MiMeDB: Showing metabocard for Aqabamycin D (MMDBc0010761)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 02:50:56 UTC

Update Date

2025-10-07 16:05:47 UTC

Metabolite ID

MMDBc0010761

Metabolite Identification

Common Name

Aqabamycin D

Description

Aqabamycin D is a maleimide derivative, a chemical class known for its diverse biological activities. It was isolated alongside several other novel compounds, including aqabamycin A, B, C, E, F, and G, as well as known metabolites such as 3-nitro-1H-indazole and indazole-3-carbaldehyde (PMID: 32931234 ). The maleimide structure is characterized by a five-membered ring containing a carbonyl group and a nitrogen atom, which can engage in various chemical reactions, making these compounds of interest for potential therapeutic applications. The biological significance of aqabamycin D, along with its analogs, stems from their potential interactions with cellular processes, although detailed studies on their specific mechanisms of action are still required. The isolation of such compounds highlights the ongoing exploration of natural products in drug discovery, particularly those derived from microbial sources, which often yield novel structures with promising biological activities. Further research is necessary to fully elucidate the pharmacological properties and potential applications of aqabamycin D in medicine.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152104502D          

 27 29  0  0  0  0            999 V2000
    0.7429    1.5082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6078    3.5277    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5275    1.7631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6078    4.3527    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3014    2.8672    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0367    3.5277    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1298    2.0602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    3.1152    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0860    3.1221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0367    4.3527    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6991    2.5701    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    4.7652    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6548    1.8053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    2.2902    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9097    1.0206    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9897    1.8053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7347    1.0206    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2575    3.9291    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7512    4.7652    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4837    2.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    5.5902    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4248    0.3532    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7743    2.0602    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0421    4.1840    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6444    4.4811    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7512    5.5902    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4656    4.3527    0.0000 O   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
  7  1  1  0  0  0  0
  7  5  2  0  0  0  0
  8  2  1  0  0  0  0
  8  6  2  0  0  0  0
  9  5  1  0  0  0  0
 10  6  1  0  0  0  0
 11  3  1  0  0  0  0
 11  9  2  0  0  0  0
 12  4  1  0  0  0  0
 12 10  2  0  0  0  0
 13  7  1  0  0  0  0
 14  8  1  0  0  0  0
 14 13  2  0  0  0  0
 15 13  1  0  0  0  0
 16 14  1  0  0  0  0
 17 15  2  0  0  0  0
 17 16  1  0  0  0  0
 18  9  1  0  0  0  0
 19 10  1  0  0  0  0
 20 11  1  0  0  0  0
 21 12  1  0  0  0  0
 22 15  1  0  0  0  0
 23 16  2  0  0  0  0
 24 18  2  0  0  0  0
 25 18  2  0  0  0  0
 26 19  2  0  0  0  0
 27 19  2  0  0  0  0
M  END


  Mrv1652305152104502D          

 27 29  0  0  0  0            999 V2000
    0.7429    1.5082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6078    3.5277    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5275    1.7631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6078    4.3527    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3014    2.8672    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0367    3.5277    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1298    2.0602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    3.1152    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0860    3.1221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0367    4.3527    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6991    2.5701    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    4.7652    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6548    1.8053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    2.2902    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9097    1.0206    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9897    1.8053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7347    1.0206    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2575    3.9291    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7512    4.7652    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4837    2.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    5.5902    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4248    0.3532    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7743    2.0602    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0421    4.1840    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6444    4.4811    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7512    5.5902    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4656    4.3527    0.0000 O   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
  7  1  1  0  0  0  0
  7  5  2  0  0  0  0
  8  2  1  0  0  0  0
  8  6  2  0  0  0  0
  9  5  1  0  0  0  0
 10  6  1  0  0  0  0
 11  3  1  0  0  0  0
 11  9  2  0  0  0  0
 12  4  1  0  0  0  0
 12 10  2  0  0  0  0
 13  7  1  0  0  0  0
 14  8  1  0  0  0  0
 14 13  2  0  0  0  0
 15 13  1  0  0  0  0
 16 14  1  0  0  0  0
 17 15  2  0  0  0  0
 17 16  1  0  0  0  0
 18  9  1  0  0  0  0
 19 10  1  0  0  0  0
 20 11  1  0  0  0  0
 21 12  1  0  0  0  0
 22 15  1  0  0  0  0
 23 16  2  0  0  0  0
 24 18  2  0  0  0  0
 25 18  2  0  0  0  0
 26 19  2  0  0  0  0
 27 19  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0010761

> <DATABASE_NAME>
MIME

> <SMILES>
OC1=NC(=O)C(=C1C1=CC(=C(O)C=C1)N(=O)=O)C1=CC(=C(O)C=C1)N(=O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C16H9N3O8/c20-11-3-1-7(5-9(11)18(24)25)13-14(16(23)17-15(13)22)8-2-4-12(21)10(6-8)19(26)27/h1-6,20-21H,(H,17,22,23)

> <INCHI_KEY>
ORKTZLAOMXYSNI-UHFFFAOYSA-N

> <FORMULA>
C16H9N3O8

> <MOLECULAR_WEIGHT>
371.261

> <EXACT_MASS>
371.038964262

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
32.00876562911209

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-hydroxy-3,4-bis(4-hydroxy-3-nitrophenyl)-2H-pyrrol-2-one

> <ALOGPS_LOGP>
2.21

> <JCHEM_LOGP>
2.340611205333333

> <ALOGPS_LOGS>
-4.53

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
5.610537938713868

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.095891786637991

> <JCHEM_PKA_STRONGEST_BASIC>
-4.229167356176603

> <JCHEM_POLAR_SURFACE_AREA>
181.76

> <JCHEM_REFRACTIVITY>
91.18849999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.10e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-hydroxy-3,4-bis(4-hydroxy-3-nitrophenyl)pyrrol-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       1.387   2.815   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.134   6.585   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.851   3.291   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.134   8.125   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.563   5.352   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.802   6.585   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.242   3.846   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.468   5.815   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.027   5.828   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -3.802   8.125   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.172   4.797   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.468   8.895   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.222   3.370   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.468   4.275   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.698   1.905   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -3.714   3.370   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0      -3.238   1.905   0.000  0.00  0.00           N+0
HETATM   18  N   UNK     0       2.347   7.334   0.000  0.00  0.00           N+0
HETATM   19  N   UNK     0      -5.136   8.895   0.000  0.00  0.00           N+0
HETATM   20  O   UNK     0       4.636   5.273   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -2.468  10.435   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -0.793   0.659   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -5.179   3.846   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       3.812   7.810   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       1.203   8.365   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -5.136  10.435   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      -6.469   8.125   0.000  0.00  0.00           O+0
CONECT    1    3    7                                                       
CONECT    2    4    8                                                       
CONECT    3    1   11                                                       
CONECT    4    2   12                                                       
CONECT    5    7    9                                                       
CONECT    6    8   10                                                       
CONECT    7    1    5   13                                                  
CONECT    8    2    6   14                                                  
CONECT    9    5   11   18                                                  
CONECT   10    6   12   19                                                  
CONECT   11    3    9   20                                                  
CONECT   12    4   10   21                                                  
CONECT   13    7   14   15                                                  
CONECT   14    8   13   16                                                  
CONECT   15   13   17   22                                                  
CONECT   16   14   17   23                                                  
CONECT   17   15   16                                                       
CONECT   18    9   24   25                                                  
CONECT   19   10   26   27                                                  
CONECT   20   11                                                            
CONECT   21   12                                                            
CONECT   22   15                                                            
CONECT   23   16                                                            
CONECT   24   18                                                            
CONECT   25   18                                                            
CONECT   26   19                                                            
CONECT   27   19                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   58    0
END

Synonyms

Not Available

Molecular Formula

C₁₆H₉N₃O₈

Average Mass

371.261

Monoisotopic Mass

371.038964262

IUPAC Name

5-hydroxy-3,4-bis(4-hydroxy-3-nitrophenyl)-2H-pyrrol-2-one

Traditional Name

5-hydroxy-3,4-bis(4-hydroxy-3-nitrophenyl)pyrrol-2-one

CAS Registry Number

Not Available

SMILES

OC1=NC(=O)C(=C1C1=CC(=C(O)C=C1)N(=O)=O)C1=CC(=C(O)C=C1)N(=O)=O

InChI Identifier

InChI=1S/C16H9N3O8/c20-11-3-1-7(5-9(11)18(24)25)13-14(16(23)17-15(13)22)8-2-4-12(21)10(6-8)19(26)27/h1-6,20-21H,(H,17,22,23)

InChI Key

ORKTZLAOMXYSNI-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as stilbenes. These are organic compounds containing a 1,2-diphenylethylene moiety. Stilbenes (C6-C2-C6 ) are derived from the common phenylpropene (C6-C3) skeleton building block. The introduction of one or more hydroxyl groups to a phenyl ring lead to stilbenoids.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Stilbenes

Sub Class

Not Available

Direct Parent

Stilbenes

Alternative Parents

Substituents

Stilbene
Nitrophenol
Nitrobenzene
Nitroaromatic compound
1-hydroxy-2-unsubstituted benzenoid
Phenol
Maleimide
Monocyclic benzene moiety
Benzenoid
Carboxylic acid imide
Dicarboximide
Carboxylic acid imide, n-unsubstituted
Pyrroline
Organic nitro compound
C-nitro compound
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Allyl-type 1,3-dipolar organic compound
Carboxylic acid derivative
Azacycle
Organic oxoazanium
Organic salt
Carbonyl group
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Organic cation
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic 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	2.21	ALOGPS
logP	2.34	ChemAxon
logS	-4.5	ALOGPS
pKa (Strongest Acidic)	4.1	ChemAxon
pKa (Strongest Basic)	-4.2	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	181.76 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	91.19 m³·mol⁻¹	ChemAxon
Polarizability	32.01 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	Proteobacteria	1		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

27024979

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

46846128

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 Aqabamycin D (MMDBc0010761)

MOL for #<Metabolite:0x00007f2ad3aacaf8>

3D MOL for #<Metabolite:0x00007f2ad3aacaf8>

3D SDF for #<Metabolite:0x00007f2ad3aacaf8>

3D-SDF for #<Metabolite:0x00007f2ad3aacaf8>

PDB for #<Metabolite:0x00007f2ad3aacaf8>

3D PDB for #<Metabolite:0x00007f2ad3aacaf8>

SMILES for #<Metabolite:0x00007f2ad3aacaf8>

INCHI for #<Metabolite:0x00007f2ad3aacaf8>

Structure for #<Metabolite:0x00007f2ad3aacaf8>

3D Structure for #<Metabolite:0x00007f2ad3aacaf8>