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Showing metabocard for Deoxyribose (HMDB0003224)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2006-05-22 15:12:42 UTC
Update Date2023-02-21 17:16:34 UTC
HMDB IDHMDB0003224
Secondary Accession Numbers
  • HMDB03224
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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0003224 (Deoxyribose)

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 HMDB0003224 (Deoxyribose)

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 HMDB0003224 (Deoxyribose)

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>
HMDB0003224

> <DATABASE_NAME>
hmdb

> <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 HMDB0003224 (Deoxyribose)

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 HMDB0003224 (Deoxyribose)

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 HMDB0003224 (Deoxyribose)

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 HMDB0003224 (Deoxyribose)

OC[C@@H]1O[C@H](O)C[C@H]1O
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INCHI for HMDB0003224 (Deoxyribose)

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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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2'-Deoxy-D-riboseHMDB
Chemical FormulaC5H10O4
Average Molecular Weight134.1305
Monoisotopic Molecular Weight134.057908808
IUPAC Name(2S,4R,5S)-5-(hydroxymethyl)oxolane-2,4-diol
Traditional Name2-deoxyribose
CAS Registry Number533-67-5
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
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.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPentoses
Alternative Parents
Substituents
  • Pentose monosaccharide
  • Tetrahydrofuran
  • Secondary alcohol
  • Hemiacetal
  • Oxacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point91 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility1000000 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Extracellular
Biospecimen Locations
  • Feces
Tissue Locations
  • Fibroblasts
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023126
KNApSAcK IDC00001115
Chemspider ID17216222
KEGG Compound IDC01801
BioCyc IDCPD-7298
BiGG ID38440
Wikipedia LinkDeoxyribose
METLIN ID3258
PubChem Compound22833604
PDB IDNot Available
ChEBI ID28816
Food Biomarker OntologyNot Available
VMH IDDRIB
MarkerDB IDNot Available
Good Scents IDrw1175031
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Formichi P, Radi E, Battisti C, Tarquini E, Leonini A, Di Stefano A, Federico A: Human fibroblasts undergo oxidative stress-induced apoptosis without internucleosomal DNA fragmentation. J Cell Physiol. 2006 Aug;208(2):289-97. [PubMed:16646085 ]
  2. Lapenna D, Ciofani G, Festi D, Neri M, Pierdomenico SD, Giamberardino MA, Cuccurullo F: Antioxidant properties of ursodeoxycholic acid. Biochem Pharmacol. 2002 Dec 1;64(11):1661-7. [PubMed:12429355 ]
  3. Gutteridge JM, Quinlan GJ: Antioxidant protection against organic and inorganic oxygen radicals by normal human plasma: the important primary role for iron-binding and iron-oxidising proteins. Biochim Biophys Acta. 1993 Feb 13;1156(2):144-50. [PubMed:8427873 ]
  4. Truscott RJ, Halpern B, Hammond J, Hunt S, Cotton RG, Haan EA, Danks DM: Abnormal deoxyribose metabolites in the urine of a child with a possible new inborn error of metabolism. Biomed Mass Spectrom. 1979 Oct;6(10):453-9. [PubMed:526564 ]
  5. Gutteridge JM, Quinlan GJ: Antioxidant protection against organic and inorganic oxygen radicals by normal human plasma: the important primary role for iron-binding and iron-oxidising proteins. Biochim Biophys Acta. 1992 Oct 20;1159(3):248-54. [PubMed:1327159 ]
  6. Chappel A, Scholem RD, Brown GK, Truscott RM, Cotton RG, Haan EA, Danks DM: Deoxyribose-5-phosphate aldolase deficiency--a harmless inborn error of metabolism. J Inherit Metab Dis. 1983;6(3):105-7. [PubMed:6422138 ]

Enzymes

Enzyme Details
1. Ribokinase
General function:
Involved in ribokinase activity
Specific function:
Not Available
Gene Name:
RBKS
Uniprot ID:
Q9H477
Molecular weight:
34142.685
Reactions
Deoxyribose 5-monophosphate + ADP → Deoxyribose + Adenosine triphosphatedetails