MiMeDB: Showing metabocard for L-Rhamnulose 1-phosphate (MMDBc0030074)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:52:55 UTC

Update Date

2022-08-31 17:39:30 UTC

Metabolite ID

MMDBc0030074

Metabolite Identification

Common Name

L-Rhamnulose 1-phosphate

Description

L-rhamnulose 1-phosphate is a member of the chemical class known as Hexoses. These are monosaccharides in which the sugar unit is a hexose.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 03281501142D          

 15 14  0  0  0  0            999 V2000
   -2.8599    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1454    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4309    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7165    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0020    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7124    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4268    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5744    0.4125    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3117    0.4120    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5744    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5744   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4309   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7165    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0020   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7124    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  8 10  1  0  0  0  0
  8 11  2  0  0  0  0
  1  2  1  0  0  0  0
  1  8  1  0  0  0  0
  3 12  2  0  0  0  0
  8  9  1  0  0  0  0
  4 13  1  0  0  0  0
  5 14  1  0  0  0  0
  6 15  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030074

> <DATABASE_NAME>
MIME

> <SMILES>
CC(O)C(O)C(O)C(=C)COP(C)(O)=C

> <INCHI_IDENTIFIER>
InChI=1S/C9H19O5P/c1-6(5-14-15(3,4)13)8(11)9(12)7(2)10/h7-13H,1,3,5H2,2,4H3

> <INCHI_KEY>
QRXAIBTYLQNPRQ-UHFFFAOYSA-N

> <FORMULA>
C9H19O5P

> <MOLECULAR_WEIGHT>
238.22

> <EXACT_MASS>
238.09701071

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
23.216887397064983

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl(methylidene)[(3,4,5-trihydroxy-2-methylidenehexyl)oxy]phosphinous acid

> <ALOGPS_LOGP>
-0.71

> <JCHEM_LOGP>
-1.0948999999999995

> <ALOGPS_LOGS>
-1.34

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.99954998210018

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.78194411757761

> <JCHEM_PKA_STRONGEST_BASIC>
-3.051633989886165

> <JCHEM_POLAR_SURFACE_AREA>
90.15

> <JCHEM_REFRACTIVITY>
57.30829999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.10e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl(methylidene)(3,4,5-trihydroxy-2-methylidenehexyl)oxyphosphinous acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-MAR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-MAR-15         0                                  
HETATM    1  O   UNK     0      -5.338   0.000   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -4.005   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.671   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.337   0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.004   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.330   0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.663   0.000   0.000  0.00  0.00           C+0
HETATM    8  P   UNK     0      -6.672   0.770   0.000  0.00  0.00           P+0
HETATM    9  O   UNK     0      -8.049   0.769   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -6.672   2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -6.672  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.671  -1.540   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -1.337   2.310   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -0.004  -1.540   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       1.330   2.310   0.000  0.00  0.00           O+0
CONECT    1    2    8                                                       
CONECT    2    3    1                                                       
CONECT    3    2    4   12                                                  
CONECT    4    3    5   13                                                  
CONECT    5    4    6   14                                                  
CONECT    6    5    7   15                                                  
CONECT    7    6                                                            
CONECT    8   10   11    1    9                                             
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    8                                                            
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
L-Rhamnulose 1-phosphoric acid	Generator

Molecular Formula

C₉H₁₉O₅P

Average Mass

238.22

Monoisotopic Mass

238.09701071

IUPAC Name

methyl(methylidene)[(3,4,5-trihydroxy-2-methylidenehexyl)oxy]phosphinous acid

Traditional Name

methyl(methylidene)(3,4,5-trihydroxy-2-methylidenehexyl)oxyphosphinous acid

CAS Registry Number

444-09-7

SMILES

CC(O)C(O)C(O)C(=C)COP(C)(O)=C

InChI Identifier

InChI=1S/C9H19O5P/c1-6(5-14-15(3,4)13)8(11)9(12)7(2)10/h7-13H,1,3,5H2,2,4H3

InChI Key

QRXAIBTYLQNPRQ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as secondary alcohols. Secondary alcohols are compounds containing a secondary alcohol functional group, with the general structure HOC(R)(R') (R,R'=alkyl, aryl).

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Alcohols and polyols

Direct Parent

Secondary alcohols

Alternative Parents

Substituents

Secondary alcohol
Polyol
Organopnictogen compound
Hydrocarbon derivative
Organophosphorus compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	11 g/L	ALOGPS
logP	-0.71	ALOGPS
logP	-1.1	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	9.78	ChemAxon
pKa (Strongest Basic)	-3.1	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	6	ChemAxon
Refractivity	57.31 m³·mol⁻¹	ChemAxon
Polarizability	23.22 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_2_3) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-09	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

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0007958	L-Rhamnulose	L-Rhamnulose 1-phosphate	Not Available		VMH	30371894
MMDBr0007959	L-Rhamnulose 1-phosphate	Dihydroxyacetone phosphate	Not Available		VMH	30371894

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	119	Pig ; Human feces; Human ; Human feces; pleural fluid plaque; bal; Human stool; Human sputum; Human pleural fluid plaque	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	135	Human feces; Human pleural fluid plaque; Human ; Human stool; Pig ; Catfish	Metabolic reconstruction
Bacteria	Actinobacteria	50	Human feces; Human pleural fluid plaque; Human dental plaque; Human sputum; Human ; Human mucosa; Human supragingival plaque; Human subgingival plaque	Metabolic reconstruction
Bacteria	Bacteroidetes	68	Human feces; Human stool; Human saliva; Human ; Human gastric fluid; Human urine	Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction

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

Not Available

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

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

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 ]
Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]
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-Rhamnulose 1-phosphate (MMDBc0030074)

MOL for #<Metabolite:0x00007fed14e9ab70>

3D MOL for #<Metabolite:0x00007fed14e9ab70>

3D SDF for #<Metabolite:0x00007fed14e9ab70>

3D-SDF for #<Metabolite:0x00007fed14e9ab70>

PDB for #<Metabolite:0x00007fed14e9ab70>

3D PDB for #<Metabolite:0x00007fed14e9ab70>

SMILES for #<Metabolite:0x00007fed14e9ab70>

INCHI for #<Metabolite:0x00007fed14e9ab70>

Structure for #<Metabolite:0x00007fed14e9ab70>

3D Structure for #<Metabolite:0x00007fed14e9ab70>