

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@H](OC[C@H]2OC(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-ABXHMFFYSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Arabidopsis thaliana	LOTUS Database	35616633
Daphnia pulex	LOTUS Database	35616633
Medicago sativa	LOTUS Database	35616633
Paris polyphylla	LOTUS Database	35616633

Chemical Taxonomy

Description

This compound 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.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

O-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 Framework

Aliphatic heteromonocyclic compounds

External Descriptors

glycosylglucose (CHEBI:28053 )
Disaccharides (C05402 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-3	ALOGPS
logP	-4.7	ChemAxon
logS	0.17	ALOGPS
pKa (Strongest Acidic)	11.25	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	189.53 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	68.34 m³·mol⁻¹	ChemAxon
Polarizability	30.97 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB00048

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Melibiose

METLIN ID

3478

PubChem Compound

440658

PDB ID

Not Available

ChEBI ID

28053

Good Scents ID

Not Available

References

General References

Vaughan HA, Loveland BE, Sandrin MS: Gal alpha(1,3)Gal is the major xenoepitope expressed on pig endothelial cells recognized by naturally occurring cytotoxic human antibodies. Transplantation. 1994 Oct 27;58(8):879-82. [PubMed:7524207 ]
PARDEE AB: An inducible mechanism for accumulation of melibiose in Escherichia coli. J Bacteriol. 1957 Mar;73(3):376-85. doi: 10.1128/jb.73.3.376-385.1957. [PubMed:13416199 ]
WINGE O, ROBERTS C: A genetic analysis of melibiose and raffinose fermentation. Cr Trav Lab Carlsberg Ser Physiol. 1957;25(18-19):419-59. [PubMed:13437610 ]
Piguet JD: [Arabinose, melibiose and xylose oxidation and fermentation in "Serratia" (author's transl)]. Ann Microbiol (Paris). 1978 Aug-Sep;129B(2):167-73. [PubMed:718021 ]
LOTUS database [Link]

Showing NP-Card for d-melibiose (NP0255047)

MOL for NP0255047 (d-melibiose)

3D MOL for NP0255047 (d-melibiose)

3D SDF for NP0255047 (d-melibiose)

3D-SDF for NP0255047 (d-melibiose)

PDB for NP0255047 (d-melibiose)

3D PDB for NP0255047 (d-melibiose)

SMILES for NP0255047 (d-melibiose)

INCHI for NP0255047 (d-melibiose)

Structure for NP0255047 (d-melibiose)

3D Structure for NP0255047 (d-melibiose)