MiMeDB: Showing metabocard for 6,7-seco-Agroclavine (MMDBc0013361)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 04:40:53 UTC

Update Date

2022-08-31 06:35:58 UTC

Metabolite ID

MMDBc0013361

Metabolite Identification

Common Name

6,7-seco-Agroclavine

Description

Benz(cd)indol-4-amine, 1,3,4,5-tetrahydro-N-methyl-5-(2-methyl-1-propenyl)-, (4R,5R)- belongs to the class of organic compounds known as clavines and derivatives. These are hydroxy and dehydro derivatives of 6,8-dimethylergolenes and the corresponding ergolines. Benz(cd)indol-4-amine, 1,3,4,5-tetrahydro-N-methyl-5-(2-methyl-1-propenyl)-, (4R,5R)- is a very strong basic compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152106402D          

 20 22  0  0  1  0            999 V2000
    1.8992    3.0034    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7798    4.1288    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7060    2.6578    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8514    1.5017    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5189    1.9867    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9377    0.6813    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3141    2.8035    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7799    0.6813    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7713   -0.4389    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6644    3.3119    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0262    0.3457    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2725    1.6511    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1987    1.9867    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6913    0.3457    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8661    1.5017    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3588    0.8306    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6198    1.8373    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9463   -0.4389    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5581    2.5065    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9524    2.3222    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  4  2  0  0  0  0
  6  4  1  0  0  0  0
 10  1  1  0  0  0  0
 10  2  1  0  0  0  0
 10  7  2  0  0  0  0
 11  8  1  0  0  0  0
 11  9  2  0  0  0  0
 12  5  1  0  0  0  0
 13  7  1  1  0  0  0
 13 12  1  0  0  0  0
 14  6  2  0  0  0  0
 15  8  1  0  0  0  0
 15 13  1  0  0  0  0
 16 11  1  0  0  0  0
 16 12  2  0  0  0  0
 16 14  1  0  0  0  0
 17  3  1  0  0  0  0
 15 17  1  6  0  0  0
 18  9  1  0  0  0  0
 18 14  1  0  0  0  0
 13 19  1  6  0  0  0
 15 20  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0013361

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(CC2=CNC3=CC=CC(=C23)[C@@]1([H])C=C(C)C)NC

> <INCHI_IDENTIFIER>
InChI=1S/C16H20N2/c1-10(2)7-13-12-5-4-6-14-16(12)11(9-18-14)8-15(13)17-3/h4-7,9,13,15,17-18H,8H2,1-3H3/t13-,15-/m1/s1

> <INCHI_KEY>
NGJMPUDCQIYVMS-UKRRQHHQSA-N

> <FORMULA>
C16H20N2

> <MOLECULAR_WEIGHT>
240.35

> <EXACT_MASS>
240.162648652

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
28.23777391874981

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(6R,7R)-N-methyl-7-(2-methylprop-1-en-1-yl)-2-azatricyclo[6.3.1.0^{4,12}]dodeca-1(11),3,8(12),9-tetraen-6-amine

> <ALOGPS_LOGP>
2.70

> <JCHEM_LOGP>
3.154223191333333

> <ALOGPS_LOGS>
-4.19

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.049513721699228

> <JCHEM_PKA_STRONGEST_BASIC>
10.340167035746916

> <JCHEM_POLAR_SURFACE_AREA>
27.82

> <JCHEM_REFRACTIVITY>
77.1995

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.55e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(6R,7R)-N-methyl-7-(2-methylprop-1-en-1-yl)-2-azatricyclo[6.3.1.0^{4,12}]dodeca-1(11),3,8(12),9-tetraen-6-amine

> <JCHEM_VEBER_RULE>
1

$$$$

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       3.545   5.606   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.189   7.707   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.785   4.961   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.589   2.803   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.835   3.708   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.750   1.272   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.186   5.233   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.056   1.272   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.173  -0.819   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.973   6.182   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.649   0.645   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.242   3.082   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.971   3.708   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.157   0.645   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.217   2.803   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.403   1.550   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       8.624   3.430   0.000  0.00  0.00           N+0
HETATM   18  N   UNK     0       3.633  -0.819   0.000  0.00  0.00           N+0
HETATM   19  H   UNK     0       4.775   4.679   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       7.378   4.335   0.000  0.00  0.00           H+0
CONECT    1   10                                                            
CONECT    2   10                                                            
CONECT    3   17                                                            
CONECT    4    5    6                                                       
CONECT    5    4   12                                                       
CONECT    6    4   14                                                       
CONECT    7   10   13                                                       
CONECT    8   11   15                                                       
CONECT    9   11   18                                                       
CONECT   10    1    2    7                                                  
CONECT   11    8    9   16                                                  
CONECT   12    5   13   16                                                  
CONECT   13    7   12   15   19                                             
CONECT   14    6   16   18                                                  
CONECT   15    8   13   17   20                                             
CONECT   16   11   12   14                                                  
CONECT   17    3   15                                                       
CONECT   18    9   14                                                       
CONECT   19   13                                                            
CONECT   20   15                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

Synonyms

Not Available

Molecular Formula

C₁₆H₂₀N₂

Average Mass

240.35

Monoisotopic Mass

240.162648652

IUPAC Name

(6R,7R)-N-methyl-7-(2-methylprop-1-en-1-yl)-2-azatricyclo[6.3.1.0^{4,12}]dodeca-1(11),3,8(12),9-tetraen-6-amine

Traditional Name

(6R,7R)-N-methyl-7-(2-methylprop-1-en-1-yl)-2-azatricyclo[6.3.1.0^{4,12}]dodeca-1(11),3,8(12),9-tetraen-6-amine

CAS Registry Number

Not Available

SMILES

[H][C@]1(CC2=CNC3=CC=CC(=C23)[C@@]1([H])C=C(C)C)NC

InChI Identifier

InChI=1S/C16H20N2/c1-10(2)7-13-12-5-4-6-14-16(12)11(9-18-14)8-15(13)17-3/h4-7,9,13,15,17-18H,8H2,1-3H3/t13-,15-/m1/s1

InChI Key

NGJMPUDCQIYVMS-UKRRQHHQSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as clavines and derivatives. These are hydroxy and dehydro derivatives of 6,8-dimethylergolenes and the corresponding ergolines.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Ergoline and derivatives

Sub Class

Clavines and derivatives

Direct Parent

Clavines and derivatives

Alternative Parents

Substituents

Chanoclavine skeleton
3-alkylindole
Indole
Indole or derivatives
Isoindole or derivatives
Aralkylamine
Benzenoid
Pyrrole
Heteroaromatic compound
Organoheterocyclic compound
Azacycle
Secondary amine
Secondary aliphatic amine
Organonitrogen compound
Hydrocarbon derivative
Organopnictogen compound
Organic nitrogen compound
Amine
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	0.016 g/L	ALOGPS
logP	2.7	ALOGPS
logP	3.15	ChemAxon
logS	-4.2	ALOGPS
pKa (Strongest Acidic)	17.05	ChemAxon
pKa (Strongest Basic)	10.34	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	27.82 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	77.2 m³·mol⁻¹	ChemAxon
Polarizability	28.24 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	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_2) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-09	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	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	4	Human feces	Metabolic reconstruction

Exposure Sources

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

136632

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

155090

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 6,7-seco-Agroclavine (MMDBc0013361)

MOL for #<Metabolite:0x00007fdb38755e98>

3D MOL for #<Metabolite:0x00007fdb38755e98>

3D SDF for #<Metabolite:0x00007fdb38755e98>

3D-SDF for #<Metabolite:0x00007fdb38755e98>

PDB for #<Metabolite:0x00007fdb38755e98>

3D PDB for #<Metabolite:0x00007fdb38755e98>

SMILES for #<Metabolite:0x00007fdb38755e98>

INCHI for #<Metabolite:0x00007fdb38755e98>

Structure for #<Metabolite:0x00007fdb38755e98>

3D Structure for #<Metabolite:0x00007fdb38755e98>