NP-MRD: Showing NP-Card for Paerucumarin (NP0007918)

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Record Information

Version

2.0

Created at

2020-12-09 05:28:35 UTC

Updated at

2021-07-15 16:58:55 UTC

NP-MRD ID

NP0007918

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Paerucumarin

Provided By

NPAtlas

Description

Paerucumarin is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Paerucumarin is found in Pseudomonas aeruginosa. Paerucumarin was first documented in 2008 (PMID: 18689486). Based on a literature review a small amount of articles have been published on Paerucumarin (PMID: 23646138) (PMID: 27480638) (PMID: 30528249).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242106053D          

 20 21  0  0  0  0            999 V2000
   -5.1183    0.0945   -0.6104 C   0  5  0  0  0  3  0  0  0  0  0  0
   -3.9911   -0.0977   -0.3645 N   0  3  0  0  0  4  0  0  0  0  0  0
   -2.6565   -0.3011   -0.0718 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6564    0.5337   -0.5678 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3238    0.3259   -0.2721 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6893    1.1345   -0.7477 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0223    0.9095   -0.4395 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0458    1.7298   -0.9225 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3517   -0.1578    0.3695 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6918   -0.3865    0.6811 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3447   -0.9710    0.8491 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0018   -0.7392    0.5349 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9495   -1.5173    0.9951 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2225   -1.3402    0.7282 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1196   -2.1035    1.1836 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9477    1.3489   -1.1901 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4129    1.9664   -1.3805 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8510    2.5203   -1.5164 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9706   -1.1450    1.2610 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6035   -1.8043    1.4809 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14  3  1  0  0  0  0
 12  5  1  0  0  0  0
  4 16  1  0  0  0  0
  6 17  1  0  0  0  0
  8 18  1  0  0  0  0
 10 19  1  0  0  0  0
 11 20  1  0  0  0  0
M  CHG  2   1  -1   2   1
M  END
> <DATABASE_ID>
NP0007918

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC1=C(O[H])C([H])=C2C([H])=C([N+]#[C-])C(=O)OC2=C1[H]

> <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>
18.63852757891529

> <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                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  C   UNK     0      -5.118   0.095  -0.610  0.00  0.00           C-1
HETATM    2  N   UNK     0      -3.991  -0.098  -0.365  0.00  0.00           N+1
HETATM    3  C   UNK     0      -2.656  -0.301  -0.072  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.656   0.534  -0.568  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.324   0.326  -0.272  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.689   1.135  -0.748  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.022   0.910  -0.440  0.00  0.00           C+0
HETATM    8  O   UNK     0       3.046   1.730  -0.923  0.00  0.00           O+0
HETATM    9  C   UNK     0       2.352  -0.158   0.370  0.00  0.00           C+0
HETATM   10  O   UNK     0       3.692  -0.387   0.681  0.00  0.00           O+0
HETATM   11  C   UNK     0       1.345  -0.971   0.849  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.002  -0.739   0.535  0.00  0.00           C+0
HETATM   13  O   UNK     0      -0.950  -1.517   0.995  0.00  0.00           O+0
HETATM   14  C   UNK     0      -2.223  -1.340   0.728  0.00  0.00           C+0
HETATM   15  O   UNK     0      -3.120  -2.103   1.184  0.00  0.00           O+0
HETATM   16  H   UNK     0      -1.948   1.349  -1.190  0.00  0.00           H+0
HETATM   17  H   UNK     0       0.413   1.966  -1.381  0.00  0.00           H+0
HETATM   18  H   UNK     0       2.851   2.520  -1.516  0.00  0.00           H+0
HETATM   19  H   UNK     0       3.971  -1.145   1.261  0.00  0.00           H+0
HETATM   20  H   UNK     0       1.603  -1.804   1.481  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   14                                                  
CONECT    4    3    5   16                                                  
CONECT    5    4    6   12                                                  
CONECT    6    5    7   17                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7   18                                                       
CONECT    9    7   10   11                                                  
CONECT   10    9   19                                                       
CONECT   11    9   12   20                                                  
CONECT   12   11   13    5                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15    3                                                  
CONECT   15   14                                                            
CONECT   16    4                                                            
CONECT   17    6                                                            
CONECT   18    8                                                            
CONECT   19   10                                                            
CONECT   20   11                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   42    0
END

View in JSmol View NMR Assignments

Synonyms

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

Chemical Formula

C₁₀H₅NO₄

Average Mass

203.1530 Da

Monoisotopic Mass

203.02186 Da

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=C(O)C=C2C=C([N+]#[C-])C(=O)OC2=C1

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

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Pseudomonas aeruginosa	NPAtlas	18689486

Chemical Taxonomy

Classification

Not classified

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
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	18.64 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

External Links

NPAtlas ID

NPA018070

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB 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

Good Scents ID

Not Available

References

General References

Clarke-Pearson MF, Brady SF: Paerucumarin, a new metabolite produced by the pvc gene cluster from Pseudomonas aeruginosa. J Bacteriol. 2008 Oct;190(20):6927-30. doi: 10.1128/JB.00801-08. Epub 2008 Aug 8. [PubMed:18689486 ]
Qaisar U, Luo L, Haley CL, Brady SF, Carty NL, Colmer-Hamood JA, Hamood AN: The pvc operon regulates the expression of the Pseudomonas aeruginosa fimbrial chaperone/usher pathway (cup) genes. PLoS One. 2013 Apr 30;8(4):e62735. doi: 10.1371/journal.pone.0062735. Print 2013. [PubMed:23646138 ]
Qaisar U, Kruczek CJ, Azeem M, Javaid N, Colmer-Hamood JA, Hamood AN: The Pseudomonas aeruginosa extracellular secondary metabolite, Paerucumarin, chelates iron and is not localized to extracellular membrane vesicles. J Microbiol. 2016 Aug;54(8):573-81. doi: 10.1007/s12275-016-5645-3. Epub 2016 Aug 2. [PubMed:27480638 ]
Asif A, Iftikhar A, Hamood A, Colmer-Hamood JA, Qaisar U: Isonitrile-functionalized tyrosine modulates swarming motility and quorum sensing in Pseudomonas aeruginosa. Microb Pathog. 2019 Feb;127:288-295. doi: 10.1016/j.micpath.2018.12.001. Epub 2018 Dec 4. [PubMed:30528249 ]

Showing NP-Card for Paerucumarin (NP0007918)

MOL for NP0007918 (Paerucumarin)

3D MOL for NP0007918 (Paerucumarin)

3D SDF for NP0007918 (Paerucumarin)

3D-SDF for NP0007918 (Paerucumarin)

PDB for NP0007918 (Paerucumarin)

3D PDB for NP0007918 (Paerucumarin)

SMILES for NP0007918 (Paerucumarin)

INCHI for NP0007918 (Paerucumarin)

Structure for NP0007918 (Paerucumarin)

3D Structure for NP0007918 (Paerucumarin)