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

Functional Ontology

Physical Properties

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

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 (MMDBc0030093)

MOL for #<Metabolite:0x00005623080102f8>

3D MOL for #<Metabolite:0x00005623080102f8>

3D SDF for #<Metabolite:0x00005623080102f8>

3D-SDF for #<Metabolite:0x00005623080102f8>

PDB for #<Metabolite:0x00005623080102f8>

3D PDB for #<Metabolite:0x00005623080102f8>

SMILES for #<Metabolite:0x00005623080102f8>

INCHI for #<Metabolite:0x00005623080102f8>

Structure for #<Metabolite:0x00005623080102f8>

3D Structure for #<Metabolite:0x00005623080102f8>