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

Spectrum Type	Description	Splash Key	Deposition Date	View
GC-MS	GC-MS Spectrum - GC-MS (1 MEOX; 4 TMS)	splash10-014i-0920000000-3f32654cd6b207d5192c	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (1 MEOX; 4 TMS)	splash10-014i-0910000000-3efed9ba21b4acc1a0a7	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-014i-0920000000-15cadd38d19e98599380	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-014i-0920000000-845777ce5ccb02564dd4	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-014i-0910000000-a3998948f1f154365fea	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-014i-0900000000-09ff33efc7ead61776ac	2017-09-12	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , positive	splash10-000i-0900000000-c17a9df600308d9b31be	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 10V, negative	splash10-0a4i-9300000000-aba9c0e75315919d15ca	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - QqQ 2V, negative	splash10-03di-0900000000-5bc4a1e81d1743e4d888	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - QqQ 6V, negative	splash10-114r-4900000000-cce3aaf678cc70d6861a	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - QqQ 8V, negative	splash10-0pb9-9700000000-4f6230f5365dba6dd52f	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - QqQ 12V, negative	splash10-0a4i-9100000000-9477982822aed3518682	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - QqQ 16V, negative	splash10-0a4i-9000000000-594366ab16c0cac99671	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - QqQ 20V, negative	splash10-0a4i-9000000000-f0b38b5601df3611821c	2020-07-21	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - n/a 11V, negative	splash10-0udi-3900000000-a5276b0d1c6f7703894f	2020-07-22	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - n/a 11V, negative	splash10-004i-2900000000-2a20cb5f730a3fd74448	2020-07-22	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - n/a 11V, negative	splash10-0089-9000000000-643fd0369e6935a5767c	2020-07-22	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - n/a 11V, negative	splash10-0532-9400000000-2e4332a61dcaf8add5aa	2020-07-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-014j-3900000000-ff3539fb021325c23c4a	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0a6r-9200000000-b270b5d83d44008211ba	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9000000000-f516852459b277fdb157	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0ly9-9600000000-efc90d58c6475abfcecd	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0abi-9100000000-3b89500afd7b488df6fa	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9000000000-7b10fe17f3ce9401fd3f	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum

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

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0007162	Hydrogen Ion	Hydrogen Ion	Not Available	L-rhamnose transport via proton symport	VMH	30371894
MMDBr0007957	L-Rhamnose	L-Rhamnulose	Not Available	L-rhamnose isomerase	VMH	30371894
MMDBr0010929	Hydrogen Ion	Hydrogen Ion	Not Available	L-rhamnose transport via proton symport (2 per proton)	VMH	30371894
MMDBr0014298	Rhamnose	L-Rhamnulose	L-rhamnose isomerase	Isomerization	RHEA	34755880
MMDBr0014648	beta-D-galactosyl-(1->4)-L-rhamnose	Galactose 1-phosphate	D-galactosyl-beta-1->4-L-rhamnose phosphorylase	Phosphorylation	RHEA	34755880
MMDBr0015022	2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnose	5-Dehydro-4-deoxy-D-glucuronate	Unsaturated rhamnogalacturonyl hydrolase YesR	Hydrolysis of bond	RHEA	34755880
MMDBr0015320	3-O-alpha-D-glucosyl-L-rhamnose	beta-D-Glucose 1-phosphate	3-O-alpha-D-glucosyl-L-rhamnose phosphorylase	Phosphorylation	RHEA	34755880

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	127	Human feces; Human ; Human feces; pleural fluid plaque; bal; Human stool; Human subgingival plaque; Human sputum	Unknown; Metabolic reconstruction
Bacteria	Bacteroidetes	95	Human feces; Human appendix biopsy; Human stool; Human saliva; Human ; Human gastric fluid; Human urine	Metabolic reconstruction
Bacteria	Firmicutes	105	Human feces; Human ; Catfish ; Human supragingival plaque; Human saliva	Metabolic reconstruction
Bacteria	Actinobacteria	29	Human ; Human feces; Human subgingival plaque; Human pleural fluid plaque; Human dental plaque	Metabolic reconstruction
Archaea	Crenarchaeota	2	Human feces	Metabolic reconstruction
Bacteria	Planctomycetes	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
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

References

Synthesis Reference

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:0x00007f5ab0052320>

3D MOL for #<Metabolite:0x00007f5ab0052320>

3D SDF for #<Metabolite:0x00007f5ab0052320>

3D-SDF for #<Metabolite:0x00007f5ab0052320>

PDB for #<Metabolite:0x00007f5ab0052320>

3D PDB for #<Metabolite:0x00007f5ab0052320>

SMILES for #<Metabolite:0x00007f5ab0052320>

INCHI for #<Metabolite:0x00007f5ab0052320>

Structure for #<Metabolite:0x00007f5ab0052320>

3D Structure for #<Metabolite:0x00007f5ab0052320>