MiMeDB: Showing metabocard for alpha-L-Rhamnose (MMDBc0029511)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:25:20 UTC

Update Date

2022-08-31 13:37:30 UTC

Metabolite ID

MMDBc0029511

Metabolite Identification

Common Name

alpha-L-Rhamnose

Description

Rhamnose is a methylpentose whose L- isomer is found naturally in many plant glycosides and some gram-negative bacterial lipopolysaccharides.

Structure

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>
MMDBc0029511

> <DATABASE_NAME>
MIME

> <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

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

Molecular Formula

C₆H₁₂O₅

Average Mass

164.1565

Monoisotopic Mass

164.068473494

IUPAC Name

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

Traditional Name

α-L-rhamnopyranose

CAS Registry Number

3615-41-6

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

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 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	827 g/L	ALOGPS
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

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-014i-1900000000-73abedcfedce730de924	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-014j-1900000000-5f2bd8fc908e0f2d17d8	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4s-9000000000-4ae8072a5651434f44b4	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-3900000000-e7a20de995c932bdb5d1	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-03dj-6900000000-03f10dd2373a0985cc0e	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9000000000-1ef6b887ff1a4477de1f	2015-09-15	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-23	View Spectrum

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
Bacteria	Proteobacteria	84	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown
Bacteria	Firmicutes	11	Human feces; Human
Bacteria	Bacteroidetes	4	Human ; Human feces
Bacteria	Verrucomicrobia	1

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

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

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 alpha-L-Rhamnose (MMDBc0029511)

MOL for #<Metabolite:0x00007fecaf471e88>

3D MOL for #<Metabolite:0x00007fecaf471e88>

3D SDF for #<Metabolite:0x00007fecaf471e88>

3D-SDF for #<Metabolite:0x00007fecaf471e88>

PDB for #<Metabolite:0x00007fecaf471e88>

3D PDB for #<Metabolite:0x00007fecaf471e88>

SMILES for #<Metabolite:0x00007fecaf471e88>

INCHI for #<Metabolite:0x00007fecaf471e88>

Structure for #<Metabolite:0x00007fecaf471e88>

3D Structure for #<Metabolite:0x00007fecaf471e88>