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

Functional Ontology

Physical Properties

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01b9-1590000000-42b048d2c23ca96f5908	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0gb9-2930000000-4919a12118e6bf75521f	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03dr-9400000000-1a13f170188e308b164a	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0292-2690000000-68581f80437bb7da635e	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00kb-3960000000-21c3f9415cf6a4b74a29	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0aos-9700000000-dd64ac19f6fcc0bb8d5c	2019-02-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-17	View Spectrum

Biological Properties

Human Proteins and Enzymes

Human Pathways

Metabolic Reactions

Health Effects and Bioactivity

Microbial Sources

Exposure Sources

Host Biospecimen and Location

External Links

References

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

MOL for #<Metabolite:0x00007fd5f927b330>

3D MOL for #<Metabolite:0x00007fd5f927b330>

3D SDF for #<Metabolite:0x00007fd5f927b330>

3D-SDF for #<Metabolite:0x00007fd5f927b330>

PDB for #<Metabolite:0x00007fd5f927b330>

3D PDB for #<Metabolite:0x00007fd5f927b330>

SMILES for #<Metabolite:0x00007fd5f927b330>

INCHI for #<Metabolite:0x00007fd5f927b330>

Structure for #<Metabolite:0x00007fd5f927b330>

3D Structure for #<Metabolite:0x00007fd5f927b330>