NP-MRD: Showing NP-Card for sydowinin a (NP0224374)

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Record Information

Version

2.0

Created at

2022-09-06 02:43:12 UTC

Updated at

2022-09-06 02:43:13 UTC

NP-MRD ID

NP0224374

Secondary Accession Numbers

None

Natural Product Identification

Common Name

sydowinin a

Description

Sydowinin A 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. Sydowinin A is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 34 36  0  0  0  0  0  0  0  0999 V2000
    5.4664   -1.8398   -0.1242 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6319   -0.7342    0.1576 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2657   -0.6988   -0.2726 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9419   -1.7056   -0.8844 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5152    0.4755    0.0733 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2038    1.6802    0.3347 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5734    2.8573    0.6120 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2074    2.8573    0.6355 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4914    1.7246    0.3925 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8313    1.8087    0.4389 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6051    0.7953    0.2303 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9857    0.8557    0.2721 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7804   -0.2487    0.0441 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2771   -0.1465    0.0975 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6033    1.1745    0.3963 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1651   -1.4659   -0.2380 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7843   -1.5583   -0.2869 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1761   -2.7681   -0.5672 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0468   -0.4288   -0.0522 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3536   -0.5593   -0.1112 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8436   -1.6691   -0.3626 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1551    0.5357    0.1121 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9065   -2.7219   -0.4696 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2141   -1.5262   -0.9079 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0724   -2.0300    0.7916 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2792    1.6294    0.3048 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1558    3.7468    0.8033 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6745    3.7848    0.8536 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4393    1.8148    0.4937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6863   -0.3581   -0.9321 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7025   -0.8427    0.8539 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3709    1.5123   -0.1080 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8046   -2.3372   -0.4176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6931   -3.6138   -0.7437 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 22  2  0
 22 20  1  0
 20 21  2  0
 20 19  1  0
 19 17  2  0
 17 18  1  0
 17 16  1  0
 16 13  2  0
 13 14  1  0
 14 15  1  0
 13 12  1  0
 12 11  2  0
 11 10  1  0
 22  5  1  0
 11 19  1  0
 10  9  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  6 26  1  0
  7 27  1  0
  8 28  1  0
 18 34  1  0
 16 33  1  0
 14 30  1  0
 14 31  1  0
 15 32  1  0
 12 29  1  0
M  END

  Mrv1533004241501202D          

 22 24  0  0  0  0            999 V2000
    1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    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   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 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  1  0  0  0  0
 13 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  2  0  0  0  0
 11 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
  5 22  1  0  0  0  0
  9 22  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0224374

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C1=CC=CC2=C1C(=O)C1=C(O)C=C(CO)C=C1O2

> <INCHI_IDENTIFIER>
InChI=1S/C16H12O6/c1-21-16(20)9-3-2-4-11-13(9)15(19)14-10(18)5-8(7-17)6-12(14)22-11/h2-6,17-18H,7H2,1H3

> <INCHI_KEY>
UBYOEDLUKKPPPN-UHFFFAOYSA-N

> <FORMULA>
C16H12O6

> <MOLECULAR_WEIGHT>
300.266

> <EXACT_MASS>
300.063388106

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
29.849530522958204

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl 8-hydroxy-6-(hydroxymethyl)-9-oxo-9H-xanthene-1-carboxylate

> <ALOGPS_LOGP>
1.85

> <JCHEM_LOGP>
2.5422020953333333

> <ALOGPS_LOGS>
-3.41

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.95194561689934

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.228310618430662

> <JCHEM_PKA_STRONGEST_BASIC>
-2.91503368347251

> <JCHEM_POLAR_SURFACE_AREA>
93.06

> <JCHEM_REFRACTIVITY>
77.6384

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.17e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl 8-hydroxy-6-(hydroxymethyl)-9-oxoxanthene-1-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       5.335  -7.700   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      12.003  -2.310   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      12.003  -0.770   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       9.336  -6.930   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       6.668  -6.930   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   22                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   22                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   19                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   16                                                  
CONECT   14   13   15                                                       
CONECT   15   14                                                            
CONECT   16   13   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   11   20                                                  
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20    5    9                                                  
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₆H₁₂O₆

Average Mass

300.2660 Da

Monoisotopic Mass

300.06339 Da

IUPAC Name

methyl 8-hydroxy-6-(hydroxymethyl)-9-oxo-9H-xanthene-1-carboxylate

Traditional Name

methyl 8-hydroxy-6-(hydroxymethyl)-9-oxoxanthene-1-carboxylate

CAS Registry Number

Not Available

SMILES

COC(=O)C1=CC=CC2=C1C(=O)C1=C(O)C=C(CO)C=C1O2

InChI Identifier

InChI=1S/C16H12O6/c1-21-16(20)9-3-2-4-11-13(9)15(19)14-10(18)5-8(7-17)6-12(14)22-11/h2-6,17-18H,7H2,1H3

InChI Key

UBYOEDLUKKPPPN-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

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
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Pyranone
Pyran
Benzenoid
Heteroaromatic compound
Vinylogous acid
Methyl ester
Carboxylic acid ester
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Oxacycle
Primary alcohol
Organooxygen compound
Organic oxide
Organic oxygen compound
Hydrocarbon derivative
Alcohol
Aromatic alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

phenols (CHEBI:68227 )
aromatic ester (CHEBI:68227 )
xanthones (CHEBI:68227 )

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	1.85	ALOGPS
logP	2.54	ChemAxon
logS	-3.4	ALOGPS
pKa (Strongest Acidic)	8.23	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	93.06 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	77.64 m³·mol⁻¹	ChemAxon
Polarizability	29.85 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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

68227

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for sydowinin a (NP0224374)

MOL for NP0224374 (sydowinin a)

3D MOL for NP0224374 (sydowinin a)

3D SDF for NP0224374 (sydowinin a)

3D-SDF for NP0224374 (sydowinin a)

PDB for NP0224374 (sydowinin a)

3D PDB for NP0224374 (sydowinin a)

SMILES for NP0224374 (sydowinin a)

INCHI for NP0224374 (sydowinin a)

Structure for NP0224374 (sydowinin a)

3D Structure for NP0224374 (sydowinin a)