Showing metabocard for D-Ribose (MMDBc0000091)

Plant
Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:30:02 UTC
Update Date2022-08-30 23:33:50 UTC
Metabolite IDMMDBc0000091
Metabolite Identification
Common NameD-Ribose
DescriptionD-Ribose, commonly referred to as simply ribose, is a five-carbon sugar found in all living cells. Ribose is not an essential nutrient because it can be synthesized by almost every tissue in the body from other substances, such as glucose. It is vital for life as a component of DNA, RNA, ATP, ADP, and AMP. In nature, small amounts of ribose can be found in ripe fruits and vegetables. Brewer's yeast, which has a high concentration of RNA, is another rich source of ribose. D-ribose is also a component of many so-called energy drinks and anti-ageing products available on the market today. Ribose is a structural component of ATP, which is the primary energy source for exercising muscle. The adenosine component is an adenine base attached to the five-carbon sugar ribose. ATP provides energy to working muscles by releasing a phosphate group, hence becoming ADP, which in turn may release a phosphate group, then becoming AMP. During intense muscular activity, the total amount of ATP available is quickly depleted. In an effort to correct this imbalance, AMP is broken down in the muscle and secreted from the cell. Once the breakdown products of AMP are released from the cell, the energy potential (TAN pool) of the muscle is reduced and ATP must then be reformed using ribose. Ribose helps restore the level of adenine nucleotides by bypassing the rate-limiting step in the de novo (oxidative pentose phosphate) pathway, which regenerates phosphoribosyl pyrophosphate (PRPP), the essential precursor for ATP. If ribose is not readily available to a cell, glucose may be converted to ribose. Ribose supplementation has been shown to increase the rate of ATP resynthesis following intense exercise. The use of ribose in men with severe coronary artery disease resulted in improved exercise tolerance. Hence, there is interest in the potential of ribose supplements to boost muscular performance in athletic activities (PMID: 17618002 , Curr Sports Med Rep. 2007 Jul;6(4):254-7.).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f12407b4928>


  Mrv1652305271900072D          

 10 10  0  0  1  0            999 V2000
   12.9398   -2.8516    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0424   -4.7885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8374   -4.7885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.3163   -2.2746    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.5274   -4.1211    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   12.2725   -3.3365    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.3524   -4.1211    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   13.6075   -3.3365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4878   -3.0816    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3920   -3.0816    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  0  0  0
  1  8  1  0  0  0  0
  5  2  1  6  0  0  0
  7  3  1  6  0  0  0
  4  9  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  9  1  1  0  0  0
  7  8  1  0  0  0  0
  8 10  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f12407b4928>

HMDB0000283
     RDKit          3D
D-Ribose
 20 20  0  0  0  0  0  0  0  0999 V2000
    2.5759   -1.6543   -0.0424 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8696   -0.5817    0.4914 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7707   -0.1109   -0.4628 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1386   -1.1041   -0.7295 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4117   -0.5249   -0.6620 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4202   -1.4315   -0.6017 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2545    0.2758    0.6333 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3100    1.1436    0.8199 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0327    0.9985    0.2672 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3235    1.9954   -0.6558 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2839   -1.2959   -0.6307 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5925    0.2610    0.5944 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4462   -0.8077    1.4821 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2073    0.2296   -1.4053 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4710    0.1849   -1.5214 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1741   -2.3697   -0.5457 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0830   -0.4053    1.4698 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1655    1.6315    1.6460 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5708    1.3795    1.1299 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4026    2.1862   -1.2765 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  3  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  6
  5 15  1  0
  6 16  1  0
  7 17  1  1
  8 18  1  0
  9 19  1  1
 10 20  1  0
M  END
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3D SDF for #<Metabolite:0x00007f12407b4928>


  Mrv1652305271900072D          

 10 10  0  0  1  0            999 V2000
   12.9398   -2.8516    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0424   -4.7885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8374   -4.7885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.3163   -2.2746    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.5274   -4.1211    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   12.2725   -3.3365    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.3524   -4.1211    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   13.6075   -3.3365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4878   -3.0816    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3920   -3.0816    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  0  0  0
  1  8  1  0  0  0  0
  5  2  1  6  0  0  0
  7  3  1  6  0  0  0
  4  9  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  9  1  1  0  0  0
  7  8  1  0  0  0  0
  8 10  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000091

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4-,5?/m1/s1

> <INCHI_KEY>
HMFHBZSHGGEWLO-SOOFDHNKSA-N

> <FORMULA>
C5H10O5

> <MOLECULAR_WEIGHT>
150.1299

> <EXACT_MASS>
150.05282343

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.681345802838806

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4S,5R)-5-(hydroxymethyl)oxolane-2,3,4-triol

> <ALOGPS_LOGP>
-2.65

> <JCHEM_LOGP>
-2.302204276

> <ALOGPS_LOGS>
0.85

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.899514700313038

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.30569577774193

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9811390578102284

> <JCHEM_POLAR_SURFACE_AREA>
90.15

> <JCHEM_REFRACTIVITY>
29.9609

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.07e+03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-ribofuranoside

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f12407b4928>

HMDB0000283
     RDKit          3D
D-Ribose
 20 20  0  0  0  0  0  0  0  0999 V2000
    2.5759   -1.6543   -0.0424 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8696   -0.5817    0.4914 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7707   -0.1109   -0.4628 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1386   -1.1041   -0.7295 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4117   -0.5249   -0.6620 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4202   -1.4315   -0.6017 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2545    0.2758    0.6333 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3100    1.1436    0.8199 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0327    0.9985    0.2672 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3235    1.9954   -0.6558 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2839   -1.2959   -0.6307 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5925    0.2610    0.5944 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4462   -0.8077    1.4821 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2073    0.2296   -1.4053 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4710    0.1849   -1.5214 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1741   -2.3697   -0.5457 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0830   -0.4053    1.4698 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1655    1.6315    1.6460 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5708    1.3795    1.1299 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4026    2.1862   -1.2765 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  3  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  6
  5 15  1  0
  6 16  1  0
  7 17  1  1
  8 18  1  0
  9 19  1  1
 10 20  1  0
M  END
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PDB for #<Metabolite:0x00007f12407b4928>

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  O   UNK     0      24.154  -5.323   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      22.479  -8.939   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      25.830  -8.939   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      21.124  -4.246   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      23.384  -7.693   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      22.909  -6.228   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      24.924  -7.693   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      25.401  -6.228   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      21.444  -5.752   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      26.865  -5.752   0.000  0.00  0.00           O+0
CONECT    1    6    8                                                       
CONECT    2    5                                                            
CONECT    3    7                                                            
CONECT    4    9                                                            
CONECT    5    2    6    7                                                  
CONECT    6    1    5    9                                                  
CONECT    7    3    5    8                                                  
CONECT    8    1    7   10                                                  
CONECT    9    4    6                                                       
CONECT   10    8                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END
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3D PDB for #<Metabolite:0x00007f12407b4928>

COMPND    HMDB0000283
HETATM    1  O1  UNL     1       2.576  -1.654  -0.042  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.870  -0.582   0.491  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.771  -0.111  -0.463  1.00  0.00           C  
HETATM    4  O2  UNL     1      -0.139  -1.104  -0.730  1.00  0.00           O  
HETATM    5  C3  UNL     1      -1.412  -0.525  -0.662  1.00  0.00           C  
HETATM    6  O3  UNL     1      -2.420  -1.432  -0.602  1.00  0.00           O  
HETATM    7  C4  UNL     1      -1.255   0.276   0.633  1.00  0.00           C  
HETATM    8  O4  UNL     1      -2.310   1.144   0.820  1.00  0.00           O  
HETATM    9  C5  UNL     1       0.033   0.998   0.267  1.00  0.00           C  
HETATM   10  O5  UNL     1      -0.323   1.995  -0.656  1.00  0.00           O  
HETATM   11  H1  UNL     1       3.284  -1.296  -0.631  1.00  0.00           H  
HETATM   12  H2  UNL     1       2.592   0.261   0.594  1.00  0.00           H  
HETATM   13  H3  UNL     1       1.446  -0.808   1.482  1.00  0.00           H  
HETATM   14  H4  UNL     1       1.207   0.230  -1.405  1.00  0.00           H  
HETATM   15  H5  UNL     1      -1.471   0.185  -1.521  1.00  0.00           H  
HETATM   16  H6  UNL     1      -2.174  -2.370  -0.546  1.00  0.00           H  
HETATM   17  H7  UNL     1      -1.083  -0.405   1.470  1.00  0.00           H  
HETATM   18  H8  UNL     1      -2.165   1.631   1.646  1.00  0.00           H  
HETATM   19  H9  UNL     1       0.571   1.380   1.130  1.00  0.00           H  
HETATM   20  H10 UNL     1       0.403   2.186  -1.277  1.00  0.00           H  
CONECT    1    2   11
CONECT    2    3   12   13
CONECT    3    4    9   14
CONECT    4    5
CONECT    5    6    7   15
CONECT    6   16
CONECT    7    8    9   17
CONECT    8   18
CONECT    9   10   19
CONECT   10   20
END
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SMILES for #<Metabolite:0x00007f12407b4928>

OC[C@H]1OC(O)[C@H](O)[C@@H]1O
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INCHI for #<Metabolite:0x00007f12407b4928>

InChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4-,5?/m1/s1
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Synonyms
ValueSource
(3R,4S,5R)-5-(Hydroxymethyl)tetrahydrofuran-2,3,4-triolChEBI
RiboseChEBI
D-RibofuranosideHMDB
D-​RibofuranoseHMDB
RibofuranosideHMDB
RibofuranoseHMDB
Molecular FormulaC5H10O5
Average Mass150.1299
Monoisotopic Mass150.05282343
IUPAC Name(3R,4S,5R)-5-(hydroxymethyl)oxolane-2,3,4-triol
Traditional NameD-ribofuranoside
CAS Registry Number613-83-2
SMILES
OC[C@H]1OC(O)[C@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4-,5?/m1/s1
InChI KeyHMFHBZSHGGEWLO-SOOFDHNKSA-N