MiMeDB: Showing metabocard for Penicamedine A (MMDBc0014485)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 05:30:48 UTC

Update Date

2025-10-07 16:06:17 UTC

Metabolite ID

MMDBc0014485

Metabolite Identification

Common Name

Penicamedine A

Description

Penicamedine A is a highly oxygenated hexacyclic indole alkaloid, a chemical class known for its diverse biological activities and structural complexity. Isolated from the culture broth of the fungus Penicillium camemberti, penicamedine A features a rare furan ring within its structure, which contributes to its unique chemical properties (PMID:26460559 ). This compound was identified alongside two known analogs, iso-α-cyclopiazonic acid and cyclopiazonic acid, highlighting its potential significance in the biosynthetic pathways of secondary metabolites produced by fungi (PMID:26460559 ). The structural intricacies of penicamedine A suggest possible interactions with biological systems, although further research is needed to elucidate its specific biological roles and potential applications in pharmacology. The discovery of such metabolites underscores the importance of fungal species like Penicillium camemberti in the search for novel bioactive compounds that may have therapeutic implications.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152107302D          

 32 37  0  0  1  0            999 V2000
   -0.8153    2.5216    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9639    0.4347    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9098    0.7049    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9689    4.8214    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2368    2.4548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7136    1.8026    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9346    3.2261    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2453    1.2963    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3333    3.1912    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8647    1.8925    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4086    1.4586    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.1132    3.3451    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5844    2.6912    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2990    2.2723    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8930    3.8146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3102    2.2829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5908    1.1705    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7685    2.9664    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4876    3.1085    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5300    2.4338    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3257    3.2116    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6766    4.0499    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0210    1.8069    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6721    3.9433    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2686    4.3538    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4546    1.9735    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4785    3.9335    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7236    2.6078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1134    4.0088    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1032    3.5386    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4693    0.6359    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1022    2.0839    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  2  0  0  0  0
  7  5  1  0  0  0  0
  9  1  1  0  0  0  0
 10  6  1  0  0  0  0
 10  8  1  0  0  0  0
 11  8  1  0  0  0  0
 12  7  2  0  0  0  0
 13 10  2  0  0  0  0
 13 12  1  0  0  0  0
 14 11  1  0  0  0  0
 17  2  1  0  0  0  0
 17  3  1  0  0  0  0
 17 11  1  0  0  0  0
 18 13  1  0  0  0  0
 18 14  1  0  0  0  0
 18 15  1  0  0  0  0
 19  9  1  6  0  0  0
 19 16  1  0  0  0  0
 20 14  1  0  0  0  0
 21 19  1  0  0  0  0
 21 20  1  0  0  0  0
 22  4  1  0  0  0  0
 22 12  1  0  0  0  0
 22 15  1  0  0  0  0
 23 16  1  0  0  0  0
 23 17  1  0  0  0  0
 23 20  1  0  0  0  0
 24  9  2  0  0  0  0
 25 15  2  0  0  0  0
 26 16  2  0  0  0  0
 19 27  1  1  0  0  0
 20 28  1  6  0  0  0
 21 29  1  6  0  0  0
 18 30  1  1  0  0  0
 30 21  1  0  0  0  0
 11 31  1  6  0  0  0
 14 32  1  6  0  0  0
M  END


  Mrv1652305152107302D          

 32 37  0  0  1  0            999 V2000
   -0.8153    2.5216    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9639    0.4347    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9098    0.7049    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9689    4.8214    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2368    2.4548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7136    1.8026    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9346    3.2261    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2453    1.2963    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3333    3.1912    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8647    1.8925    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4086    1.4586    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.1132    3.3451    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5844    2.6912    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2990    2.2723    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8930    3.8146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3102    2.2829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5908    1.1705    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7685    2.9664    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4876    3.1085    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5300    2.4338    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3257    3.2116    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6766    4.0499    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0210    1.8069    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6721    3.9433    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2686    4.3538    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4546    1.9735    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4785    3.9335    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7236    2.6078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1134    4.0088    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1032    3.5386    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4693    0.6359    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1022    2.0839    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  2  0  0  0  0
  7  5  1  0  0  0  0
  9  1  1  0  0  0  0
 10  6  1  0  0  0  0
 10  8  1  0  0  0  0
 11  8  1  0  0  0  0
 12  7  2  0  0  0  0
 13 10  2  0  0  0  0
 13 12  1  0  0  0  0
 14 11  1  0  0  0  0
 17  2  1  0  0  0  0
 17  3  1  0  0  0  0
 17 11  1  0  0  0  0
 18 13  1  0  0  0  0
 18 14  1  0  0  0  0
 18 15  1  0  0  0  0
 19  9  1  6  0  0  0
 19 16  1  0  0  0  0
 20 14  1  0  0  0  0
 21 19  1  0  0  0  0
 21 20  1  0  0  0  0
 22  4  1  0  0  0  0
 22 12  1  0  0  0  0
 22 15  1  0  0  0  0
 23 16  1  0  0  0  0
 23 17  1  0  0  0  0
 23 20  1  0  0  0  0
 24  9  2  0  0  0  0
 25 15  2  0  0  0  0
 26 16  2  0  0  0  0
 19 27  1  1  0  0  0
 20 28  1  6  0  0  0
 21 29  1  6  0  0  0
 18 30  1  1  0  0  0
 30 21  1  0  0  0  0
 11 31  1  6  0  0  0
 14 32  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0014485

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]12CC3=C4C(=CC=C3)N(C)C(=O)[C@]43O[C@@]4(O)[C@](O)(N(C(=O)[C@]4(O)C(C)=O)C1(C)C)[C@]23[H]

> <INCHI_IDENTIFIER>
InChI=1S/C21H22N2O7/c1-9(24)19(27)16(26)23-17(2,3)11-8-10-6-5-7-12-13(10)18(15(25)22(12)4)14(11)20(23,28)21(19,29)30-18/h5-7,11,14,27-29H,8H2,1-4H3/t11-,14-,18+,19-,20+,21-/m1/s1

> <INCHI_KEY>
QLOOWQVCXQPADP-UMHNQWNOSA-N

> <FORMULA>
C21H22N2O7

> <MOLECULAR_WEIGHT>
414.414

> <EXACT_MASS>
414.142701056

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
52

> <JCHEM_AVERAGE_POLARIZABILITY>
40.539480998185724

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,2R,3S,4R,5S,9R)-5-acetyl-3,4,5-trihydroxy-8,8,16-trimethyl-19-oxa-7,16-diazahexacyclo[9.6.1.1^{1,4}.0^{2,9}.0^{3,7}.0^{15,18}]nonadeca-11(18),12,14-triene-6,17-dione

> <ALOGPS_LOGP>
0.23

> <JCHEM_LOGP>
0.0035241466666673382

> <ALOGPS_LOGS>
-1.84

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.285971063984375

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.935505138439085

> <JCHEM_PKA_STRONGEST_BASIC>
-4.5255037419688495

> <JCHEM_POLAR_SURFACE_AREA>
127.61000000000001

> <JCHEM_REFRACTIVITY>
100.0903

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.06e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,3S,4R,5S,9R)-5-acetyl-3,4,5-trihydroxy-8,8,16-trimethyl-19-oxa-7,16-diazahexacyclo[9.6.1.1^{1,4}.0^{2,9}.0^{3,7}.0^{15,18}]nonadeca-11(18),12,14-triene-6,17-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      -1.522   4.707   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.666   0.811   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.698   1.316   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.409   9.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.775   4.582   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.799   3.365   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.211   6.022   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.058   2.420   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.622   5.957   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.214   3.533   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.496   2.723   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.678   6.244   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.691   5.024   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.292   4.242   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.400   7.121   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.579   4.261   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.970   2.185   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.168   5.537   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.910   5.803   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.856   4.543   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.475   5.995   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0       6.863   7.560   0.000  0.00  0.00           N+0
HETATM   23  N   UNK     0       1.906   3.373   0.000  0.00  0.00           N+0
HETATM   24  O   UNK     0      -1.255   7.361   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       4.235   8.127   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -0.849   3.684   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       0.893   7.342   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       1.351   4.868   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       2.078   7.483   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       3.926   6.605   0.000  0.00  0.00           O+0
HETATM   31  H   UNK     0       4.609   1.187   0.000  0.00  0.00           H+0
HETATM   32  H   UNK     0       5.791   3.890   0.000  0.00  0.00           H+0
CONECT    1    9                                                            
CONECT    2   17                                                            
CONECT    3   17                                                            
CONECT    4   22                                                            
CONECT    5    6    7                                                       
CONECT    6    5   10                                                       
CONECT    7    5   12                                                       
CONECT    8   10   11                                                       
CONECT    9    1   19   24                                                  
CONECT   10    6    8   13                                                  
CONECT   11    8   14   17   31                                             
CONECT   12    7   13   22                                                  
CONECT   13   10   12   18                                                  
CONECT   14   11   18   20   32                                             
CONECT   15   18   22   25                                                  
CONECT   16   19   23   26                                                  
CONECT   17    2    3   11   23                                             
CONECT   18   13   14   15   30                                             
CONECT   19    9   16   21   27                                             
CONECT   20   14   21   23   28                                             
CONECT   21   19   20   29   30                                             
CONECT   22    4   12   15                                                  
CONECT   23   16   17   20                                                  
CONECT   24    9                                                            
CONECT   25   15                                                            
CONECT   26   16                                                            
CONECT   27   19                                                            
CONECT   28   20                                                            
CONECT   29   21                                                            
CONECT   30   18   21                                                       
CONECT   31   11                                                            
CONECT   32   14                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   74    0
END

Synonyms

Not Available

Molecular Formula

C₂₁H₂₂N₂O₇

Average Mass

414.414

Monoisotopic Mass

414.142701056

IUPAC Name

(1R,2R,3S,4R,5S,9R)-5-acetyl-3,4,5-trihydroxy-8,8,16-trimethyl-19-oxa-7,16-diazahexacyclo[9.6.1.1^{1,4}.0^{2,9}.0^{3,7}.0^{15,18}]nonadeca-11(18),12,14-triene-6,17-dione

Traditional Name

(1R,2R,3S,4R,5S,9R)-5-acetyl-3,4,5-trihydroxy-8,8,16-trimethyl-19-oxa-7,16-diazahexacyclo[9.6.1.1^{1,4}.0^{2,9}.0^{3,7}.0^{15,18}]nonadeca-11(18),12,14-triene-6,17-dione

CAS Registry Number

Not Available

SMILES

[H][C@]12CC3=C4C(=CC=C3)N(C)C(=O)[C@]43O[C@@]4(O)[C@](O)(N(C(=O)[C@]4(O)C(C)=O)C1(C)C)[C@]23[H]

InChI Identifier

InChI=1S/C21H22N2O7/c1-9(24)19(27)16(26)23-17(2,3)11-8-10-6-5-7-12-13(10)18(15(25)22(12)4)14(11)20(23,28)21(19,29)30-18/h5-7,11,14,27-29H,8H2,1-4H3/t11-,14-,18+,19-,20+,21-/m1/s1

InChI Key

QLOOWQVCXQPADP-UMHNQWNOSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as naphthofurans. Naphthofurans are compounds containing a furan ring fused to a naphthalene moiety. Furan is a 5 membered- ring aromatic ring with four carbon and one oxygen atoms. Naphthalene is a polycyclic aromatic hydrocarbon made up of two fused benzene rings.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Naphthofurans

Sub Class

Not Available

Direct Parent

Naphthofurans

Alternative Parents

Substituents

Naphthofuran
Tetralin
Isoindolone
Pyrrolizidinone
Isoindole or derivatives
Isoindoline
Indole or derivatives
Pyrrolizidine
Benzenoid
N-alkylpyrrolidine
2-pyrrolidone
Pyrrolidone
Tetrahydrofuran
Tertiary carboxylic acid amide
Tertiary alcohol
Pyrrolidine
Alpha-hydroxy ketone
Lactam
Ketone
Hemiacetal
Carboxamide group
Oxacycle
Azacycle
Polyol
Carboxylic acid derivative
Alkanolamine
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	6.06 g/L	ALOGPS
logP	0.23	ALOGPS
logP	0.0035	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	8.94	ChemAxon
pKa (Strongest Basic)	-4.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	127.61 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	100.09 m³·mol⁻¹	ChemAxon
Polarizability	40.54 Å³	ChemAxon
Number of Rings	6	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_3_4) - 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
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	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

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-23	308.0
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	105.3
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-23	285.3
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	417.8
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	276.0
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-23	173.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	1618.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (void)	2025-10-23	134.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	309.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	223.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	237.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	147.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	118.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	102.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	245.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	57.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	247.8
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	1150.1
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	726.8

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	Penicamedine A_TMS_1	CC(=O)[C@@]1(O)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O[Si](C)(C)C)[C@@]2(O)[C@H]34)C(=O)N5C	standard non polar	2025-10-23	1874.24
Gas Chromatography	Penicamedine A_TMS_2	CC(=O)[C@@]1(O)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O)[C@@]2(O[Si](C)(C)C)[C@H]34)C(=O)N5C	standard non polar	2025-10-23	2099.61
Gas Chromatography	Penicamedine A_TMS_3	CC(=O)[C@@]1(O[Si](C)(C)C)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O)[C@@]2(O)[C@H]34)C(=O)N5C	standard non polar	2025-10-23	1710.6
Gas Chromatography	Penicamedine A_TMS_4	C=C(O[Si](C)(C)C)[C@@]1(O)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O)[C@@]2(O)[C@H]34)C(=O)N5C	standard non polar	2025-10-23	2667.73
Gas Chromatography	Penicamedine A_TMS_5	CC(=O)[C@@]1(O[Si](C)(C)C)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O[Si](C)(C)C)[C@@]2(O)[C@H]34)C(=O)N5C	standard non polar	2025-10-23	1861.13
Gas Chromatography	Penicamedine A_TMS_6	CC(=O)[C@@]1(O)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O[Si](C)(C)C)[C@@]2(O[Si](C)(C)C)[C@H]34)C(=O)N5C	standard non polar	2025-10-23	2975.04
Gas Chromatography	Penicamedine A_TMS_7	C=C(O[Si](C)(C)C)[C@@]1(O)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O[Si](C)(C)C)[C@@]2(O)[C@H]34)C(=O)N5C	standard non polar	2025-10-23	2534.94
Gas Chromatography	Penicamedine A_TMS_8	CC(=O)[C@@]1(O[Si](C)(C)C)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O)[C@@]2(O[Si](C)(C)C)[C@H]34)C(=O)N5C	standard non polar	2025-10-23	1426.28
Gas Chromatography	Penicamedine A_TMS_9	C=C(O[Si](C)(C)C)[C@@]1(O)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O)[C@@]2(O[Si](C)(C)C)[C@H]34)C(=O)N5C	standard non polar	2025-10-23	2887.57
Gas Chromatography	Penicamedine A_TMS_10	C=C(O[Si](C)(C)C)[C@@]1(O[Si](C)(C)C)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O)[C@@]2(O)[C@H]34)C(=O)N5C	standard non polar	2025-10-23	3240.47
Gas Chromatography	Penicamedine A_TMS_11	CC(=O)[C@@]1(O[Si](C)(C)C)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O[Si](C)(C)C)[C@@]2(O[Si](C)(C)C)[C@H]34)C(=O)N5C	standard non polar	2025-10-23	2885.11
Gas Chromatography	Penicamedine A_TMS_12	C=C(O[Si](C)(C)C)[C@@]1(O[Si](C)(C)C)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O[Si](C)(C)C)[C@@]2(O)[C@H]34)C(=O)N5C	standard non polar	2025-10-23	2344.46
Gas Chromatography	Penicamedine A_TMS_13	C=C(O[Si](C)(C)C)[C@@]1(O)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O[Si](C)(C)C)[C@@]2(O[Si](C)(C)C)[C@H]34)C(=O)N5C	standard non polar	2025-10-23	2267.87
Gas Chromatography	Penicamedine A_TMS_14	C=C(O[Si](C)(C)C)[C@@]1(O[Si](C)(C)C)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O)[C@@]2(O[Si](C)(C)C)[C@H]34)C(=O)N5C	standard non polar	2025-10-23	3731.71
Gas Chromatography	Penicamedine A_TMS_15	C=C(O[Si](C)(C)C)[C@@]1(O[Si](C)(C)C)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O[Si](C)(C)C)[C@@]2(O[Si](C)(C)C)[C@H]34)C(=O)N5C	standard non polar	2025-10-23	1889.47
Gas Chromatography	Penicamedine A_TMS_1	CC(=O)[C@@]1(O)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O[Si](C)(C)C)[C@@]2(O)[C@H]34)C(=O)N5C	standard polar	2025-10-23	2640.86
Gas Chromatography	Penicamedine A_TMS_2	CC(=O)[C@@]1(O)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O)[C@@]2(O[Si](C)(C)C)[C@H]34)C(=O)N5C	standard polar	2025-10-23	1484.84
Gas Chromatography	Penicamedine A_TMS_3	CC(=O)[C@@]1(O[Si](C)(C)C)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O)[C@@]2(O)[C@H]34)C(=O)N5C	standard polar	2025-10-23	2159.45
Gas Chromatography	Penicamedine A_TMS_4	C=C(O[Si](C)(C)C)[C@@]1(O)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O)[C@@]2(O)[C@H]34)C(=O)N5C	standard polar	2025-10-23	1616.25
Gas Chromatography	Penicamedine A_TMS_5	CC(=O)[C@@]1(O[Si](C)(C)C)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O[Si](C)(C)C)[C@@]2(O)[C@H]34)C(=O)N5C	standard polar	2025-10-23	-118.345
Gas Chromatography	Penicamedine A_TMS_6	CC(=O)[C@@]1(O)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O[Si](C)(C)C)[C@@]2(O[Si](C)(C)C)[C@H]34)C(=O)N5C	standard polar	2025-10-23	2224.61
Gas Chromatography	Penicamedine A_TMS_7	C=C(O[Si](C)(C)C)[C@@]1(O)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O[Si](C)(C)C)[C@@]2(O)[C@H]34)C(=O)N5C	standard polar	2025-10-23	2811.5
Gas Chromatography	Penicamedine A_TMS_8	CC(=O)[C@@]1(O[Si](C)(C)C)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O)[C@@]2(O[Si](C)(C)C)[C@H]34)C(=O)N5C	standard polar	2025-10-23	1754.17
Gas Chromatography	Penicamedine A_TMS_9	C=C(O[Si](C)(C)C)[C@@]1(O)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O)[C@@]2(O[Si](C)(C)C)[C@H]34)C(=O)N5C	standard polar	2025-10-23	1968.26
Gas Chromatography	Penicamedine A_TMS_10	C=C(O[Si](C)(C)C)[C@@]1(O[Si](C)(C)C)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O)[C@@]2(O)[C@H]34)C(=O)N5C	standard polar	2025-10-23	2467.91
Gas Chromatography	Penicamedine A_TMS_11	CC(=O)[C@@]1(O[Si](C)(C)C)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O[Si](C)(C)C)[C@@]2(O[Si](C)(C)C)[C@H]34)C(=O)N5C	standard polar	2025-10-23	2138.08
Gas Chromatography	Penicamedine A_TMS_12	C=C(O[Si](C)(C)C)[C@@]1(O[Si](C)(C)C)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O[Si](C)(C)C)[C@@]2(O)[C@H]34)C(=O)N5C	standard polar	2025-10-23	2811.54
Gas Chromatography	Penicamedine A_TMS_13	C=C(O[Si](C)(C)C)[C@@]1(O)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O[Si](C)(C)C)[C@@]2(O[Si](C)(C)C)[C@H]34)C(=O)N5C	standard polar	2025-10-23	3181.68
Gas Chromatography	Penicamedine A_TMS_14	C=C(O[Si](C)(C)C)[C@@]1(O[Si](C)(C)C)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O)[C@@]2(O[Si](C)(C)C)[C@H]34)C(=O)N5C	standard polar	2025-10-23	2876.41
Gas Chromatography	Penicamedine A_TMS_15	C=C(O[Si](C)(C)C)[C@@]1(O[Si](C)(C)C)C(=O)N2C(C)(C)[C@@H]3CC4=CC=CC5=C4[C@@]4(O[C@@]1(O[Si](C)(C)C)[C@@]2(O[Si](C)(C)C)[C@H]34)C(=O)N5C	standard polar	2025-10-23	2155.38

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

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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

Other Exposures

Source Type	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

34982091

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139587045

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 Penicamedine A (MMDBc0014485)

MOL for #<Metabolite:0x00007fc951295e88>

3D MOL for #<Metabolite:0x00007fc951295e88>

3D SDF for #<Metabolite:0x00007fc951295e88>

3D-SDF for #<Metabolite:0x00007fc951295e88>

PDB for #<Metabolite:0x00007fc951295e88>

3D PDB for #<Metabolite:0x00007fc951295e88>

SMILES for #<Metabolite:0x00007fc951295e88>

INCHI for #<Metabolite:0x00007fc951295e88>

Structure for #<Metabolite:0x00007fc951295e88>

3D Structure for #<Metabolite:0x00007fc951295e88>