MiMeDB: Showing metabocard for Brevianamide F (MMDBc0020318)

Xenobiotic

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 10:18:34 UTC

Update Date

2025-10-07 16:07:04 UTC

Metabolite ID

MMDBc0020318

Metabolite Identification

Common Name

Brevianamide F

Description

Brevianamide F is a diketopiperazine alkaloid, a class of compounds known for their diverse biological activities. Chemically, it is characterized by its unique cyclic structure, which contributes to its interaction with various biological pathways. Notably, Brevianamide F has been linked to a new biosynthetic gene cluster (BGC) through integrative analyses of LC-ESI(+)-HRMS/MS data, indicating its potential for novel metabolic functions (PMID:40182618 ). In biological studies, Brevianamide F has demonstrated significant antithrombotic effects by modulating the MAPK signaling pathway and the coagulation cascade. In a zebrafish thrombosis model, it was shown to reduce platelet aggregation, increase circulating platelet counts, enhance blood return to the heart, elevate heart rate, and restore caudal blood flow velocity (PMID:39452847 ). Transcriptome sequencing and RT-qPCR analyses further confirmed its role in these pathways (PMID:39452847 ). Additionally, Brevianamide F is part of a broader array of bioactive compounds synthesized by certain microorganisms, highlighting its potential in pharmaceutical applications (PMID:38344285 ). Its structural properties and biological interactions make Brevianamide F a compound of interest in both chemical and biological research contexts.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05041410132D          

 23 26  0  0  1  0            999 V2000
    5.2115   -1.3932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0185   -1.5647    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9565   -0.6086    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5705   -0.9516    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7079    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1760    1.1606    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4223    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5086    0.0045    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3155   -0.1670    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7280    0.5475    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4782   -0.8205    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  6  3  1  0  0  0  0
  7  3  1  0  0  0  0
 10  8  1  0  0  0  0
 10  9  2  0  0  0  0
 11  4  2  0  0  0  0
 11 10  1  0  0  0  0
 12  5  2  0  0  0  0
 12 11  1  0  0  0  0
 13  8  1  6  0  0  0
 14  6  1  0  0  0  0
 15 14  1  0  0  0  0
 16 13  1  0  0  0  0
 17  9  1  0  0  0  0
 17 12  1  0  0  0  0
 18 13  1  0  0  0  0
 18 15  2  0  0  0  0
 19  7  1  0  0  0  0
 19 14  1  0  0  0  0
 19 16  1  0  0  0  0
 20 15  1  0  0  0  0
 21 16  2  0  0  0  0
 13 22  1  1  0  0  0
 14 23  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0020318

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]12CCCN1C(=O)[C@]([H])(CC1=CNC3=CC=CC=C13)N=C2O

> <INCHI_IDENTIFIER>
InChI=1S/C16H17N3O2/c20-15-14-6-3-7-19(14)16(21)13(18-15)8-10-9-17-12-5-2-1-4-11(10)12/h1-2,4-5,9,13-14,17H,3,6-8H2,(H,18,20)/t13-,14-/m0/s1

> <INCHI_KEY>
RYFZBPVMVYTEKZ-KBPBESRZSA-N

> <FORMULA>
C16H17N3O2

> <MOLECULAR_WEIGHT>
283.3251

> <EXACT_MASS>
283.132076803

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
29.521915008095156

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3S,8aS)-1-hydroxy-3-(1H-indol-3-ylmethyl)-3H,4H,6H,7H,8H,8aH-pyrrolo[1,2-a]pyrazin-4-one

> <ALOGPS_LOGP>
1.48

> <JCHEM_LOGP>
1.7743200706666662

> <ALOGPS_LOGS>
-2.99

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
16.15248260428442

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.385837793110378

> <JCHEM_PKA_STRONGEST_BASIC>
1.384424460335783

> <JCHEM_POLAR_SURFACE_AREA>
68.69

> <JCHEM_REFRACTIVITY>
78.5111

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.90e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S,8aS)-1-hydroxy-3-(1H-indol-3-ylmethyl)-3H,6H,7H,8H,8aH-pyrrolo[1,2-a]pyrazin-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   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       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   18  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   19  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   20  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   22  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    2    4                                                       
CONECT    2    1    5                                                       
CONECT    3    6    7                                                       
CONECT    4    1   11                                                       
CONECT    5    2   12                                                       
CONECT    6    3   14                                                       
CONECT    7    3   19                                                       
CONECT    8   10   13                                                       
CONECT    9   10   17                                                       
CONECT   10    8    9   11                                                  
CONECT   11    4   10   12                                                  
CONECT   12    5   11   17                                                  
CONECT   13    8   16   18   22                                             
CONECT   14    6   15   19   23                                             
CONECT   15   14   18   20                                                  
CONECT   16   13   19   21                                                  
CONECT   17    9   12                                                       
CONECT   18   13   15                                                       
CONECT   19    7   14   16                                                  
CONECT   20   15                                                            
CONECT   21   16                                                            
CONECT   22   13                                                            
CONECT   23   14                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   52    0
END

Synonyms

Value	Source
Cyclo-(TRP-pro)	ChEBI
Cyclo-L-TRP-L-pro	ChEBI
Cyclo-L-tryptophanyl-L-proline	ChEBI
L-Prolyl-L-tryptophan anhydride	ChEBI
L-Tryptophyl-L-proline cyclic anhydride	ChEBI
Tryptophan-proline diketopiperazine	ChEBI
Cyclo(L-TRP-L-pro)	Kegg

Molecular Formula

C₁₆H₁₇N₃O₂

Average Mass

283.3251

Monoisotopic Mass

283.132076803

IUPAC Name

(3S,8aS)-1-hydroxy-3-(1H-indol-3-ylmethyl)-3H,4H,6H,7H,8H,8aH-pyrrolo[1,2-a]pyrazin-4-one

Traditional Name

(3S,8aS)-1-hydroxy-3-(1H-indol-3-ylmethyl)-3H,6H,7H,8H,8aH-pyrrolo[1,2-a]pyrazin-4-one

CAS Registry Number

Not Available

SMILES

[H][C@@]12CCCN1C(=O)[C@]([H])(CC1=CNC3=CC=CC=C13)N=C2O

InChI Identifier

InChI=1S/C16H17N3O2/c20-15-14-6-3-7-19(14)16(21)13(18-15)8-10-9-17-12-5-2-1-4-11(10)12/h1-2,4-5,9,13-14,17H,3,6-8H2,(H,18,20)/t13-,14-/m0/s1

InChI Key

RYFZBPVMVYTEKZ-KBPBESRZSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids and derivatives

Alternative Parents

Substituents

Alpha-amino acid or derivatives
3-alkylindole
Indole
Indole or derivatives
Dioxopiperazine
2,5-dioxopiperazine
N-alkylpiperazine
1,4-diazinane
Piperazine
Benzenoid
Substituted pyrrole
Heteroaromatic compound
Pyrrole
Tertiary carboxylic acid amide
Pyrrolidine
Carboxamide group
Lactam
Secondary carboxylic acid amide
Azacycle
Organoheterocyclic compound
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Carbonyl group
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

indoles (CHEBI:64530 )
dipeptide (CHEBI:64530 )
pyrrolopyrazine (CHEBI:64530 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.29 g/L	ALOGPS
logP	1.48	ALOGPS
logP	1.77	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	6.39	ChemAxon
pKa (Strongest Basic)	1.38	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	68.69 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	78.51 m³·mol⁻¹	ChemAxon
Polarizability	29.52 Å³	ChemAxon
Number of Rings	4	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

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	12	Human feces; Human sputum; Human	Metabolic reconstruction; Microbial culture
Bacteria/Eubacteria	Firmicutes	1	Human	Microbial culture
Bacteria	Actinobacteria	2		Microbial culture

Exposure Sources

Other Exposures

Source Type	Data Source	Reference
Cosmetics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox

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

Not Available

KEGG Compound ID

C20563

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Brevianamide F

METLIN ID

Not Available

PubChem Compound

181567

PDB ID

Not Available

ChEBI ID

64530

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

RYFZBPVMVYTEKZ-KBPBESRZSA-N

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for Brevianamide F (MMDBc0020318)

MOL for #<Metabolite:0x00007f8de8e0f3f8>

3D MOL for #<Metabolite:0x00007f8de8e0f3f8>

3D SDF for #<Metabolite:0x00007f8de8e0f3f8>

3D-SDF for #<Metabolite:0x00007f8de8e0f3f8>

PDB for #<Metabolite:0x00007f8de8e0f3f8>

3D PDB for #<Metabolite:0x00007f8de8e0f3f8>

SMILES for #<Metabolite:0x00007f8de8e0f3f8>

INCHI for #<Metabolite:0x00007f8de8e0f3f8>

Structure for #<Metabolite:0x00007f8de8e0f3f8>

3D Structure for #<Metabolite:0x00007f8de8e0f3f8>