MiMeDB: Showing metabocard for Limazepine D (MMDBc0012490)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 04:00:46 UTC

Update Date

2025-10-07 16:06:00 UTC

Metabolite ID

MMDBc0012490

Metabolite Identification

Common Name

Limazepine D

Description

Limazepine D is a metabolite belonging to the class of benzodiazepines, which are known for their psychoactive properties. This compound has garnered attention in biomedical research due to its biological activity, particularly its efficacy against various pathogens. Notably, Limazepine D was found to exhibit activity against Staphylococcus species, as indicated in the literature (PMID:19388705 ). The presence of a benzodiazepine structure suggests potential interactions with GABA receptors, which may contribute to its biological effects, although specific mechanisms of action in the context of its antimicrobial activity remain to be fully elucidated. The exploration of Limazepine D's properties not only highlights its significance as a metabolite but also opens avenues for further investigation into its therapeutic potential, especially in the realm of infectious diseases. Understanding the pharmacological profile of Limazepine D could lead to the development of novel treatments, leveraging its unique chemical characteristics to combat resistant strains of bacteria.

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004191522002D          

 20 22  0  0  0  0            999 V2000
   -0.5455   -2.1235    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3111   -1.3325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4911   -1.1399    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8068   -0.3777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6293   -0.4425    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1364    0.2082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9614    0.2175    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4829   -0.4218    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2685   -0.1698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4431    0.6365    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8795   -0.7241    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6651   -0.4722    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8397    0.3341    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7050   -1.5305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9194   -1.7824    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3084   -1.2281    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5691   -1.5943    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5783   -2.4193    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8219   -1.2447    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1184   -1.6757    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 11 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
  8 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
  5 19  1  0  0  0  0
 19 20  1  0  0  0  0
  3 20  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0012490

> <DATABASE_NAME>
MIME

> <SMILES>
CCC1=CN2C(=C1)C=NC1=C(O)C(OC)=CC=C1C2=O

> <INCHI_IDENTIFIER>
InChI=1S/C15H14N2O3/c1-3-9-6-10-7-16-13-11(15(19)17(10)8-9)4-5-12(20-2)14(13)18/h4-8,18H,3H2,1-2H3

> <INCHI_KEY>
SKMAAAVNEKWJHB-UHFFFAOYSA-N

> <FORMULA>
C15H14N2O3

> <MOLECULAR_WEIGHT>
270.288

> <EXACT_MASS>
270.100442319

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
28.7452339145213

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-ethyl-11-hydroxy-12-methoxy-3,9-diazatricyclo[8.4.0.0³,⁷]tetradeca-1(14),4,6,8,10,12-hexaen-2-one

> <ALOGPS_LOGP>
2.84

> <JCHEM_LOGP>
2.3173164969999993

> <ALOGPS_LOGS>
-3.16

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.247418383485613

> <JCHEM_PKA_STRONGEST_BASIC>
-2.1121830807348605

> <JCHEM_POLAR_SURFACE_AREA>
63.82000000000001

> <JCHEM_REFRACTIVITY>
77.993

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.85e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-ethyl-11-hydroxy-12-methoxy-3,9-diazatricyclo[8.4.0.0³,⁷]tetradeca-1(14),4,6,8,10,12-hexaen-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 19-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-15         0                                  
HETATM    1  C   UNK     0      -1.018  -3.964   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.581  -2.487   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.917  -2.128   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.506  -0.705   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.041  -0.826   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.988   0.389   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       5.528   0.406   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       6.501  -0.787   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.968  -0.317   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       8.294   1.188   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       9.108  -1.352   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      10.575  -0.881   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      10.901   0.624   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.783  -2.857   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.316  -3.327   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.176  -2.292   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.796  -2.976   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       4.813  -4.516   0.000  0.00  0.00           O+0
HETATM   19  N   UNK     0       3.401  -2.323   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0       2.088  -3.128   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   20                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   19                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   16                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   14                                                  
CONECT   12   11   13                                                       
CONECT   13   12                                                            
CONECT   14   11   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15    8   17                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17    5   20                                                  
CONECT   20   19    3                                                       
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

Synonyms

Not Available

Molecular Formula

C₁₅H₁₄N₂O₃

Average Mass

270.288

Monoisotopic Mass

270.100442319

IUPAC Name

5-ethyl-11-hydroxy-12-methoxy-3,9-diazatricyclo[8.4.0.0³,⁷]tetradeca-1(14),4,6,8,10,12-hexaen-2-one

Traditional Name

5-ethyl-11-hydroxy-12-methoxy-3,9-diazatricyclo[8.4.0.0³,⁷]tetradeca-1(14),4,6,8,10,12-hexaen-2-one

CAS Registry Number

Not Available

SMILES

CCC1=CN2C(=C1)C=NC1=C(O)C(OC)=CC=C1C2=O

InChI Identifier

InChI=1S/C15H14N2O3/c1-3-9-6-10-7-16-13-11(15(19)17(10)8-9)4-5-12(20-2)14(13)18/h4-8,18H,3H2,1-2H3

InChI Key

SKMAAAVNEKWJHB-UHFFFAOYSA-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
Anisole
Phenol ether
Alkyl aryl ether
1-hydroxy-4-unsubstituted benzenoid
Phenol
Benzenoid
Substituted pyrrole
Heteroaromatic compound
Pyrrole
Lactam
Ether
Azacycle
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen 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	0.18 g/L	ALOGPS
logP	2.84	ALOGPS
logP	2.32	ChemAxon
logS	-3.2	ALOGPS
pKa (Strongest Acidic)	8.25	ChemAxon
pKa (Strongest Basic)	-2.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	63.82 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	77.99 m³·mol⁻¹	ChemAxon
Polarizability	28.75 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

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

42639335

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 D (MMDBc0012490)

MOL for #<Metabolite:0x00007f2ad594dc28>

3D MOL for #<Metabolite:0x00007f2ad594dc28>

3D SDF for #<Metabolite:0x00007f2ad594dc28>

3D-SDF for #<Metabolite:0x00007f2ad594dc28>

PDB for #<Metabolite:0x00007f2ad594dc28>

3D PDB for #<Metabolite:0x00007f2ad594dc28>

SMILES for #<Metabolite:0x00007f2ad594dc28>

INCHI for #<Metabolite:0x00007f2ad594dc28>

Structure for #<Metabolite:0x00007f2ad594dc28>

3D Structure for #<Metabolite:0x00007f2ad594dc28>