MiMeDB: Showing metabocard for L-Rhamnonate (MMDBc0031745)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:47:28 UTC

Update Date

2022-08-31 18:24:13 UTC

Metabolite ID

MMDBc0031745

Metabolite Identification

Common Name

L-Rhamnonate

Description

L-Rhamnoate (6-deoxy-L-mannonate) is a mono-acid sugar. It is the preferred substrate for the E. coli enzyme called L-Rhamnoate dehydratase (YfaW). L-Rhamnonate, L-mannonate, and L-lyxonate share the same configurations at carbons-2, -3, and -4; D-gulonate differs from L-rhamnonate and L-mannonate by the configuration of carbon-5.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 10101211152D          

 16 15  0  0  0  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    2.2539    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.0164    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    2.2539    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.0164    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  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
  2  7  1  6  0  0  0
  3  8  1  1  0  0  0
  4  9  1  1  0  0  0
  5 10  1  6  0  0  0
 11  6  2  0  0  0  0
 12  6  1  0  0  0  0
  2 13  1  6  0  0  0
  3 14  1  1  0  0  0
  4 15  1  1  0  0  0
  5 16  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031745

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O6/c1-2(7)3(8)4(9)5(10)6(11)12/h2-5,7-10H,1H3,(H,11,12)/t2-,3-,4+,5+/m0/s1

> <INCHI_KEY>
NBFWIISVIFCMDK-QMKXCQHVSA-N

> <FORMULA>
C6H12O6

> <MOLECULAR_WEIGHT>
180.1559

> <EXACT_MASS>
180.063388116

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
16.183090460044713

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-2.07

> <JCHEM_LOGP>
-2.362834344

> <ALOGPS_LOGS>
-0.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.704809226791319

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.533365129686107

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0491138226804058

> <JCHEM_POLAR_SURFACE_AREA>
118.22000000000001

> <JCHEM_REFRACTIVITY>
36.7273

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.69e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-rhamnonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-OCT-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-OCT-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   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       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   13  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   14  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   16  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3    7   13                                             
CONECT    3    2    4    8   14                                             
CONECT    4    3    5    9   15                                             
CONECT    5    4    6   10   16                                             
CONECT    6    5   11   12                                                  
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    6                                                            
CONECT   12    6                                                            
CONECT   13    2                                                            
CONECT   14    3                                                            
CONECT   15    4                                                            
CONECT   16    5                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   30    0
END

Synonyms

Value	Source
6-Deoxy-L-mannonic acid	Kegg
6-Deoxy-L-mannonate	Generator
L-Rhamnonic acid	Generator
L-Rhamnonate	ChEBI

Molecular Formula

C₆H₁₂O₆

Average Mass

180.1559

Monoisotopic Mass

180.063388116

IUPAC Name

(2R,3R,4S,5S)-2,3,4,5-tetrahydroxyhexanoic acid

Traditional Name

L-rhamnonic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C6H12O6/c1-2(7)3(8)4(9)5(10)6(11)12/h2-5,7-10H,1H3,(H,11,12)/t2-,3-,4+,5+/m0/s1

InChI Key

NBFWIISVIFCMDK-QMKXCQHVSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Hydroxy acids and derivatives

Sub Class

Medium-chain hydroxy acids and derivatives

Direct Parent

Medium-chain hydroxy acids and derivatives

Alternative Parents

Substituents

Medium-chain hydroxy acid
Medium-chain fatty acid
Beta-hydroxy acid
Hydroxy fatty acid
Alpha-hydroxy acid
Monosaccharide
Fatty acyl
Fatty acid
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Polyol
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Carbonyl group
Alcohol
Organic oxygen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

rhamnonic acid (CHEBI:17357 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	169 g/L	ALOGPS
logP	-2.1	ALOGPS
logP	-2.4	ChemAxon
logS	-0.03	ALOGPS
pKa (Strongest Acidic)	3.53	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	118.22 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	36.73 m³·mol⁻¹	ChemAxon
Polarizability	16.18 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
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_7) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03e9-2900000000-9044f12679ca05d4a3b3	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0a70-9500000000-b6b42ceebf4868143af1	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a6r-9100000000-a4eebfc103952104e418	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00b9-9700000000-39bbdaba9e867f404bb5	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-05i9-9400000000-c325f8306fafd678aa0a	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9100000000-0f819a95990bc10662e2	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-21	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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0012881	Water	Hydrogen Ion	L-rhamnono-gamma-lactonase	Hydrolysis	RHEA	34755880
MMDBr0014285	L-Rhamnonate	2-Dehydro-3-deoxy-L-rhamnonate	L-rhamnonate dehydratase	Hydration/dehydration of C-O bond	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	45	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown
Eukaryota/Fungi	Ascomycota	1
Archaea/Archaea	Crenarchaeota	1
Bacteria	Actinobacteria	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

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C01934

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6602429

PDB ID

Not Available

ChEBI ID

17357

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 L-Rhamnonate (MMDBc0031745)

MOL for #<Metabolite:0x00007f5a587c68e8>

3D MOL for #<Metabolite:0x00007f5a587c68e8>

3D SDF for #<Metabolite:0x00007f5a587c68e8>

3D-SDF for #<Metabolite:0x00007f5a587c68e8>

PDB for #<Metabolite:0x00007f5a587c68e8>

3D PDB for #<Metabolite:0x00007f5a587c68e8>

SMILES for #<Metabolite:0x00007f5a587c68e8>

INCHI for #<Metabolite:0x00007f5a587c68e8>

Structure for #<Metabolite:0x00007f5a587c68e8>

3D Structure for #<Metabolite:0x00007f5a587c68e8>