NP-MRD: Showing NP-Card for Flavidin (NP0051653)

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Record Information

Version

2.0

Created at

2022-04-27 22:56:24 UTC

Updated at

2022-04-27 22:56:24 UTC

NP-MRD ID

NP0051653

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Flavidin

Description

Flavidin belongs to the class of organic compounds known as phenanthrenes and derivatives. These are polycyclic compounds containing a phenanthrene moiety, which is a tricyclic aromatic compound with three non-linearly fused benzene. Flavidin is found in Acampe praemorsa, Arundina graminifolia, Bulbophyllum fuscopurpureum, Bulbophyllum protractum, Coelogyne barbata, Coelogyne elata, Coelogyne flavida, Coelogyne nitida, Coelogyne ovalis, Coelogyne stricta, Dendrobium pierardii, Otochilus fusta, Otochilus porrectus , Pholidota articulata and Pholidota imbricata. Flavidin is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 30 33  0  0  0  0  0  0  0  0999 V2000
   -4.7481   -0.1574   -0.6589 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3696   -0.0641   -0.4508 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5842   -1.1516   -0.7221 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2018   -1.0588   -0.5137 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6900    0.1213   -0.0448 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4765    1.2169    0.2292 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8624    1.1126    0.0163 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9232    2.4813    0.7327 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4354    2.4761    0.9007 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2700    1.4425    0.6580 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6393    1.5689    0.8769 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4469    0.4840    0.6132 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8072    0.6215    0.8346 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9233   -0.7002    0.1447 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5539   -0.8281   -0.0747 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7514    0.2524    0.1881 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0711   -2.1160   -0.5704 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3735   -2.2319   -0.8120 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2979   -0.4789    0.1280 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9500   -2.0944   -1.0911 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4709    1.9957    0.2403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4748    2.7751    1.6751 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1552    3.2406   -0.0698 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0667    2.5035    1.2485 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4133    0.9560    0.0769 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5697   -1.5274   -0.0525 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6048   -2.3153   -1.5310 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3835   -2.8768    0.1990 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7647   -3.1433   -0.2690 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5937   -2.5043   -1.9015 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  7  2  0
  7  6  1  0
  6  5  2  0
  5  4  1  0
  4 18  1  0
 18 17  1  0
 17 15  1  0
 15 14  2  0
 14 12  1  0
 12 13  1  0
 12 11  2  0
 11 10  1  0
 10  9  1  0
  9  8  1  0
 10 16  2  0
  4  3  2  0
  3  2  1  0
  8  6  1  0
 16  5  1  0
 16 15  1  0
  1 19  1  0
  7 21  1  0
 18 29  1  0
 18 30  1  0
 17 27  1  0
 17 28  1  0
 14 26  1  0
 13 25  1  0
 11 24  1  0
  8 22  1  0
  8 23  1  0
  3 20  1  0
M  END


  Mrv1533004241518472D          

 18 21  0  0  0  0            999 V2000
    0.8250    0.2211    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.2211    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.9355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875    0.9355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875    2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    3.0789    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    3.0789    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    2.3645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.9355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.9355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1250    1.6500    0.0000 O   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
  4  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
  3  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
  7 12  1  0  0  0  0
 10 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
  9 16  1  0  0  0  0
  1 16  1  0  0  0  0
 14 17  1  0  0  0  0
  5 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0051653

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1=CC2=C3C(CCC4=CC(O)=CC(OC2)=C34)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C15H12O3/c16-11-3-8-1-2-9-4-12(17)6-13-15(9)14(8)10(5-11)7-18-13/h3-6,16-17H,1-2,7H2

> <INCHI_KEY>
QMOLHJKSZMURCV-UHFFFAOYSA-N

> <FORMULA>
C15H12O3

> <MOLECULAR_WEIGHT>
240.258

> <EXACT_MASS>
240.078644246

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
25.34947897856248

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-oxatetracyclo[6.6.2.0⁴,¹⁶.0¹¹,¹⁵]hexadeca-1(15),4(16),5,7,11,13-hexaene-6,13-diol

> <ALOGPS_LOGP>
2.49

> <JCHEM_LOGP>
3.170013446333333

> <ALOGPS_LOGS>
-3.00

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.852609221395987

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.114629128203921

> <JCHEM_PKA_STRONGEST_BASIC>
-4.896258809535004

> <JCHEM_POLAR_SURFACE_AREA>
49.69

> <JCHEM_REFRACTIVITY>
68.45400000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.40e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-oxatetracyclo[6.6.2.0⁴,¹⁶.0¹¹,¹⁵]hexadeca-1(15),4(16),5,7,11,13-hexaene-6,13-diol

> <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       1.540   0.413   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.080   0.413   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.850   1.746   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.390   1.746   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.160   3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.390   4.414   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.850   4.414   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.080   3.080   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.540   3.080   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.770   4.414   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.540   5.747   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       3.080   5.747   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -0.770   4.414   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.540   3.080   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.770   1.746   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.770   1.746   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -3.080   3.080   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       7.700   3.080   0.000  0.00  0.00           O+0
CONECT    1    2   16                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   18                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   12                                                  
CONECT    8    7    3    9                                                  
CONECT    9    8   10   16                                                  
CONECT   10    9   11   13                                                  
CONECT   11   10   12                                                       
CONECT   12   11    7                                                       
CONECT   13   10   14                                                       
CONECT   14   13   15   17                                                  
CONECT   15   14   16                                                       
CONECT   16   15    9    1                                                  
CONECT   17   14                                                            
CONECT   18    5                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   42    0
END

View in JSmol

Synonyms

Value	Source
9,10-Dihydro-5H-phenanthro[4,5-BCD]pyran-2,7-diol	Kegg
2,7-Dihydroxy-9,10-dihydro-phenanthro-4,5-BCD-pyran	MeSH

Chemical Formula

C₁₅H₁₂O₃

Average Mass

240.2580 Da

Monoisotopic Mass

240.07864 Da

IUPAC Name

2-oxatetracyclo[6.6.2.0⁴,¹⁶.0¹¹,¹⁵]hexadeca-1(15),4(16),5,7,11,13-hexaene-6,13-diol

Traditional Name

2-oxatetracyclo[6.6.2.0⁴,¹⁶.0¹¹,¹⁵]hexadeca-1(15),4(16),5,7,11,13-hexaene-6,13-diol

CAS Registry Number

Not Available

SMILES

OC1=CC2=C3C(CCC4=CC(O)=CC(OC2)=C34)=C1

InChI Identifier

InChI=1S/C15H12O3/c16-11-3-8-1-2-9-4-12(17)6-13-15(9)14(8)10(5-11)7-18-13/h3-6,16-17H,1-2,7H2

InChI Key

QMOLHJKSZMURCV-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
Acampe praemorsa	LOTUS Database	35616633
Arundina graminifolia	LOTUS Database	35616633
Bulbophyllum fuscopurpureum	Plant	KNApSAcK
Bulbophyllum protractum	LOTUS Database	35616633
Coelogyne barbata	Plant	KNApSAcK
Coelogyne elata	Plant	KNApSAcK
Coelogyne flavida	Plant	KNApSAcK
Coelogyne nitida	Plant	KNApSAcK
Coelogyne ovalis	Plant	KNApSAcK
Coelogyne stricta	LOTUS Database	35616633
Dendrobium pierardii	Plant	KNApSAcK
Otochilus fusta	Plant	KNApSAcK
Otochilus porrectus	Plant	KNApSAcK
Pholidota articulata	Plant	KNApSAcK
Pholidota imbricata	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenanthrenes and derivatives. These are polycyclic compounds containing a phenanthrene moiety, which is a tricyclic aromatic compound with three non-linearly fused benzene.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Phenanthrenes and derivatives

Sub Class

Not Available

Direct Parent

Phenanthrenes and derivatives

Alternative Parents

Substituents

Phenanthrene
Dibenzopyran
2-benzopyran
1-benzopyran
Naphthalene
Benzopyran
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Oxacycle
Organoheterocyclic compound
Ether
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

phenanthrenes (CHEBI:5072 )
Dihydrophenanthrenes (C10258 )

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	2.49	ALOGPS
logP	3.17	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	9.11	ChemAxon
pKa (Strongest Basic)	-4.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	49.69 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	68.45 m³·mol⁻¹	ChemAxon
Polarizability	25.35 Å³	ChemAxon
Number of Rings	4	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

C00002881

Chemspider ID

Not Available

KEGG Compound ID

C10258

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

158594

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Flavidin (NP0051653)

MOL for NP0051653 (Flavidin)

3D MOL for NP0051653 (Flavidin)

3D SDF for NP0051653 (Flavidin)

3D-SDF for NP0051653 (Flavidin)

PDB for NP0051653 (Flavidin)

3D PDB for NP0051653 (Flavidin)

SMILES for NP0051653 (Flavidin)

INCHI for NP0051653 (Flavidin)

Structure for NP0051653 (Flavidin)

3D Structure for NP0051653 (Flavidin)