NP-MRD: Showing NP-Card for 2,3,5,7-Tetrahydroxy-9,10-dihydrophenanthrene (NP0061042)

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Record Information

Version

2.0

Created at

2022-04-28 05:58:59 UTC

Updated at

2022-04-28 05:58:59 UTC

NP-MRD ID

NP0061042

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2,3,5,7-Tetrahydroxy-9,10-dihydrophenanthrene

Description

9,10-Dihydro-2,3,5,7-Phenanthrenetetrol, also known as 2,3,5,7-tetrahydroxy-9,10-dihydrophenanthrene, belongs to the class of organic compounds known as hydrophenanthrenes. These are a phenanthrene derivative where at least one ring CC bond is substituted by hydrogenation. 9,10-Dihydro-2,3,5,7-Phenanthrenetetrol is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, 9,10-Dihydro-2,3,5,7-Phenanthrenetetrol has been detected, but not quantified in, root vegetables. 2,3,5,7-Tetrahydroxy-9,10-dihydrophenanthrene is found in Cassia garrettiana, Dioscorea bulbifera and Senna garrettiana. This could make 9,10-dihydro-2,3,5,7-phenanthrenetetrol a potential biomarker for the consumption of these foods.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 30 32  0  0  0  0  0  0  0  0999 V2000
   -4.9398   -0.3481    0.3271 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5440   -0.3581    0.2426 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8228   -1.5203    0.2349 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4180   -1.5367    0.1501 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7676   -2.7477    0.1483 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7845   -0.3275    0.0741 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4879    0.8715    0.0796 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8722    0.8312    0.1649 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9069    2.2122    0.0026 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5532    2.2774   -0.0878 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2500    0.9902   -0.0903 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6362    1.0803   -0.1773 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4343   -0.0349   -0.1912 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8218    0.0964   -0.2796 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8216   -1.2401   -0.1166 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5825   -2.3886   -0.1272 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4300   -1.4060   -0.0269 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6717   -0.2620   -0.0163 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4536   -0.3729   -0.5479 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3084   -2.4674    0.2938 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2790   -3.6120    0.2062 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4439    1.7481    0.1711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2634    2.7736    0.9162 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4006    2.7613   -0.8499 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9834    2.8780    0.7662 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8449    2.8061   -1.0425 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1474    2.0488   -0.2384 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2912    0.9657   -0.3350 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1883   -3.3191   -0.0744 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0363   -2.3995    0.0278 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  4  6  2  0
  6  7  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 13 15  2  0
 15 16  1  0
 15 17  1  0
 17 18  2  0
  7  8  2  0
  8  2  1  0
 18  6  1  0
 18 11  1  0
  1 19  1  0
  3 20  1  0
  5 21  1  0
  9 23  1  0
  9 24  1  0
 10 25  1  0
 10 26  1  0
 12 27  1  0
 14 28  1  0
 16 29  1  0
 17 30  1  0
  8 22  1  0
M  END


  Mrv0541 05061311082D          

 18 20  0  0  0  0            999 V2000
    4.5079    0.6039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6829    0.6039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4454   -0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7454   -0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4454   -1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9204   -1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9204   -0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2704   -0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0329   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5079   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1579   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7454   -1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2704   -1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6829   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2079   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.9829   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1579   -2.2539    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6829   -2.2539    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  7  1  1  0  0  0  0
  7  4  2  0  0  0  0
  8  2  1  0  0  0  0
  8  3  2  0  0  0  0
  9  3  1  0  0  0  0
  9  5  2  0  0  0  0
 10  6  2  0  0  0  0
 10  7  1  0  0  0  0
 11  4  1  0  0  0  0
 12  6  1  0  0  0  0
 12 11  2  0  0  0  0
 13  5  1  0  0  0  0
 14  8  1  0  0  0  0
 14 10  1  0  0  0  0
 14 13  2  0  0  0  0
 15  9  1  0  0  0  0
 16 11  1  0  0  0  0
 17 12  1  0  0  0  0
 18 13  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0061042

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1=CC(O)=C2C(CCC3=CC(O)=C(O)C=C23)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C14H12O4/c15-9-3-8-2-1-7-4-11(16)12(17)6-10(7)14(8)13(18)5-9/h3-6,15-18H,1-2H2

> <INCHI_KEY>
NIGUICNPKCJLJQ-UHFFFAOYSA-N

> <FORMULA>
C14H12O4

> <MOLECULAR_WEIGHT>
244.2427

> <EXACT_MASS>
244.073558872

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
24.942593310101444

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
9,10-dihydrophenanthrene-2,3,5,7-tetrol

> <ALOGPS_LOGP>
1.63

> <JCHEM_LOGP>
2.9693267673333334

> <ALOGPS_LOGS>
-3.00

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.574537682420557

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.92498431563987

> <JCHEM_PKA_STRONGEST_BASIC>
-5.657146181168007

> <JCHEM_POLAR_SURFACE_AREA>
80.92

> <JCHEM_REFRACTIVITY>
67.39800000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.45e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
9,10-dihydrophenanthrene-2,3,5,7-tetrol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       8.415   1.127   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.875   1.127   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.565  -0.206   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.725  -0.206   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.565  -2.874   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.185  -2.874   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.185  -0.206   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.105  -0.206   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.795  -1.540   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.415  -1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      11.495  -1.540   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.725  -2.874   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.105  -2.874   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.875  -1.540   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       2.255  -1.540   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      13.035  -1.540   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      11.495  -4.207   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       6.875  -4.207   0.000  0.00  0.00           O+0
CONECT    1    2    7                                                       
CONECT    2    1    8                                                       
CONECT    3    8    9                                                       
CONECT    4    7   11                                                       
CONECT    5    9   13                                                       
CONECT    6   10   12                                                       
CONECT    7    1    4   10                                                  
CONECT    8    2    3   14                                                  
CONECT    9    3    5   15                                                  
CONECT   10    6    7   14                                                  
CONECT   11    4   12   16                                                  
CONECT   12    6   11   17                                                  
CONECT   13    5   14   18                                                  
CONECT   14    8   10   13                                                  
CONECT   15    9                                                            
CONECT   16   11                                                            
CONECT   17   12                                                            
CONECT   18   13                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   40    0
END

View in JSmol

Synonyms

Value	Source
2,3,5,7-Tetrahydroxy-9,10-dihydrophenanthrene	HMDB
2,4,6,7-Tetrahydroxy-9-10-dihydrophenanthrene	HMDB

Chemical Formula

C₁₄H₁₂O₄

Average Mass

244.2427 Da

Monoisotopic Mass

244.07356 Da

IUPAC Name

9,10-dihydrophenanthrene-2,3,5,7-tetrol

Traditional Name

9,10-dihydrophenanthrene-2,3,5,7-tetrol

CAS Registry Number

Not Available

SMILES

OC1=CC(O)=C2C(CCC3=CC(O)=C(O)C=C23)=C1

InChI Identifier

InChI=1S/C14H12O4/c15-9-3-8-2-1-7-4-11(16)12(17)6-10(7)14(8)13(18)5-9/h3-6,15-18H,1-2H2

InChI Key

NIGUICNPKCJLJQ-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
Cassia garrettiana	Plant	KNApSAcK
Dioscorea bulbifera	Plant	KNApSAcK
Senna garrettiana	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydrophenanthrenes. These are a phenanthrene derivative where at least one ring CC bond is substituted by hydrogenation.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Phenanthrenes and derivatives

Sub Class

Hydrophenanthrenes

Direct Parent

Hydrophenanthrenes

Alternative Parents

Substituents

Hydrophenanthrene
1-naphthol
2-naphthol
Naphthalene
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Polyol
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Aromatic homopolycyclic compound

Molecular Framework

Aromatic homopolycyclic compounds

External Descriptors

Not Available

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	1.63	ALOGPS
logP	2.97	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	8.92	ChemAxon
pKa (Strongest Basic)	-5.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	80.92 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	67.4 m³·mol⁻¹	ChemAxon
Polarizability	24.94 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

HMDB0039430

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB019025

KNApSAcK ID

C00015202

Chemspider ID

15356228

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

22753774

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for 2,3,5,7-Tetrahydroxy-9,10-dihydrophenanthrene (NP0061042)

MOL for NP0061042 (2,3,5,7-Tetrahydroxy-9,10-dihydrophenanthrene)

3D MOL for NP0061042 (2,3,5,7-Tetrahydroxy-9,10-dihydrophenanthrene)

3D SDF for NP0061042 (2,3,5,7-Tetrahydroxy-9,10-dihydrophenanthrene)

3D-SDF for NP0061042 (2,3,5,7-Tetrahydroxy-9,10-dihydrophenanthrene)

PDB for NP0061042 (2,3,5,7-Tetrahydroxy-9,10-dihydrophenanthrene)

3D PDB for NP0061042 (2,3,5,7-Tetrahydroxy-9,10-dihydrophenanthrene)

SMILES for NP0061042 (2,3,5,7-Tetrahydroxy-9,10-dihydrophenanthrene)

INCHI for NP0061042 (2,3,5,7-Tetrahydroxy-9,10-dihydrophenanthrene)

Structure for NP0061042 (2,3,5,7-Tetrahydroxy-9,10-dihydrophenanthrene)

3D Structure for NP0061042 (2,3,5,7-Tetrahydroxy-9,10-dihydrophenanthrene)