MiMeDB: Showing metabocard for S-Ribosyl-L-homocysteine (MMDBc0030093)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:53:38 UTC

Update Date

2022-08-31 17:39:40 UTC

Metabolite ID

MMDBc0030093

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 10231213092D          

 22 22  0  0  0  0            999 V2000
    0.0078   -0.1494    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7066    0.2631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1356    0.2631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7223    0.2631    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8501   -0.1494    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.6037    0.1862    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.1558   -0.4269    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4368   -0.1494    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7433   -1.1414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7223    1.0881    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7753    0.9932    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9762   -0.3407    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1512    0.2631    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4368   -0.9744    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0788   -1.8950    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9363   -0.9698    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4211   -0.1494    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.7223   -0.5619    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1724    0.6101    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1788    0.8934    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4514    0.3433    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5671   -1.1845    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  1  1  0  0  0  0
  5  3  1  1  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  4  1  0  0  0  0
  9  7  1  0  0  0  0
  4 10  1  1  0  0  0
  6 11  1  6  0  0  0
  7 12  1  6  0  0  0
 13  8  2  0  0  0  0
 14  8  1  0  0  0  0
 15  9  1  0  0  0  0
 16  5  1  0  0  0  0
 16  9  1  0  0  0  0
 17  2  1  0  0  0  0
 17  3  1  0  0  0  0
  4 18  1  1  0  0  0
  5 19  1  6  0  0  0
  6 20  1  1  0  0  0
  7 21  1  1  0  0  0
 22  9  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030093

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](N)(CCSC[C@@]1([H])OC([H])(O)[C@]([H])(O)[C@]1([H])O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H17NO6S/c10-4(8(13)14)1-2-17-3-5-6(11)7(12)9(15)16-5/h4-7,9,11-12,15H,1-3,10H2,(H,13,14)/t4-,5+,6+,7+,9?/m0/s1

> <INCHI_KEY>
IQFWYNFDWRYSRA-BLELIYKESA-N

> <FORMULA>
C9H17NO6S

> <MOLECULAR_WEIGHT>
267.299

> <EXACT_MASS>
267.077657971

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
26.514823027923654

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-4-({[(2S,3S,4R)-3,4,5-trihydroxyoxolan-2-yl]methyl}sulfanyl)butanoic acid

> <ALOGPS_LOGP>
-2.58

> <JCHEM_LOGP>
-4.233186655917743

> <ALOGPS_LOGS>
-0.81

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.315163773646933

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8022463307785994

> <JCHEM_PKA_STRONGEST_BASIC>
9.495582400043908

> <JCHEM_POLAR_SURFACE_AREA>
133.24

> <JCHEM_REFRACTIVITY>
59.4888

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.10e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
ribose-5-S-homocysteine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-OCT-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-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  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+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  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   17  S   UNK     0       0.000   0.000   0.000  0.00  0.00           S+0
HETATM   18  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   19  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    2    4                                                       
CONECT    2    1   17                                                       
CONECT    3    5   17                                                       
CONECT    4    1    8   10   18                                             
CONECT    5    3    6   16   19                                             
CONECT    6    5    7   11   20                                             
CONECT    7    6    9   12   21                                             
CONECT    8    4   13   14                                                  
CONECT    9    7   15   16   22                                             
CONECT   10    4                                                            
CONECT   11    6                                                            
CONECT   12    7                                                            
CONECT   13    8                                                            
CONECT   14    8                                                            
CONECT   15    9                                                            
CONECT   16    5    9                                                       
CONECT   17    2    3                                                       
CONECT   18    4                                                            
CONECT   19    5                                                            
CONECT   20    6                                                            
CONECT   21    7                                                            
CONECT   22    9                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   44    0
END

Synonyms

Value	Source
Ribose-5-S-homocysteine	ChEBI

Molecular Formula

C₉H₁₇NO₆S

Average Mass

267.299

Monoisotopic Mass

267.077657971

IUPAC Name

(2S)-2-amino-4-({[(2S,3S,4R)-3,4,5-trihydroxyoxolan-2-yl]methyl}sulfanyl)butanoic acid

Traditional Name

ribose-5-S-homocysteine

CAS Registry Number

15912-98-8

SMILES

[H][C@](N)(CCSC[C@@]1([H])OC([H])(O)[C@]([H])(O)[C@]1([H])O)C(O)=O

InChI Identifier

InChI=1S/C9H17NO6S/c10-4(8(13)14)1-2-17-3-5-6(11)7(12)9(15)16-5/h4-7,9,11-12,15H,1-3,10H2,(H,13,14)/t4-,5+,6+,7+,9?/m0/s1

InChI Key

IQFWYNFDWRYSRA-BLELIYKESA-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

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

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

homocysteines (CHEBI:17575 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	41 g/L	ALOGPS
logP	-2.6	ALOGPS
logP	-4.2	ChemAxon
logS	-0.81	ALOGPS
pKa (Strongest Acidic)	1.8	ChemAxon
pKa (Strongest Basic)	9.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	133.24 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	59.49 m³·mol⁻¹	ChemAxon
Polarizability	26.51 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 (TMS_4_11) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0v4i-1490000000-a563ced55f82e8070620	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0awl-6940000000-6f3b4a6abff4c6480a68	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000i-9300000000-ec0c015f9099ed6a02a3	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-1980000000-d38c80c34d9b3ddb390f	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00lr-2910000000-6a40a387796ae281b565	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a59-9600000000-eb2fe9f3863fefa956e0	2015-09-15	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-22	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
MMDBr0007223	S-Adenosylhomocysteine	Adenine	Not Available	S-adenosylhomocysteine nucleosidase	VMH	30371894
MMDBr0007224	Water	Homocysteine	Not Available	Ribosylhomocysteinase	VMH	30371894
MMDBr0007562	S-Ribosyl-L-homocysteine	4,5-Dihydroxy-2,3-pentanedione	Not Available	S-ribosylhomocysteine cleavage enzyme	VMH	30371894
MMDBr0007705	S-Adenosylhomocysteine	Adenine	Not Available	S-adenosylhomocysteine nucleosidase reversible	VMH	30371894
MMDBr0013683	S-Ribosyl-L-homocysteine	(4S)-4,5-Dihydroxypentan-2,3-dione	S-ribosylhomocysteine lyase	Non-hydrolytic bond cleavage (or its reversal)	RHEA	34755880
MMDBr0013686	Water	Adenine	Aminodeoxyfutalosine nucleosidase	Hydrolysis of a nucleotide	RHEA	34755880
MMDBr0013687	Water	Adenine	5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase	Hydrolysis of a nucleotide	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	306	Human feces; Human sputum; Human ; Pig ; Human unknown; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal; Human stool; Cattle ; River trout ; Lion ; Chicken ; Human subgingival plaque	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	448	Pig ; Human feces; Human ; Cattle ; Human pleural fluid plaque; Human stool; Human subgingival plaque; Human saliva; Catfish	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Bacteroidetes	109	Human feces; Human appendix biopsy; Human ; Human gastric fluid; Human saliva; Human subgingival plaque; Human supragingival plaque; Human stool; Human urine	Metabolic reconstruction
Bacteria	Actinobacteria	117	Human ; Human feces; Human nasopharyngeal swab; Human sputum; Human pleural fluid plaque; Human dental plaque; Human supragingival plaque; Human subgingival plaque; Human mucosa; Human saliva; Cattle	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria	Synergistetes	2	Human feces	Metabolic reconstruction
Archaea	Euryarchaeota	4		Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Bacteria	Spirochaetes	6	Human feces; Human	Metabolic reconstruction
Bacteria	Fusobacteria	19	Human feces; Human	Metabolic reconstruction
Bacteria	Tenericutes	3	Human feces	Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Bacteria	Deinococcus-thermus	5
Bacteria/NULL	Proteobacteria	1	Human feces; Human sputum; Human ; Pig ; Human unknown; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal; Human stool; Cattle ; River trout ; Lion ; Chicken ; Human subgingival plaque	Unknown; Metabolic reconstruction
Bacteria	Thermotogae	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

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

24798681

PDB ID

Not Available

ChEBI ID

17575

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 S-Ribosyl-L-homocysteine (MMDBc0030093)

MOL for #<Metabolite:0x00007f5a8c7a0c68>

3D MOL for #<Metabolite:0x00007f5a8c7a0c68>

3D SDF for #<Metabolite:0x00007f5a8c7a0c68>

3D-SDF for #<Metabolite:0x00007f5a8c7a0c68>

PDB for #<Metabolite:0x00007f5a8c7a0c68>

3D PDB for #<Metabolite:0x00007f5a8c7a0c68>

SMILES for #<Metabolite:0x00007f5a8c7a0c68>

INCHI for #<Metabolite:0x00007f5a8c7a0c68>

Structure for #<Metabolite:0x00007f5a8c7a0c68>

3D Structure for #<Metabolite:0x00007f5a8c7a0c68>