NP-MRD: Showing NP-Card for 4-thiouridine (NP0004824)

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Record Information

Version

2.0

Created at

2020-12-09 02:14:00 UTC

Updated at

2021-07-15 16:50:16 UTC

NP-MRD ID

NP0004824

Secondary Accession Numbers

None

Natural Product Identification

Common Name

4-thiouridine

Provided By

NPAtlas

Description

1-[(2R,3S,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-sulfanyl-1,2-dihydropyrimidin-2-one 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 found in Streptomyces, Streptomyces libani and Streptomyces libani NK-110134 (FERM 10638). 4-thiouridine was first documented in 1992 (PMID: 1399860). Based on a literature review very few articles have been published on 1-[(2R,3S,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-sulfanyl-1,2-dihydropyrimidin-2-one.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242121113D          

 29 30  0  0  0  0            999 V2000
   -2.1663   -0.8539    2.0555 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2501   -0.2093    0.9781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4919   -0.1357    0.4187 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7159    0.5245   -0.7332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2079    0.6130   -1.4055 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6449    1.1345   -1.3452 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3876    1.0413   -0.7485 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1921    0.3780    0.3984 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1190    0.3142    0.9667 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0116    1.1351    0.3320 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7627    0.4339   -0.5718 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2546    0.6183   -0.2597 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6157    1.9631   -0.3296 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4838   -1.0364   -0.4056 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7022   -1.5491   -1.4218 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7458   -1.0422    0.9161 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1248   -2.0947    0.9539 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3097   -0.5923    0.8711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8016    1.6713   -2.2729 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5903    1.5419   -1.2781 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0397    0.6879    2.0296 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6349    0.7339   -1.6296 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4658    0.1857    0.7459 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8366    0.0323   -0.9899 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9065    2.5588    0.0223 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4055   -1.6472   -0.3194 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0639   -2.4170   -1.7865 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5126   -1.0910    1.7253 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3222   -2.8991    1.3420 H   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  1  0  0  0  0
  4  5  2  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
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 11 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
  8  2  1  0  0  0  0
 16  9  1  0  0  0  0
  3 18  1  0  0  0  0
  6 19  1  0  0  0  0
  7 20  1  0  0  0  0
  9 21  1  1  0  0  0
 11 22  1  6  0  0  0
 12 23  1  0  0  0  0
 12 24  1  0  0  0  0
 13 25  1  0  0  0  0
 14 26  1  1  0  0  0
 15 27  1  0  0  0  0
 16 28  1  1  0  0  0
 17 29  1  0  0  0  0
M  END

     RDKit          3D

 29 30  0  0  0  0  0  0  0  0999 V2000
   -2.1663   -0.8539    2.0555 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2501   -0.2093    0.9781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4919   -0.1357    0.4187 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7159    0.5245   -0.7332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2079    0.6130   -1.4055 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6449    1.1345   -1.3452 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3876    1.0413   -0.7485 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1921    0.3780    0.3984 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1190    0.3142    0.9667 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0116    1.1351    0.3320 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7627    0.4339   -0.5718 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2546    0.6183   -0.2597 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6157    1.9631   -0.3296 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4838   -1.0364   -0.4056 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7022   -1.5491   -1.4218 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7458   -1.0422    0.9161 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1248   -2.0947    0.9539 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3097   -0.5923    0.8711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8016    1.6713   -2.2729 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5903    1.5419   -1.2781 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0397    0.6879    2.0296 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6349    0.7339   -1.6296 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4658    0.1857    0.7459 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8366    0.0323   -0.9899 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9065    2.5588    0.0223 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4055   -1.6472   -0.3194 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0639   -2.4170   -1.7865 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5126   -1.0910    1.7253 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3222   -2.8991    1.3420 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  2  0
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
  8  2  1  0
 16  9  1  0
  3 18  1  0
  6 19  1  0
  7 20  1  0
  9 21  1  1
 11 22  1  6
 12 23  1  0
 12 24  1  0
 13 25  1  0
 14 26  1  1
 15 27  1  0
 16 28  1  1
 17 29  1  0
M  END


  Mrv1652306242121113D          

 29 30  0  0  0  0            999 V2000
   -2.1663   -0.8539    2.0555 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2501   -0.2093    0.9781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4919   -0.1357    0.4187 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7159    0.5245   -0.7332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2079    0.6130   -1.4055 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6449    1.1345   -1.3452 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3876    1.0413   -0.7485 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1921    0.3780    0.3984 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1190    0.3142    0.9667 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0116    1.1351    0.3320 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7627    0.4339   -0.5718 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2546    0.6183   -0.2597 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6157    1.9631   -0.3296 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4838   -1.0364   -0.4056 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7022   -1.5491   -1.4218 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7458   -1.0422    0.9161 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1248   -2.0947    0.9539 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3097   -0.5923    0.8711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8016    1.6713   -2.2729 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5903    1.5419   -1.2781 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0397    0.6879    2.0296 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6349    0.7339   -1.6296 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4658    0.1857    0.7459 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8366    0.0323   -0.9899 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9065    2.5588    0.0223 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4055   -1.6472   -0.3194 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0639   -2.4170   -1.7865 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5126   -1.0910    1.7253 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3222   -2.8991    1.3420 H   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  1  0  0  0  0
  4  5  2  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
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 11 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
  8  2  1  0  0  0  0
 16  9  1  0  0  0  0
  3 18  1  0  0  0  0
  6 19  1  0  0  0  0
  7 20  1  0  0  0  0
  9 21  1  1  0  0  0
 11 22  1  6  0  0  0
 12 23  1  0  0  0  0
 12 24  1  0  0  0  0
 13 25  1  0  0  0  0
 14 26  1  1  0  0  0
 15 27  1  0  0  0  0
 16 28  1  1  0  0  0
 17 29  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0004824

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC([H])([H])[C@]1([H])O[C@@]([H])(N2C([H])=C([H])C(=S)N([H])C2=O)[C@@]([H])(O[H])[C@@]1([H])O[H]

> <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+/m0/s1

> <INCHI_KEY>
ZLOIGESWDJYCTF-YDLFOAGRSA-N

> <FORMULA>
C9H12N2O5S

> <MOLECULAR_WEIGHT>
260.26

> <EXACT_MASS>
260.046692668

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
23.929977225271944

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.79

> <JCHEM_LOGP>
-1.5253725573333334

> <ALOGPS_LOGS>
-1.41

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.556386825892353

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.898778473908594

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9802996389052714

> <JCHEM_POLAR_SURFACE_AREA>
102.26000000000002

> <JCHEM_REFRACTIVITY>
60.5565

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.01e+01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 29 30  0  0  0  0  0  0  0  0999 V2000
   -2.1663   -0.8539    2.0555 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2501   -0.2093    0.9781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4919   -0.1357    0.4187 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7159    0.5245   -0.7332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2079    0.6130   -1.4055 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6449    1.1345   -1.3452 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3876    1.0413   -0.7485 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1921    0.3780    0.3984 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1190    0.3142    0.9667 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0116    1.1351    0.3320 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7627    0.4339   -0.5718 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2546    0.6183   -0.2597 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6157    1.9631   -0.3296 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4838   -1.0364   -0.4056 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7022   -1.5491   -1.4218 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7458   -1.0422    0.9161 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1248   -2.0947    0.9539 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3097   -0.5923    0.8711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8016    1.6713   -2.2729 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5903    1.5419   -1.2781 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0397    0.6879    2.0296 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6349    0.7339   -1.6296 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4658    0.1857    0.7459 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8366    0.0323   -0.9899 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9065    2.5588    0.0223 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4055   -1.6472   -0.3194 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0639   -2.4170   -1.7865 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5126   -1.0910    1.7253 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3222   -2.8991    1.3420 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  2  0
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
  8  2  1  0
 16  9  1  0
  3 18  1  0
  6 19  1  0
  7 20  1  0
  9 21  1  1
 11 22  1  6
 12 23  1  0
 12 24  1  0
 13 25  1  0
 14 26  1  1
 15 27  1  0
 16 28  1  1
 17 29  1  0
M  END

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  O   UNK     0      -2.166  -0.854   2.055  0.00  0.00           O+0
HETATM    2  C   UNK     0      -2.250  -0.209   0.978  0.00  0.00           C+0
HETATM    3  N   UNK     0      -3.492  -0.136   0.419  0.00  0.00           N+0
HETATM    4  C   UNK     0      -3.716   0.525  -0.733  0.00  0.00           C+0
HETATM    5  S   UNK     0      -5.208   0.613  -1.406  0.00  0.00           S+0
HETATM    6  C   UNK     0      -2.645   1.135  -1.345  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.388   1.041  -0.749  0.00  0.00           C+0
HETATM    8  N   UNK     0      -1.192   0.378   0.398  0.00  0.00           N+0
HETATM    9  C   UNK     0       0.119   0.314   0.967  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.012   1.135   0.332  0.00  0.00           O+0
HETATM   11  C   UNK     0       1.763   0.434  -0.572  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.255   0.618  -0.260  0.00  0.00           C+0
HETATM   13  O   UNK     0       3.616   1.963  -0.330  0.00  0.00           O+0
HETATM   14  C   UNK     0       1.484  -1.036  -0.406  0.00  0.00           C+0
HETATM   15  O   UNK     0       0.702  -1.549  -1.422  0.00  0.00           O+0
HETATM   16  C   UNK     0       0.746  -1.042   0.916  0.00  0.00           C+0
HETATM   17  O   UNK     0      -0.125  -2.095   0.954  0.00  0.00           O+0
HETATM   18  H   UNK     0      -4.310  -0.592   0.871  0.00  0.00           H+0
HETATM   19  H   UNK     0      -2.802   1.671  -2.273  0.00  0.00           H+0
HETATM   20  H   UNK     0      -0.590   1.542  -1.278  0.00  0.00           H+0
HETATM   21  H   UNK     0       0.040   0.688   2.030  0.00  0.00           H+0
HETATM   22  H   UNK     0       1.635   0.734  -1.630  0.00  0.00           H+0
HETATM   23  H   UNK     0       3.466   0.186   0.746  0.00  0.00           H+0
HETATM   24  H   UNK     0       3.837   0.032  -0.990  0.00  0.00           H+0
HETATM   25  H   UNK     0       2.906   2.559   0.022  0.00  0.00           H+0
HETATM   26  H   UNK     0       2.406  -1.647  -0.319  0.00  0.00           H+0
HETATM   27  H   UNK     0       1.064  -2.417  -1.787  0.00  0.00           H+0
HETATM   28  H   UNK     0       1.513  -1.091   1.725  0.00  0.00           H+0
HETATM   29  H   UNK     0       0.322  -2.899   1.342  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4   18                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   19                                                  
CONECT    7    6    8   20                                                  
CONECT    8    7    9    2                                                  
CONECT    9    8   10   16   21                                             
CONECT   10    9   11                                                       
CONECT   11   10   12   14   22                                             
CONECT   12   11   13   23   24                                             
CONECT   13   12   25                                                       
CONECT   14   11   15   16   26                                             
CONECT   15   14   27                                                       
CONECT   16   14   17    9   28                                             
CONECT   17   16   29                                                       
CONECT   18    3                                                            
CONECT   19    6                                                            
CONECT   20    7                                                            
CONECT   21    9                                                            
CONECT   22   11                                                            
CONECT   23   12                                                            
CONECT   24   12                                                            
CONECT   25   13                                                            
CONECT   26   14                                                            
CONECT   27   15                                                            
CONECT   28   16                                                            
CONECT   29   17                                                            
MASTER        0    0    0    0    0    0    0    0   29    0   60    0
END

RDKit          3D

29 30  0  0  0  0  0  0  0  0999 V2000
   -2.1663   -0.8539    2.0555 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2501   -0.2093    0.9781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4919   -0.1357    0.4187 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7159    0.5245   -0.7332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2079    0.6130   -1.4055 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6449    1.1345   -1.3452 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3876    1.0413   -0.7485 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1921    0.3780    0.3984 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1190    0.3142    0.9667 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0116    1.1351    0.3320 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7627    0.4339   -0.5718 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2546    0.6183   -0.2597 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6157    1.9631   -0.3296 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4838   -1.0364   -0.4056 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7022   -1.5491   -1.4218 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7458   -1.0422    0.9161 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1248   -2.0947    0.9539 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3097   -0.5923    0.8711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8016    1.6713   -2.2729 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5903    1.5419   -1.2781 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0397    0.6879    2.0296 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6349    0.7339   -1.6296 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4658    0.1857    0.7459 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8366    0.0323   -0.9899 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9065    2.5588    0.0223 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4055   -1.6472   -0.3194 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0639   -2.4170   -1.7865 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5126   -1.0910    1.7253 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3222   -2.8991    1.3420 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  2  0
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 11 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
  8  2  1  0
 16  9  1  0
  3 18  1  0
  6 19  1  0
  7 20  1  0
  9 21  1  1
 11 22  1  6
 12 23  1  0
 12 24  1  0
 13 25  1  0
 14 26  1  1
 15 27  1  0
 16 28  1  1
 17 29  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
1-[(2R,3S,4R,5S)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-sulphanyl-1,2-dihydropyrimidin-2-one	Generator

Chemical Formula

C₉H₁₂N₂O₅S

Average Mass

260.2600 Da

Monoisotopic Mass

260.04669 Da

IUPAC Name

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

Traditional Name

1-[(2R,3S,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-sulfanylidene-3H-pyrimidin-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+/m0/s1

InChI Key

ZLOIGESWDJYCTF-YDLFOAGRSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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	NPAtlas	1399860
Streptomyces libani	LOTUS Database	35616633
Streptomyces libani NK-110134 (FERM 10638)	Bacteria	KNApSAcK

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
Pyrimidinethione
Hydropyrimidine
Monosaccharide
Pyrimidine
Heteroaromatic compound
Oxolane
Thiolactam
1,2-diol
Urea
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Alcohol
Primary alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

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	-0.79	ALOGPS
logP	-1.5	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	7.9	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	102.26 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	60.56 m³·mol⁻¹	ChemAxon
Polarizability	23.93 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

NPAtlas ID

NPA020621

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

18827887

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

22865605

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Nishikiori T, Hiruma S, Kurokawa T, Saito S, Shimada N: Microbial production of 4-thiouridine. J Antibiot (Tokyo). 1992 Aug;45(8):1376-7. doi: 10.7164/antibiotics.45.1376. [PubMed:1399860 ]

Showing NP-Card for 4-thiouridine (NP0004824)

MOL for NP0004824 (4-thiouridine)

3D MOL for NP0004824 (4-thiouridine)

3D SDF for NP0004824 (4-thiouridine)

3D-SDF for NP0004824 (4-thiouridine)

PDB for NP0004824 (4-thiouridine)

3D PDB for NP0004824 (4-thiouridine)

SMILES for NP0004824 (4-thiouridine)

INCHI for NP0004824 (4-thiouridine)

Structure for NP0004824 (4-thiouridine)

3D Structure for NP0004824 (4-thiouridine)