MiMeDB: Showing metabocard for 5-Methylthioribose 1-phosphate (MMDBc0032910)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:26:59 UTC

Update Date

2022-12-15 22:51:51 UTC

MiMeDB ID

MMDBc0032910

Metabolite Identification

Common Name

5-Methylthioribose 1-phosphate

Description

5-Methylthioribose 1-phosphate, also known as 1-phospho-5-S-methylthioribose or D-ribofuranoside, belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. 5-Methylthioribose 1-phosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). 5-methylthioribose 1-phosphate and L-methionine can be biosynthesized from 5'-methylthioadenosine; which is mediated by the enzyme S-methyl-5'-thioadenosine phosphorylase. In humans, 5-methylthioribose 1-phosphate is involved in the metabolic disorder called hypermethioninemia. In the methionine salvage pathway 5-methylthioribose 1-phosphate isomerase (M1Pi) catalyzes the conversion of 5-methylthioribose 1-phosphate (MTR-1-P) to 5-methylthioribulose 1-phosphate (MTRu-1-P).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02231218512D          

 15 15  0  0  1  0            999 V2000
   10.9690   -9.7595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9071  -10.7156    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1000  -10.8872    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7645  -11.6408    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.9440  -11.5546    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.7725  -10.7476    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1770  -12.3554    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3920  -12.1677    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.7530   -9.5054    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1121   -9.6778    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8463   -8.7711    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.4869  -10.3351    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0188  -10.4121    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9326   -9.5916    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   10.1620   -9.9310    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  1 15  1  0  0  0  0
  2 15  1  0  0  0  0
  2  3  1  6  0  0  0
  3  4  1  0  0  0  0
  3 12  1  0  0  0  0
  4  7  1  1  0  0  0
  4  5  1  0  0  0  0
  5  8  1  1  0  0  0
  5  6  1  0  0  0  0
  6 12  1  0  0  0  0
  6 13  1  0  0  0  0
  9 14  1  0  0  0  0
 10 14  1  0  0  0  0
 11 14  2  0  0  0  0
 13 14  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0032910

> <DATABASE_NAME>
MIME

> <SMILES>
CSCC1OC(OP(O)(O)=O)[C@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C6H13O7PS/c1-15-2-3-4(7)5(8)6(12-3)13-14(9,10)11/h3-8H,2H2,1H3,(H2,9,10,11)/t3?,4-,5-,6?/m1/s1

> <INCHI_KEY>
JTFITTQBRJDSTL-WATOWXBHSA-N

> <FORMULA>
C6H13O7PS

> <MOLECULAR_WEIGHT>
260.202

> <EXACT_MASS>
260.011959972

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
22.52691291319853

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(3R,4S)-3,4-dihydroxy-5-[(methylsulfanyl)methyl]oxolan-2-yl]oxy}phosphonic acid

> <ALOGPS_LOGP>
-1.16

> <JCHEM_LOGP>
-0.943299161333333

> <ALOGPS_LOGS>
-0.96

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.219263382330931

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.1557362714105084

> <JCHEM_PKA_STRONGEST_BASIC>
-3.659561681639288

> <JCHEM_POLAR_SURFACE_AREA>
116.45000000000002

> <JCHEM_REFRACTIVITY>
51.6674

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.87e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(3R,4S)-3,4-dihydroxy-5-[(methylsulfanyl)methyl]oxolan-2-yl]oxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      20.475 -18.218   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      18.493 -20.002   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      16.987 -20.323   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      16.360 -21.729   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      14.829 -21.569   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      14.509 -20.062   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      17.130 -23.063   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      13.798 -22.713   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      14.472 -17.743   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      11.409 -18.065   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      12.780 -16.373   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      15.842 -19.292   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      13.102 -19.436   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0      12.941 -17.904   0.000  0.00  0.00           P+0
HETATM   15  S   UNK     0      18.969 -18.538   0.000  0.00  0.00           S+0
CONECT    1   15                                                            
CONECT    2   15    3                                                       
CONECT    3    2    4   12                                                  
CONECT    4    3    7    5                                                  
CONECT    5    4    8    6                                                  
CONECT    6    5   12   13                                                  
CONECT    7    4                                                            
CONECT    8    5                                                            
CONECT    9   14                                                            
CONECT   10   14                                                            
CONECT   11   14                                                            
CONECT   12    3    6                                                       
CONECT   13    6   14                                                       
CONECT   14    9   10   11   13                                             
CONECT   15    1    2                                                       
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

Synonyms

Value	Source
5-Methylthioribose 1-phosphoric acid	Generator
1-Phospho-5-S-methylthioribose	HMDB
1-Phosphomethylthioribose	HMDB
5-Methylthio-5-deoxy-D-ribose 1-phosphate	HMDB
5-Methylthio-5-deoxy-D-ribose-1-phosphate	HMDB
5-Methylthio-D-ribose-1-phosphate	HMDB
5-Methylthioribose-1-phosphate	HMDB
D-Ribofuranoside	HMDB
S-Methyl-5-thio-alpha-D-ribose 1-phosphate	HMDB
S5-Methyl-5-thio-D-ribose-1-phosphate	HMDB

Chemical Formula

C₆H₁₃O₇PS

Average Molecular Weight

260.202

Monoisotopic Molecular Weight

260.011959972

IUPAC Name

{[(3R,4S)-3,4-dihydroxy-5-[(methylsulfanyl)methyl]oxolan-2-yl]oxy}phosphonic acid

Traditional Name

[(3R,4S)-3,4-dihydroxy-5-[(methylsulfanyl)methyl]oxolan-2-yl]oxyphosphonic acid

CAS Registry Number

72843-83-5

SMILES

CSCC1OC(OP(O)(O)=O)[C@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C6H13O7PS/c1-15-2-3-4(7)5(8)6(12-3)13-14(9,10)11/h3-8H,2H2,1H3,(H2,9,10,11)/t3?,4-,5-,6?/m1/s1

InChI Key

JTFITTQBRJDSTL-WATOWXBHSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentoses

Alternative Parents

Substituents

Pentose monosaccharide
Monoalkyl phosphate
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Tetrahydrofuran
1,2-diol
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Dialkylthioether
Sulfenyl compound
Thioether
Organic oxide
Alcohol
Hydrocarbon derivative
Organosulfur compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	28.7 g/L	ALOGPS
logP	-1.2	ALOGPS
logP	-0.94	ChemAxon
logS	-0.96	ALOGPS
pKa (Strongest Acidic)	1.16	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	116.45 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	51.67 m³·mol⁻¹	ChemAxon
Polarizability	22.53 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 (Non-derivatized) - 70eV, Positive	splash10-0002-9100000000-2488064947bfab511f5e	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-0002-9011000000-4ba10accddc39548ffac	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0002-9340000000-81076180aee84a287f34	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-9330000000-16cc1e6103ea1cca9414	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-001j-9200000000-e1e1c3a051f24524c0f3	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-9010000000-6e1ba60f11f69a1cb95a	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004j-9000000000-138587ed5d90d657c9c1	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-41783131ed46fc1d13e5	2016-09-12	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Feces

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Proteins

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Related Health Condition	Evidence Type	Measured in Matrix	Data Source	Reference

Microbial Sources

Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Fungi	Ascomycota	1	Human Feces	Unknown
	Firmicutes	92	Pig ; Human Feces; Human	Metabolic reconstruction
	Proteobacteria	68	Human Feces; Human	Metabolic reconstruction
	Thaumarchaeota	1	Human Feces	Metabolic reconstruction
	Fusobacteria	8	Human Feces; Human	Metabolic reconstruction
	Actinobacteria	13	Human Feces; Human	Metabolic reconstruction
	Euryarchaeota	5	Human Feces; Cattle ; Human	Metabolic reconstruction
	Crenarchaeota	1	Human Feces	Metabolic reconstruction
	Synergistetes	2	Human Feces	Metabolic reconstruction
	Bacteroidetes	14	Human Feces; Human	Metabolic reconstruction
	Spirochaetes	1	Human Feces	Metabolic reconstruction
	Planctomycetes	1	Human Feces	Metabolic reconstruction

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference	Details

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		details

External Links

HMDB ID

HMDB0000963

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022341

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C04188

BioCyc ID

Not Available

BiGG ID

43318

Wikipedia Link

Not Available

METLIN ID

5909

PubChem Compound

53477720

PDB ID

Not Available

ChEBI ID

27859

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 ]

Showing metabocard for 5-Methylthioribose 1-phosphate (MMDBc0032910)

MOL for #<Metabolite:0x0000564abdaa6b18>

3D MOL for #<Metabolite:0x0000564abdaa6b18>

3D SDF for #<Metabolite:0x0000564abdaa6b18>

3D-SDF for #<Metabolite:0x0000564abdaa6b18>

PDB for #<Metabolite:0x0000564abdaa6b18>

3D PDB for #<Metabolite:0x0000564abdaa6b18>

SMILES for #<Metabolite:0x0000564abdaa6b18>

INCHI for #<Metabolite:0x0000564abdaa6b18>

Structure for #<Metabolite:0x0000564abdaa6b18>

3D Structure for #<Metabolite:0x0000564abdaa6b18>