MiMeDB: Showing metabocard for Penicillenol C2 (MMDBc0014447)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 05:28:01 UTC

Update Date

2022-08-31 06:37:42 UTC

Metabolite ID

MMDBc0014447

Metabolite Identification

Common Name

Penicillenol C2

Description

penicillenol C2 belongs to the class of organic compounds known as n-alkylpyrrolidines. N-alkylpyrrolidines are compounds containing a pyrrolidine moiety that is substituted at the N1-position with an alkyl group. Pyrrolidine is a five-membered saturated aliphatic heterocycle with one nitrogen atom and four carbon atoms. penicillenol C2 is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152107282D          

 26 26  0  0  1  0            999 V2000
   -4.0203   -2.6108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2665   -3.4358    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7447   -4.4427    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8217   -2.8021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3058   -2.1983    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5913   -2.6108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8769   -2.1983    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1624   -2.6108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4479   -2.1983    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2665   -2.6108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9242   -4.3565    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6955   -2.6108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5887   -3.6028    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9810   -2.1983    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7817   -3.4313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4492   -2.2752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0012   -2.8883    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4393   -5.0239    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9810   -1.3733    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1686   -3.9833    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6207   -1.4683    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3058   -1.3733    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5913   -3.4358    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4479   -3.0233    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4092   -3.6891    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0695   -4.2440    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  1  0  0  0  0
  6  5  2  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  2  1  0  0  0  0
 10  9  1  0  0  0  0
 11  3  1  0  0  0  0
 13 11  1  6  0  0  0
 14 10  1  0  0  0  0
 14 12  2  0  0  0  0
 15 12  1  0  0  0  0
 15 13  1  0  0  0  0
 16 12  1  0  0  0  0
 17  4  1  0  0  0  0
 17 13  1  0  0  0  0
 17 16  1  0  0  0  0
 18 11  1  0  0  0  0
 19 14  1  0  0  0  0
 20 15  2  0  0  0  0
 21 16  2  0  0  0  0
 22  5  1  0  0  0  0
 23  6  1  0  0  0  0
 24 10  1  0  0  0  0
 25 11  1  0  0  0  0
 13 26  1  1  0  0  0
M  END


  Mrv1652305152107282D          

 26 26  0  0  1  0            999 V2000
   -4.0203   -2.6108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2665   -3.4358    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7447   -4.4427    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8217   -2.8021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3058   -2.1983    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5913   -2.6108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8769   -2.1983    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1624   -2.6108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4479   -2.1983    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2665   -2.6108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9242   -4.3565    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6955   -2.6108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5887   -3.6028    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9810   -2.1983    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7817   -3.4313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4492   -2.2752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0012   -2.8883    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4393   -5.0239    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9810   -1.3733    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1686   -3.9833    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6207   -1.4683    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3058   -1.3733    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5913   -3.4358    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4479   -3.0233    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4092   -3.6891    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0695   -4.2440    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  1  0  0  0  0
  6  5  2  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  2  1  0  0  0  0
 10  9  1  0  0  0  0
 11  3  1  0  0  0  0
 13 11  1  6  0  0  0
 14 10  1  0  0  0  0
 14 12  2  0  0  0  0
 15 12  1  0  0  0  0
 15 13  1  0  0  0  0
 16 12  1  0  0  0  0
 17  4  1  0  0  0  0
 17 13  1  0  0  0  0
 17 16  1  0  0  0  0
 18 11  1  0  0  0  0
 19 14  1  0  0  0  0
 20 15  2  0  0  0  0
 21 16  2  0  0  0  0
 22  5  1  0  0  0  0
 23  6  1  0  0  0  0
 24 10  1  0  0  0  0
 25 11  1  0  0  0  0
 13 26  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0014447

> <DATABASE_NAME>
MIME

> <SMILES>
[H]\C(C)=C(\[H])CCCC([H])(C)C(\O)=C1\C(=O)N(C)[C@@]([H])(C1=O)C([H])(C)O

> <INCHI_IDENTIFIER>
InChI=1S/C16H25NO4/c1-5-6-7-8-9-10(2)14(19)12-15(20)13(11(3)18)17(4)16(12)21/h5-6,10-11,13,18-19H,7-9H2,1-4H3/b6-5+,14-12-/t10?,11?,13-/m1/s1

> <INCHI_KEY>
DRDBTDHUTFJYHV-WSUZUZABSA-N

> <FORMULA>
C16H25NO4

> <MOLECULAR_WEIGHT>
295.379

> <EXACT_MASS>
295.178358289

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
46

> <JCHEM_AVERAGE_POLARIZABILITY>
32.82066430434697

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3Z,5R)-3-[(6E)-1-hydroxy-2-methyloct-6-en-1-ylidene]-5-(1-hydroxyethyl)-1-methylpyrrolidine-2,4-dione

> <ALOGPS_LOGP>
1.91

> <JCHEM_LOGP>
1.9603275396666664

> <ALOGPS_LOGS>
-2.25

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
10.40214606566389

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.10736811686038

> <JCHEM_PKA_STRONGEST_BASIC>
-0.7936249422382539

> <JCHEM_POLAR_SURFACE_AREA>
77.84

> <JCHEM_REFRACTIVITY>
83.34370000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.65e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3Z,5R)-3-[(6E)-1-hydroxy-2-methyloct-6-en-1-ylidene]-5-(1-hydroxyethyl)-1-methylpyrrolidine-2,4-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      -7.505  -4.874   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.498  -6.414   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.990  -8.293   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.134  -5.231   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -6.171  -4.104   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.837  -4.874   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.504  -4.104   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.170  -4.874   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.836  -4.104   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.498  -4.874   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.459  -8.132   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.165  -4.874   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.832  -6.725   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.831  -4.104   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.326  -6.405   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.572  -4.247   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       5.602  -5.392   0.000  0.00  0.00           N+0
HETATM   18  O   UNK     0       4.553  -9.378   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       1.831  -2.564   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       2.181  -7.436   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       4.892  -2.741   0.000  0.00  0.00           O+0
HETATM   22  H   UNK     0      -6.171  -2.564   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0      -4.837  -6.414   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0      -0.836  -5.644   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0       6.364  -6.886   0.000  0.00  0.00           H+0
HETATM   26  H   UNK     0       3.863  -7.922   0.000  0.00  0.00           H+0
CONECT    1    5                                                            
CONECT    2   10                                                            
CONECT    3   11                                                            
CONECT    4   17                                                            
CONECT    5    1    6   22                                                  
CONECT    6    5    7   23                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    2    9   14   24                                             
CONECT   11    3   13   18   25                                             
CONECT   12   14   15   16                                                  
CONECT   13   11   15   17   26                                             
CONECT   14   10   12   19                                                  
CONECT   15   12   13   20                                                  
CONECT   16   12   17   21                                                  
CONECT   17    4   13   16                                                  
CONECT   18   11                                                            
CONECT   19   14                                                            
CONECT   20   15                                                            
CONECT   21   16                                                            
CONECT   22    5                                                            
CONECT   23    6                                                            
CONECT   24   10                                                            
CONECT   25   11                                                            
CONECT   26   13                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   52    0
END

Synonyms

Not Available

Molecular Formula

C₁₆H₂₅NO₄

Average Mass

295.379

Monoisotopic Mass

295.178358289

IUPAC Name

(3Z,5R)-3-[(6E)-1-hydroxy-2-methyloct-6-en-1-ylidene]-5-(1-hydroxyethyl)-1-methylpyrrolidine-2,4-dione

Traditional Name

(3Z,5R)-3-[(6E)-1-hydroxy-2-methyloct-6-en-1-ylidene]-5-(1-hydroxyethyl)-1-methylpyrrolidine-2,4-dione

CAS Registry Number

Not Available

SMILES

[H]\C(C)=C(\[H])CCCC([H])(C)C(\O)=C1\C(=O)N(C)[C@@]([H])(C1=O)C([H])(C)O

InChI Identifier

InChI=1S/C16H25NO4/c1-5-6-7-8-9-10(2)14(19)12-15(20)13(11(3)18)17(4)16(12)21/h5-6,10-11,13,18-19H,7-9H2,1-4H3/b6-5+,14-12-/t10?,11?,13-/m1/s1

InChI Key

DRDBTDHUTFJYHV-WSUZUZABSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as n-alkylpyrrolidines. N-alkylpyrrolidines are compounds containing a pyrrolidine moiety that is substituted at the N1-position with an alkyl group. Pyrrolidine is a five-membered saturated aliphatic heterocycle with one nitrogen atom and four carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyrrolidines

Sub Class

N-alkylpyrrolidines

Direct Parent

N-alkylpyrrolidines

Alternative Parents

Substituents

Pyrrolidone
2-pyrrolidone
3-pyrrolidone
N-alkylpyrrolidine
Tertiary carboxylic acid amide
Vinylogous acid
Carboxamide group
Ketone
Lactam
Secondary alcohol
Cyclic ketone
Enol
Carboxylic acid derivative
Azacycle
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Carbonyl group
Alcohol
Organic oxide
Hydrocarbon derivative
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	1.65 g/L	ALOGPS
logP	1.91	ALOGPS
logP	1.96	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	5.11	ChemAxon
pKa (Strongest Basic)	-0.79	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	77.84 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	83.34 m³·mol⁻¹	ChemAxon
Polarizability	32.82 Å³	ChemAxon
Number of Rings	1	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 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

27023250

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

135550826

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 Penicillenol C2 (MMDBc0014447)

MOL for #<Metabolite:0x00007fecec8569a8>

3D MOL for #<Metabolite:0x00007fecec8569a8>

3D SDF for #<Metabolite:0x00007fecec8569a8>

3D-SDF for #<Metabolite:0x00007fecec8569a8>

PDB for #<Metabolite:0x00007fecec8569a8>

3D PDB for #<Metabolite:0x00007fecec8569a8>

SMILES for #<Metabolite:0x00007fecec8569a8>

INCHI for #<Metabolite:0x00007fecec8569a8>

Structure for #<Metabolite:0x00007fecec8569a8>

3D Structure for #<Metabolite:0x00007fecec8569a8>