MiMeDB: Showing metabocard for L-Rhamnose (MMDBc0031145)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 00:37:05 UTC

Update Date

2022-08-31 17:58:52 UTC

Metabolite ID

MMDBc0031145

Metabolite Identification

Common Name

L-Rhamnose

Description

Rhamnose (Rham) is a naturally occurring deoxy sugar. It can be classified as either a methyl-pentose or a 6-deoxy-hexose. Rhamnose occurs in nature in its L-form as L-rhamnose (6-deoxy-L-mannose). This is unusual, since most of the naturally occurring sugars are in D-form. Rhamnose is commonly bound to other sugars in nature. It is a common glycone component of glycosides from many plants. Rhamnose is also a component of the outer cell membrane of certain bacteria. L-rhamnose is metabolized to L-Lactaldehyde, which is a branching point in the metabolic pathway of L-fucose and L-rhamnose utilization. It exists in two anomeric forms, alpha-L-rhamnose and beta-L-rhamnose.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652303202019012D          

 15 14  0  0  1  0            999 V2000
    2.3349   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6204   -0.7145    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5230   -1.1270    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9059   -1.1270    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1914   -0.7145    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.9520   -1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6204    0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5230   -1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9059   -1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1914    0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6204   -1.5395    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5230   -0.3020    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9059   -0.3020    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1914   -1.5395    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  2  2  0  0  0  0
  3  8  1  6  0  0  0
  4  9  1  6  0  0  0
  5 10  1  1  0  0  0
  6 11  1  1  0  0  0
  3 12  1  6  0  0  0
  4 13  1  6  0  0  0
  5 14  1  1  0  0  0
  6 15  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031145

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O5/c1-3(8)5(10)6(11)4(9)2-7/h2-6,8-11H,1H3/t3-,4-,5-,6-/m0/s1

> <INCHI_KEY>
PNNNRSAQSRJVSB-BXKVDMCESA-N

> <FORMULA>
C6H12O5

> <MOLECULAR_WEIGHT>
164.1565

> <EXACT_MASS>
164.068473494

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
15.243832455630093

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5S)-2,3,4,5-tetrahydroxyhexanal

> <ALOGPS_LOGP>
-2.02

> <JCHEM_LOGP>
-2.5214505963333327

> <ALOGPS_LOGS>
0.20

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.294570156223926

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.305727419271797

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0490444234470298

> <JCHEM_POLAR_SURFACE_AREA>
97.99000000000001

> <JCHEM_REFRACTIVITY>
35.801899999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.58e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-deoxy-L-mannose

> <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       4.358  -2.104   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.025  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.976  -2.104   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.691  -2.104   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.357  -1.334   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -3.644  -2.104   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       3.025   0.206   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -0.976  -3.644   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       1.691  -3.644   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.357   0.206   0.000  0.00  0.00           O+0
HETATM   12  H   UNK     0       3.025  -2.874   0.000  0.00  0.00           H+0
HETATM   13  H   UNK     0      -0.976  -0.564   0.000  0.00  0.00           H+0
HETATM   14  H   UNK     0       1.691  -0.564   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0       0.357  -2.874   0.000  0.00  0.00           H+0
CONECT    1    3                                                            
CONECT    2    4    7                                                       
CONECT    3    1    5    8   12                                             
CONECT    4    2    6    9   13                                             
CONECT    5    3    6   10   14                                             
CONECT    6    4    5   11   15                                             
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    6                                                            
CONECT   12    3                                                            
CONECT   13    4                                                            
CONECT   14    5                                                            
CONECT   15    6                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END

Synonyms

Value	Source
(2R,3R,4S,5S)-2,3,4,5-Tetrahydroxyhexanal	ChEBI
L-Rha	ChEBI
L-Rhamnose	ChEBI
Deoxymannose	MeSH
Rhamnose	MeSH
Rhamnose, L isomer	MeSH
Rhamnose, L-isomer	MeSH

Molecular Formula

C₆H₁₂O₅

Average Mass

164.1565

Monoisotopic Mass

164.068473494

IUPAC Name

(2R,3R,4S,5S)-2,3,4,5-tetrahydroxyhexanal

Traditional Name

6-deoxy-L-mannose

CAS Registry Number

3615-41-6

SMILES

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

InChI Identifier

InChI=1S/C6H12O5/c1-3(8)5(10)6(11)4(9)2-7/h2-6,8-11H,1H3/t3-,4-,5-,6-/m0/s1

InChI Key

PNNNRSAQSRJVSB-BXKVDMCESA-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
Medium-chain aldehyde
Beta-hydroxy aldehyde
Alpha-hydroxyaldehyde
Secondary alcohol
Polyol
Organic oxide
Hydrocarbon derivative
Carbonyl group
Aldehyde
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

aldehyde (CHEBI:16055 )
L-rhamnose (CHEBI:16055 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	258 g/L	ALOGPS
logP	-2	ALOGPS
logP	-2.5	ChemAxon
logS	0.2	ALOGPS
pKa (Strongest Acidic)	12.31	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	97.99 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	35.8 m³·mol⁻¹	ChemAxon
Polarizability	15.24 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

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

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated 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	100	Human feces; Human ; Human feces; pleural fluid plaque; bal	Unknown; Metabolic reconstruction
Bacteria	Bacteroidetes	69	Human feces; Human appendix biopsy; Human	Metabolic reconstruction
Bacteria	Firmicutes	89	Human feces; Human ; Catfish	Metabolic reconstruction
Bacteria	Actinobacteria	25	Human ; Human feces; Human pleural fluid plaque; Human dental plaque	Metabolic reconstruction
Archaea	Crenarchaeota	1	Human feces	Metabolic reconstruction
Bacteria	Planctomycetes	1

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

Not Available

DrugBank ID

DB02961

Phenol Explorer Compound ID

Not Available

FooDB 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

Rhamnose

METLIN ID

Not Available

PubChem Compound

19233

PDB ID

Not Available

ChEBI ID

16055

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]
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 L-Rhamnose (MMDBc0031145)

MOL for #<Metabolite:0x0000560be2309280>

3D MOL for #<Metabolite:0x0000560be2309280>

3D SDF for #<Metabolite:0x0000560be2309280>

3D-SDF for #<Metabolite:0x0000560be2309280>

PDB for #<Metabolite:0x0000560be2309280>

3D PDB for #<Metabolite:0x0000560be2309280>

SMILES for #<Metabolite:0x0000560be2309280>

INCHI for #<Metabolite:0x0000560be2309280>

Structure for #<Metabolite:0x0000560be2309280>

3D Structure for #<Metabolite:0x0000560be2309280>