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Showing NP-Card for (5r)-3,4-dihydroxy-5-(hydroxymethyl)-5h-furan-2-one (NP0263382)

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Record Information
Version2.0
Created at2022-09-08 06:33:08 UTC
Updated at2022-09-08 06:33:08 UTC
NP-MRD IDNP0263382
Secondary Accession NumbersNone
Natural Product Identification
Common Name(5r)-3,4-dihydroxy-5-(hydroxymethyl)-5h-furan-2-one
DescriptionDehydro-D-arabinono-1,4-lactone, also known as D-erythroascorbic acid or D-glycero-2-pentenono-L,4-lactone, belongs to the class of organic compounds known as butenolides. These are dihydrofurans with a carbonyl group at the C2 carbon atom. Dehydro-D-arabinono-1,4-lactone is an extremely weak basic (essentially neutral) compound (based on its pKa). Dehydro-D-arabinono-1,4-lactone may be a unique S. (5r)-3,4-dihydroxy-5-(hydroxymethyl)-5h-furan-2-one is found in Sclerotinia sclerotiorum and Trypanosoma brucei. (5r)-3,4-dihydroxy-5-(hydroxymethyl)-5h-furan-2-one was first documented in 1998 (PMID: 10094636). Cerevisiae (yeast) metabolite (PMID: 10508108) (PMID: 11349062) (PMID: 15809004) (PMID: 17151466).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0263382 ((5r)-3,4-dihydroxy-5-(hydroxymethyl)-5h-furan-2-one)


  Mrv0541 02241222092D          

 10 10  0  0  1  0            999 V2000
    4.7008  -11.9845    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.9658  -12.7658    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3754  -11.5060    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7988  -12.7658    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4943  -13.4405    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0432  -11.9948    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2875  -13.4370    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6249  -11.4062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9174  -11.7306    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3059  -12.2821    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  2  4  2  0  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  4  7  1  0  0  0  0
  6  8  2  0  0  0  0
  4  6  1  0  0  0  0
  1  9  1  1  0  0  0
  1  2  1  0  0  0  0
  9 10  1  0  0  0  0
M  END
Download

3D MOL for NP0263382 ((5r)-3,4-dihydroxy-5-(hydroxymethyl)-5h-furan-2-one)

     RDKit          3D

 16 16  0  0  0  0  0  0  0  0999 V2000
    1.3137   -2.8535    0.2954 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8572   -1.6679    0.2478 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4095   -1.2912    0.6334 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5552    0.0879    0.4404 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7012    0.3554   -0.5064 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8495   -0.1949    0.1090 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7387    0.5241   -0.0993 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0747    1.8300   -0.4513 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5713   -0.4906   -0.2164 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8895   -0.5056   -0.6845 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7572    0.5344    1.4391 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8351    1.4366   -0.6386 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5815   -0.1877   -1.4504 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9615    0.1751    1.0210 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5240    2.6031   -0.0976 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6817   -0.3553   -0.0417 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0
  5  4  1  0
  4  3  1  0
  3  2  1  0
  2  1  2  0
  2  9  1  0
  9 10  1  0
  9  7  2  0
  7  8  1  0
  7  4  1  0
  6 14  1  0
  5 12  1  0
  5 13  1  0
  4 11  1  1
 10 16  1  0
  8 15  1  0
M  END
Download

3D SDF for NP0263382 ((5r)-3,4-dihydroxy-5-(hydroxymethyl)-5h-furan-2-one)


  Mrv0541 02241222092D          

 10 10  0  0  1  0            999 V2000
    4.7008  -11.9845    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.9658  -12.7658    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3754  -11.5060    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7988  -12.7658    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4943  -13.4405    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0432  -11.9948    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2875  -13.4370    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6249  -11.4062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9174  -11.7306    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3059  -12.2821    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  2  4  2  0  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  4  7  1  0  0  0  0
  6  8  2  0  0  0  0
  4  6  1  0  0  0  0
  1  9  1  1  0  0  0
  1  2  1  0  0  0  0
  9 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0263382

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1OC(=O)C(O)=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C5H6O5/c6-1-2-3(7)4(8)5(9)10-2/h2,6-8H,1H2/t2-/m1/s1

> <INCHI_KEY>
ZZZCUOFIHGPKAK-UWTATZPHSA-N

> <FORMULA>
C5H6O5

> <MOLECULAR_WEIGHT>
146.0981

> <EXACT_MASS>
146.021523302

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
12.156867187605773

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.46

> <JCHEM_LOGP>
-1.2832239336666666

> <ALOGPS_LOGS>
0.53

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.216438546152538

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.429998328105595

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0087905384401648

> <JCHEM_POLAR_SURFACE_AREA>
86.99

> <JCHEM_REFRACTIVITY>
31.069599999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.92e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(5R)-3,4-dihydroxy-5-(hydroxymethyl)-5H-furan-2-one

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0263382 ((5r)-3,4-dihydroxy-5-(hydroxymethyl)-5h-furan-2-one)

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PDB for NP0263382 ((5r)-3,4-dihydroxy-5-(hydroxymethyl)-5h-furan-2-one)
HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       8.775 -22.371   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.269 -23.829   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      10.034 -21.478   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      10.824 -23.829   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       8.389 -25.089   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      11.281 -22.390   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      11.737 -25.082   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      12.366 -21.292   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       7.312 -21.897   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       6.171 -22.927   0.000  0.00  0.00           O+0
CONECT    1    3    9    2                                                  
CONECT    2    4    5    1                                                  
CONECT    3    1    6                                                       
CONECT    4    2    7    6                                                  
CONECT    5    2                                                            
CONECT    6    3    8    4                                                  
CONECT    7    4                                                            
CONECT    8    6                                                            
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 NP0263382 ((5r)-3,4-dihydroxy-5-(hydroxymethyl)-5h-furan-2-one)
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SMILES for NP0263382 ((5r)-3,4-dihydroxy-5-(hydroxymethyl)-5h-furan-2-one)
OC[C@H]1OC(=O)C(O)=C1O
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INCHI for NP0263382 ((5r)-3,4-dihydroxy-5-(hydroxymethyl)-5h-furan-2-one)
InChI=1S/C5H6O5/c6-1-2-3(7)4(8)5(9)10-2/h2,6-8H,1H2/t2-/m1/s1
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View in JSmol
Synonyms
ValueSource
(5R)-3,4-Dihydroxy-5-(hydroxymethyl)furan-2(5H)-oneChEBI
D-Erythroascorbic acidChEBI
D-Glycero-2-pentenono-L,4-lactoneChEBI
D-ErythroascorbateGenerator
D-erythro-Ascorbic acidChEBI
D-erythro-AscorbateGenerator
Chemical FormulaC5H6O5
Average Mass146.0981 Da
Monoisotopic Mass146.02152 Da
IUPAC Name(5R)-3,4-dihydroxy-5-(hydroxymethyl)-2,5-dihydrofuran-2-one
Traditional Name(5R)-3,4-dihydroxy-5-(hydroxymethyl)-5H-furan-2-one
CAS Registry NumberNot Available
SMILES
OC[C@H]1OC(=O)C(O)=C1O
InChI Identifier
InChI=1S/C5H6O5/c6-1-2-3(7)4(8)5(9)10-2/h2,6-8H,1H2/t2-/m1/s1
InChI KeyZZZCUOFIHGPKAK-UWTATZPHSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Sclerotinia sclerotiorumLOTUS Database
Trypanosoma bruceiLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as butenolides. These are dihydrofurans with a carbonyl group at the C2 carbon atom.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassDihydrofurans  
Sub ClassFuranones  
Direct ParentButenolides  
Alternative Parents
Substituents
  • 2-furanone
    • 

  • Monosaccharide
    • 

  • Enoate ester
    • 

  • Alpha,beta-unsaturated carboxylic ester
    • 

  • Vinylogous acid
    • 

  • Lactone
    • 

  • Enediol
    • 

  • Carboxylic acid ester
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid derivative
    • 

  • Oxacycle
    • 

  • Alcohol
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Organic oxide
    • 

  • Carbonyl group
    • 

  • Organic oxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-1.5ALOGPS
logP-1.3ChemAxon
logS0.53ALOGPS
pKa (Strongest Acidic)4.43ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area86.99 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity31.07 m³·mol⁻¹ChemAxon
Polarizability12.16 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC06316  
BioCyc IDCPD-1789  
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound54675775  
PDB IDNot Available
ChEBI ID17803  
Good Scents IDNot Available
References
General References
  1. Huh WK, Lee BH, Kim ST, Kim YR, Rhie GE, Baek YW, Hwang CS, Lee JS, Kang SO: D-Erythroascorbic acid is an important antioxidant molecule in Saccharomyces cerevisiae. Mol Microbiol. 1998 Nov;30(4):895-903. doi: 10.1046/j.1365-2958.1998.01133.x. [PubMed:10094636  ] 
  2. Lee BH, Huh WK, Kim ST, Lee JS, Kang SO: Bacterial production of D-erythroascorbic acid and L-ascorbic acid through functional expression of Saccharomyces cerevisiae D-arabinono-1,4-lactone oxidase in Escherichia coli. Appl Environ Microbiol. 1999 Oct;65(10):4685-7. doi:  10.1128/AEM.65.10.4685-4687.1999. [PubMed:10508108  ] 
  3. Huh WK, Kim ST, Kim H, Jeong G, Kang SO: Deficiency of D-erythroascorbic acid attenuates hyphal growth and virulence of Candida albicans. Infect Immun. 2001 Jun;69(6):3939-46. doi: 10.1128/IAI.69.6.3939-3946.2001. [PubMed:11349062  ] 
  4. Baroja-Mazo A, del Valle P, Rua J, de Cima S, Busto F, de Arriaga D, Smirnoff N: Characterisation and biosynthesis of D-erythroascorbic acid in Phycomyces blakesleeanus. Fungal Genet Biol. 2005 May;42(5):390-402. doi: 10.1016/j.fgb.2005.01.005. [PubMed:15809004  ] 
  5. Amako K, Fujita K, Iwamoto C, Sengee M, Fuchigami K, Fukumoto J, Ogishi Y, Kishimoto R, Goda K: NADP(+)-dependent D-arabinose dehydrogenase shows a limited contribution to erythroascorbic acid biosynthesis and oxidative stress resistance in Saccharomyces cerevisiae. Biosci Biotechnol Biochem. 2006 Dec;70(12):3004-12. doi: 10.1271/bbb.60399. Epub  2006 Dec 7. [PubMed:17151466  ] 
  6. LOTUS database [Link]