MiMeDB: Showing metabocard for S-ribosyl-L-homocysteine (MMDBc0032151)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 02:04:30 UTC

Update Date

2022-08-31 18:30:55 UTC

Metabolite ID

MMDBc0032151

Metabolite Identification

Common Name

S-ribosyl-L-homocysteine

Description

S-Ribosyl-L-homocysteine is a member of the chemical class known as Alpha Amino Acids and Derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon). AI-2 is spontaneously derived from 4,5-dihydroxy-2,3-pentanedione that, along with homocysteine, is produced by cleavage of S-adenosylhomocysteine (SAH) and S-ribosylhomocysteine by the Pfs and LuxS enzymes. (PMID 16885435 )

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 04051517092D          

 17 17  0  0  0  0            999 V2000
    4.5923   -2.9518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8778   -3.3643    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1633   -2.9518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1633   -2.1268    0.0000 N   0  3  0  0  0  1  0  0  0  0  0  0
    2.4489   -3.3643    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7344   -2.9518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4489   -4.1893    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.3067   -3.3643    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    6.0212   -2.9518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7357   -3.3643    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4894   -3.0288    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0414   -3.6418    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8619   -3.5556    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6289   -4.3563    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9645   -5.1100    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8219   -4.1848    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2088   -4.7368    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  1  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 10 16  1  0  0  0  0
M  CHG  2   4   1   7  -1
M  RAD  1   4   2
M  END
> <DATABASE_ID>
MMDBc0032151

> <DATABASE_NAME>
MIME

> <SMILES>
[N+]C(CCSCC1OC(O)C(O)C1O)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H15NO6S/c10-4(8(13)14)1-2-17-3-5-6(11)7(12)9(15)16-5/h4-7,9,11-12,15H,1-3H2,(H,13,14)/q+1/p-1

> <INCHI_KEY>
QUDMRZABJLFLCP-UHFFFAOYSA-M

> <FORMULA>
C9H14NO6S

> <MOLECULAR_WEIGHT>
264.27

> <EXACT_MASS>
264.054183349

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
25.516731805126057

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1-carboxylato-3-{[(3,4,5-trihydroxyoxolan-2-yl)methyl]sulfanyl}propyl)azaniumyl

> <ALOGPS_LOGP>
-2.10

> <JCHEM_LOGP>
-2.862882262209279

> <ALOGPS_LOGS>
-1.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.308592212670076

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.626919858940398

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6587446413644464

> <JCHEM_POLAR_SURFACE_AREA>
133.11

> <JCHEM_REFRACTIVITY>
68.80380000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.69e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1-carboxylato-3-{[(3,4,5-trihydroxyoxolan-2-yl)methyl]sulfanyl}propyl)ammonio

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-APR-15         0                                  
HETATM    1  C   UNK     0       8.572  -5.510   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.239  -6.280   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.905  -5.510   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       5.905  -3.970   0.000  0.00  0.00           N+1
HETATM    5  C   UNK     0       4.571  -6.280   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       3.238  -5.510   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       4.571  -7.820   0.000  0.00  0.00           O-1
HETATM    8  S   UNK     0       9.906  -6.280   0.000  0.00  0.00           S+0
HETATM    9  C   UNK     0      11.240  -5.510   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      12.573  -6.280   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      13.980  -5.654   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      15.011  -6.798   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      16.542  -6.637   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      14.241  -8.132   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      14.867  -9.539   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      12.734  -7.812   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      11.590  -8.842   0.000  0.00  0.00           O+0
CONECT    1    2    8                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    1    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   16                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   10                                                  
CONECT   17   16                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   34    0
END

Synonyms

Not Available

Molecular Formula

C₉H₁₄NO₆S

Average Mass

264.27

Monoisotopic Mass

264.054183349

IUPAC Name

(1-carboxylato-3-{[(3,4,5-trihydroxyoxolan-2-yl)methyl]sulfanyl}propyl)azaniumyl

Traditional Name

(1-carboxylato-3-{[(3,4,5-trihydroxyoxolan-2-yl)methyl]sulfanyl}propyl)ammonio

CAS Registry Number

Not Available

SMILES

[N+]C(CCSCC1OC(O)C(O)C1O)C([O-])=O

InChI Identifier

InChI=1S/C9H15NO6S/c10-4(8(13)14)1-2-17-3-5-6(11)7(12)9(15)16-5/h4-7,9,11-12,15H,1-3H2,(H,13,14)/q+1/p-1

InChI Key

QUDMRZABJLFLCP-UHFFFAOYSA-M

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

Alpha-amino acid or derivatives
Pentose monosaccharide
Heterocyclic fatty acid
Hydroxy fatty acid
Thia fatty acid
Fatty acyl
Fatty acid
Tetrahydrofuran
1,2-diol
Carboxylic acid salt
Hemiacetal
Secondary alcohol
Dialkylthioether
Sulfenyl compound
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Polyol
Oxacycle
Organoheterocyclic compound
Thioether
Organic oxide
Organopnictogen compound
Carbonyl group
Organonitrogen compound
Organosulfur compound
Hydrocarbon derivative
Organic zwitterion
Organic nitrogen compound
Alcohol
Organic salt
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	26.9 g/L	ALOGPS
logP	-2.1	ALOGPS
logP	-2.9	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	1.63	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	133.11 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	68.8 m³·mol⁻¹	ChemAxon
Polarizability	25.52 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

Not Available

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

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0018410	S-Adenosylhomocysteine	Adenine	5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase	Hydrolysis of a nucleotide	PathBank	31602464
MMDBr0018411	S-ribosyl-L-homocysteine	Homocysteine	S-ribosylhomocysteine lyase	Non-hydrolytic bond cleavage (or its reversal)	PathBank	31602464
MMDBr0019197	S-ribosyl-L-homocysteine	4,5-Dihydroxy-2,3-pentanedione	S-ribosylhomocysteine lyase	Non-hydrolytic bond cleavage (or its reversal)	PathBank	31602464

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/Eubacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

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

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

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 S-ribosyl-L-homocysteine (MMDBc0032151)

MOL for #<Metabolite:0x00007f920382c020>

3D MOL for #<Metabolite:0x00007f920382c020>

3D SDF for #<Metabolite:0x00007f920382c020>

3D-SDF for #<Metabolite:0x00007f920382c020>

PDB for #<Metabolite:0x00007f920382c020>

3D PDB for #<Metabolite:0x00007f920382c020>

SMILES for #<Metabolite:0x00007f920382c020>

INCHI for #<Metabolite:0x00007f920382c020>

Structure for #<Metabolite:0x00007f920382c020>

3D Structure for #<Metabolite:0x00007f920382c020>