MiMeDB: Showing metabocard for 2-Thiouridine (MMDBc0030121)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:54:44 UTC

Update Date

2022-08-31 17:39:52 UTC

Metabolite ID

MMDBc0030121

Metabolite Identification

Common Name

2-Thiouridine

Description

2-thiouridine is a member of the chemical class known as Pyrimidine Nucleosides and Analogues. These are compounds comprising a pyrimidine base attached to a sugar. 2-thiouridine is invovled in tRNA-s2U34 biosynthesis. Thionucleosides are uniquely present in tRNA. In many organisms, tRNA specific for Lys, Glu, and Gln contain hypermodified 2-thiouridine (s(2)U) derivatives at wobble position 34. The s(2) group of s(2)U34 stabilizes anticodon structure, confers ribosome binding ability to tRNA and improves reading frame maintenance. [PMID:12549933 ]

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 08131209352D          

 21 22  0  0  0  0            999 V2000
    1.7044   -3.4197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1893   -2.7523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2032   -0.2916    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4186   -0.5465    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8839   -3.3335    0.0000 C   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
    2.0837   -0.5465    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3387   -1.3312    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0333   -1.9124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5484   -2.5798    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8538   -1.9986    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3748    0.5154    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3990   -4.0009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    0.7634    0.0000 O   0  0  0  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
    3.1637   -1.3312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6977   -1.1587    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.2612    0.2633    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3138    0.5418    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9547    0.2683    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5238   -1.2021    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  4  3  1  1  0  0  0
  5  1  1  0  0  0  0
  6  4  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
 10  5  2  0  0  0  0
 10  9  1  0  0  0  0
 11  2  1  0  0  0  0
  8 11  1  1  0  0  0
 11  9  1  0  0  0  0
 12  3  1  0  0  0  0
 13  5  1  0  0  0  0
  6 14  1  6  0  0  0
  7 15  1  6  0  0  0
 16  4  1  0  0  0  0
 16  8  1  0  0  0  0
 17  9  2  0  0  0  0
  4 18  1  6  0  0  0
  6 19  1  1  0  0  0
  7 20  1  1  0  0  0
  8 21  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030121

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(CO)O[C@@]([H])(N2C=CC(O)=NC2=S)[C@]([H])(O)[C@]1([H])O

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

> <INCHI_KEY>
GJTBSTBJLVYKAU-XVFCMESISA-N

> <FORMULA>
C9H12N2O5S

> <MOLECULAR_WEIGHT>
260.267

> <EXACT_MASS>
260.046692194

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
24.151976372229804

> <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-hydroxy-1,2-dihydropyrimidine-2-thione

> <ALOGPS_LOGP>
-1.01

> <JCHEM_LOGP>
-1.1578717530000002

> <ALOGPS_LOGS>
-1.84

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.555810056516567

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.255811519177492

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9558700002163762

> <JCHEM_POLAR_SURFACE_AREA>
105.75000000000001

> <JCHEM_REFRACTIVITY>
60.87819999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.80e+00 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 13-AUG-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-AUG-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   17  S   UNK     0       0.000   0.000   0.000  0.00  0.00           S+0
HETATM   18  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   19  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    2    5                                                       
CONECT    2    1   11                                                       
CONECT    3    4   12                                                       
CONECT    4    3    6   16   18                                             
CONECT    5    1   10   13                                                  
CONECT    6    4    7   14   19                                             
CONECT    7    6    8   15   20                                             
CONECT    8    7   11   16   21                                             
CONECT    9   10   11   17                                                  
CONECT   10    5    9                                                       
CONECT   11    2    8    9                                                  
CONECT   12    3                                                            
CONECT   13    5                                                            
CONECT   14    6                                                            
CONECT   15    7                                                            
CONECT   16    4    8                                                       
CONECT   17    9                                                            
CONECT   18    4                                                            
CONECT   19    6                                                            
CONECT   20    7                                                            
CONECT   21    8                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   44    0
END

Synonyms

Value	Source
1-beta-D-Ribofuranosyl-2-thiouracil	ChEBI
s2u	ChEBI
1-b-D-Ribofuranosyl-2-thiouracil	Generator
1-Β-D-ribofuranosyl-2-thiouracil	Generator

Molecular Formula

C₉H₁₂N₂O₅S

Average Mass

260.267

Monoisotopic Mass

260.046692194

IUPAC Name

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

Traditional Name

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

CAS Registry Number

20235-78-3

SMILES

[H][C@]1(CO)O[C@@]([H])(N2C=CC(O)=NC2=S)[C@]([H])(O)[C@]1([H])O

InChI Identifier

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

InChI Key

GJTBSTBJLVYKAU-XVFCMESISA-N

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
2-thiopyrimidine
Thiopyrimidine
Hydropyrimidine
Pyrimidine
Monosaccharide
Vinylogous amide
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Thiourea
Lactam
Oxacycle
Azacycle
Organoheterocyclic compound
Alcohol
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Primary alcohol
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

thiouridine (CHEBI:60731 )
nucleoside analogue (CHEBI:60731 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	3.8 g/L	ALOGPS
logP	-1	ALOGPS
logP	-1.2	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	8.26	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	105.75 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	60.88 m³·mol⁻¹	ChemAxon
Polarizability	24.15 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

Spectra

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal	Unknown

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

2-THIOURIDINE

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

146517

PDB ID

Not Available

ChEBI ID

60731

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Winder CL, Dunn WB, Schuler S, Broadhurst D, Jarvis R, Stephens GM, Goodacre R: Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites. Anal Chem. 2008 Apr 15;80(8):2939-48. doi: 10.1021/ac7023409. Epub 2008 Mar 11. [PubMed:18331064 ]
Keseler IM, Collado-Vides J, Santos-Zavaleta A, Peralta-Gil M, Gama-Castro S, Muniz-Rascado L, Bonavides-Martinez C, Paley S, Krummenacker M, Altman T, Kaipa P, Spaulding A, Pacheco J, Latendresse M, Fulcher C, Sarker M, Shearer AG, Mackie A, Paulsen I, Gunsalus RP, Karp PD: EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res. 2011 Jan;39(Database issue):D583-90. doi: 10.1093/nar/gkq1143. Epub 2010 Nov 21. [PubMed:21097882 ]

Showing metabocard for 2-Thiouridine (MMDBc0030121)

MOL for #<Metabolite:0x00007f121c02a910>

3D MOL for #<Metabolite:0x00007f121c02a910>

3D SDF for #<Metabolite:0x00007f121c02a910>

3D-SDF for #<Metabolite:0x00007f121c02a910>

PDB for #<Metabolite:0x00007f121c02a910>

3D PDB for #<Metabolite:0x00007f121c02a910>

SMILES for #<Metabolite:0x00007f121c02a910>

INCHI for #<Metabolite:0x00007f121c02a910>

Structure for #<Metabolite:0x00007f121c02a910>

3D Structure for #<Metabolite:0x00007f121c02a910>