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Showing metabocard for Ribonic acid (HMDB0000867)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:15:15 UTC
HMDB IDHMDB0000867
Secondary Accession Numbers
  • HMDB00867
Metabolite Identification
Common NameRibonic acid
DescriptionRibonic acid, also known as D-ribonate, belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group. Ribonic acid has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make ribonic acid a potential biomarker for the consumption of these foods. Ribonic acid is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on Ribonic acid.
Structure
Data?1676999715
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000867 (Ribonic acid)

  Mrv1652307171918042D          

 11 10  0  0  0  0            999 V2000
   -3.4819    0.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1964   -0.2008    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4819    1.0366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7674   -0.2008    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7674   -1.0258    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0530    0.2116    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0530    1.0366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3385   -0.2008    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6240    0.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0903   -0.2008    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3385   -1.0258    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  4  6  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  6  7  1  6  0  0  0
  4  5  1  1  0  0  0
  1  3  2  0  0  0  0
  2  1  1  0  0  0  0
  8 11  1  1  0  0  0
M  END
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3D MOL for HMDB0000867 (Ribonic acid)

HMDB0000867
     RDKit          3D
Ribonic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
    1.6115   -2.2965   -0.4232 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9320   -1.2542    0.1779 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6792   -1.3478    1.3286 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5202    0.0490   -0.3318 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9677    1.0970    0.4669 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0457    0.1700   -0.5956 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1988    1.3771   -1.2487 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7851    0.1375    0.6524 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5334   -1.0771    1.3013 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2454    0.1404    0.2644 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6095    1.3060   -0.3907 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2693   -0.5938    1.6841 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0335    0.1928   -1.3267 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5345    1.0063    1.3656 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2865   -0.6413   -1.2743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1975    2.1330   -0.5906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5724    0.9457    1.3528 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8509   -1.8464    0.7574 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8782    0.0923    1.1940 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4851   -0.7138   -0.3735 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9507    1.1240   -1.3208 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
  3 12  1  0
  4 13  1  6
  5 14  1  0
  6 15  1  6
  7 16  1  0
  8 17  1  1
  9 18  1  0
 10 19  1  0
 10 20  1  0
 11 21  1  0
M  END
Download

3D SDF for HMDB0000867 (Ribonic acid)

  Mrv1652307171918042D          

 11 10  0  0  0  0            999 V2000
   -3.4819    0.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1964   -0.2008    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4819    1.0366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7674   -0.2008    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7674   -1.0258    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0530    0.2116    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0530    1.0366    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3385   -0.2008    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6240    0.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0903   -0.2008    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3385   -1.0258    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  4  6  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  6  7  1  6  0  0  0
  4  5  1  1  0  0  0
  1  3  2  0  0  0  0
  2  1  1  0  0  0  0
  8 11  1  1  0  0  0
M  END
> <DATABASE_ID>
HMDB0000867

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O6/c6-1-2(7)3(8)4(9)5(10)11/h2-4,6-9H,1H2,(H,10,11)/t2-,3-,4-/m1/s1

> <INCHI_KEY>
QXKAIJAYHKCRRA-BXXZVTAOSA-N

> <FORMULA>
C5H10O6

> <MOLECULAR_WEIGHT>
166.1293

> <EXACT_MASS>
166.047738052

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
14.346660109400801

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4R)-2,3,4,5-tetrahydroxypentanoic acid

> <ALOGPS_LOGP>
-2.48

> <JCHEM_LOGP>
-2.7794093686666668

> <ALOGPS_LOGS>
0.19

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.768659694136133

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.393139811550542

> <JCHEM_PKA_STRONGEST_BASIC>
-2.974562302797298

> <JCHEM_POLAR_SURFACE_AREA>
118.22000000000001

> <JCHEM_REFRACTIVITY>
32.308499999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.58e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
ribonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0000867 (Ribonic acid)

HMDB0000867
     RDKit          3D
Ribonic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
    1.6115   -2.2965   -0.4232 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9320   -1.2542    0.1779 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6792   -1.3478    1.3286 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5202    0.0490   -0.3318 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9677    1.0970    0.4669 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0457    0.1700   -0.5956 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1988    1.3771   -1.2487 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7851    0.1375    0.6524 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5334   -1.0771    1.3013 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2454    0.1404    0.2644 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6095    1.3060   -0.3907 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2693   -0.5938    1.6841 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0335    0.1928   -1.3267 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5345    1.0063    1.3656 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2865   -0.6413   -1.2743 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1975    2.1330   -0.5906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5724    0.9457    1.3528 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8509   -1.8464    0.7574 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8782    0.0923    1.1940 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4851   -0.7138   -0.3735 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9507    1.1240   -1.3208 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
  3 12  1  0
  4 13  1  6
  5 14  1  0
  6 15  1  6
  7 16  1  0
  8 17  1  1
  9 18  1  0
 10 19  1  0
 10 20  1  0
 11 21  1  0
M  END
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PDB for HMDB0000867 (Ribonic acid)

HEADER    PROTEIN                                 17-JUL-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUL-19         0                                  
HETATM    1  C   UNK     0      -6.500   0.395   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -7.833  -0.375   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      -6.500   1.935   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -5.166  -0.375   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -5.166  -1.915   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -3.832   0.395   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -3.832   1.935   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -2.499  -0.375   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.165   0.395   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       0.169  -0.375   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -2.499  -1.915   0.000  0.00  0.00           O+0
CONECT    1    4    3    2                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1    6    5                                                  
CONECT    5    4                                                            
CONECT    6    4    8    7                                                  
CONECT    7    6                                                            
CONECT    8    6    9   11                                                  
CONECT    9    8   10                                                       
CONECT   10    9                                                            
CONECT   11    8                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for HMDB0000867 (Ribonic acid)

COMPND    HMDB0000867
HETATM    1  O1  UNL     1       1.611  -2.296  -0.423  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.932  -1.254   0.178  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.679  -1.348   1.329  1.00  0.00           O  
HETATM    4  C2  UNL     1       1.520   0.049  -0.332  1.00  0.00           C  
HETATM    5  O3  UNL     1       1.968   1.097   0.467  1.00  0.00           O  
HETATM    6  C3  UNL     1       0.046   0.170  -0.596  1.00  0.00           C  
HETATM    7  O4  UNL     1      -0.199   1.377  -1.249  1.00  0.00           O  
HETATM    8  C4  UNL     1      -0.785   0.137   0.652  1.00  0.00           C  
HETATM    9  O5  UNL     1      -0.533  -1.077   1.301  1.00  0.00           O  
HETATM   10  C5  UNL     1      -2.245   0.140   0.264  1.00  0.00           C  
HETATM   11  O6  UNL     1      -2.609   1.306  -0.391  1.00  0.00           O  
HETATM   12  H1  UNL     1       3.269  -0.594   1.684  1.00  0.00           H  
HETATM   13  H2  UNL     1       2.033   0.193  -1.327  1.00  0.00           H  
HETATM   14  H3  UNL     1       1.535   1.006   1.366  1.00  0.00           H  
HETATM   15  H4  UNL     1      -0.286  -0.641  -1.274  1.00  0.00           H  
HETATM   16  H5  UNL     1      -0.197   2.133  -0.591  1.00  0.00           H  
HETATM   17  H6  UNL     1      -0.572   0.946   1.353  1.00  0.00           H  
HETATM   18  H7  UNL     1      -0.851  -1.846   0.757  1.00  0.00           H  
HETATM   19  H8  UNL     1      -2.878   0.092   1.194  1.00  0.00           H  
HETATM   20  H9  UNL     1      -2.485  -0.714  -0.374  1.00  0.00           H  
HETATM   21  H10 UNL     1      -2.951   1.124  -1.321  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   12
CONECT    4    5    6   13
CONECT    5   14
CONECT    6    7    8   15
CONECT    7   16
CONECT    8    9   10   17
CONECT    9   18
CONECT   10   11   19   20
CONECT   11   21
END
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SMILES for HMDB0000867 (Ribonic acid)

OC[C@@H](O)[C@@H](O)[C@@H](O)C(O)=O
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INCHI for HMDB0000867 (Ribonic acid)

InChI=1S/C5H10O6/c6-1-2(7)3(8)4(9)5(10)11/h2-4,6-9H,1H2,(H,10,11)/t2-,3-,4-/m1/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
D-Ribonic acidKegg
D-RibonateGenerator
RibonateGenerator
2,3,4,5-Tetrahydroxypentanoic acidHMDB
Ribonic acidHMDB
Chemical FormulaC5H10O6
Average Molecular Weight166.1293
Monoisotopic Molecular Weight166.047738052
IUPAC Name(2R,3R,4R)-2,3,4,5-tetrahydroxypentanoic acid
Traditional Nameribonic acid
CAS Registry Number642-98-8
SMILES
OC[C@@H](O)[C@@H](O)[C@@H](O)C(O)=O
InChI Identifier
InChI=1S/C5H10O6/c6-1-2(7)3(8)4(9)5(10)11/h2-4,6-9H,1H2,(H,10,11)/t2-,3-,4-/m1/s1
InChI KeyQXKAIJAYHKCRRA-BXXZVTAOSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentSugar acids and derivatives
Alternative Parents
Substituents
  • Pentose monosaccharide
  • Beta-hydroxy acid
  • Sugar acid
  • Short-chain hydroxy acid
  • Alpha-hydroxy acid
  • Fatty acid
  • Hydroxy acid
  • Monosaccharide
  • Secondary alcohol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Polyol
  • Primary alcohol
  • Alcohol
  • Carbonyl group
  • Hydrocarbon derivative
  • Organic oxide
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-Not Available128.367http://allccs.zhulab.cn/database/detail?ID=AllCCS00001838
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue Locations
  • Placenta
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedInfant (0-1 year old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothBladder cancer details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022289
KNApSAcK IDC00053747
Chemspider ID4574162
KEGG Compound IDC01685
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID3290
PubChem Compound5460677
PDB IDNot Available
ChEBI ID21077
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceLockwood, L. B. Pentoic acids from pentoses. (1949), US 2463784 19490308 CAN 43:20773 AN 1949:20773 CAPLUS
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Roux A, Xu Y, Heilier JF, Olivier MF, Ezan E, Tabet JC, Junot C: Annotation of the human adult urinary metabolome and metabolite identification using ultra high performance liquid chromatography coupled to a linear quadrupole ion trap-Orbitrap mass spectrometer. Anal Chem. 2012 Aug 7;84(15):6429-37. doi: 10.1021/ac300829f. Epub 2012 Jul 17. [PubMed:22770225 ]
  2. Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]