MiMeDB: Showing metabocard for Paerucumarin (MMDBc0018184)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 08:25:45 UTC

Update Date

2025-10-07 16:06:47 UTC

Metabolite ID

MMDBc0018184

Metabolite Identification

Common Name

Paerucumarin

Description

Paerucumarin is a novel isonitrile functionalized coumarin belonging to the class of secondary metabolites. It is synthesized by the pvcABCD operon in Pseudomonas aeruginosa, where the gene pvcA catalyzes the production of isonitrile functionalized tyrosine (IFT), which is then converted to mature paerucumarin by the actions of pvcB, pvcC, and pvcD (PMID:30528249 ). As an iron-binding molecule, paerucumarin plays a significant role in modulating biofilm formation and is involved in the expression of various genes, including mexT and mexEF-oprN, which confer resistance to antibiotics such as chloramphenicol and ciprofloxacin (PMID:32941967 ). Additionally, exogenous addition of paerucumarin enhances pyoverdine production and the expression of pvdS in P. aeruginosa (PMID:27480638 ). This metabolite is not localized to extracellular membrane vesicles and has been shown to influence the fimbrial chaperone/usher pathway genes, indicating its potential involvement in bacterial pathogenesis, although further investigation is required to elucidate its direct functions (PMID:27480638 ). Overall, paerucumarin represents a critical component in the complex biochemical pathways of Pseudomonas aeruginosa.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152110252D          

 15 16  0  0  0  0            999 V2000
   -0.7145    0.4125    0.0000 C   0  5  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
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    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
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    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
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  5  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  2  2  0  0  0  0
  7  3  2  0  0  0  0
  8  4  2  0  0  0  0
  8  7  1  0  0  0  0
  9  4  1  0  0  0  0
  9  5  2  0  0  0  0
 10  6  1  0  0  0  0
 11  1  3  0  0  0  0
 11  6  1  0  0  0  0
 12  7  1  0  0  0  0
 13  8  1  0  0  0  0
 14 10  2  0  0  0  0
 15  9  1  0  0  0  0
 15 10  1  0  0  0  0
M  CHG  2   1  -1  11   1
M  END
> <DATABASE_ID>
MMDBc0018184

> <DATABASE_NAME>
MIME

> <SMILES>
OC1=CC2=C(C=C1O)C=C([N+]#[C-])C(=O)O2

> <INCHI_IDENTIFIER>
InChI=1S/C10H5NO4/c1-11-6-2-5-3-7(12)8(13)4-9(5)15-10(6)14/h2-4,12-13H

> <INCHI_KEY>
PBXVYKHISUQHKY-UHFFFAOYSA-N

> <FORMULA>
C10H5NO4

> <MOLECULAR_WEIGHT>
203.153

> <EXACT_MASS>
203.021857645

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
18.517442621944866

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6,7-dihydroxy-3-isocyano-2H-chromen-2-one

> <ALOGPS_LOGP>
2.14

> <JCHEM_LOGP>
-1.0407264248759456

> <ALOGPS_LOGS>
-2.74

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
12.058644152218326

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.453827201527036

> <JCHEM_PKA_STRONGEST_BASIC>
-6.273894416000368

> <JCHEM_POLAR_SURFACE_AREA>
71.12

> <JCHEM_REFRACTIVITY>
60.72810000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.69e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6,7-dihydroxy-3-isocyanochromen-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      -1.334   0.770   0.000  0.00  0.00           C-1
HETATM    2  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       0.000  -0.000   0.000  0.00  0.00           N+1
HETATM   12  O   UNK     0       8.002  -0.000   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
CONECT    1   11                                                            
CONECT    2    5    6                                                       
CONECT    3    5    7                                                       
CONECT    4    8    9                                                       
CONECT    5    2    3    9                                                  
CONECT    6    2   10   11                                                  
CONECT    7    3    8   12                                                  
CONECT    8    4    7   13                                                  
CONECT    9    4    5   15                                                  
CONECT   10    6   14   15                                                  
CONECT   11    1    6                                                       
CONECT   12    7                                                            
CONECT   13    8                                                            
CONECT   14   10                                                            
CONECT   15    9   10                                                       
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

Synonyms

Value	Source
6,7-Dihydroxy-3-isocyano-2H-1-benzopyran-2-one	ChEBI
6,7-Dihydroxy-3-isocyanochromen-2-one	ChEBI

Molecular Formula

C₁₀H₅NO₄

Average Mass

203.153

Monoisotopic Mass

203.021857645

IUPAC Name

6,7-dihydroxy-3-isocyano-2H-chromen-2-one

Traditional Name

6,7-dihydroxy-3-isocyanochromen-2-one

CAS Registry Number

Not Available

SMILES

OC1=CC2=C(C=C1O)C=C([N+]#[C-])C(=O)O2

InChI Identifier

InChI=1S/C10H5NO4/c1-11-6-2-5-3-7(12)8(13)4-9(5)15-10(6)14/h2-4,12-13H

InChI Key

PBXVYKHISUQHKY-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 6,7-dihydroxycoumarins. These are coumarins bearing two hydroxyl groups at positions 6 and 7 of the coumarin skeleton, respectively.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Coumarins and derivatives

Sub Class

Hydroxycoumarins

Direct Parent

6,7-dihydroxycoumarins

Alternative Parents

Substituents

6,7-dihydroxycoumarin
7-hydroxycoumarin
Benzopyran
1-benzopyran
1-hydroxy-2-unsubstituted benzenoid
Pyranone
Benzenoid
Pyran
Heteroaromatic compound
Lactone
Oxacycle
Organoheterocyclic compound
Organic nitrogen compound
Organic zwitterion
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
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	0.47 g/L	ALOGPS
logP	2.14	ALOGPS
logP	-1	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Acidic)	7.45	ChemAxon
pKa (Strongest Basic)	-6.3	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	71.12 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	60.73 m³·mol⁻¹	ChemAxon
Polarizability	18.52 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-18	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

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
Bacteria/Eubacteria	Proteobacteria	1	Human ; Human sputum; Human subgingival plaque; 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

60832997

KEGG Compound ID

Not Available

BioCyc ID

CPD-20762

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

130034774

PDB ID

Not Available

ChEBI ID

140649

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 Paerucumarin (MMDBc0018184)

MOL for #<Metabolite:0x00007f8de97f8bf8>

3D MOL for #<Metabolite:0x00007f8de97f8bf8>

3D SDF for #<Metabolite:0x00007f8de97f8bf8>

3D-SDF for #<Metabolite:0x00007f8de97f8bf8>

PDB for #<Metabolite:0x00007f8de97f8bf8>

3D PDB for #<Metabolite:0x00007f8de97f8bf8>

SMILES for #<Metabolite:0x00007f8de97f8bf8>

INCHI for #<Metabolite:0x00007f8de97f8bf8>

Structure for #<Metabolite:0x00007f8de97f8bf8>

3D Structure for #<Metabolite:0x00007f8de97f8bf8>