MiMeDB: Showing metabocard for 1,2-Dihydroxy-3-keto-5-methylthiopentene (MMDBc0032940)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:28:11 UTC

Update Date

2024-04-30 19:55:26 UTC

Metabolite ID

MMDBc0032940

Metabolite Identification

Common Name

1,2-Dihydroxy-3-keto-5-methylthiopentene

Description

At physiological pH, this molecule, 1,2-dihydroxy-3-keto-5-methylthiopentene, is a monoanion, 1,2-dihydroxy-3-keto-5-methylthiopentene anion. 1,2-dihydroxy-3-keto-5-methylthiopentene anion, an aci-reductone, is believed to be an unstable intermediate in the methionine salvage pathway in Klebsiella pneumoniae. (MetaCyc).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652311192105282D          

 20 19  0  0  0  0            999 V2000
   -2.3349    1.1270    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6204    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9059    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9059    1.9520    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9059   -0.5230    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8672   -0.0228    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6078   -0.0228    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3222    1.8642    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5817    1.8642    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7934    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0954    1.5395    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684    1.8414    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  4  0  0  0
  3  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 10 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 13 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 17 20  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0032940

> <DATABASE_NAME>
MIME

> <SMILES>
[H]OC([H])=C(O[H])C(=O)C([H])([H])C([H])([H])SC([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O3S/c1-10-3-2-5(8)6(9)4-7/h4,7,9H,2-3H2,1H3

> <INCHI_KEY>
CILXJJLQPTUUSS-UHFFFAOYSA-N

> <FORMULA>
C6H10O3S

> <MOLECULAR_WEIGHT>
162.2

> <EXACT_MASS>
162.035065356

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
16.223016630748496

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one

> <ALOGPS_LOGP>
0.07

> <JCHEM_LOGP>
0.8116459593333338

> <ALOGPS_LOGS>
-1.27

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.558186339804077

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.30665894402364

> <JCHEM_PKA_STRONGEST_BASIC>
-3.967606300887529

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
41.86879999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.75e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 19-NOV-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-NOV-21         0                                  
HETATM    1  H   UNK     0      -4.358   2.104   0.000  0.00  0.00           H+0
HETATM    2  O   UNK     0      -3.025   1.334   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -1.691   2.104   0.000  0.00  0.00           C+0
HETATM    4  H   UNK     0      -1.691   3.644   0.000  0.00  0.00           H+0
HETATM    5  C   UNK     0      -0.357   1.334   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -0.357  -0.206   0.000  0.00  0.00           O+0
HETATM    7  H   UNK     0      -1.691  -0.976   0.000  0.00  0.00           H+0
HETATM    8  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       0.976   3.644   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM   11  H   UNK     0       1.619  -0.043   0.000  0.00  0.00           H+0
HETATM   12  H   UNK     0       3.001  -0.043   0.000  0.00  0.00           H+0
HETATM   13  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM   14  H   UNK     0       4.335   3.480   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0       2.953   3.480   0.000  0.00  0.00           H+0
HETATM   16  S   UNK     0       4.977   1.334   0.000  0.00  0.00           S+0
HETATM   17  C   UNK     0       6.311   2.104   0.000  0.00  0.00           C+0
HETATM   18  H   UNK     0       7.081   0.770   0.000  0.00  0.00           H+0
HETATM   19  H   UNK     0       7.645   2.874   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       5.541   3.437   0.000  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    8                                                  
CONECT    6    5    7                                                       
CONECT    7    6                                                            
CONECT    8    5    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12   13                                             
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13   10   14   15   16                                             
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16   13   17                                                       
CONECT   17   16   18   19   20                                             
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   17                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   38    0
END

Synonyms

Not Available

Molecular Formula

C₆H₁₀O₃S

Average Mass

162.2

Monoisotopic Mass

162.035065356

IUPAC Name

1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one

Traditional Name

1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one

CAS Registry Number

746507-19-7

SMILES

[H]OC([H])=C(O[H])C(=O)C([H])([H])C([H])([H])SC([H])([H])[H]

InChI Identifier

InChI=1S/C6H10O3S/c1-10-3-2-5(8)6(9)4-7/h4,7,9H,2-3H2,1H3

InChI Key

CILXJJLQPTUUSS-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha-branched alpha,beta-unsaturated ketones. These are alpha,beta-unsaturated ketones that carry a branch on the alpha carbon. They have the generic structure RC(=O)C(R')=C, R = organyl group and R'= any heteroatom.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

Alpha-branched alpha,beta-unsaturated ketones

Alternative Parents

Substituents

Alpha-branched alpha,beta-unsaturated-ketone
Vinylogous acid
Enone
Alpha-hydroxy ketone
Acryloyl-group
Ketone
Enediol
Dialkylthioether
Sulfenyl compound
Thioether
Organic oxide
Hydrocarbon derivative
Organosulfur compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	8.75 g/L	ALOGPS
logP	0.07	ALOGPS
logP	0.81	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	8.31	ChemAxon
pKa (Strongest Basic)	-4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	57.53 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	41.87 m³·mol⁻¹	ChemAxon
Polarizability	16.22 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

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

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0019450	1,2-Dihydroxy-3-keto-5-methylthiopentene	Formic acid	1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase	Oxygenation	PathBank	31602464
MMDBr0019451	5-(methylsulfanyl)-2,3-dioxopentyl phosphate	1,2-Dihydroxy-3-keto-5-methylthiopentene	Enolase-phosphatase E1	Dephosphorylation	PathBank	31602464

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
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown
Bacteria/Eubacteria	Proteobacteria	39	Human feces; Human sputum; Human	Metabolic reconstruction
Bacteria/Eubacteria	Firmicutes	38	Human feces; Human	Metabolic reconstruction
Bacteria	Proteobacteria	4	Human feces; Human sputum; Human	Metabolic reconstruction

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
Human Feces	Detected but not Quantified									HMDB

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

546

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

562

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]

Showing metabocard for 1,2-Dihydroxy-3-keto-5-methylthiopentene (MMDBc0032940)

MOL for #<Metabolite:0x00005645c9db8138>

3D MOL for #<Metabolite:0x00005645c9db8138>

3D SDF for #<Metabolite:0x00005645c9db8138>

3D-SDF for #<Metabolite:0x00005645c9db8138>

PDB for #<Metabolite:0x00005645c9db8138>

3D PDB for #<Metabolite:0x00005645c9db8138>

SMILES for #<Metabolite:0x00005645c9db8138>

INCHI for #<Metabolite:0x00005645c9db8138>

Structure for #<Metabolite:0x00005645c9db8138>

3D Structure for #<Metabolite:0x00005645c9db8138>