MiMeDB: Showing metabocard for Penidiamide (MMDBc0010190)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 02:26:58 UTC

Update Date

2025-10-07 16:05:42 UTC

Metabolite ID

MMDBc0010190

Metabolite Identification

Common Name

Penidiamide

Description

Penidiamide is a metabolite belonging to the class of tripetides. It consists of dehydrotryptamine, glycine, and anthranilic acid linked by two amide bonds, along with an oxindole moiety. This compound was isolated from submerged cultures of Penicillium sp. using preparative chromatography (PMID:38814060 ). The structure of penidiamide was elucidated through spectroscopic methods, confirming its unique composition (PMID:9528122 ). In terms of biological activity, penidiamide exhibits preferential inhibition of human synovial phospholipase A2, with an IC50 value of 30 microM, while oxindole shows a significantly higher IC50 of 380 microM (PMID:9528122 ). Although penidiamide demonstrates weak antibacterial activity, no antimicrobial activity was detected for oxindole (PMID:9528122 ). This highlights penidiamide's potential relevance in biochemical pathways, particularly concerning phospholipase inhibition, while also indicating limited antibacterial properties.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152104262D          

 27 29  0  0  0  0            999 V2000
   -4.7650   -1.1298    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0200   -1.9144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9580   -0.9583    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4679   -2.5275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768   -0.1006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2400   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4060   -1.5714    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6610   -2.3560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9851   -1.0568    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5990   -1.3998    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1089   -2.9691    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1781   -0.8853    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0470   -2.0129    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5371   -0.4437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3441   -0.6152    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4358   -0.5422    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4752    0.5124    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  2  0  0  0  0
  4  2  2  0  0  0  0
  5  2  1  0  0  0  0
  6  1  1  0  0  0  0
  7  3  1  0  0  0  0
  8  4  1  0  0  0  0
 10  9  2  0  0  0  0
 13  9  1  0  0  0  0
 13 11  2  0  0  0  0
 14  5  2  0  0  0  0
 14 13  1  0  0  0  0
 15  6  2  0  0  0  0
 16  7  2  0  0  0  0
 16 15  1  0  0  0  0
 17  8  2  0  0  0  0
 17 14  1  0  0  0  0
 18 12  1  0  0  0  0
 19 15  1  0  0  0  0
 20 16  1  0  0  0  0
 21 10  1  4  0  0  0
 21 18  2  0  0  0  0
 22 11  1  0  0  0  0
 22 17  1  0  0  0  0
 23 12  1  4  0  0  0
 23 19  2  0  0  0  0
 24 18  1  0  0  0  0
 25 19  1  0  0  0  0
 26  9  1  0  0  0  0
 27 10  1  0  0  0  0
M  END


  Mrv1652305152104262D          

 27 29  0  0  0  0            999 V2000
   -4.7650   -1.1298    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0200   -1.9144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9580   -0.9583    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4679   -2.5275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768   -0.1006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2400   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4060   -1.5714    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6610   -2.3560    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9851   -1.0568    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5990   -1.3998    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1089   -2.9691    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1781   -0.8853    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0470   -2.0129    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5371   -0.4437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3441   -0.6152    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4358   -0.5422    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4752    0.5124    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  2  0  0  0  0
  4  2  2  0  0  0  0
  5  2  1  0  0  0  0
  6  1  1  0  0  0  0
  7  3  1  0  0  0  0
  8  4  1  0  0  0  0
 10  9  2  0  0  0  0
 13  9  1  0  0  0  0
 13 11  2  0  0  0  0
 14  5  2  0  0  0  0
 14 13  1  0  0  0  0
 15  6  2  0  0  0  0
 16  7  2  0  0  0  0
 16 15  1  0  0  0  0
 17  8  2  0  0  0  0
 17 14  1  0  0  0  0
 18 12  1  0  0  0  0
 19 15  1  0  0  0  0
 20 16  1  0  0  0  0
 21 10  1  4  0  0  0
 21 18  2  0  0  0  0
 22 11  1  0  0  0  0
 22 17  1  0  0  0  0
 23 12  1  4  0  0  0
 23 19  2  0  0  0  0
 24 18  1  0  0  0  0
 25 19  1  0  0  0  0
 26  9  1  0  0  0  0
 27 10  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0010190

> <DATABASE_NAME>
MIME

> <SMILES>
[H]\C(N=C(O)CN=C(O)C1=CC=CC=C1N)=C(\[H])C1=CNC2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C19H18N4O2/c20-16-7-3-1-6-15(16)19(25)23-12-18(24)21-10-9-13-11-22-17-8-4-2-5-14(13)17/h1-11,22H,12,20H2,(H,21,24)(H,23,25)/b10-9+

> <INCHI_KEY>
DCQDGRBMXXRGIN-MDZDMXLPSA-N

> <FORMULA>
C19H18N4O2

> <MOLECULAR_WEIGHT>
334.379

> <EXACT_MASS>
334.142975836

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
43

> <JCHEM_AVERAGE_POLARIZABILITY>
35.48101471689031

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-{[(2-aminophenyl)(hydroxy)methylidene]amino}-N-[(E)-2-(1H-indol-3-yl)ethenyl]ethanimidic acid

> <ALOGPS_LOGP>
2.50

> <JCHEM_LOGP>
0.3134415839435755

> <ALOGPS_LOGS>
-4.66

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
8.922335987664093

> <JCHEM_PKA_STRONGEST_ACIDIC>
-3.8755207745903872

> <JCHEM_PKA_STRONGEST_BASIC>
11.51382139885487

> <JCHEM_POLAR_SURFACE_AREA>
106.99000000000001

> <JCHEM_REFRACTIVITY>
99.12759999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.31e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-{[(2-aminophenyl)(hydroxy)methylidene]amino}-N-[(E)-2-(1H-indol-3-yl)ethenyl]ethanimidic acid

> <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      -8.895  -2.109   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -9.371  -3.574   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -7.388  -1.789   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -8.340  -4.718   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.650   0.132   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.143  -0.188   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.315  -3.437   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.126   1.597   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -6.358  -2.933   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -6.834  -4.398   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -1.839  -1.973   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -4.852  -2.613   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0      -5.803  -5.542   0.000  0.00  0.00           N+0
HETATM   21  N   UNK     0      -0.333  -1.652   0.000  0.00  0.00           N+0
HETATM   22  N   UNK     0       2.126   4.089   0.000  0.00  0.00           N+0
HETATM   23  N   UNK     0      -3.821  -3.757   0.000  0.00  0.00           N+0
HETATM   24  O   UNK     0      -2.869  -0.828   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      -4.376  -1.148   0.000  0.00  0.00           O+0
HETATM   26  H   UNK     0       2.680  -1.012   0.000  0.00  0.00           H+0
HETATM   27  H   UNK     0      -0.887   0.957   0.000  0.00  0.00           H+0
CONECT    1    3    6                                                       
CONECT    2    4    5                                                       
CONECT    3    1    7                                                       
CONECT    4    2    8                                                       
CONECT    5    2   14                                                       
CONECT    6    1   15                                                       
CONECT    7    3   16                                                       
CONECT    8    4   17                                                       
CONECT    9   10   13   26                                                  
CONECT   10    9   21   27                                                  
CONECT   11   13   22                                                       
CONECT   12   18   23                                                       
CONECT   13    9   11   14                                                  
CONECT   14    5   13   17                                                  
CONECT   15    6   16   19                                                  
CONECT   16    7   15   20                                                  
CONECT   17    8   14   22                                                  
CONECT   18   12   21   24                                                  
CONECT   19   15   23   25                                                  
CONECT   20   16                                                            
CONECT   21   10   18                                                       
CONECT   22   11   17                                                       
CONECT   23   12   19                                                       
CONECT   24   18                                                            
CONECT   25   19                                                            
CONECT   26    9                                                            
CONECT   27   10                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   58    0
END

Synonyms

Not Available

Molecular Formula

C₁₉H₁₈N₄O₂

Average Mass

334.379

Monoisotopic Mass

334.142975836

IUPAC Name

2-{[(2-aminophenyl)(hydroxy)methylidene]amino}-N-[(E)-2-(1H-indol-3-yl)ethenyl]ethanimidic acid

Traditional Name

2-{[(2-aminophenyl)(hydroxy)methylidene]amino}-N-[(E)-2-(1H-indol-3-yl)ethenyl]ethanimidic acid

CAS Registry Number

Not Available

SMILES

[H]\C(N=C(O)CN=C(O)C1=CC=CC=C1N)=C(\[H])C1=CNC2=CC=CC=C12

InChI Identifier

InChI=1S/C19H18N4O2/c20-16-7-3-1-6-15(16)19(25)23-12-18(24)21-10-9-13-11-22-17-8-4-2-5-14(13)17/h1-11,22H,12,20H2,(H,21,24)(H,23,25)/b10-9+

InChI Key

DCQDGRBMXXRGIN-MDZDMXLPSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hippuric acids and derivatives. Hippuric acids and derivatives are compounds containing a hippuric acid or a derivative, with a structure characterized the presence of a benzoyl group linked to the N-terminal of a glycine.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Benzoic acids and derivatives

Direct Parent

Hippuric acids and derivatives

Alternative Parents

Substituents

Hippuric acid or derivatives
N-acyl-alpha amino acid or derivatives
Alpha-amino acid amide
Anthranilamide
N-substituted-alpha-amino acid
Alpha-amino acid or derivatives
Aminobenzamide
Aminobenzoic acid or derivatives
2-aminobenzamide
Indole
Indole or derivatives
Benzoyl
Aniline or substituted anilines
Substituted pyrrole
Pyrrole
Heteroaromatic compound
Vinylogous amide
Secondary carboxylic acid amide
Amino acid or derivatives
Carboxamide group
Azacycle
Carboxylic acid derivative
Organoheterocyclic compound
Organic oxide
Carbonyl group
Organic nitrogen compound
Organooxygen compound
Hydrocarbon derivative
Primary amine
Amine
Organic oxygen compound
Organonitrogen 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	0.0073 g/L	ALOGPS
logP	2.5	ALOGPS
logP	0.31	ChemAxon
logS	-4.7	ALOGPS
pKa (Strongest Acidic)	-3.9	ChemAxon
pKa (Strongest Basic)	11.51	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	106.99 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	99.13 m³·mol⁻¹	ChemAxon
Polarizability	35.48 Å³	ChemAxon
Number of Rings	3	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

Microbial Pathways

Pathways

This table shows at most 5 pathways. For the full list of associated pathways:

See All Associated Bacterial Pathways

Name	SMPDB/PathBank

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

8624961

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10449544

PDB ID

Not Available

ChEBI ID

Not Available

CMMC Knowledgebase

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 Penidiamide (MMDBc0010190)

MOL for #<Metabolite:0x00007fd448d01c08>

3D MOL for #<Metabolite:0x00007fd448d01c08>

3D SDF for #<Metabolite:0x00007fd448d01c08>

3D-SDF for #<Metabolite:0x00007fd448d01c08>

PDB for #<Metabolite:0x00007fd448d01c08>

3D PDB for #<Metabolite:0x00007fd448d01c08>

SMILES for #<Metabolite:0x00007fd448d01c08>

INCHI for #<Metabolite:0x00007fd448d01c08>

Structure for #<Metabolite:0x00007fd448d01c08>

3D Structure for #<Metabolite:0x00007fd448d01c08>