NP-MRD: Showing NP-Card for α-l-rhamnopyranose (NP0199585)

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Record Information

Version

1.0

Created at

2022-09-04 18:15:35 UTC

Updated at

2022-09-04 18:15:35 UTC

NP-MRD ID

NP0199585

Secondary Accession Numbers

None

Natural Product Identification

Common Name

α-l-rhamnopyranose

Description

α-l-rhamnopyranose is found in Cussonia spicata, Ipomoea muricata, Joannesia princeps, Primula veris and Prunus avium. It was first documented in 2009 (PMID: 19443021).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652303202019012D          

 16 16  0  0  1  0            999 V2000
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    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
   -0.7145   -0.4125    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
    1.4289   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  3  7  1  1  0  0  0
  4  8  1  1  0  0  0
  5  9  1  6  0  0  0
  6 10  1  1  0  0  0
 11  2  1  0  0  0  0
 11  6  1  0  0  0  0
  2 12  1  1  0  0  0
  3 13  1  6  0  0  0
  4 14  1  1  0  0  0
  5 15  1  1  0  0  0
  6 16  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0199585

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O5/c1-2-3(7)4(8)5(9)6(10)11-2/h2-10H,1H3/t2-,3-,4+,5+,6+/m0/s1

> <INCHI_KEY>
SHZGCJCMOBCMKK-HGVZOGFYSA-N

> <FORMULA>
C6H12O5

> <MOLECULAR_WEIGHT>
164.1565

> <EXACT_MASS>
164.068473494

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
15.255669877749114

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4R,5R,6S)-6-methyloxane-2,3,4,5-tetrol

> <ALOGPS_LOGP>
-2.39

> <JCHEM_LOGP>
-1.885629251333333

> <ALOGPS_LOGS>
0.70

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.724419195509512

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.30218058050956

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6121738272477764

> <JCHEM_POLAR_SURFACE_AREA>
90.15

> <JCHEM_REFRACTIVITY>
34.3797

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.27e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
α-L-rhamnopyranose

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 20-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-MAR-20         0                                  
HETATM    1  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+0
HETATM   12  H   UNK     0       2.667   3.080   0.000  0.00  0.00           H+0
HETATM   13  H   UNK     0       0.000   3.080   0.000  0.00  0.00           H+0
HETATM   14  H   UNK     0       1.334   0.770   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0      -1.334   0.770   0.000  0.00  0.00           H+0
HETATM   16  H   UNK     0      -0.000  -1.540   0.000  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3   11   12                                             
CONECT    3    2    4    7   13                                             
CONECT    4    3    5    8   14                                             
CONECT    5    4    6    9   15                                             
CONECT    6    5   10   11   16                                             
CONECT    7    3                                                            
CONECT    8    4                                                            
CONECT    9    5                                                            
CONECT   10    6                                                            
CONECT   11    2    6                                                       
CONECT   12    2                                                            
CONECT   13    3                                                            
CONECT   14    4                                                            
CONECT   15    5                                                            
CONECT   16    6                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END

View in JSmol

Synonyms

Value	Source
alpha-6-Deoxy-L-mannose	ChEBI
alpha-L-Mannomethylose	ChEBI
alpha-L-Rha	ChEBI
alpha-L-Rhamnose	ChEBI
alpha-L-Rhap	ChEBI
alpha-L-Rhamnopyranose	Kegg
a-6-Deoxy-L-mannose	Generator
Α-6-deoxy-L-mannose	Generator
a-L-Mannomethylose	Generator
Α-L-mannomethylose	Generator
a-L-Rha	Generator
Α-L-rha	Generator
a-L-Rhamnose	Generator
Α-L-rhamnose	Generator
a-L-Rhap	Generator
Α-L-rhap	Generator
a-L-Rhamnopyranose	Generator

Chemical Formula

C₆H₁₂O₅

Average Mass

164.1565 Da

Monoisotopic Mass

164.06847 Da

IUPAC Name

(2R,3R,4R,5R,6S)-6-methyloxane-2,3,4,5-tetrol

Traditional Name

α-L-rhamnopyranose

CAS Registry Number

Not Available

SMILES

[H][C@@]1(C)O[C@@]([H])(O)[C@]([H])(O)[C@]([H])(O)[C@@]1([H])O

InChI Identifier

InChI=1S/C6H12O5/c1-2-3(7)4(8)5(9)6(10)11-2/h2-10H,1H3/t2-,3-,4+,5+,6+/m0/s1

InChI Key

SHZGCJCMOBCMKK-HGVZOGFYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Cussonia spicata	LOTUS Database	35616633
Ipomoea muricata	LOTUS Database	35616633
Joannesia princeps	LOTUS Database	35616633
Primula veris	LOTUS Database	35616633
Prunus avium	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hexoses. These are monosaccharides in which the sugar unit is a is a six-carbon containing moeity.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Hexoses

Alternative Parents

Substituents

Hexose monosaccharide
Oxane
Secondary alcohol
Hemiacetal
Oxacycle
Organoheterocyclic compound
Polyol
Hydrocarbon derivative
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

L-rhamnopyranose (CHEBI:27907 )

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	-2.4	ALOGPS
logP	-1.9	ChemAxon
logS	0.7	ALOGPS
pKa (Strongest Acidic)	11.3	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	90.15 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	34.38 m³·mol⁻¹	ChemAxon
Polarizability	15.26 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

C00001129

Chemspider ID

Not Available

KEGG Compound ID

C02476

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

439710

PDB ID

Not Available

ChEBI ID

27907

Good Scents ID

Not Available

References

General References

von Gunten S, Smith DF, Cummings RD, Riedel S, Miescher S, Schaub A, Hamilton RG, Bochner BS: Intravenous immunoglobulin contains a broad repertoire of anticarbohydrate antibodies that is not restricted to the IgG2 subclass. J Allergy Clin Immunol. 2009 Jun;123(6):1268-76.e15. doi: 10.1016/j.jaci.2009.03.013. Epub 2009 May 13. [PubMed:19443021 ]
Schneider C, Smith DF, Cummings RD, Boligan KF, Hamilton RG, Bochner BS, Miescher S, Simon HU, Pashov A, Vassilev T, von Gunten S: The human IgG anti-carbohydrate repertoire exhibits a universal architecture and contains specificity for microbial attachment sites. Sci Transl Med. 2015 Jan 7;7(269):269ra1. doi: 10.1126/scitranslmed.3010524. [PubMed:25568069 ]
Martin CE, Broecker F, Oberli MA, Komor J, Mattner J, Anish C, Seeberger PH: Immunological evaluation of a synthetic Clostridium difficile oligosaccharide conjugate vaccine candidate and identification of a minimal epitope. J Am Chem Soc. 2013 Jul 3;135(26):9713-22. doi: 10.1021/ja401410y. Epub 2013 Jun 24. [PubMed:23795894 ]
Martin CE, Broecker F, Eller S, Oberli MA, Anish C, Pereira CL, Seeberger PH: Glycan arrays containing synthetic Clostridium difficile lipoteichoic acid oligomers as tools toward a carbohydrate vaccine. Chem Commun (Camb). 2013 Aug 18;49(64):7159-61. doi: 10.1039/c3cc43545h. [PubMed:23836132 ]
Broecker F, Hanske J, Martin CE, Baek JY, Wahlbrink A, Wojcik F, Hartmann L, Rademacher C, Anish C, Seeberger PH: Multivalent display of minimal Clostridium difficile glycan epitopes mimics antigenic properties of larger glycans. Nat Commun. 2016 Apr 19;7:11224. doi: 10.1038/ncomms11224. [PubMed:27091615 ]
LOTUS database [Link]

Showing NP-Card for α-l-rhamnopyranose (NP0199585)

MOL for NP0199585 (α-l-rhamnopyranose)

3D MOL for NP0199585 (α-l-rhamnopyranose)

3D SDF for NP0199585 (α-l-rhamnopyranose)

3D-SDF for NP0199585 (α-l-rhamnopyranose)

PDB for NP0199585 (α-l-rhamnopyranose)

3D PDB for NP0199585 (α-l-rhamnopyranose)

SMILES for NP0199585 (α-l-rhamnopyranose)

INCHI for NP0199585 (α-l-rhamnopyranose)

Structure for NP0199585 (α-l-rhamnopyranose)

3D Structure for NP0199585 (α-l-rhamnopyranose)