MiMeDB: Showing metabocard for Sclerotigenin (MMDBc0003418)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-14 21:27:45 UTC

Update Date

2022-08-31 06:20:53 UTC

Metabolite ID

MMDBc0003418

Metabolite Identification

Common Name

Sclerotigenin

Description

sclerotigenin belongs to the class of organic compounds known as pyrimidodiazepines. Pyrimidodiazepines are compounds containing a pyrimidoazepine moiety, which consists of a pyrimidine fused to a piperazine ring by a bond. Pyrimidine is 6-membered ring consisting of five carbon atoms and two nitrogen atoms at ring positions 1 and 3. Diazepine is a 7-membered ring consisting of five carbon atoms and two nitrogen centers. sclerotigenin is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004191521522D          

 21 24  0  0  0  0            999 V2000
    1.6120    1.7168    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3623    1.3738    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9969    1.9009    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8047    1.7334    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1774    0.9973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9987    1.0754    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.4769    0.4031    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2982    0.4811    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7765   -0.1911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4334   -0.9414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6121   -1.0194    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1339   -0.3472    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3126   -0.4252    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9695   -1.1755    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8343    0.2471    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0338    0.0475    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9271   -0.7706    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1653   -1.0872    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5102   -0.5858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6169    0.2323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3787    0.5489    0.0000 C   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  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
  7 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
  5 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
  2 21  1  0  0  0  0
 16 21  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0003418

> <DATABASE_NAME>
MIME

> <SMILES>
O=C1N2C(CNC(=O)C3=CC=CC=C23)=NC2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C16H11N3O2/c20-15-11-6-2-4-8-13(11)19-14(9-17-15)18-12-7-3-1-5-10(12)16(19)21/h1-8H,9H2,(H,17,20)

> <INCHI_KEY>
NGYKOTTXJAPLPC-UHFFFAOYSA-N

> <FORMULA>
C16H11N3O2

> <MOLECULAR_WEIGHT>
277.283

> <EXACT_MASS>
277.085126606

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
28.167692050397807

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1,9,12-triazatetracyclo[9.8.0.0²,⁷.0¹³,¹⁸]nonadeca-2,4,6,11,13,15,17-heptaene-8,19-dione

> <ALOGPS_LOGP>
1.17

> <JCHEM_LOGP>
1.430720398333333

> <ALOGPS_LOGS>
-3.15

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.938288774625647

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.202076431361274

> <JCHEM_PKA_STRONGEST_BASIC>
-1.4388682595111693

> <JCHEM_POLAR_SURFACE_AREA>
61.77

> <JCHEM_REFRACTIVITY>
79.48020000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.95e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1,9,12-triazatetracyclo[9.8.0.0²,⁷.0¹³,¹⁸]nonadeca-2,4,6,11,13,15,17-heptaene-8,19-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 19-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-15         0                                  
HETATM    1  O   UNK     0       3.009   3.205   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.410   2.564   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       5.594   3.548   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       7.102   3.236   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.798   1.862   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       9.331   2.007   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      10.224   0.752   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      11.757   0.898   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      12.649  -0.357   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      12.009  -1.757   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.476  -1.903   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.583  -0.648   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.050  -0.794   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       7.410  -2.194   0.000  0.00  0.00           O+0
HETATM   15  N   UNK     0       7.157   0.461   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       5.663   0.089   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.464  -1.438   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.042  -2.029   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.819  -1.093   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.018   0.434   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.440   1.025   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   21                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   15                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   12                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11    7   13                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13    5   16                                                  
CONECT   16   15   17   21                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20    2   16                                                  
MASTER        0    0    0    0    0    0    0    0   21    0   48    0
END

Synonyms

Not Available

Molecular Formula

C₁₆H₁₁N₃O₂

Average Mass

277.283

Monoisotopic Mass

277.085126606

IUPAC Name

1,9,12-triazatetracyclo[9.8.0.0²,⁷.0¹³,¹⁸]nonadeca-2,4,6,11,13,15,17-heptaene-8,19-dione

Traditional Name

1,9,12-triazatetracyclo[9.8.0.0²,⁷.0¹³,¹⁸]nonadeca-2,4,6,11,13,15,17-heptaene-8,19-dione

CAS Registry Number

Not Available

SMILES

O=C1N2C(CNC(=O)C3=CC=CC=C23)=NC2=CC=CC=C12

InChI Identifier

InChI=1S/C16H11N3O2/c20-15-11-6-2-4-8-13(11)19-14(9-17-15)18-12-7-3-1-5-10(12)16(19)21/h1-8H,9H2,(H,17,20)

InChI Key

NGYKOTTXJAPLPC-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidodiazepines. Pyrimidodiazepines are compounds containing a pyrimidoazepine moiety, which consists of a pyrimidine fused to a piperazine ring by a bond. Pyrimidine is 6-membered ring consisting of five carbon atoms and two nitrogen atoms at ring positions 1 and 3. Diazepine is a 7-membered ring consisting of five carbon atoms and two nitrogen centers.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyrimidodiazepines

Sub Class

Not Available

Direct Parent

Pyrimidodiazepines

Alternative Parents

Substituents

Benzodiazepine
Pyrimidodiazepine
1,4-benzodiazepine
Quinazoline
Pyrimidone
Pyrimidine
Benzenoid
Heteroaromatic compound
Vinylogous amide
Carboxamide group
Lactam
Secondary carboxylic acid amide
Carboxylic acid derivative
Azacycle
Organooxygen compound
Organonitrogen compound
Organic oxide
Organic oxygen compound
Hydrocarbon derivative
Organic nitrogen 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	0.2 g/L	ALOGPS
logP	1.17	ALOGPS
logP	1.43	ChemAxon
logS	-3.2	ALOGPS
pKa (Strongest Acidic)	14.2	ChemAxon
pKa (Strongest Basic)	-1.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	61.77 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	79.48 m³·mol⁻¹	ChemAxon
Polarizability	28.17 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-10	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum

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	3	Human sputum; Human ; 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

10802469

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 Sclerotigenin (MMDBc0003418)

MOL for #<Metabolite:0x00007fed141badb0>

3D MOL for #<Metabolite:0x00007fed141badb0>

3D SDF for #<Metabolite:0x00007fed141badb0>

3D-SDF for #<Metabolite:0x00007fed141badb0>

PDB for #<Metabolite:0x00007fed141badb0>

3D PDB for #<Metabolite:0x00007fed141badb0>

SMILES for #<Metabolite:0x00007fed141badb0>

INCHI for #<Metabolite:0x00007fed141badb0>

Structure for #<Metabolite:0x00007fed141badb0>

3D Structure for #<Metabolite:0x00007fed141badb0>