NP-MRD: Showing NP-Card for 1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-sulfanylpyrimidin-2-one (NP0252340)

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Record Information

Version

2.0

Created at

2022-09-07 15:48:56 UTC

Updated at

2022-09-07 15:48:56 UTC

NP-MRD ID

NP0252340

Secondary Accession Numbers

None

Natural Product Identification

Common Name

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

Description

4-Thiouridine, also known as S4U, 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. 4-Thiouridine 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. 1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-sulfanylpyrimidin-2-one is found in Streptomyces libani. Based on a literature review very few articles have been published on 4-thiouridine.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 29 30  0  0  0  0  0  0  0  0999 V2000
   -1.7209    0.2770   -2.6930 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0999   -0.2232   -1.6019 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4126   -0.5060   -1.4250 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8774   -1.0384   -0.2884 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6227   -1.3980   -0.0941 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9631   -1.2950    0.7155 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6281   -0.9950    0.5049 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1801   -0.4629   -0.6376 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1824   -0.1360   -0.9042 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1041   -0.9752   -0.3399 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2895   -0.3166   -0.1681 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7111   -0.2443    1.2926 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9241    0.4411    1.3683 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0843    1.1247   -0.6177 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2517    1.2711   -1.9870 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5736    1.2331   -0.3532 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0025    2.2692   -1.0350 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2960   -0.2506    0.3926 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3327   -1.7266    1.6400 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9007   -1.1902    1.2814 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3665   -0.0896   -1.9978 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0762   -0.8192   -0.7335 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9638    0.3187    1.8991 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7751   -1.2653    1.6814 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6303   -0.2017    1.1553 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6551    1.8430   -0.0225 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8052    0.5285   -2.3801 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4529    1.2745    0.7442 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8141    2.5527   -0.5139 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  1
 17 29  1  0
 14 26  1  1
 15 27  1  0
  7 20  1  0
  6 19  1  0
  5 18  1  0
M  END


  Mrv1652309072217482D          

 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 S   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  1  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  1  0  0  0
M  END
> <DATABASE_ID>
NP0252340

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C9H12N2O5S/c12-3-4-6(13)7(14)8(16-4)11-2-1-5(17)10-9(11)15/h1-2,4,6-8,12-14H,3H2,(H,10,15,17)/t4-,6-,7-,8-/m1/s1

> <INCHI_KEY>
ZLOIGESWDJYCTF-XVFCMESISA-N

> <FORMULA>
C9H12N2O5S

> <MOLECULAR_WEIGHT>
260.26

> <EXACT_MASS>
260.046692668

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
24.25082824621767

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-1.5342269843333334

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.553244009757055

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.9969123149506

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9802998329226336

> <JCHEM_POLAR_SURFACE_AREA>
102.59

> <JCHEM_REFRACTIVITY>
59.01429999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-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  S   UNK     0       5.136   6.045   0.000  0.00  0.00           S+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
1-beta-D-Ribofuranosyl-4-thiouracil	ChEBI
s4u	ChEBI
Thiouridine	ChEBI
1-b-D-Ribofuranosyl-4-thiouracil	Generator
1-Β-D-ribofuranosyl-4-thiouracil	Generator

Chemical Formula

C₉H₁₂N₂O₅S

Average Mass

260.2600 Da

Monoisotopic Mass

260.04669 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C9H12N2O5S/c12-3-4-6(13)7(14)8(16-4)11-2-1-5(17)10-9(11)15/h1-2,4,6-8,12-14H,3H2,(H,10,15,17)/t4-,6-,7-,8-/m1/s1

InChI Key

ZLOIGESWDJYCTF-XVFCMESISA-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
Streptomyces libani	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
Pyrimidinethione
Pyrimidone
Hydropyrimidine
Monosaccharide
Pyrimidine
Heteroaromatic compound
Thiolactam
Tetrahydrofuran
Urea
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Primary alcohol
Hydrocarbon derivative
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Organic oxide
Organopnictogen compound
Organic oxygen compound
Alcohol
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

thiouridine (CHEBI:20480 )
nucleoside analogue (CHEBI:20480 )

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	-1.5	ChemAxon
pKa (Strongest Acidic)	6	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	102.59 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	59.01 m³·mol⁻¹	ChemAxon
Polarizability	24.25 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

C00016743

Chemspider ID

2297547

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

26347

PDB ID

Not Available

ChEBI ID

20480

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-sulfanylpyrimidin-2-one (NP0252340)

MOL for NP0252340 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-sulfanylpyrimidin-2-one)

3D MOL for NP0252340 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-sulfanylpyrimidin-2-one)

3D SDF for NP0252340 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-sulfanylpyrimidin-2-one)

3D-SDF for NP0252340 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-sulfanylpyrimidin-2-one)

PDB for NP0252340 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-sulfanylpyrimidin-2-one)

3D PDB for NP0252340 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-sulfanylpyrimidin-2-one)

SMILES for NP0252340 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-sulfanylpyrimidin-2-one)

INCHI for NP0252340 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-sulfanylpyrimidin-2-one)

Structure for NP0252340 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-sulfanylpyrimidin-2-one)

3D Structure for NP0252340 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-sulfanylpyrimidin-2-one)