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Showing NP-Card for Ribonolactone (NP0000374)

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Record Information
Version1.0
Created at2006-03-09 14:33:53 UTC
Updated at2021-08-19 23:58:03 UTC
NP-MRD IDNP0000374
Secondary Accession NumbersNone
Natural Product Identification
Common NameRibonolactone
DescriptionRibonolactone, also known as D-ribono-1,4-lactone is a five-membered form of ribonolactone having D-configuration. It has a role as a metabolite. It is a ribonolactone and a butan-4-olide. It derives from a D-ribonic acid. Ribonolactone belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. Ribonolactone is a metabolite normally not detectable in human biofluids; however, it has been found in the urine of patients with neuroblastoma.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000374 (Ribonolactone)

Untitled Document-2
  Mrv1652305271900282D          

 10 10  0  0  0  0            999 V2000
   -0.7136    0.2796    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7136   -0.5454    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0711   -0.8004    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5560   -0.1329    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0711    0.5345    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3810   -0.1329    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3810   -1.0303    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3260   -1.5850    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3810    0.7645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2948    1.5850    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
  4  6  2  0  0  0  0
  2  7  1  6  0  0  0
  3  8  1  6  0  0  0
  1  9  1  1  0  0  0
  9 10  1  0  0  0  0
M  END
Download

3D MOL for NP0000374 (Ribonolactone)

HMDB0001900
     RDKit          3D
Ribonolactone
 18 18  0  0  0  0  0  0  0  0999 V2000
   -1.2728   -1.9281   -1.5959 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8367   -0.8364   -1.0966 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2812   -0.1029   -1.4494 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8448    0.3913   -0.2597 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6461   -0.7314    0.3661 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6628   -1.1724   -0.4781 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3374    0.6946    0.5946 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6430    2.0511    0.6436 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4750   -0.1036    0.0153 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4472    0.7253   -0.5361 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5199    1.2469   -0.4304 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0661   -0.3747    1.3211 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9920   -1.6015    0.5770 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9873   -0.3924   -1.0128 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1407    0.3653    1.6236 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6676    2.4042    1.5510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8914   -0.8267    0.7357 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2884    0.1912   -0.5689 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  4  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  2  1  0
  4 11  1  6
  5 12  1  0
  5 13  1  0
  6 14  1  0
  7 15  1  1
  8 16  1  0
  9 17  1  1
 10 18  1  0
M  END
Download

3D SDF for NP0000374 (Ribonolactone)

Untitled Document-2
  Mrv1652305271900282D          

 10 10  0  0  0  0            999 V2000
   -0.7136    0.2796    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7136   -0.5454    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0711   -0.8004    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5560   -0.1329    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0711    0.5345    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3810   -0.1329    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3810   -1.0303    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3260   -1.5850    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3810    0.7645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2948    1.5850    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
  4  6  2  0  0  0  0
  2  7  1  6  0  0  0
  3  8  1  6  0  0  0
  1  9  1  1  0  0  0
  9 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000374

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O5/c6-1-2-3(7)4(8)5(9)10-2/h2-4,6-8H,1H2/t2-,3-,4-/m1/s1

> <INCHI_KEY>
CUOKHACJLGPRHD-BXXZVTAOSA-N

> <FORMULA>
C5H8O5

> <MOLECULAR_WEIGHT>
148.114

> <EXACT_MASS>
148.037173366

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
12.798132681177856

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-one

> <ALOGPS_LOGP>
-1.98

> <JCHEM_LOGP>
-2.114938244

> <ALOGPS_LOGS>
0.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.66228265576019

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.633837675631321

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9894265691123385

> <JCHEM_POLAR_SURFACE_AREA>
86.99000000000001

> <JCHEM_REFRACTIVITY>
28.8163

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.47e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-ribosone

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000374 (Ribonolactone)

HMDB0001900
     RDKit          3D
Ribonolactone
 18 18  0  0  0  0  0  0  0  0999 V2000
   -1.2728   -1.9281   -1.5959 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8367   -0.8364   -1.0966 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2812   -0.1029   -1.4494 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8448    0.3913   -0.2597 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6461   -0.7314    0.3661 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6628   -1.1724   -0.4781 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3374    0.6946    0.5946 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6430    2.0511    0.6436 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4750   -0.1036    0.0153 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4472    0.7253   -0.5361 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5199    1.2469   -0.4304 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0661   -0.3747    1.3211 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9920   -1.6015    0.5770 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9873   -0.3924   -1.0128 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1407    0.3653    1.6236 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6676    2.4042    1.5510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8914   -0.8267    0.7357 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2884    0.1912   -0.5689 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  4  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  2  1  0
  4 11  1  6
  5 12  1  0
  5 13  1  0
  6 14  1  0
  7 15  1  1
  8 16  1  0
  9 17  1  1
 10 18  1  0
M  END
Download

PDB for NP0000374 (Ribonolactone)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Untitled Document-2                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0      -1.332   0.522   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.332  -1.018   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.133  -1.494   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.038  -0.248   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.133   0.998   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       2.578  -0.248   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -2.578  -1.923   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.609  -2.959   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -2.578   1.427   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -2.417   2.959   0.000  0.00  0.00           O+0
CONECT    1    2    5    9                                                  
CONECT    2    1    3    7                                                  
CONECT    3    2    4    8                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4    1                                                       
CONECT    6    4                                                            
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    1   10                                                       
CONECT   10    9                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END
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3D PDB for NP0000374 (Ribonolactone)

COMPND    HMDB0001900
HETATM    1  O1  UNL     1      -1.273  -1.928  -1.596  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.837  -0.836  -1.097  1.00  0.00           C  
HETATM    3  O2  UNL     1       0.281  -0.103  -1.449  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.845   0.391  -0.260  1.00  0.00           C  
HETATM    5  C3  UNL     1       1.646  -0.731   0.366  1.00  0.00           C  
HETATM    6  O3  UNL     1       2.663  -1.172  -0.478  1.00  0.00           O  
HETATM    7  C4  UNL     1      -0.337   0.695   0.595  1.00  0.00           C  
HETATM    8  O4  UNL     1      -0.643   2.051   0.644  1.00  0.00           O  
HETATM    9  C5  UNL     1      -1.475  -0.104   0.015  1.00  0.00           C  
HETATM   10  O5  UNL     1      -2.447   0.725  -0.536  1.00  0.00           O  
HETATM   11  H1  UNL     1       1.520   1.247  -0.430  1.00  0.00           H  
HETATM   12  H2  UNL     1       2.066  -0.375   1.321  1.00  0.00           H  
HETATM   13  H3  UNL     1       0.992  -1.602   0.577  1.00  0.00           H  
HETATM   14  H4  UNL     1       2.987  -0.392  -1.013  1.00  0.00           H  
HETATM   15  H5  UNL     1      -0.141   0.365   1.624  1.00  0.00           H  
HETATM   16  H6  UNL     1      -0.668   2.404   1.551  1.00  0.00           H  
HETATM   17  H7  UNL     1      -1.891  -0.827   0.736  1.00  0.00           H  
HETATM   18  H8  UNL     1      -3.288   0.191  -0.569  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    9
CONECT    3    4
CONECT    4    5    7   11
CONECT    5    6   12   13
CONECT    6   14
CONECT    7    8    9   15
CONECT    8   16
CONECT    9   10   17
CONECT   10   18
END
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SMILES for NP0000374 (Ribonolactone)

OC[C@H]1OC(=O)[C@H](O)[C@@H]1O
Download

INCHI for NP0000374 (Ribonolactone)

InChI=1S/C5H8O5/c6-1-2-3(7)4(8)5(9)10-2/h2-4,6-8H,1H2/t2-,3-,4-/m1/s1
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View in JSmol
Synonyms
ValueSource
D-(+)-Ribonic acid gamma-lactoneChEBI
D-Ribonic acid-1,4-lactoneChEBI
D-Ribono-gamma-lactoneChEBI
D-RibonolactoneChEBI
D-Ribopentono-1,4-lactoneChEBI
Ribono-gamma-lactoneChEBI
D-(+)-Ribonate g-lactoneGenerator
D-(+)-Ribonate gamma-lactoneGenerator
D-(+)-Ribonate γ-lactoneGenerator
D-(+)-Ribonic acid g-lactoneGenerator
D-(+)-Ribonic acid γ-lactoneGenerator
D-Ribonate-1,4-lactoneGenerator
D-Ribono-g-lactoneGenerator
D-Ribono-γ-lactoneGenerator
Ribono-g-lactoneGenerator
Ribono-γ-lactoneGenerator
D(+)-Ribonic acid gamma-lactoneHMDB
D-(+)-Ribonone-1.4-lactoneHMDB
D-Ribono-1,4-lactoneHMDB
delta-(+)-Ribonic acid g-lactoneHMDB
delta-(+)-Ribonic acid gamma-lactoneHMDB
delta-(+)-Ribonone-1.4-lactoneHMDB
delta-Ribono-1,4-lactoneHMDB
delta-Ribono-gamma-lactoneHMDB
delta-RibonolactoneHMDB
delta-Ribopentono-1,4-lactoneHMDB
DeoxyribonolactoneHMDB
gamma-Lactone OF ribonateHMDB
gamma-Lactone OF ribonic acidHMDB
gamma-Lactone-ribonateHMDB
gamma-Lactone-ribonic acidHMDB
RibonolactoneChEBI
Chemical FormulaC5H8O5
Average Mass148.1140 Da
Monoisotopic Mass148.03717 Da
IUPAC Name(3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-one
Traditional NameD-ribosone
CAS Registry Number5336-08-3
SMILES
OC[C@H]1OC(=O)[C@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C5H8O5/c6-1-2-3(7)4(8)5(9)10-2/h2-4,6-8H,1H2/t2-,3-,4-/m1/s1
InChI KeyCUOKHACJLGPRHD-BXXZVTAOSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
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
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
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
  • Gamma butyrolactone
  • Tetrahydrofuran
  • Carboxylic acid ester
  • Lactone
  • Secondary alcohol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid derivative
  • Oxacycle
  • Organoheterocyclic compound
  • Primary alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Alcohol
  • Carbonyl group
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point83 - 85 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility1000000 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility847 g/LALOGPS
logP-2ALOGPS
logP-2.1ChemAxon
logS0.76ALOGPS
pKa (Strongest Acidic)11.63ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area86.99 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity28.82 m³·mol⁻¹ChemAxon
Polarizability12.8 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0001900
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022728
KNApSAcK IDNot Available
Chemspider ID99702
KEGG Compound IDC02674
BioCyc IDCPD-13413
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID6380
PubChem Compound111064
PDB IDNot Available
ChEBI ID74168
Good Scents IDrw1233571
References
General References
  1. Lewis S, Kenyon CN, Meili J, Burlingame AL: High resolution gas chromatographic/real-time high resolution mass spectrometric identification of organic acids in human urine. Anal Chem. 1979 Jul;51(8):1275-85. [PubMed:484857 ]
  2. Chamberlin BA, Sweeley CC: Metabolic profiles of urinary organic acids recovered from absorbent filter paper. Clin Chem. 1987 Apr;33(4):572-6. [PubMed:3829393 ]
  3. Gates SC, Sweeley CC, Krivit W, DeWitt D, Blaisdell BE: Automated metabolic profiling of organic acids in human urine. II. Analysis of urine samples from "healthy" adults, sick children, and children with neuroblastoma. Clin Chem. 1978 Oct;24(10):1680-9. [PubMed:699273 ]
  4. Xie Y, Hu T, Zhang Y, Wei D, Zheng W, Zhu F, Tian G, Aisa HA, Shen J: Weinreb Amide Approach to the Practical Synthesis of a Key Remdesivir Intermediate. J Org Chem. 2021 Apr 2;86(7):5065-5072. doi: 10.1021/acs.joc.0c02986. Epub 2021 Mar 18. [PubMed:33733767 ]
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