MiMeDB: Showing metabocard for Limazepine A (MMDBc0007978)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 00:57:53 UTC

Update Date

2025-10-07 16:05:24 UTC

Metabolite ID

MMDBc0007978

Metabolite Identification

Common Name

Limazepine A

Description

Limazepine A is a secondary metabolite belonging to the class of phenazine derivatives. It has been identified in various biological contexts, suggesting its potential role in microbial ecology and interactions. The biosynthetic pathways of limazepine A exhibit notable similarities to those of phenazine compounds, indicating tight evolutionary links between these groups and highlighting the importance of secondary metabolites in evolutionary biology (PMID:29773836 ). Furthermore, limazepine A has been characterized alongside other known metabolites, such as cyclo(D)-Pro-(D)-Val and cyclo(D)-Pro-(D)-Leu, which underscores its relevance in the study of microbial secondary metabolism (PMID:24423655 ). The exploration of limazepine A and its biosynthetic origins may provide insights into its ecological functions and potential applications in biotechnology or medicine.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152102572D          

 22 24  0  0  1  0            999 V2000
   -0.5455    0.6537    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8397    3.1114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3111    1.4448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9194    0.9948    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7050    1.2468    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8068    2.3995    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1184    1.1015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4911    1.6373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3084    1.5491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6293    2.3347    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.8795    2.0531    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4829    2.3555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2685    2.6074    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1364    2.9855    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5691    1.1829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9614    2.9947    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8219    1.5325    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4431    3.4137    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7702    3.7247    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5783    0.3580    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6651    2.3051    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4356    2.1602    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  5  4  2  0  0  0  0
  8  3  1  0  0  0  0
  8  6  1  0  0  0  0
  8  7  2  0  0  0  0
  9  4  1  0  0  0  0
 10  6  1  0  0  0  0
 11  5  1  0  0  0  0
 12  9  2  0  0  0  0
 13 11  2  0  0  0  0
 13 12  1  0  0  0  0
 14 10  1  0  0  0  0
 15  9  1  0  0  0  0
 16 12  1  0  0  0  0
 16 14  2  0  0  0  0
 17  7  1  0  0  0  0
 17 10  1  0  0  0  0
 17 15  1  0  0  0  0
 18 13  1  0  0  0  0
 19 14  1  0  0  0  0
 20 15  2  0  0  0  0
 21  2  1  0  0  0  0
 21 11  1  0  0  0  0
 10 22  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0007978

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]12CC(CC)=CN1C(=O)C1=C(N=C2O)C(O)=C(OC)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C15H16N2O4/c1-3-8-6-10-14(19)16-12-9(15(20)17(10)7-8)4-5-11(21-2)13(12)18/h4-5,7,10,18H,3,6H2,1-2H3,(H,16,19)/t10-/m0/s1

> <INCHI_KEY>
WFFPORSPDSBCLL-JTQLQIEISA-N

> <FORMULA>
C15H16N2O4

> <MOLECULAR_WEIGHT>
288.303

> <EXACT_MASS>
288.111007003

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
29.64362539314437

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(7S)-5-ethyl-8,11-dihydroxy-12-methoxy-3,9-diazatricyclo[8.4.0.0^{3,7}]tetradeca-1(10),4,8,11,13-pentaen-2-one

> <ALOGPS_LOGP>
1.02

> <JCHEM_LOGP>
2.444160450666667

> <ALOGPS_LOGS>
-2.85

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.370311991591496

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.630386708675981

> <JCHEM_PKA_STRONGEST_BASIC>
-1.3261388129591123

> <JCHEM_POLAR_SURFACE_AREA>
82.36

> <JCHEM_REFRACTIVITY>
78.69530000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.05e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(7S)-5-ethyl-8,11-dihydroxy-12-methoxy-3,9-diazatricyclo[8.4.0.0^{3,7}]tetradeca-1(10),4,8,11,13-pentaen-2-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      -1.018   1.220   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.901   5.808   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.581   2.697   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.316   1.857   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.783   2.327   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.506   4.479   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.088   2.056   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.917   3.056   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.176   2.892   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.041   4.358   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.108   3.832   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.501   4.397   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.968   4.867   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.988   5.573   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.796   2.208   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       5.528   5.590   0.000  0.00  0.00           N+0
HETATM   17  N   UNK     0       3.401   2.861   0.000  0.00  0.00           N+0
HETATM   18  O   UNK     0       8.294   6.372   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       3.304   6.953   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       4.813   0.668   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      10.575   4.303   0.000  0.00  0.00           O+0
HETATM   22  H   UNK     0       4.546   4.032   0.000  0.00  0.00           H+0
CONECT    1    3                                                            
CONECT    2   21                                                            
CONECT    3    1    8                                                       
CONECT    4    5    9                                                       
CONECT    5    4   11                                                       
CONECT    6    8   10                                                       
CONECT    7    8   17                                                       
CONECT    8    3    6    7                                                  
CONECT    9    4   12   15                                                  
CONECT   10    6   14   17   22                                             
CONECT   11    5   13   21                                                  
CONECT   12    9   13   16                                                  
CONECT   13   11   12   18                                                  
CONECT   14   10   16   19                                                  
CONECT   15    9   17   20                                                  
CONECT   16   12   14                                                       
CONECT   17    7   10   15                                                  
CONECT   18   13                                                            
CONECT   19   14                                                            
CONECT   20   15                                                            
CONECT   21    2   11                                                       
CONECT   22   10                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

Synonyms

Not Available

Molecular Formula

C₁₅H₁₆N₂O₄

Average Mass

288.303

Monoisotopic Mass

288.111007003

IUPAC Name

(7S)-5-ethyl-8,11-dihydroxy-12-methoxy-3,9-diazatricyclo[8.4.0.0^{3,7}]tetradeca-1(10),4,8,11,13-pentaen-2-one

Traditional Name

(7S)-5-ethyl-8,11-dihydroxy-12-methoxy-3,9-diazatricyclo[8.4.0.0^{3,7}]tetradeca-1(10),4,8,11,13-pentaen-2-one

CAS Registry Number

Not Available

SMILES

[H][C@@]12CC(CC)=CN1C(=O)C1=C(N=C2O)C(O)=C(OC)C=C1

InChI Identifier

InChI=1S/C15H16N2O4/c1-3-8-6-10-14(19)16-12-9(15(20)17(10)7-8)4-5-11(21-2)13(12)18/h4-5,7,10,18H,3,6H2,1-2H3,(H,16,19)/t10-/m0/s1

InChI Key

WFFPORSPDSBCLL-JTQLQIEISA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 1,4-benzodiazepines. These are organic compounds containing a benzene ring fused to a 1,4-azepine.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzodiazepines

Sub Class

1,4-benzodiazepines

Direct Parent

1,4-benzodiazepines

Alternative Parents

Substituents

1,4-benzodiazepine
Alpha-amino acid or derivatives
Anisole
Phenol ether
Alkyl aryl ether
1-hydroxy-4-unsubstituted benzenoid
Phenol
Benzenoid
Vinylogous amide
Tertiary carboxylic acid amide
Pyrroline
Amino acid or derivatives
Carboxamide group
Lactam
Tertiary amine
Secondary carboxylic acid amide
Ether
Carboxylic acid derivative
Azacycle
Organonitrogen compound
Organic oxide
Carbonyl group
Organooxygen compound
Organic oxygen compound
Amine
Hydrocarbon derivative
Organic nitrogen 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	0.4 g/L	ALOGPS
logP	1.02	ALOGPS
logP	2.44	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Acidic)	3.63	ChemAxon
pKa (Strongest Basic)	-1.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	82.36 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	78.7 m³·mol⁻¹	ChemAxon
Polarizability	29.64 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	Species

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
Bacteria	Actinobacteria	2	Human urine; 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

C00047493

Chemspider ID

24625714

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

42639334

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 Limazepine A (MMDBc0007978)

MOL for #<Metabolite:0x0000564fa0045268>

3D MOL for #<Metabolite:0x0000564fa0045268>

3D SDF for #<Metabolite:0x0000564fa0045268>

3D-SDF for #<Metabolite:0x0000564fa0045268>

PDB for #<Metabolite:0x0000564fa0045268>

3D PDB for #<Metabolite:0x0000564fa0045268>

SMILES for #<Metabolite:0x0000564fa0045268>

INCHI for #<Metabolite:0x0000564fa0045268>

Structure for #<Metabolite:0x0000564fa0045268>

3D Structure for #<Metabolite:0x0000564fa0045268>