Showing metabocard for Deoxyribose (MMDBc0000422)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:37:24 UTC
Update Date2022-08-31 06:06:51 UTC
Metabolite IDMMDBc0000422
Metabolite Identification
Common NameDeoxyribose
DescriptionDeoxyribose is an aldopentose, a monosaccharide containing five carbon atoms, and including an aldehyde functional group. It is derived from the pentose sugar ribose by the replacement of the hydroxyl group at the 2 position with hydrogen, leading to the net loss of an oxygen atom, and has chemical formula C5H10O4. In deoxyribose, the carbon furthest from the attached carbon is stripped of the oxygen atom in what would be a hydroxyl group in ribose. The common base adenine (a purine derivative) coupled to deoxyribose is called deoxyadenosine. The 5-triphosphate derivative of adenosine, commonly called adenosine triphosphate (ATP) is an important energy transport molecule in cells. -- Wikipedia .
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x0000560be19fa608>

Untitled Document-9
  Mrv0541 02231219402D          

  9  9  0  0  0  0            999 V2000
   -0.7136    0.0023    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7136   -0.8227    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0711   -1.0777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5560   -0.4102    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0711    0.2572    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3810   -1.3077    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3810    0.4872    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3810   -0.4102    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2948    1.3077    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
  4  5  1  0  0  0  0
  5  1  1  0  0  0  0
  2  6  1  1  0  0  0
  1  7  1  6  0  0  0
  4  8  1  6  0  0  0
  7  9  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x0000560be19fa608>

HMDB0003224
     RDKit          3D
Deoxyribose
 19 19  0  0  0  0  0  0  0  0999 V2000
    2.5558   -0.0872    1.0010 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0036    0.4782   -0.1244 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5185    0.3790   -0.1971 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1351    1.0006    0.8643 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4674    0.7423    0.5017 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3527    1.0354    1.5183 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5087   -0.7204    0.1051 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0168   -1.0148   -0.1088 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2008   -1.7772   -1.2334 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5473   -0.1310    0.8440 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2836    1.5471   -0.1919 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4188   -0.0152   -1.0272 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1703    0.8224   -1.1389 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6461    1.3837   -0.4084 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3795    1.9970    1.6545 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9816   -0.8149   -0.8912 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9435   -1.3543    0.8746 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3345   -1.5398    0.8079 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6018   -1.9309   -1.7743 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
  8  9  1  0
  8  3  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  6
  5 14  1  6
  6 15  1  0
  7 16  1  0
  7 17  1  0
  8 18  1  1
  9 19  1  0
M  END
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3D SDF for #<Metabolite:0x0000560be19fa608>

Untitled Document-9
  Mrv0541 02231219402D          

  9  9  0  0  0  0            999 V2000
   -0.7136    0.0023    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7136   -0.8227    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0711   -1.0777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5560   -0.4102    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0711    0.2572    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3810   -1.3077    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3810    0.4872    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3810   -0.4102    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2948    1.3077    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
  4  5  1  0  0  0  0
  5  1  1  0  0  0  0
  2  6  1  1  0  0  0
  1  7  1  6  0  0  0
  4  8  1  6  0  0  0
  7  9  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000422

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O4/c6-2-4-3(7)1-5(8)9-4/h3-8H,1-2H2/t3-,4+,5+/m1/s1

> <INCHI_KEY>
PDWIQYODPROSQH-WISUUJSJSA-N

> <FORMULA>
C5H10O4

> <MOLECULAR_WEIGHT>
134.1305

> <EXACT_MASS>
134.057908808

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
12.672116914961766

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-2.06

> <JCHEM_LOGP>
-1.4015662129999997

> <ALOGPS_LOGS>
0.89

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.970472920803942

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.360977999134441

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9789221500650536

> <JCHEM_POLAR_SURFACE_AREA>
69.92

> <JCHEM_REFRACTIVITY>
28.450199999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.05e+03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-deoxyribose

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x0000560be19fa608>

HMDB0003224
     RDKit          3D
Deoxyribose
 19 19  0  0  0  0  0  0  0  0999 V2000
    2.5558   -0.0872    1.0010 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0036    0.4782   -0.1244 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5185    0.3790   -0.1971 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1351    1.0006    0.8643 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4674    0.7423    0.5017 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3527    1.0354    1.5183 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5087   -0.7204    0.1051 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0168   -1.0148   -0.1088 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2008   -1.7772   -1.2334 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5473   -0.1310    0.8440 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2836    1.5471   -0.1919 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4188   -0.0152   -1.0272 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1703    0.8224   -1.1389 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6461    1.3837   -0.4084 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3795    1.9970    1.6545 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9816   -0.8149   -0.8912 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9435   -1.3543    0.8746 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3345   -1.5398    0.8079 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6018   -1.9309   -1.7743 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
  8  9  1  0
  8  3  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  6
  5 14  1  6
  6 15  1  0
  7 16  1  0
  7 17  1  0
  8 18  1  1
  9 19  1  0
M  END
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PDB for #<Metabolite:0x0000560be19fa608>

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Untitled Document-9                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      -1.332   0.004   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.332  -1.536   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.133  -2.012   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.038  -0.766   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.133   0.480   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      -2.578  -2.441   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -2.578   0.909   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       2.578  -0.766   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -2.417   2.441   0.000  0.00  0.00           O+0
CONECT    1    2    5    7                                                  
CONECT    2    1    3    6                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    8                                                  
CONECT    5    4    1                                                       
CONECT    6    2                                                            
CONECT    7    1    9                                                       
CONECT    8    4                                                            
CONECT    9    7                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
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3D PDB for #<Metabolite:0x0000560be19fa608>

COMPND    HMDB0003224
HETATM    1  O1  UNL     1       2.556  -0.087   1.001  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.004   0.478  -0.124  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.519   0.379  -0.197  1.00  0.00           C  
HETATM    4  O2  UNL     1      -0.135   1.001   0.864  1.00  0.00           O  
HETATM    5  C3  UNL     1      -1.467   0.742   0.502  1.00  0.00           C  
HETATM    6  O3  UNL     1      -2.353   1.035   1.518  1.00  0.00           O  
HETATM    7  C4  UNL     1      -1.509  -0.720   0.105  1.00  0.00           C  
HETATM    8  C5  UNL     1      -0.017  -1.015  -0.109  1.00  0.00           C  
HETATM    9  O4  UNL     1       0.201  -1.777  -1.233  1.00  0.00           O  
HETATM   10  H1  UNL     1       3.547  -0.131   0.844  1.00  0.00           H  
HETATM   11  H2  UNL     1       2.284   1.547  -0.192  1.00  0.00           H  
HETATM   12  H3  UNL     1       2.419  -0.015  -1.027  1.00  0.00           H  
HETATM   13  H4  UNL     1       0.170   0.822  -1.139  1.00  0.00           H  
HETATM   14  H5  UNL     1      -1.646   1.384  -0.408  1.00  0.00           H  
HETATM   15  H6  UNL     1      -2.379   1.997   1.654  1.00  0.00           H  
HETATM   16  H7  UNL     1      -1.982  -0.815  -0.891  1.00  0.00           H  
HETATM   17  H8  UNL     1      -1.943  -1.354   0.875  1.00  0.00           H  
HETATM   18  H9  UNL     1       0.334  -1.540   0.808  1.00  0.00           H  
HETATM   19  H10 UNL     1      -0.602  -1.931  -1.774  1.00  0.00           H  
CONECT    1    2   10
CONECT    2    3   11   12
CONECT    3    4    8   13
CONECT    4    5
CONECT    5    6    7   14
CONECT    6   15
CONECT    7    8   16   17
CONECT    8    9   18
CONECT    9   19
END
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SMILES for #<Metabolite:0x0000560be19fa608>

OC[C@@H]1O[C@H](O)C[C@H]1O
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INCHI for #<Metabolite:0x0000560be19fa608>

InChI=1S/C5H10O4/c6-2-4-3(7)1-5(8)9-4/h3-8H,1-2H2/t3-,4+,5+/m1/s1
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Synonyms
ValueSource
2'-Deoxy-D-riboseHMDB
Molecular FormulaC5H10O4
Average Mass134.1305
Monoisotopic Mass134.057908808
IUPAC Name(2S,4R,5S)-5-(hydroxymethyl)oxolane-2,4-diol
Traditional Name2-deoxyribose
CAS Registry NumberNot Available
SMILES
OC[C@@H]1O[C@H](O)C[C@H]1O
InChI Identifier
InChI=1S/C5H10O4/c6-2-4-3(7)1-5(8)9-4/h3-8H,1-2H2/t3-,4+,5+/m1/s1
InChI KeyPDWIQYODPROSQH-WISUUJSJSA-N