MiMeDB: Showing metabocard for Sporidesmin B (MMDBc0000955)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-14 18:39:40 UTC

Update Date

2022-08-31 06:17:21 UTC

Metabolite ID

MMDBc0000955

Metabolite Identification

Common Name

Sporidesmin B

Description

SPORIDESMIN B, also known as sporidesmin a, belongs to the class of organic compounds known as pyrroloindoles. Pyrroloindoles are compounds containing a pyrroloindole moiety, which is a tricyclic heterocycle which consists of a pyrrole ring fused to an indole. Pyrrole is 5-membered ring consisting of four carbon atoms and one nitrogen atom. Indole is a bicyclic compound consisting of a six-membered benzene ring fused to a five-membered nitrogen-containing pyrrole ring. SPORIDESMIN B is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004251508262D          

 29 33  0  0  0  0            999 V2000
    7.4464   -0.4458    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2751    0.3612    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4905    0.6163    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3192    1.4233    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9324    1.9752    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    5.5346    1.6784    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9214    1.1265    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0927    0.3195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3782   -0.0929    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2918   -0.9133    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7652    0.4593    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9030    0.5504    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3240   -0.1819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6240   -0.9504    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3884   -0.0334    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8437   -0.6529    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0351    0.3442    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.9758    1.0892    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.6444    1.4279    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4356    1.7419    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1009    1.2129    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4133    1.9765    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6859    1.5702    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3710    2.3327    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1347    0.8302    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3226    0.9756    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8773    0.0644    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0487   -0.7426    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8332   -0.9977    0.0000 C   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  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
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 12 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
  7 21  1  0  0  0  0
 11 21  1  0  0  0  0
 21 22  1  0  0  0  0
 19 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 15 25  1  0  0  0  0
 25 26  1  0  0  0  0
  8 27  2  0  0  0  0
  3 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
M  END


  Mrv1533004251508262D          

 29 33  0  0  0  0            999 V2000
    7.4464   -0.4458    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2751    0.3612    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4905    0.6163    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3192    1.4233    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9324    1.9752    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    5.5346    1.6784    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9214    1.1265    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0927    0.3195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3782   -0.0929    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2918   -0.9133    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7652    0.4593    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9030    0.5504    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3240   -0.1819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6240   -0.9504    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3884   -0.0334    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8437   -0.6529    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0351    0.3442    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.9758    1.0892    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.6444    1.4279    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4356    1.7419    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1009    1.2129    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4133    1.9765    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6859    1.5702    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3710    2.3327    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1347    0.8302    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3226    0.9756    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8773    0.0644    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0487   -0.7426    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8332   -0.9977    0.0000 C   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  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
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 12 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
  7 21  1  0  0  0  0
 11 21  1  0  0  0  0
 21 22  1  0  0  0  0
 19 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 15 25  1  0  0  0  0
 25 26  1  0  0  0  0
  8 27  2  0  0  0  0
  3 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000955

> <DATABASE_NAME>
MIME

> <SMILES>
COC1=C2N(C)C3N4C(=O)C5(C)SSC4(CC3(O)C2=CC(Cl)=C1OC)C(=O)N5C

> <INCHI_IDENTIFIER>
InChI=1S/C18H20ClN3O5S2/c1-16-14(23)22-13-17(25,7-18(22,29-28-16)15(24)21(16)3)8-6-9(19)11(26-4)12(27-5)10(8)20(13)2/h6,13,25H,7H2,1-5H3

> <INCHI_KEY>
HCAHETRFJITQNU-UHFFFAOYSA-N

> <FORMULA>
C18H20ClN3O5S2

> <MOLECULAR_WEIGHT>
457.94

> <EXACT_MASS>
457.0532908

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
49

> <JCHEM_AVERAGE_POLARIZABILITY>
44.11913729847496

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
6-chloro-3-hydroxy-7,8-dimethoxy-10,14,18-trimethyl-15,16-dithia-10,12,18-triazapentacyclo[12.2.2.0¹,¹².0³,¹¹.0⁴,⁹]octadeca-4,6,8-triene-13,17-dione

> <ALOGPS_LOGP>
1.97

> <JCHEM_LOGP>
2.4997129289999998

> <ALOGPS_LOGS>
-2.57

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.877702775297166

> <JCHEM_PKA_STRONGEST_BASIC>
-3.727092806085019

> <JCHEM_POLAR_SURFACE_AREA>
82.55000000000001

> <JCHEM_REFRACTIVITY>
111.22369999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.22e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-chloro-3-hydroxy-7,8-dimethoxy-10,14,18-trimethyl-15,16-dithia-10,12,18-triazapentacyclo[12.2.2.0¹,¹².0³,¹¹.0⁴,⁹]octadeca-4,6,8-triene-13,17-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-APR-15         0                                  
HETATM    1  C   UNK     0      13.900  -0.832   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      13.580   0.674   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      12.116   1.150   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      11.796   2.657   0.000  0.00  0.00           C+0
HETATM    5 Cl   UNK     0      12.940   3.687   0.000  0.00  0.00          Cl+0
HETATM    6  C   UNK     0      10.331   3.133   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.187   2.103   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.506   0.596   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       8.173  -0.173   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       8.011  -1.705   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.028   0.857   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       5.419   1.027   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       4.338  -0.340   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       4.898  -1.774   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       2.592  -0.062   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.575  -1.219   0.000  0.00  0.00           C+0
HETATM   17  S   UNK     0       3.799   0.643   0.000  0.00  0.00           S+0
HETATM   18  S   UNK     0       3.688   2.033   0.000  0.00  0.00           S+0
HETATM   19  C   UNK     0       4.936   2.665   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.413   3.252   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       7.655   2.264   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       8.238   3.689   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       3.147   2.931   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       2.559   4.354   0.000  0.00  0.00           O+0
HETATM   25  N   UNK     0       2.118   1.550   0.000  0.00  0.00           N+0
HETATM   26  C   UNK     0       0.602   1.821   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      10.971   0.120   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      11.291  -1.386   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      12.755  -1.862   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   27                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8   21                                                  
CONECT    8    7    9   27                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   21                                                  
CONECT   12   11   13   19                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17   25                                             
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   12   20   23                                             
CONECT   20   19   21                                                       
CONECT   21   20    7   11   22                                             
CONECT   22   21                                                            
CONECT   23   19   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   15   26                                                  
CONECT   26   25                                                            
CONECT   27    8    3   28                                                  
CONECT   28   27   29                                                       
CONECT   29   28                                                            
MASTER        0    0    0    0    0    0    0    0   29    0   66    0
END

Synonyms

Value	Source
Sporidesmin a	MeSH
Sporidesmin g	MeSH
Sporidesmin H	MeSH
Sporidesmin D	MeSH
Sporidesmin e	MeSH
Isosporidesmin b	MeSH
Sporidesmin F	MeSH
Sporidesmin	MeSH
Sporidesmin C	MeSH

Molecular Formula

C₁₈H₂₀ClN₃O₅S₂

Average Mass

457.94

Monoisotopic Mass

457.0532908

IUPAC Name

6-chloro-3-hydroxy-7,8-dimethoxy-10,14,18-trimethyl-15,16-dithia-10,12,18-triazapentacyclo[12.2.2.0¹,¹².0³,¹¹.0⁴,⁹]octadeca-4,6,8-triene-13,17-dione

Traditional Name

6-chloro-3-hydroxy-7,8-dimethoxy-10,14,18-trimethyl-15,16-dithia-10,12,18-triazapentacyclo[12.2.2.0¹,¹².0³,¹¹.0⁴,⁹]octadeca-4,6,8-triene-13,17-dione

CAS Registry Number

Not Available

SMILES

COC1=C2N(C)C3N4C(=O)C5(C)SSC4(CC3(O)C2=CC(Cl)=C1OC)C(=O)N5C

InChI Identifier

InChI=1S/C18H20ClN3O5S2/c1-16-14(23)22-13-17(25,7-18(22,29-28-16)15(24)21(16)3)8-6-9(19)11(26-4)12(27-5)10(8)20(13)2/h6,13,25H,7H2,1-5H3

InChI Key

HCAHETRFJITQNU-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrroloindoles. Pyrroloindoles are compounds containing a pyrroloindole moiety, which is a tricyclic heterocycle which consists of a pyrrole ring fused to an indole. Pyrrole is 5-membered ring consisting of four carbon atoms and one nitrogen atom. Indole is a bicyclic compound consisting of a six-membered benzene ring fused to a five-membered nitrogen-containing pyrrole ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Pyrroloindoles

Direct Parent

Pyrroloindoles

Alternative Parents

Substituents

Pyrroloindole
Alpha-amino acid or derivatives
Epipolythiodioxopiperazine
Indole
Thiodioxopiperazine
Anisole
Dioxopiperazine
Dialkylarylamine
2,5-dioxopiperazine
Alkyl aryl ether
N-alkylpiperazine
N-methylpiperazine
Aryl chloride
Aryl halide
1,4-diazinane
Dithiazinane
Piperazine
Benzenoid
Tertiary carboxylic acid amide
Tertiary alcohol
Pyrrolidine
Pyrrole
Carboxamide group
Lactam
Organic disulfide
Ether
Carboxylic acid derivative
Azacycle
Hydrocarbon derivative
Organopnictogen compound
Organic oxide
Organic oxygen compound
Alcohol
Carbonyl group
Organic nitrogen compound
Organochloride
Organonitrogen compound
Organooxygen compound
Organohalogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	1.22 g/L	ALOGPS
logP	1.97	ALOGPS
logP	2.5	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	12.88	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	82.55 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	111.22 m³·mol⁻¹	ChemAxon
Polarizability	44.12 Å³	ChemAxon
Number of Rings	5	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	1	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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

99878

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 Sporidesmin B (MMDBc0000955)

MOL for #<Metabolite:0x00007f46e0ee0b00>

3D MOL for #<Metabolite:0x00007f46e0ee0b00>

3D SDF for #<Metabolite:0x00007f46e0ee0b00>

3D-SDF for #<Metabolite:0x00007f46e0ee0b00>

PDB for #<Metabolite:0x00007f46e0ee0b00>

3D PDB for #<Metabolite:0x00007f46e0ee0b00>

SMILES for #<Metabolite:0x00007f46e0ee0b00>

INCHI for #<Metabolite:0x00007f46e0ee0b00>

Structure for #<Metabolite:0x00007f46e0ee0b00>

3D Structure for #<Metabolite:0x00007f46e0ee0b00>