MiMeDB: Showing metabocard for Benzomalvin A (MMDBc0004478)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-14 22:26:34 UTC

Update Date

2025-10-07 16:04:52 UTC

Metabolite ID

MMDBc0004478

Metabolite Identification

Common Name

Benzomalvin A

Description

Benzomalvin A is a benzodiazepine and a specialized metabolite derived from fungi, classified within the chemical class of quinazolinone natural products. This compound is biosynthesized by a three-gene nonribosomal peptide synthetase cluster and exhibits significant biological activity as an inhibitor of the substance P receptor NK1, with reported inhibitory constants (Ki) of 12, 42, and 43 µM at guinea pig, rat, and human receptors, respectively (PMID:7518818 ). Benzomalvin A has been isolated from the solid culture of Penicillium spathulatum B35, alongside other metabolites such as quinolactacins and asperphenamate (PMID:27399232 ). The unique Csp3-Csp2 bond forming reaction utilized in the synthesis of Benzomalvin A has been demonstrated in the context of producing various quinazolinone derivatives (PMID:37177871 ). Additionally, the growth characteristics of Penicillium spathulatum, including its ability to produce benzomalvin A, highlight its ecological niche and metabolic capabilities (PMID:23173673 ). A two-step total synthesis of (+/-)-benzomalvin A has also been successfully achieved, yielding 16% overall (PMID:16323862 ).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152100262D          

 30 34  0  0  1  0            999 V2000
    6.7173   -3.8597    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1584   -5.8322    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6598   -5.1771    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3403   -5.7255    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
    6.3432   -4.4153    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0237   -4.9637    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
    5.5251   -4.3086    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  1  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
    4.8884   -2.8156    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  1  1  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
 21 30  1  6  0  0  0
M  END


  Mrv1652305152100262D          

 30 34  0  0  1  0            999 V2000
    6.7173   -3.8597    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1584   -5.8322    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6598   -5.1771    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3403   -5.7255    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
    6.3432   -4.4153    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0237   -4.9637    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
    5.5251   -4.3086    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  1  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
    4.8884   -2.8156    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  1  1  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
 21 30  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0004478

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]1(CC2=CC=CC=C2)N(C)C(=O)C2=CC=CC=C2N2C(=O)C3=CC=CC=C3N=C12

> <INCHI_IDENTIFIER>
InChI=1S/C24H19N3O2/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/h2-14,21H,15H2,1H3/t21-/m0/s1

> <INCHI_KEY>
YYWUABJYAOCACI-NRFANRHFSA-N

> <FORMULA>
C24H19N3O2

> <MOLECULAR_WEIGHT>
381.435

> <EXACT_MASS>
381.147726864

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
48

> <JCHEM_AVERAGE_POLARIZABILITY>
40.84478182279412

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(10S)-10-benzyl-9-methyl-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>
2.70

> <JCHEM_LOGP>
3.879487074

> <ALOGPS_LOGS>
-4.53

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
19.735663033802236

> <JCHEM_PKA_STRONGEST_BASIC>
-1.6030327117030816

> <JCHEM_POLAR_SURFACE_AREA>
52.980000000000004

> <JCHEM_REFRACTIVITY>
113.48980000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.14e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(10S)-10-benzyl-9-methyl-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      11.496 -10.887   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      12.432  -9.664   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.969 -10.688   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      11.841  -8.242   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.378  -9.266   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      10.314  -8.043   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       9.125  -5.256   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                                                       
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   30                                             
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   21                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   68    0
END

Synonyms

Not Available

Molecular Formula

C₂₄H₁₉N₃O₂

Average Mass

381.435

Monoisotopic Mass

381.147726864

IUPAC Name

(10S)-10-benzyl-9-methyl-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

(10S)-10-benzyl-9-methyl-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@@]1(CC2=CC=CC=C2)N(C)C(=O)C2=CC=CC=C2N2C(=O)C3=CC=CC=C3N=C12

InChI Identifier

InChI=1S/C24H19N3O2/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/h2-14,21H,15H2,1H3/t21-/m0/s1

InChI Key

YYWUABJYAOCACI-NRFANRHFSA-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
Pyrimidodiazepine
1,4-benzodiazepine
Quinazoline
Pyrimidone
Monocyclic benzene moiety
Pyrimidine
Benzenoid
Heteroaromatic compound
Vinylogous amide
Tertiary carboxylic acid amide
Carboxamide group
Lactam
Carboxylic acid derivative
Azacycle
Organic oxide
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Organic oxygen compound
Hydrocarbon derivative
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	0.011 g/L	ALOGPS
logP	2.7	ALOGPS
logP	3.88	ChemAxon
logS	-4.5	ALOGPS
pKa (Strongest Acidic)	19.74	ChemAxon
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	2	ChemAxon
Refractivity	113.49 m³·mol⁻¹	ChemAxon
Polarizability	40.84 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

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
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

C00016956

Chemspider ID

8243946

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10068406

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

YYWUABJYAOCACI-NRFANRHFSA-N

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 Benzomalvin A (MMDBc0004478)

MOL for #<Metabolite:0x00007f2ad483b2c8>

3D MOL for #<Metabolite:0x00007f2ad483b2c8>

3D SDF for #<Metabolite:0x00007f2ad483b2c8>

3D-SDF for #<Metabolite:0x00007f2ad483b2c8>

PDB for #<Metabolite:0x00007f2ad483b2c8>

3D PDB for #<Metabolite:0x00007f2ad483b2c8>

SMILES for #<Metabolite:0x00007f2ad483b2c8>

INCHI for #<Metabolite:0x00007f2ad483b2c8>

Structure for #<Metabolite:0x00007f2ad483b2c8>

3D Structure for #<Metabolite:0x00007f2ad483b2c8>