MiMeDB: Showing metabocard for Penicilindole B (MMDBc0022572)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 12:39:54 UTC

Update Date

2022-08-31 06:47:42 UTC

Metabolite ID

MMDBc0022572

Metabolite Identification

Common Name

Penicilindole B

Description

Penicilindole B belongs to the class of organic compounds known as 3-alkylindoles. 3-alkylindoles are compounds containing an indole moiety that carries an alkyl chain at the 3-position. Penicilindole B is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152114392D          

 33 36  0  0  1  0            999 V2000
    0.7145    5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4256    2.8377    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9590    2.4208    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5110    3.0339    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1520    2.5923    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2561    3.8185    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2296    4.5330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8971    3.3769    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4491    3.9900    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0366    4.7045    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4849    3.1424    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9559    1.9192    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.8875    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  6  2  0  0  0  0
  9  8  1  0  0  0  0
 10  6  1  0  0  0  0
 11  7  1  0  0  0  0
 13 12  1  0  0  0  0
 14  8  1  0  0  0  0
 16 15  1  0  0  0  0
 19  1  1  0  0  0  0
 19  2  1  0  0  0  0
 19  9  2  0  0  0  0
 20  3  1  1  0  0  0
 20 12  1  0  0  0  0
 21 17  1  0  0  0  0
 21 18  2  0  0  0  0
 22 10  2  0  0  0  0
 22 21  1  0  0  0  0
 23 11  2  0  0  0  0
 23 22  1  0  0  0  0
 24 17  1  6  0  0  0
 25 13  1  0  0  0  0
 26  4  1  6  0  0  0
 26 15  1  0  0  0  0
 26 20  1  0  0  0  0
 27  5  1  1  0  0  0
 27 16  1  0  0  0  0
 27 24  1  0  0  0  0
 28 14  1  6  0  0  0
 28 24  1  0  0  0  0
 28 25  1  0  0  0  0
 28 26  1  0  0  0  0
 29 18  1  0  0  0  0
 29 23  1  0  0  0  0
 30 25  2  0  0  0  0
 27 31  1  6  0  0  0
 20 32  1  1  0  0  0
 24 33  1  1  0  0  0
M  END


  Mrv1652305152114392D          

 33 36  0  0  1  0            999 V2000
    0.7145    5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4256    2.8377    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9590    2.4208    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5110    3.0339    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1520    2.5923    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2561    3.8185    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2296    4.5330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8971    3.3769    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4491    3.9900    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0366    4.7045    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4849    3.1424    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9559    1.9192    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.8875    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  6  2  0  0  0  0
  9  8  1  0  0  0  0
 10  6  1  0  0  0  0
 11  7  1  0  0  0  0
 13 12  1  0  0  0  0
 14  8  1  0  0  0  0
 16 15  1  0  0  0  0
 19  1  1  0  0  0  0
 19  2  1  0  0  0  0
 19  9  2  0  0  0  0
 20  3  1  1  0  0  0
 20 12  1  0  0  0  0
 21 17  1  0  0  0  0
 21 18  2  0  0  0  0
 22 10  2  0  0  0  0
 22 21  1  0  0  0  0
 23 11  2  0  0  0  0
 23 22  1  0  0  0  0
 24 17  1  6  0  0  0
 25 13  1  0  0  0  0
 26  4  1  6  0  0  0
 26 15  1  0  0  0  0
 26 20  1  0  0  0  0
 27  5  1  1  0  0  0
 27 16  1  0  0  0  0
 27 24  1  0  0  0  0
 28 14  1  6  0  0  0
 28 24  1  0  0  0  0
 28 25  1  0  0  0  0
 28 26  1  0  0  0  0
 29 18  1  0  0  0  0
 29 23  1  0  0  0  0
 30 25  2  0  0  0  0
 27 31  1  6  0  0  0
 20 32  1  1  0  0  0
 24 33  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0022572

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]1(C)CCC(=O)[C@@]2(CCC=C(C)C)[C@]([H])(CC3=CNC4=CC=CC=C34)[C@](C)(O)CC[C@@]12C

> <INCHI_IDENTIFIER>
InChI=1S/C28H39NO2/c1-19(2)9-8-14-28-24(17-21-18-29-23-11-7-6-10-22(21)23)27(5,31)16-15-26(28,4)20(3)12-13-25(28)30/h6-7,9-11,18,20,24,29,31H,8,12-17H2,1-5H3/t20-,24-,26+,27-,28-/m1/s1

> <INCHI_KEY>
KPIWQVIPQWGFNG-VFRRUXMTSA-N

> <FORMULA>
C28H39NO2

> <MOLECULAR_WEIGHT>
421.625

> <EXACT_MASS>
421.2980795

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
70

> <JCHEM_AVERAGE_POLARIZABILITY>
50.12542176546097

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4R,4aS,7R,8S,8aS)-7-hydroxy-8-[(1H-indol-3-yl)methyl]-4,4a,7-trimethyl-8a-(4-methylpent-3-en-1-yl)-decahydronaphthalen-1-one

> <ALOGPS_LOGP>
6.00

> <JCHEM_LOGP>
6.482371458333332

> <ALOGPS_LOGS>
-6.23

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
16.18351391851684

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.727476270961517

> <JCHEM_PKA_STRONGEST_BASIC>
-2.910949029228358

> <JCHEM_POLAR_SURFACE_AREA>
53.09

> <JCHEM_REFRACTIVITY>
128.6594

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.47e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4R,4aS,7R,8S,8aS)-7-hydroxy-8-(1H-indol-3-ylmethyl)-4,4a,7-trimethyl-8a-(4-methylpent-3-en-1-yl)-hexahydronaphthalen-1-one

> <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       1.334  10.010   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   7.700   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334   0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.528   5.297   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.390   4.519   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.421   5.663   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   6.160   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   7.700   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.884   4.839   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.945   7.128   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334   5.390   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.667   6.160   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.162   8.462   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.334   8.470   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -0.000   1.540   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.001   6.930   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.408   6.304   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       6.438   7.448   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM   29  N   UNK     0       5.668   8.782   0.000  0.00  0.00           N+0
HETATM   30  O   UNK     0      -0.905   5.866   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       5.518   3.583   0.000  0.00  0.00           O+0
HETATM   32  H   UNK     0       0.000   3.080   0.000  0.00  0.00           H+0
HETATM   33  H   UNK     0       4.001   5.390   0.000  0.00  0.00           H+0
CONECT    1   19                                                            
CONECT    2   19                                                            
CONECT    3   20                                                            
CONECT    4   26                                                            
CONECT    5   27                                                            
CONECT    6    7   10                                                       
CONECT    7    6   11                                                       
CONECT    8    9   14                                                       
CONECT    9    8   19                                                       
CONECT   10    6   22                                                       
CONECT   11    7   23                                                       
CONECT   12   13   20                                                       
CONECT   13   12   25                                                       
CONECT   14    8   28                                                       
CONECT   15   16   26                                                       
CONECT   16   15   27                                                       
CONECT   17   21   24                                                       
CONECT   18   21   29                                                       
CONECT   19    1    2    9                                                  
CONECT   20    3   12   26   32                                             
CONECT   21   17   18   22                                                  
CONECT   22   10   21   23                                                  
CONECT   23   11   22   29                                                  
CONECT   24   17   27   28   33                                             
CONECT   25   13   28   30                                                  
CONECT   26    4   15   20   28                                             
CONECT   27    5   16   24   31                                             
CONECT   28   14   24   25   26                                             
CONECT   29   18   23                                                       
CONECT   30   25                                                            
CONECT   31   27                                                            
CONECT   32   20                                                            
CONECT   33   24                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   72    0
END

Synonyms

Not Available

Molecular Formula

C₂₈H₃₉NO₂

Average Mass

421.625

Monoisotopic Mass

421.2980795

IUPAC Name

(4R,4aS,7R,8S,8aS)-7-hydroxy-8-[(1H-indol-3-yl)methyl]-4,4a,7-trimethyl-8a-(4-methylpent-3-en-1-yl)-decahydronaphthalen-1-one

Traditional Name

(4R,4aS,7R,8S,8aS)-7-hydroxy-8-(1H-indol-3-ylmethyl)-4,4a,7-trimethyl-8a-(4-methylpent-3-en-1-yl)-hexahydronaphthalen-1-one

CAS Registry Number

Not Available

SMILES

[H][C@@]1(C)CCC(=O)[C@@]2(CCC=C(C)C)[C@]([H])(CC3=CNC4=CC=CC=C34)[C@](C)(O)CC[C@@]12C

InChI Identifier

InChI=1S/C28H39NO2/c1-19(2)9-8-14-28-24(17-21-18-29-23-11-7-6-10-22(21)23)27(5,31)16-15-26(28,4)20(3)12-13-25(28)30/h6-7,9-11,18,20,24,29,31H,8,12-17H2,1-5H3/t20-,24-,26+,27-,28-/m1/s1

InChI Key

KPIWQVIPQWGFNG-VFRRUXMTSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 3-alkylindoles. 3-Alkylindoles are compounds containing an indole moiety that carries an alkyl chain at the 3-position.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Indoles

Direct Parent

3-alkylindoles

Alternative Parents

Substituents

3-alkylindole
Benzenoid
Substituted pyrrole
Heteroaromatic compound
Tertiary alcohol
Pyrrole
Cyclic alcohol
Ketone
Azacycle
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Alcohol
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	0.00025 g/L	ALOGPS
logP	6	ALOGPS
logP	6.48	ChemAxon
logS	-6.2	ALOGPS
pKa (Strongest Acidic)	14.73	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	53.09 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	128.66 m³·mol⁻¹	ChemAxon
Polarizability	50.13 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	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

65323288

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139589954

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 Penicilindole B (MMDBc0022572)

MOL for #<Metabolite:0x00007f46f8023460>

3D MOL for #<Metabolite:0x00007f46f8023460>

3D SDF for #<Metabolite:0x00007f46f8023460>

3D-SDF for #<Metabolite:0x00007f46f8023460>

PDB for #<Metabolite:0x00007f46f8023460>

3D PDB for #<Metabolite:0x00007f46f8023460>

SMILES for #<Metabolite:0x00007f46f8023460>

INCHI for #<Metabolite:0x00007f46f8023460>

Structure for #<Metabolite:0x00007f46f8023460>

3D Structure for #<Metabolite:0x00007f46f8023460>