MiMeDB: Showing metabocard for Benzodiazepinedione (MMDBc0015501)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 06:19:32 UTC

Update Date

2025-10-07 16:06:25 UTC

Metabolite ID

MMDBc0015501

Metabolite Identification

Common Name

Benzodiazepinedione

Description

Benzodiazepinedione is a chemical class of compounds characterized by a fused benzodiazepine structure containing a diketone moiety. This class has garnered attention in biomedical research for its diverse biological activities, particularly its antiparasitic properties, as demonstrated by the identification of various benzodiazepinediones that operate through a novel mechanism of action (PMID:40599586 ). The structural versatility of benzodiazepinediones is evident in studies revealing rare geometric isomers and the significance of the 2,5-diketopiperazine ring in their acceptance (PMID:32315839 , PMID:31989220 ). Furthermore, these compounds have been explored as inhibitors of Clostridium difficile toxin B, highlighting their potential in therapeutic applications (PMID:30392779 ). The enzymatic synthesis of benzodiazepinediones, particularly through the Fe(II)/2-oxoglutarate-dependent dioxygenase AsqJ, showcases their role in the biosynthesis of quinolone antibiotics, underscoring their importance in both chemistry and biology (PMID:29876666 , PMID:26553478 ). Additionally, benzodiazepinediones have been identified as promising MDM2 inhibitors, further emphasizing their relevance in drug discovery (PMID:27888811 ).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05031418572D          

 24 27  0  0  1  0            999 V2000
    5.8545   -0.3122    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8374   -0.4033    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0260    0.4948    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8374   -1.2283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0699   -0.5671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1230    0.0092    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4129    1.0468    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1230   -1.6408    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2238   -0.8158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3007    0.6524    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6363   -0.1013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4568   -0.0151    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5915   -0.4033    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6283    0.7919    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5915   -1.2283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3988   -0.8158    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2365    0.1111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0408   -1.5591    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9138    1.2044    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2365   -1.7427    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0408   -0.0725    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0529    0.9154    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5552   -2.2041    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8377   -1.5143    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  1  1  0  0  0  0
  6  2  1  0  0  0  0
  7  3  1  0  0  0  0
  8  4  1  0  0  0  0
 11  9  1  0  0  0  0
 11 10  2  0  0  0  0
 12  5  2  0  0  0  0
 12 11  1  0  0  0  0
 13  6  2  0  0  0  0
 14  7  2  0  0  0  0
 14 12  1  0  0  0  0
 15  8  2  0  0  0  0
 15 13  1  0  0  0  0
 16  9  1  1  0  0  0
 17 13  1  0  0  0  0
 18 16  1  0  0  0  0
 19 10  1  0  0  0  0
 19 14  1  0  0  0  0
 20 15  1  0  0  0  0
 20 18  2  0  0  0  0
 21 16  1  0  0  0  0
 21 17  2  0  0  0  0
 22 17  1  0  0  0  0
 23 18  1  0  0  0  0
 16 24  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0015501

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]1(CC2=CNC3=CC=CC=C23)N=C(O)C2=CC=CC=C2N=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C18H15N3O2/c22-17-13-6-2-4-8-15(13)20-18(23)16(21-17)9-11-10-19-14-7-3-1-5-12(11)14/h1-8,10,16,19H,9H2,(H,20,23)(H,21,22)/t16-/m0/s1

> <INCHI_KEY>
AQDZAHJUWYRHGM-INIZCTEOSA-N

> <FORMULA>
C18H15N3O2

> <MOLECULAR_WEIGHT>
305.3306

> <EXACT_MASS>
305.116426739

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
31.81500661187718

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3S)-3-(1H-indol-3-ylmethyl)-3H-1,4-benzodiazepine-2,5-diol

> <ALOGPS_LOGP>
2.49

> <JCHEM_LOGP>
3.544268803964709

> <ALOGPS_LOGS>
-4.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
8.368331433486253

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.284252140082509

> <JCHEM_PKA_STRONGEST_BASIC>
4.446736097492526

> <JCHEM_POLAR_SURFACE_AREA>
80.97

> <JCHEM_REFRACTIVITY>
89.81320000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.55e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S)-3-(1H-indol-3-ylmethyl)-3H-1,4-benzodiazepine-2,5-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-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  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   20  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   21  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   22  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   24  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    3    5                                                       
CONECT    2    4    6                                                       
CONECT    3    1    7                                                       
CONECT    4    2    8                                                       
CONECT    5    1   12                                                       
CONECT    6    2   13                                                       
CONECT    7    3   14                                                       
CONECT    8    4   15                                                       
CONECT    9   11   16                                                       
CONECT   10   11   19                                                       
CONECT   11    9   10   12                                                  
CONECT   12    5   11   14                                                  
CONECT   13    6   15   17                                                  
CONECT   14    7   12   19                                                  
CONECT   15    8   13   20                                                  
CONECT   16    9   18   21   24                                             
CONECT   17   13   21   22                                                  
CONECT   18   16   20   23                                                  
CONECT   19   10   14                                                       
CONECT   20   15   18                                                       
CONECT   21   16   17                                                       
CONECT   22   17                                                            
CONECT   23   18                                                            
CONECT   24   16                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   54    0
END

Synonyms

Not Available

Molecular Formula

C₁₈H₁₅N₃O₂

Average Mass

305.3306

Monoisotopic Mass

305.116426739

IUPAC Name

(3S)-3-(1H-indol-3-ylmethyl)-3H-1,4-benzodiazepine-2,5-diol

Traditional Name

(3S)-3-(1H-indol-3-ylmethyl)-3H-1,4-benzodiazepine-2,5-diol

CAS Registry Number

Not Available

SMILES

[H][C@@]1(CC2=CNC3=CC=CC=C23)N=C(O)C2=CC=CC=C2N=C1O

InChI Identifier

InChI=1S/C18H15N3O2/c22-17-13-6-2-4-8-15(13)20-18(23)16(21-17)9-11-10-19-14-7-3-1-5-12(11)14/h1-8,10,16,19H,9H2,(H,20,23)(H,21,22)/t16-/m0/s1

InChI Key

AQDZAHJUWYRHGM-INIZCTEOSA-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
3-alkylindole
Indole
Indole or derivatives
Benzenoid
Substituted pyrrole
Heteroaromatic compound
Vinylogous amide
Pyrrole
Carboxamide group
Secondary carboxylic acid amide
Lactam
Azacycle
Carboxylic acid derivative
Hydrocarbon derivative
Organonitrogen compound
Organic nitrogen compound
Organooxygen compound
Organic oxygen compound
Carbonyl group
Organic oxide
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	0.026 g/L	ALOGPS
logP	2.49	ALOGPS
logP	3.54	ChemAxon
logS	-4.1	ALOGPS
pKa (Strongest Acidic)	5.28	ChemAxon
pKa (Strongest Basic)	4.45	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	80.97 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	89.81 m³·mol⁻¹	ChemAxon
Polarizability	31.82 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	2	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

10017963

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 Benzodiazepinedione (MMDBc0015501)

MOL for #<Metabolite:0x00007f8d88b09858>

3D MOL for #<Metabolite:0x00007f8d88b09858>

3D SDF for #<Metabolite:0x00007f8d88b09858>

3D-SDF for #<Metabolite:0x00007f8d88b09858>

PDB for #<Metabolite:0x00007f8d88b09858>

3D PDB for #<Metabolite:0x00007f8d88b09858>

SMILES for #<Metabolite:0x00007f8d88b09858>

INCHI for #<Metabolite:0x00007f8d88b09858>

Structure for #<Metabolite:0x00007f8d88b09858>

3D Structure for #<Metabolite:0x00007f8d88b09858>