NP-MRD: Showing NP-Card for 1-[(2r,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one (NP0208512)

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Record Information

Version

2.0

Created at

2022-09-05 05:32:35 UTC

Updated at

2022-09-05 05:32:35 UTC

NP-MRD ID

NP0208512

Secondary Accession Numbers

None

Natural Product Identification

Common Name

1-[(2r,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one

Description

Spongouridine, also known as arauridine or ara u, belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety. 1-[(2r,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one is found in Eunicella cavolini and Lepisorus contortus. 1-[(2r,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one was first documented in 2015 (PMID: 25668560). Based on a literature review a small amount of articles have been published on Spongouridine (PMID: 34079462) (PMID: 29912171).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 29 30  0  0  0  0  0  0  0  0999 V2000
    1.3332    1.4171    2.1994 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9356    0.6989    1.3436 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2122    0.3814    1.6404 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9561   -0.3758    0.8107 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2837   -0.7024    1.1255 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3744   -0.8175   -0.3519 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0455   -0.4704   -0.6314 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3362    0.2848    0.2176 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0029    0.6408   -0.0494 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8637    0.5100    1.0241 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1475    0.5074    0.5527 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9686   -0.6256    1.1354 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2531   -0.5331    0.5894 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0927    0.3350   -0.9511 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0810    1.5831   -1.5940 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6751   -0.2298   -1.0949 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7428   -1.5557   -0.7220 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0672   -0.3118    0.6059 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9511   -1.4320   -1.0432 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6542   -0.8527   -1.5628 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1221    1.6970   -0.4195 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7040    1.4493    0.7904 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0878   -0.4890    2.2350 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5218   -1.6064    0.9689 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3939    0.3492    0.1731 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8528   -0.3379   -1.3453 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1762    2.3341   -0.9620 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2789   -0.0621   -2.1089 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1903   -1.7857    0.0660 H   0  0  0  0  0  0  0  0  0  0  0  0
 13 12  1  0
 12 11  1  0
 11 10  1  0
 10  9  1  0
  9 16  1  0
 16 17  1  0
 16 14  1  0
 14 15  1  0
  9  8  1  0
  8  7  1  0
  7  6  2  0
  6  4  1  0
  4  5  1  0
  4  3  2  0
  3  2  1  0
  2  1  2  0
 14 11  1  0
  2  8  1  0
 13 25  1  0
 12 23  1  0
 12 24  1  0
 11 22  1  6
  9 21  1  6
 16 28  1  6
 17 29  1  0
 14 26  1  6
 15 27  1  0
  7 20  1  0
  6 19  1  0
  5 18  1  0
M  END


  Mrv1652309052207322D          

 17 18  0  0  1  0            999 V2000
    1.3222    0.7634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0367    1.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0367    2.0009    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    2.4134    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    3.2384    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4656    2.0009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4656    1.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    0.7634    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -0.0616    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4186   -0.5465    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1637   -1.3312    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6486   -1.9986    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4691   -1.9124    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3387   -1.3312    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8538   -1.9986    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0837   -0.5465    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2991   -0.2916    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  2  8  1  0  0  0  0
  9  8  1  6  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  6  0  0  0
 12 13  1  0  0  0  0
 11 14  1  0  0  0  0
 14 15  1  1  0  0  0
 14 16  1  0  0  0  0
  9 16  1  0  0  0  0
 16 17  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0208512

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@H]([C@@H](O)[C@@H]1O)N1C=CC(O)=NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H12N2O6/c12-3-4-6(14)7(15)8(17-4)11-2-1-5(13)10-9(11)16/h1-2,4,6-8,12,14-15H,3H2,(H,10,13,16)/t4-,6-,7+,8-/m1/s1

> <INCHI_KEY>
DRTQHJPVMGBUCF-CCXZUQQUSA-N

> <FORMULA>
C9H12N2O6

> <MOLECULAR_WEIGHT>
244.203

> <EXACT_MASS>
244.069536114

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
22.059543818452205

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-1,2-dihydropyrimidin-2-one

> <JCHEM_LOGP>
-2.047741337333334

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.553247165416206

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.480089429781644

> <JCHEM_PKA_STRONGEST_BASIC>
-2.98029983295402

> <JCHEM_POLAR_SURFACE_AREA>
122.82000000000001

> <JCHEM_REFRACTIVITY>
52.88729999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
1-[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  O   UNK     0       2.468   1.425   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       3.802   2.195   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       3.802   3.735   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       5.136   4.505   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       5.136   6.045   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       6.469   3.735   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.469   2.195   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       5.136   1.425   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       5.136  -0.115   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       6.381  -1.020   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       5.906  -2.485   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.811  -3.731   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       8.342  -3.570   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       4.366  -2.485   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       3.460  -3.731   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       3.890  -1.020   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       2.425  -0.544   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    2    9                                                  
CONECT    9    8   10   16                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   14                                                  
CONECT   12   11   13                                                       
CONECT   13   12                                                            
CONECT   14   11   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14    9   17                                                  
CONECT   17   16                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

View in JSmol

Synonyms

Value	Source
Arabinofuranosyluracil	MeSH
Arabinofuranoside, uracil	MeSH
Arauridine	MeSH
Uracil arabinoside	MeSH
Uracil, 1-beta-D-arabinofuranosyl	MeSH
1 beta D Arabinofuranosyl uracil	MeSH
1-beta-D-Arabinofuranosyl uracil	MeSH
Ara u	MeSH
Ara-u	MeSH
Arabinoside, uracil	MeSH
Arabinosyluracil	MeSH
Sponguridine	MeSH
Uracil arabinofuranoside	MeSH

Chemical Formula

C₉H₁₂N₂O₆

Average Mass

244.2030 Da

Monoisotopic Mass

244.06954 Da

IUPAC Name

1-[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-1,2-dihydropyrimidin-2-one

Traditional Name

1-[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@H]([C@@H](O)[C@@H]1O)N1C=CC(O)=NC1=O

InChI Identifier

InChI=1S/C9H12N2O6/c12-3-4-6(14)7(15)8(17-4)11-2-1-5(13)10-9(11)16/h1-2,4,6-8,12,14-15H,3H2,(H,10,13,16)/t4-,6-,7+,8-/m1/s1

InChI Key

DRTQHJPVMGBUCF-CCXZUQQUSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Eunicella cavolini	LOTUS Database	35616633
Lepisorus contortus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Not Available

Direct Parent

Pyrimidine nucleosides

Alternative Parents

Substituents

Pyrimidine nucleoside
Glycosyl compound
N-glycosyl compound
Pentose monosaccharide
Pyrimidone
Hydropyrimidine
Monosaccharide
Pyrimidine
Vinylogous amide
Tetrahydrofuran
Heteroaromatic compound
Urea
Secondary alcohol
Lactam
Organoheterocyclic compound
Oxacycle
Azacycle
Hydrocarbon derivative
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Primary alcohol
Alcohol
Organic oxygen compound
Organic oxide
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

N-glycosyl compound (CHEBI:68346 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-2	ChemAxon
pKa (Strongest Acidic)	7.48	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	122.82 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	52.89 m³·mol⁻¹	ChemAxon
Polarizability	22.06 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

17305

KEGG Compound ID

C16745

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

18323

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Hamoda AM, Fayed B, Ashmawy NS, El-Shorbagi AA, Hamdy R, Soliman SSM: Marine Sponge is a Promising Natural Source of Anti-SARS-CoV-2 Scaffold. Front Pharmacol. 2021 May 13;12:666664. doi: 10.3389/fphar.2021.666664. eCollection 2021. [PubMed:34079462 ]
Bertin MJ, Schwartz SL, Lee J, Korobeynikov A, Dorrestein PC, Gerwick L, Gerwick WH: Spongosine production by a Vibrio harveyi strain associated with the sponge Tectitethya crypta. J Nat Prod. 2015 Mar 27;78(3):493-9. doi: 10.1021/np5009762. Epub 2015 Feb 10. [PubMed:25668560 ]
El-Demerdash A, Tammam MA, Atanasov AG, Hooper JNA, Al-Mourabit A, Kijjoa A: Chemistry and Biological Activities of the Marine Sponges of the Genera Mycale (Arenochalina), Biemna and Clathria. Mar Drugs. 2018 Jun 18;16(6):214. doi: 10.3390/md16060214. [PubMed:29912171 ]
LOTUS database [Link]

Showing NP-Card for 1-[(2r,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one (NP0208512)

MOL for NP0208512 (1-[(2r,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one)

3D MOL for NP0208512 (1-[(2r,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one)

3D SDF for NP0208512 (1-[(2r,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one)

3D-SDF for NP0208512 (1-[(2r,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one)

PDB for NP0208512 (1-[(2r,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one)

3D PDB for NP0208512 (1-[(2r,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one)

SMILES for NP0208512 (1-[(2r,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one)

INCHI for NP0208512 (1-[(2r,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one)

Structure for NP0208512 (1-[(2r,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one)

3D Structure for NP0208512 (1-[(2r,3s,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxypyrimidin-2-one)