NP-MRD: Showing NP-Card for epimelibiose (NP0225056)

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Record Information

Version

2.0

Created at

2022-09-06 03:39:51 UTC

Updated at

2022-09-06 03:39:51 UTC

NP-MRD ID

NP0225056

Secondary Accession Numbers

None

Natural Product Identification

Common Name

epimelibiose

Description

Melibiose, also known as isomaltose, 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. Melibiose is an extremely weak basic (essentially neutral) compound (based on its pKa). Within humans, melibiose participates in a number of enzymatic reactions. In particular, melibiose and D-galactose can be biosynthesized from manninotriose through the action of the enzyme Alpha-galactosidase a. In addition, melibiose can be converted into D-galactose through its interaction with the enzyme Alpha-galactosidase a. In humans, melibiose is involved in galactose metabolism. epimelibiose is found in Daphnia pulex. epimelibiose was first documented in 1957 (PMID: 13416199). A glycosylgalactose composed of alpha-D-mannopyranose and alpha-D-galactopyranose units (PMID: 13460592) (PMID: 17345316).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305201901032D          

 23 24  0  0  1  0            999 V2000
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -5.3625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -6.1875    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4289   -6.6000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1434   -6.1875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1434   -5.3625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -6.6000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -7.4250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -6.6000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    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  0  0  0  0
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
  6  8  1  1  0  0  0
  8  9  1  0  0  0  0
 10  9  1  6  0  0  0
 10 11  1  0  0  0  0
 11 12  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
 10 15  1  0  0  0  0
 14 16  1  1  0  0  0
 13 17  1  1  0  0  0
 12 18  1  6  0  0  0
 11 19  1  6  0  0  0
  5 20  1  6  0  0  0
  4 21  1  6  0  0  0
  3 22  1  1  0  0  0
  1 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0225056

> <DATABASE_NAME>
NP-MRD

> <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-OVEBFGLASA-N

> <FORMULA>
C12H22O11

> <MOLECULAR_WEIGHT>
342.2965

> <EXACT_MASS>
342.116211546

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
45

> <JCHEM_AVERAGE_POLARIZABILITY>
30.85361818839388

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.11e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
epimelibiose

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 20-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-MAY-19         0                                  
HETATM    1  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000  -7.700   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.334 -11.550   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.667 -12.320   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -4.001 -11.550   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -2.667  -9.240   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -5.335  -9.240   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -5.335 -12.320   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -2.667 -13.860   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.000 -12.320   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       2.667  -9.240   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       5.335  -7.700   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       5.335  -4.620   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
CONECT    1    2   23                                                       
CONECT    2    1    3    7                                                  
CONECT    3    2    4   22                                                  
CONECT    4    3    5   21                                                  
CONECT    5    4    6   20                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6    2                                                       
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   15                                                  
CONECT   11   10   12   19                                                  
CONECT   12   11   13   18                                                  
CONECT   13   12   14   17                                                  
CONECT   14   13   15   16                                                  
CONECT   15   14   10                                                       
CONECT   16   14                                                            
CONECT   17   13                                                            
CONECT   18   12                                                            
CONECT   19   11                                                            
CONECT   20    5                                                            
CONECT   21    4                                                            
CONECT   22    3                                                            
CONECT   23    1                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   48    0
END

View in JSmol

Synonyms

Value	Source
6-O-(alpha-D-Galactopyranosyl)-D-mannopyranose	ChEBI
6-O-alpha-D-Mannopyranosyl-alpha-D-galactopyranose	ChEBI
6-O-(a-D-Galactopyranosyl)-D-mannopyranose	Generator
6-O-(Α-D-galactopyranosyl)-D-mannopyranose	Generator
6-O-a-D-Mannopyranosyl-a-D-galactopyranose	Generator
6-O-Α-D-mannopyranosyl-α-D-galactopyranose	Generator
Isomaltose	MeSH

Chemical Formula

C₁₂H₂₂O₁₁

Average Mass

342.2965 Da

Monoisotopic Mass

342.11621 Da

IUPAC Name

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

Traditional Name

epimelibiose

CAS Registry Number

Not 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 Key

DLRVVLDZNNYCBX-OVEBFGLASA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25.16 MHz, D₂O, 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
Daphnia pulex	LOTUS Database	35616633

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.

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

glycosylgalactose (CHEBI:4808 )

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	30.85 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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Melibiose

METLIN ID

Not Available

PubChem Compound

440656

PDB ID

Not Available

ChEBI ID

4808

Good Scents ID

Not Available

References

General References

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 ]
COURTOIS JE, PETEK F: [Obtainment of epimelibiose by the transferase action of alpha-galactosidase]. Bull Soc Chim Biol (Paris). 1957;39(7-8):715-23. [PubMed:13460592 ]
Alam N, Gupta PC: Structure of a water-soluble polysaccharide from the seeds of Cassia angustifolia. Planta Med. 1986 Aug;(4):308-10. doi: 10.1055/s-2007-969161. [PubMed:17345316 ]
LOTUS database [Link]

Showing NP-Card for epimelibiose (NP0225056)

MOL for NP0225056 (epimelibiose)

3D MOL for NP0225056 (epimelibiose)

3D SDF for NP0225056 (epimelibiose)

3D-SDF for NP0225056 (epimelibiose)

PDB for NP0225056 (epimelibiose)

3D PDB for NP0225056 (epimelibiose)

SMILES for NP0225056 (epimelibiose)

INCHI for NP0225056 (epimelibiose)

Structure for NP0225056 (epimelibiose)

3D Structure for NP0225056 (epimelibiose)