MiMeDB: Showing metabocard for Nidulalin A (MMDBc0011383)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 03:15:52 UTC

Update Date

2025-10-07 16:05:51 UTC

Metabolite ID

MMDBc0011383

Metabolite Identification

Common Name

Nidulalin A

Description

Nidulalin A is a natural product belonging to the class of xanthones, characterized by a complex caged structure. This metabolite has garnered interest due to its unique biosynthetic pathway, which remains largely unexplored, as the genes responsible for its production have not been previously described (PMID:39625876 ). The synthesis of nidulalin A has been advanced through innovative methodologies, including an asymmetric synthesis that employs acylative kinetic resolution of chiral, racemic intermediates (PMID:38319883 ). Additionally, its biosynthetic relationship with nidulaxanthone A has been established, where nidulalin A serves as a monomer that undergoes stereoselective Diels-Alder dimerization to form the latter compound (PMID:38319883 ). The compound has also been synthesized using a four-step sequence that incorporates allyl triflate for chromone ester activation and ketone desaturation via Bobbitt's oxoammonium salt (PMID:38319883 ). The biological implications of nidulalin A are still under investigation, but its production has been linked to specific fungal strains that also express other metabolites like patulin and citrinin (PMID:39625876 ).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152105152D          

 23 25  0  0  1  0            999 V2000
    3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3356    2.4037    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  5  3  2  0  0  0  0
  8  1  1  0  0  0  0
  8  6  2  0  0  0  0
  8  7  1  0  0  0  0
  9  4  2  0  0  0  0
 10  6  1  0  0  0  0
 11  7  2  0  0  0  0
 12  5  1  0  0  0  0
 13 10  2  0  0  0  0
 13 11  1  0  0  0  0
 14  9  1  0  0  0  0
 14 13  1  0  0  0  0
 16  9  1  0  0  0  0
 16 12  1  0  0  0  0
 16 15  1  6  0  0  0
 17 10  1  0  0  0  0
 12 18  1  1  0  0  0
 19 14  2  0  0  0  0
 20 15  2  0  0  0  0
 21  2  1  0  0  0  0
 21 15  1  0  0  0  0
 22 11  1  0  0  0  0
 22 16  1  0  0  0  0
 12 23  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0011383

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]1(O)C=CC=C2C(=O)C3=C(O)C=C(C)C=C3O[C@]12C(=O)OC

> <INCHI_IDENTIFIER>
InChI=1S/C16H14O6/c1-8-6-10(17)13-11(7-8)22-16(15(20)21-2)9(14(13)19)4-3-5-12(16)18/h3-7,12,17-18H,1-2H3/t12-,16+/m1/s1

> <INCHI_KEY>
BVPTZDRKEDPTOX-WBMJQRKESA-N

> <FORMULA>
C16H14O6

> <MOLECULAR_WEIGHT>
302.282

> <EXACT_MASS>
302.079038171

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
29.317944821211476

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl (4R,4aS)-4,8-dihydroxy-6-methyl-9-oxo-4a,9-dihydro-4H-xanthene-4a-carboxylate

> <ALOGPS_LOGP>
1.96

> <JCHEM_LOGP>
2.0558407663333336

> <ALOGPS_LOGS>
-2.31

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.246668108117177

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.867504335778337

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5657188664179396

> <JCHEM_POLAR_SURFACE_AREA>
93.06

> <JCHEM_REFRACTIVITY>
78.496

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.47e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl (4R,4aS)-4,8-dihydroxy-6-methyl-9-oxo-4H-xanthene-4a-carboxylate

> <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       6.668   2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334   5.390   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.335   1.540   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       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   3.080   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -1.334   3.850   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -0.626   4.487   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
HETATM   23  H   UNK     0      -2.667   3.080   0.000  0.00  0.00           H+0
CONECT    1    8                                                            
CONECT    2   21                                                            
CONECT    3    4    5                                                       
CONECT    4    3    9                                                       
CONECT    5    3   12                                                       
CONECT    6    8   10                                                       
CONECT    7    8   11                                                       
CONECT    8    1    6    7                                                  
CONECT    9    4   14   16                                                  
CONECT   10    6   13   17                                                  
CONECT   11    7   13   22                                                  
CONECT   12    5   16   18   23                                             
CONECT   13   10   11   14                                                  
CONECT   14    9   13   19                                                  
CONECT   15   16   20   21                                                  
CONECT   16    9   12   15   22                                             
CONECT   17   10                                                            
CONECT   18   12                                                            
CONECT   19   14                                                            
CONECT   20   15                                                            
CONECT   21    2   15                                                       
CONECT   22   11   16                                                       
CONECT   23   12                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   50    0
END

Synonyms

Not Available

Molecular Formula

C₁₆H₁₄O₆

Average Mass

302.282

Monoisotopic Mass

302.079038171

IUPAC Name

methyl (4R,4aS)-4,8-dihydroxy-6-methyl-9-oxo-4a,9-dihydro-4H-xanthene-4a-carboxylate

Traditional Name

methyl (4R,4aS)-4,8-dihydroxy-6-methyl-9-oxo-4H-xanthene-4a-carboxylate

CAS Registry Number

Not Available

SMILES

[H][C@@]1(O)C=CC=C2C(=O)C3=C(O)C=C(C)C=C3O[C@]12C(=O)OC

InChI Identifier

InChI=1S/C16H14O6/c1-8-6-10(17)13-11(7-8)22-16(15(20)21-2)9(14(13)19)4-3-5-12(16)18/h3-7,12,17-18H,1-2H3/t12-,16+/m1/s1

InChI Key

BVPTZDRKEDPTOX-WBMJQRKESA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as xanthones. These are polycyclic aromatic compounds containing a xanthene moiety conjugated to a ketone group at carbon 9. Xanthene is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzopyrans

Sub Class

1-benzopyrans

Direct Parent

Xanthones

Alternative Parents

Substituents

Xanthone
Chromone
Aryl ketone
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Beta-hydroxy acid
Hydroxy acid
Benzenoid
Vinylogous acid
Methyl ester
Carboxylic acid ester
Ketone
Secondary alcohol
Oxacycle
Ether
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Organic oxygen compound
Hydrocarbon derivative
Alcohol
Carbonyl group
Organic oxide
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

carboxylic ester (CHEBI:66625 )
phenols (CHEBI:66625 )
xanthones (CHEBI:66625 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	1.47 g/L	ALOGPS
logP	1.96	ALOGPS
logP	2.06	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	8.87	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	93.06 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	78.5 m³·mol⁻¹	ChemAxon
Polarizability	29.32 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-10	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum

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	3	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

C00030430

Chemspider ID

8102047

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9926413

PDB ID

Not Available

ChEBI ID

66625

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 Nidulalin A (MMDBc0011383)

MOL for #<Metabolite:0x00007f2abf86e2c8>

3D MOL for #<Metabolite:0x00007f2abf86e2c8>

3D SDF for #<Metabolite:0x00007f2abf86e2c8>

3D-SDF for #<Metabolite:0x00007f2abf86e2c8>

PDB for #<Metabolite:0x00007f2abf86e2c8>

3D PDB for #<Metabolite:0x00007f2abf86e2c8>

SMILES for #<Metabolite:0x00007f2abf86e2c8>

INCHI for #<Metabolite:0x00007f2abf86e2c8>

Structure for #<Metabolite:0x00007f2abf86e2c8>

3D Structure for #<Metabolite:0x00007f2abf86e2c8>