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Showing NP-Card for Ribitol (NP0000075)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-08-19 20:22:32 UTC
NP-MRD IDNP0000075
Secondary Accession NumbersNone
Natural Product Identification
Common NameRibitol
DescriptionRibitol is a pentose alcohol formed by the reduction of ribose. It occurs naturally in plants as well as in the cell walls of some Gram-positive bacteria. Ribitol forms part of the chemical structure of riboflavin and flavin mononucleotide (FMN). It is also a metabolic end product formed by the reduction of ribose in human fibroblasts and erythrocytes. In this regard ribitol is found in all organisms from bacteria to plants to humans. Ribitol is a normal constituent of human urine (PMID: 2736321 ). Elevated levels of ribitol in the serum or urine can be found in patients with transaldolase deficiency (PMID: 11283793 ). Transaldolase is an important enzyme in the pentose phosphate pathway (PPP). Elevated levels of ribitol in the serum or urine can be found in patients with Ribose-5-phosphate isomerase deficiency (PMID: 14988808 ). Ribose-5-phosphate isomerase is an important enzyme in the pentose phosphate pathway (PPP). Export of ribitol across the cell membrane indicates that can be cleared from the body without metabolic conversion (PMID 15234337 ). Ribitol is normally absent in Breast milk (PMID 16456418 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000075 (Ribitol)

00508.mol
  Mrv1652303202019002D          

 10  9  0  0  0  0            999 V2000
   -2.1458   -0.2063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4296    0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7134   -0.2063    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000    0.2063    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7163   -0.2063    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4296    0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1458   -0.2063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7134   -1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7163   -1.0313    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  6  1  0  0  0  0
  6  7  1  0  0  0  0
  4  8  1  1  0  0  0
  3  9  1  6  0  0  0
  5 10  1  6  0  0  0
M  END
Download

3D MOL for NP0000075 (Ribitol)

HMDB0000508
     RDKit          3D
Ribitol
 22 21  0  0  0  0  0  0  0  0999 V2000
    2.5266    0.9942   -0.5475 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3559    0.0575    0.4470 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8498   -0.0294    0.7270 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6070   -0.9645    1.7288 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1965   -0.4078   -0.5737 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4541    0.5916   -1.4951 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2813   -0.6442   -0.4258 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7866   -1.0411   -1.6913 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0230    0.5703    0.0166 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6619    1.0482    1.2633 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4613    1.1172   -0.7993 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7390   -0.9376    0.1578 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8107    0.4502    1.3739 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5600    0.9934    0.9935 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2094   -0.5348    2.5335 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6746   -1.3785   -0.9063 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6253    0.2650   -2.4057 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4746   -1.4949    0.2552 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3860   -1.8244   -1.6051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8656    1.3949   -0.7241 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1132    0.3635   -0.0160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4781    1.4113    1.6932 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
  3  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  1
  4 15  1  0
  5 16  1  6
  6 17  1  0
  7 18  1  1
  8 19  1  0
  9 20  1  0
  9 21  1  0
 10 22  1  0
M  END
Download

3D SDF for NP0000075 (Ribitol)

00508.mol
  Mrv1652303202019002D          

 10  9  0  0  0  0            999 V2000
   -2.1458   -0.2063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4296    0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7134   -0.2063    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000    0.2063    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7163   -0.2063    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4296    0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1458   -0.2063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7134   -1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7163   -1.0313    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  6  1  0  0  0  0
  6  7  1  0  0  0  0
  4  8  1  1  0  0  0
  3  9  1  6  0  0  0
  5 10  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0000075

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H12O5/c6-1-3(8)5(10)4(9)2-7/h3-10H,1-2H2/t3-,4+,5-

> <INCHI_KEY>
HEBKCHPVOIAQTA-ZXFHETKHSA-N

> <FORMULA>
C5H12O5

> <MOLECULAR_WEIGHT>
152.1458

> <EXACT_MASS>
152.068473494

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
14.381408299515499

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3s,4S)-pentane-1,2,3,4,5-pentol

> <ALOGPS_LOGP>
-2.53

> <JCHEM_LOGP>
-3.099683906666666

> <ALOGPS_LOGS>
0.64

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.742189661908146

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.760078510562963

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9742034412471314

> <JCHEM_POLAR_SURFACE_AREA>
101.15

> <JCHEM_REFRACTIVITY>
32.4411

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.64e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
ribitol

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000075 (Ribitol)

HMDB0000508
     RDKit          3D
Ribitol
 22 21  0  0  0  0  0  0  0  0999 V2000
    2.5266    0.9942   -0.5475 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3559    0.0575    0.4470 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8498   -0.0294    0.7270 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6070   -0.9645    1.7288 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1965   -0.4078   -0.5737 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4541    0.5916   -1.4951 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2813   -0.6442   -0.4258 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7866   -1.0411   -1.6913 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0230    0.5703    0.0166 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6619    1.0482    1.2633 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4613    1.1172   -0.7993 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7390   -0.9376    0.1578 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8107    0.4502    1.3739 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5600    0.9934    0.9935 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2094   -0.5348    2.5335 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6746   -1.3785   -0.9063 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6253    0.2650   -2.4057 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4746   -1.4949    0.2552 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3860   -1.8244   -1.6051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8656    1.3949   -0.7241 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1132    0.3635   -0.0160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4781    1.4113    1.6932 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
  3  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  1
  4 15  1  0
  5 16  1  6
  6 17  1  0
  7 18  1  1
  8 19  1  0
  9 20  1  0
  9 21  1  0
 10 22  1  0
M  END
Download

PDB for NP0000075 (Ribitol)

HEADER    PROTEIN                                 20-MAR-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 00508.mol                                         
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-MAR-20         0                                  
HETATM    1  O   UNK     0      -4.005  -0.385   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -2.669   0.385   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.332  -0.385   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.385   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.337  -0.385   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.669   0.385   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.005  -0.385   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   1.925   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -1.332  -1.925   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       1.337  -1.925   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    9                                                  
CONECT    4    3    5    8                                                  
CONECT    5    4    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6                                                            
CONECT    8    4                                                            
CONECT    9    3                                                            
CONECT   10    5                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
Download

3D PDB for NP0000075 (Ribitol)

COMPND    HMDB0000508
HETATM    1  O1  UNL     1       2.527   0.994  -0.547  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.356   0.057   0.447  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.850  -0.029   0.727  1.00  0.00           C  
HETATM    4  O2  UNL     1       0.607  -0.965   1.729  1.00  0.00           O  
HETATM    5  C3  UNL     1       0.196  -0.408  -0.574  1.00  0.00           C  
HETATM    6  O3  UNL     1       0.454   0.592  -1.495  1.00  0.00           O  
HETATM    7  C4  UNL     1      -1.281  -0.644  -0.426  1.00  0.00           C  
HETATM    8  O4  UNL     1      -1.787  -1.041  -1.691  1.00  0.00           O  
HETATM    9  C5  UNL     1      -2.023   0.570   0.017  1.00  0.00           C  
HETATM   10  O5  UNL     1      -1.662   1.048   1.263  1.00  0.00           O  
HETATM   11  H1  UNL     1       3.461   1.117  -0.799  1.00  0.00           H  
HETATM   12  H2  UNL     1       2.739  -0.938   0.158  1.00  0.00           H  
HETATM   13  H3  UNL     1       2.811   0.450   1.374  1.00  0.00           H  
HETATM   14  H4  UNL     1       0.560   0.993   0.993  1.00  0.00           H  
HETATM   15  H5  UNL     1       0.209  -0.535   2.533  1.00  0.00           H  
HETATM   16  H6  UNL     1       0.675  -1.378  -0.906  1.00  0.00           H  
HETATM   17  H7  UNL     1       0.625   0.265  -2.406  1.00  0.00           H  
HETATM   18  H8  UNL     1      -1.475  -1.495   0.255  1.00  0.00           H  
HETATM   19  H9  UNL     1      -2.386  -1.824  -1.605  1.00  0.00           H  
HETATM   20  H10 UNL     1      -1.866   1.395  -0.724  1.00  0.00           H  
HETATM   21  H11 UNL     1      -3.113   0.364  -0.016  1.00  0.00           H  
HETATM   22  H12 UNL     1      -2.478   1.411   1.693  1.00  0.00           H  
CONECT    1    2   11
CONECT    2    3   12   13
CONECT    3    4    5   14
CONECT    4   15
CONECT    5    6    7   16
CONECT    6   17
CONECT    7    8    9   18
CONECT    8   19
CONECT    9   10   20   21
CONECT   10   22
END
Download

SMILES for NP0000075 (Ribitol)

OC[C@H](O)[C@H](O)[C@H](O)CO
Download

INCHI for NP0000075 (Ribitol)

InChI=1S/C5H12O5/c6-1-3(8)5(10)4(9)2-7/h3-10H,1-2H2/t3-,4+,5-
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View in JSmol
Synonyms
ValueSource
(2R,3S,4S)-Pentane-1,2,3,4,5-pentolChEBI
AdonitolChEBI
D-AdonitolChEBI
D-RibitolChEBI
L-RibitolChEBI
1,2,3,4,5-PentanepentolHMDB
AdonitHMDB
AdoniteHMDB
PentitolHMDB
Chemical FormulaC5H12O5
Average Mass152.1458 Da
Monoisotopic Mass152.06847 Da
IUPAC Name(2R,3s,4S)-pentane-1,2,3,4,5-pentol
Traditional Nameribitol
CAS Registry Number488-81-3
SMILES
OC[C@H](O)[C@H](O)[C@H](O)CO
InChI Identifier
InChI=1S/C5H12O5/c6-1-3(8)5(10)4(9)2-7/h3-10H,1-2H2/t3-,4+,5-
InChI KeyHEBKCHPVOIAQTA-ZXFHETKHSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, simulated)varshavi.d26@gmail.comNot AvailableNot Available2021-08-16View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, simulated)varshavi.d26@gmail.comNot AvailableNot Available2021-08-16View Spectrum
Species
Species of Origin
Species NameSourceReference
Adonis vernalisKNApSAcK Database
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Anthriscus sylvestrisKNApSAcK Database
Arabidopsis thalianaLOTUS Database
Bergera koenegii-
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Brassica oleracea L. ssp. BotrytisKNApSAcK Database
Bubalus bubalisFooDB
Bupleurum aureumLOTUS Database
Bupleurum falcatumKNApSAcK Database
Bupleurum fruticescensLOTUS Database
Bupleurum gibraltaricumLOTUS Database
Cannabis sativaCannabisDB
      Not Available
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
Citrus X sinensis (L.) Osbeck (pro. sp.)Plant
ColumbaFooDB
ColumbidaeFooDB
Curcuma domesticaKNApSAcK Database
Curcuma longaPlant
Daphnia magnaLOTUS Database
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Eugenia lehmanniiKNApSAcK Database
Evernia prunastriLOTUS Database
Gallus gallusFooDB
Homo sapiensLOTUS Database
Homo sapiens (Urine)Animalia
Laetiporus sulphureusLOTUS Database
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Lotus burttiiLOTUS Database
Lotus corniculatusLOTUS Database
Medicago sativaLOTUS Database
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Murraya paniculataPlant
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Phoma medicaginisFungi
Prunus aviumPlant
Solanum tuberosumKNApSAcK Database
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Species Where Detected
Species NameSourceReference
Homo sapiens (Serum)KNApSAcK Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as sugar alcohols. These are hydrogenated forms of carbohydrate in which the carbonyl group (aldehyde or ketone, reducing sugar) has been reduced to a primary or secondary hydroxyl group.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentSugar alcohols
Alternative Parents
Substituents
  • Sugar alcohol
  • Monosaccharide
  • Secondary alcohol
  • Polyol
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point102 - 105 °CNot Available
Boiling Point494.50 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility936 mg/mLNot Available
LogP-3.224https://www.chemspider.com/Chemical-Structure.10254628.html
Predicted Properties
PropertyValueSource
Water Solubility664 g/LALOGPS
logP-2.5ALOGPS
logP-3.1ChemAxon
logS0.64ALOGPS
pKa (Strongest Acidic)12.76ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area101.15 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity32.44 m³·mol⁻¹ChemAxon
Polarizability14.38 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000508
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022083
KNApSAcK IDC00001171
Chemspider ID10254628
KEGG Compound IDC00474
BioCyc IDRIBITOL
BiGG ID35086
Wikipedia LinkRibitol
METLIN ID316
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID15963
Good Scents IDrw1216341
References
General References
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