MiMeDB: Showing metabocard for Gliotoxin (MMDBc0017619)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 07:57:05 UTC

Update Date

2022-08-31 06:42:42 UTC

Metabolite ID

MMDBc0017619

Metabolite Identification

Common Name

Gliotoxin

Description

NCIMech_000256 belongs to the class of organic compounds known as gliotoxins. These are polycyclic compounds containing the gliotoxin skeleton, which is structurally characterized by a epipolythiodioxopiperazine moiety fused to the pyrrolidine ring of an indol-7-ol derivative. Based on a literature review very few articles have been published on NCIMech_000256.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152109572D          

 23 26  0  0  1  0            999 V2000
    0.1598    0.8974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1879    0.7522    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6267    0.1476    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9449    1.5406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0829   -0.0675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7804    2.4228    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8224    0.3313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1406    1.7243    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5793    1.1197    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4785    0.1989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2101    2.0359    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3802    0.4190    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3237    1.8020    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9814    0.9717    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7338    1.2691    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0289    2.2627    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8975    2.5127    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1726   -0.5673    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4982    2.8089    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6783    0.7733    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.0167    1.4508    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.3363    1.9080    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3836    0.9359    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  2  2  0  0  0  0
  7  3  2  0  0  0  0
  7  5  1  0  0  0  0
  8  4  1  0  0  0  0
  9  7  1  0  0  0  0
  9  8  1  0  0  0  0
 12  5  1  0  0  0  0
 12 10  1  0  0  0  0
 13  6  1  6  0  0  0
 13 11  1  0  0  0  0
 14  1  1  0  0  0  0
 14 10  1  0  0  0  0
 14 13  1  0  0  0  0
 15  9  1  0  0  0  0
 15 11  1  0  0  0  0
 12 15  1  1  0  0  0
 16  6  1  0  0  0  0
  8 17  1  1  0  0  0
 18 10  2  0  0  0  0
 19 11  2  0  0  0  0
 20 12  1  0  0  0  0
 21 13  1  0  0  0  0
 21 20  1  0  0  0  0
  8 22  1  6  0  0  0
  9 23  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0017619

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]12N3C(=O)[C@@]4(CO)SS[C@]3(CC1=CC=C[C@]2([H])O)C(=O)N4C

> <INCHI_IDENTIFIER>
InChI=1S/C13H14N2O4S2/c1-14-10(18)12-5-7-3-2-4-8(17)9(7)15(12)11(19)13(14,6-16)21-20-12/h2-4,8-9,16-17H,5-6H2,1H3/t8-,9+,12+,13+/m0/s1

> <INCHI_KEY>
FIVPIPIDMRVLAY-HIAZDOBYSA-N

> <FORMULA>
C13H14N2O4S2

> <MOLECULAR_WEIGHT>
326.39

> <EXACT_MASS>
326.039499287

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
30.75084457519813

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,7S,8R,11R)-7-hydroxy-11-(hydroxymethyl)-15-methyl-12,13-dithia-9,15-diazatetracyclo[9.2.2.0^{1,9}.0^{3,8}]pentadeca-3,5-diene-10,14-dione

> <ALOGPS_LOGP>
-0.36

> <JCHEM_LOGP>
-0.01846358199999959

> <ALOGPS_LOGS>
-1.40

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.409874121191255

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.807188660513216

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1815361930940034

> <JCHEM_POLAR_SURFACE_AREA>
81.07999999999998

> <JCHEM_REFRACTIVITY>
81.68759999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.29e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,7S,8R,11R)-7-hydroxy-11-(hydroxymethyl)-15-methyl-12,13-dithia-9,15-diazatetracyclo[9.2.2.0^{1,9}.0^{3,8}]pentadeca-3,5-diene-10,14-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-MAY-21         0                                  
HETATM    1  C   UNK     0       0.298   1.675   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.684   1.404   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.636   0.275   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.230   2.876   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.755  -0.126   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.457   4.523   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.135   0.618   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.729   3.219   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.681   2.090   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.760   0.371   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.125   3.800   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.443   0.782   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.471   3.364   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       1.832   1.814   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       5.103   2.369   0.000  0.00  0.00           N+0
HETATM   16  O   UNK     0      -0.054   4.224   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       7.275   4.690   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       2.189  -1.059   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       4.663   5.243   0.000  0.00  0.00           O+0
HETATM   20  S   UNK     0       3.133   1.443   0.000  0.00  0.00           S+0
HETATM   21  S   UNK     0       3.765   2.708   0.000  0.00  0.00           S+0
HETATM   22  H   UNK     0       6.228   3.562   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0       8.183   1.747   0.000  0.00  0.00           H+0
CONECT    1   14                                                            
CONECT    2    3    4                                                       
CONECT    3    2    7                                                       
CONECT    4    2    8                                                       
CONECT    5    7   12                                                       
CONECT    6   13   16                                                       
CONECT    7    3    5    9                                                  
CONECT    8    4    9   17   22                                             
CONECT    9    7    8   15   23                                             
CONECT   10   12   14   18                                                  
CONECT   11   13   15   19                                                  
CONECT   12    5   10   15   20                                             
CONECT   13    6   11   14   21                                             
CONECT   14    1   10   13                                                  
CONECT   15    9   11   12                                                  
CONECT   16    6                                                            
CONECT   17    8                                                            
CONECT   18   10                                                            
CONECT   19   11                                                            
CONECT   20   12   21                                                       
CONECT   21   13   20                                                       
CONECT   22    8                                                            
CONECT   23    9                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   52    0
END

Synonyms

Not Available

Molecular Formula

C₁₃H₁₄N₂O₄S₂

Average Mass

326.39

Monoisotopic Mass

326.039499287

IUPAC Name

(1R,7S,8R,11R)-7-hydroxy-11-(hydroxymethyl)-15-methyl-12,13-dithia-9,15-diazatetracyclo[9.2.2.0^{1,9}.0^{3,8}]pentadeca-3,5-diene-10,14-dione

Traditional Name

(1R,7S,8R,11R)-7-hydroxy-11-(hydroxymethyl)-15-methyl-12,13-dithia-9,15-diazatetracyclo[9.2.2.0^{1,9}.0^{3,8}]pentadeca-3,5-diene-10,14-dione

CAS Registry Number

Not Available

SMILES

[H][C@@]12N3C(=O)[C@@]4(CO)SS[C@]3(CC1=CC=C[C@]2([H])O)C(=O)N4C

InChI Identifier

InChI=1S/C13H14N2O4S2/c1-14-10(18)12-5-7-3-2-4-8(17)9(7)15(12)11(19)13(14,6-16)21-20-12/h2-4,8-9,16-17H,5-6H2,1H3/t8-,9+,12+,13+/m0/s1

InChI Key

FIVPIPIDMRVLAY-HIAZDOBYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as gliotoxins. These are polycyclic compounds containing the gliotoxin skeleton, which is structurally characterized by a epipolythiodioxopiperazine moiety fused to the pyrrolidine ring of an indol-7-ol derivative.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazinanes

Sub Class

Piperazines

Direct Parent

Gliotoxins

Alternative Parents

Substituents

Gliotoxin-skeleton
Alpha-amino acid or derivatives
Indole or derivatives
N-alkylpiperazine
N-methylpiperazine
Dithiazinane
Tertiary carboxylic acid amide
Pyrrolidine
Carboxamide group
Lactam
Secondary alcohol
Organic disulfide
Carboxylic acid derivative
Azacycle
Primary alcohol
Hydrocarbon derivative
Organic oxide
Alcohol
Organic oxygen compound
Carbonyl group
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	12.9 g/L	ALOGPS
logP	-0.36	ALOGPS
logP	-0.018	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	13.81	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	81.08 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	81.69 m³·mol⁻¹	ChemAxon
Polarizability	30.75 Å³	ChemAxon
Number of Rings	4	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

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

Metabolic Reactions

Not Available

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	2	Human feces	Metabolic reconstruction

Exposure Sources

Source Type	Source Sub-type	Species	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

5145065

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6713040

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for Gliotoxin (MMDBc0017619)

MOL for #<Metabolite:0x00007fecfd127b58>

3D MOL for #<Metabolite:0x00007fecfd127b58>

3D SDF for #<Metabolite:0x00007fecfd127b58>

3D-SDF for #<Metabolite:0x00007fecfd127b58>

PDB for #<Metabolite:0x00007fecfd127b58>

3D PDB for #<Metabolite:0x00007fecfd127b58>

SMILES for #<Metabolite:0x00007fecfd127b58>

INCHI for #<Metabolite:0x00007fecfd127b58>

Structure for #<Metabolite:0x00007fecfd127b58>

3D Structure for #<Metabolite:0x00007fecfd127b58>