MiMeDB: Showing metabocard for Benzomalvin B (MMDBc0019941)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 09:56:58 UTC

Update Date

2025-10-07 16:07:02 UTC

Metabolite ID

MMDBc0019941

Metabolite Identification

Common Name

Benzomalvin B

Description

Benzomalvin B is a member of the chemical class of metabolites known as alkaloids. Its chemical structure has been characterized through advanced techniques such as 2-D NMR and single crystal X-ray diffraction (XRD), confirming the configuration of the compound as (E)-benzomalvin B (PMID:38349752 ). This compound is synthesized from its precursor, (±) benzomalvin E, highlighting the complexity of its biosynthetic pathways. Benzomalvin B may play a role in various metabolic processes, although specific biological pathways involving this metabolite require further exploration. The intricate synthesis and structural validation of benzomalvin B underline its potential significance in metabolic studies and its relevance in the field of natural product chemistry (PMID:38349752 ).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152111562D          

 30 34  0  0  0  0            999 V2000
    6.7173   -3.8597    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7542   -3.2267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0709   -3.9885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2557   -2.5716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0812   -0.2169    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0044   -0.5725    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7381   -0.9672    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3493   -0.0711    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8890   -4.0952    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0737   -2.6783    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9025   -0.1389    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8977   -1.3906    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2164   -1.6394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5875   -0.3877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2085   -3.5468    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3904   -3.4401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3808   -0.8111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1359   -1.7072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0377   -1.5614    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4808   -1.2058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7099   -2.8917    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3372   -2.1556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1523   -2.5321    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2021   -0.7331    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5159   -2.2337    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.5177   -3.0592    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.6803   -1.4053    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.9026   -2.8751    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5451    0.0172    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5251   -4.3086    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  4  2  1  0  0  0  0
  7  5  2  0  0  0  0
  8  6  2  0  0  0  0
  9  3  1  0  0  0  0
 10  4  2  0  0  0  0
 11  5  1  0  0  0  0
 12  6  1  0  0  0  0
 13  7  1  0  0  0  0
 14  8  1  0  0  0  0
 16  9  2  0  0  0  0
 16 10  1  0  0  0  0
 16 15  1  0  0  0  0
 17 11  2  0  0  0  0
 18 12  2  0  0  0  0
 19 13  2  0  0  0  0
 19 17  1  0  0  0  0
 20 14  2  0  0  0  0
 20 18  1  0  0  0  0
 21 15  2  0  0  0  0
 22 21  1  0  0  0  0
 23 18  1  0  0  0  0
 24 17  1  0  0  0  0
 25 19  1  0  0  0  0
 25 22  2  0  0  0  0
 26  1  1  0  0  0  0
 26 21  1  0  0  0  0
 26 23  1  0  0  0  0
 27 20  1  0  0  0  0
 27 22  1  0  0  0  0
 27 24  1  0  0  0  0
 28 23  2  0  0  0  0
 29 24  2  0  0  0  0
 30 15  1  0  0  0  0
M  END


  Mrv1652305152111562D          

 30 34  0  0  0  0            999 V2000
    6.7173   -3.8597    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7542   -3.2267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0709   -3.9885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2557   -2.5716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0812   -0.2169    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0044   -0.5725    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7381   -0.9672    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3493   -0.0711    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8890   -4.0952    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0737   -2.6783    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9025   -0.1389    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8977   -1.3906    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2164   -1.6394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5875   -0.3877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2085   -3.5468    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3904   -3.4401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3808   -0.8111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1359   -1.7072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0377   -1.5614    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4808   -1.2058    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7099   -2.8917    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3372   -2.1556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1523   -2.5321    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2021   -0.7331    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5159   -2.2337    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.5177   -3.0592    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.6803   -1.4053    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.9026   -2.8751    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5451    0.0172    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5251   -4.3086    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  2  0  0  0  0
  4  2  1  0  0  0  0
  7  5  2  0  0  0  0
  8  6  2  0  0  0  0
  9  3  1  0  0  0  0
 10  4  2  0  0  0  0
 11  5  1  0  0  0  0
 12  6  1  0  0  0  0
 13  7  1  0  0  0  0
 14  8  1  0  0  0  0
 16  9  2  0  0  0  0
 16 10  1  0  0  0  0
 16 15  1  0  0  0  0
 17 11  2  0  0  0  0
 18 12  2  0  0  0  0
 19 13  2  0  0  0  0
 19 17  1  0  0  0  0
 20 14  2  0  0  0  0
 20 18  1  0  0  0  0
 21 15  2  0  0  0  0
 22 21  1  0  0  0  0
 23 18  1  0  0  0  0
 24 17  1  0  0  0  0
 25 19  1  0  0  0  0
 25 22  2  0  0  0  0
 26  1  1  0  0  0  0
 26 21  1  0  0  0  0
 26 23  1  0  0  0  0
 27 20  1  0  0  0  0
 27 22  1  0  0  0  0
 27 24  1  0  0  0  0
 28 23  2  0  0  0  0
 29 24  2  0  0  0  0
 30 15  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0019941

> <DATABASE_NAME>
MIME

> <SMILES>
[H]\C(C1=CC=CC=C1)=C1/N(C)C(=O)C2=CC=CC=C2N2C(=O)C3=CC=CC=C3N=C12

> <INCHI_IDENTIFIER>
InChI=1S/C24H17N3O2/c1-26-21(15-16-9-3-2-4-10-16)22-25-19-13-7-5-11-17(19)24(29)27(22)20-14-8-6-12-18(20)23(26)28/h2-15H,1H3/b21-15+

> <INCHI_KEY>
HXDZMNFJQNZXKW-RCCKNPSSSA-N

> <FORMULA>
C24H17N3O2

> <MOLECULAR_WEIGHT>
379.419

> <EXACT_MASS>
379.132076799

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
46

> <JCHEM_AVERAGE_POLARIZABILITY>
39.94158518240614

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(10E)-9-methyl-10-(phenylmethylidene)-1,9,12-triazatetracyclo[9.8.0.0^{2,7}.0^{13,18}]nonadeca-2,4,6,11,13,15,17-heptaene-8,19-dione

> <ALOGPS_LOGP>
3.47

> <JCHEM_LOGP>
3.782119688666667

> <ALOGPS_LOGS>
-4.70

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-1.5980651416838403

> <JCHEM_POLAR_SURFACE_AREA>
52.980000000000004

> <JCHEM_REFRACTIVITY>
115.05829999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.53e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(10E)-9-methyl-10-(phenylmethylidene)-1,9,12-triazatetracyclo[9.8.0.0^{2,7}.0^{13,18}]nonadeca-2,4,6,11,13,15,17-heptaene-8,19-dione

> <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      12.539  -7.205   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.141  -6.023   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.732  -7.445   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.077  -4.800   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.752  -0.405   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      14.942  -1.069   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.111  -1.805   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      13.719  -0.133   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.259  -7.644   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.604  -4.999   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.285  -0.259   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      14.742  -2.596   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.004  -3.060   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      12.297  -0.724   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.722  -6.621   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.195  -6.422   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.177  -1.514   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      13.320  -3.187   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.537  -2.915   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      12.097  -2.251   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      10.658  -5.398   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       9.963  -4.024   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      13.351  -4.726   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       9.711  -1.368   0.000  0.00  0.00           C+0
HETATM   25  N   UNK     0       8.430  -4.169   0.000  0.00  0.00           N+0
HETATM   26  N   UNK     0      12.166  -5.710   0.000  0.00  0.00           N+0
HETATM   27  N   UNK     0      10.603  -2.623   0.000  0.00  0.00           N+0
HETATM   28  O   UNK     0      14.752  -5.367   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      10.351   0.032   0.000  0.00  0.00           O+0
HETATM   30  H   UNK     0      10.314  -8.043   0.000  0.00  0.00           H+0
CONECT    1   26                                                            
CONECT    2    3    4                                                       
CONECT    3    2    9                                                       
CONECT    4    2   10                                                       
CONECT    5    7   11                                                       
CONECT    6    8   12                                                       
CONECT    7    5   13                                                       
CONECT    8    6   14                                                       
CONECT    9    3   16                                                       
CONECT   10    4   16                                                       
CONECT   11    5   17                                                       
CONECT   12    6   18                                                       
CONECT   13    7   19                                                       
CONECT   14    8   20                                                       
CONECT   15   16   21   30                                                  
CONECT   16    9   10   15                                                  
CONECT   17   11   19   24                                                  
CONECT   18   12   20   23                                                  
CONECT   19   13   17   25                                                  
CONECT   20   14   18   27                                                  
CONECT   21   15   22   26                                                  
CONECT   22   21   25   27                                                  
CONECT   23   18   26   28                                                  
CONECT   24   17   27   29                                                  
CONECT   25   19   22                                                       
CONECT   26    1   21   23                                                  
CONECT   27   20   22   24                                                  
CONECT   28   23                                                            
CONECT   29   24                                                            
CONECT   30   15                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   68    0
END

Synonyms

Not Available

Molecular Formula

C₂₄H₁₇N₃O₂

Average Mass

379.419

Monoisotopic Mass

379.132076799

IUPAC Name

(10E)-9-methyl-10-(phenylmethylidene)-1,9,12-triazatetracyclo[9.8.0.0^{2,7}.0^{13,18}]nonadeca-2,4,6,11,13,15,17-heptaene-8,19-dione

Traditional Name

(10E)-9-methyl-10-(phenylmethylidene)-1,9,12-triazatetracyclo[9.8.0.0^{2,7}.0^{13,18}]nonadeca-2,4,6,11,13,15,17-heptaene-8,19-dione

CAS Registry Number

Not Available

SMILES

[H]\C(C1=CC=CC=C1)=C1/N(C)C(=O)C2=CC=CC=C2N2C(=O)C3=CC=CC=C3N=C12

InChI Identifier

InChI=1S/C24H17N3O2/c1-26-21(15-16-9-3-2-4-10-16)22-25-19-13-7-5-11-17(19)24(29)27(22)20-14-8-6-12-18(20)23(26)28/h2-15H,1H3/b21-15+

InChI Key

HXDZMNFJQNZXKW-RCCKNPSSSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidodiazepines. Pyrimidodiazepines are compounds containing a pyrimidoazepine moiety, which consists of a pyrimidine fused to a piperazine ring by a bond. Pyrimidine is 6-membered ring consisting of five carbon atoms and two nitrogen atoms at ring positions 1 and 3. Diazepine is a 7-membered ring consisting of five carbon atoms and two nitrogen centers.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyrimidodiazepines

Sub Class

Not Available

Direct Parent

Pyrimidodiazepines

Alternative Parents

Substituents

Benzodiazepine
1,4-benzodiazepine
Pyrimidodiazepine
Diazanaphthalene
Quinazoline
Pyrimidone
Monocyclic benzene moiety
Benzenoid
Pyrimidine
Heteroaromatic compound
Vinylogous amide
Tertiary carboxylic acid amide
Carboxamide group
Lactam
Carboxylic acid derivative
Azacycle
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
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	0.0075 g/L	ALOGPS
logP	3.47	ALOGPS
logP	3.78	ChemAxon
logS	-4.7	ALOGPS
pKa (Strongest Basic)	-1.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	52.98 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	115.06 m³·mol⁻¹	ChemAxon
Polarizability	39.94 Å³	ChemAxon
Number of Rings	5	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	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

C00016957

Chemspider ID

4947496

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6443512

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 Benzomalvin B (MMDBc0019941)

MOL for #<Metabolite:0x00007f8d7dc2fc10>

3D MOL for #<Metabolite:0x00007f8d7dc2fc10>

3D SDF for #<Metabolite:0x00007f8d7dc2fc10>

3D-SDF for #<Metabolite:0x00007f8d7dc2fc10>

PDB for #<Metabolite:0x00007f8d7dc2fc10>

3D PDB for #<Metabolite:0x00007f8d7dc2fc10>

SMILES for #<Metabolite:0x00007f8d7dc2fc10>

INCHI for #<Metabolite:0x00007f8d7dc2fc10>

Structure for #<Metabolite:0x00007f8d7dc2fc10>

3D Structure for #<Metabolite:0x00007f8d7dc2fc10>