NP-MRD: Showing NP-Card for 3,5-Dihydroxybibenzyl (NP0051651)

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Record Information

Version

2.0

Created at

2022-04-27 22:56:21 UTC

Updated at

2022-04-27 22:56:21 UTC

NP-MRD ID

NP0051651

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3,5-Dihydroxybibenzyl

Description

Dihydropinosylvin belongs to the class of organic compounds known as stilbenes. These are organic compounds containing a 1,2-diphenylethylene moiety. Stilbenes (C6-C2-C6 ) are derived from the common phenylpropene (C6-C3) skeleton building block. The introduction of one or more hydroxyl groups to a phenyl ring lead to stilbenoids. Thus, dihydropinosylvin is considered to be an aromatic polyketide lipid molecule. 3,5-Dihydroxybibenzyl is found in Bauhinia purpurea, Dioscorea alata , Dioscorea batatas , Dioscorea cayenensis, Dioscorea japonica, Dioscorea mangenotiana, Dioscorea opposita , Dioscorea rotundata , Oroxylum indicum, Pinus albicaulis, Pinus armandii , Pinus ayacahuite, Pinus balfouriana, Pinus cembra , Pinus flexilis , Pinus parviflora, Pinus sibirica, Pinus sylvestris, Pseudomonas cichorii, Stemona cf. pierrei, Stemona cochinchinensis, Stemona collinsiae, Stemona involuta, Stemona japonica , Stemona kerrii, Stemona lucida, Stemona phyllantha, Stemona pierrei, Stemona sessilifolia and Stemona tuberosa . 3,5-Dihydroxybibenzyl was first documented in 1992 (PMID: 1536925). Dihydropinosylvin is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral (PMID: 15679323) (PMID: 23672042).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 30 31  0  0  0  0  0  0  0  0999 V2000
   -4.0321    2.5201    0.1230 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4484    1.2537    0.0315 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1572    0.1706   -0.4514 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5558   -1.0786   -0.5331 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3068   -2.1283   -1.0224 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2469   -1.2084   -0.1242 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5445   -0.1225    0.3571 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1218   -0.2270    0.8098 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7315    0.0503   -0.4161 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1816   -0.0201   -0.1138 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8416    1.1441    0.2952 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1848    1.0911    0.5780 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8696   -0.0923    0.4599 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2129   -1.2448    0.0543 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8651   -1.2113   -0.2339 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1404    1.1238    0.4400 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0000    3.1959   -0.6230 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1827    0.3061   -0.7640 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8378   -2.6642   -0.3267 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7668   -2.1759   -0.1827 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0392   -1.2588    1.1920 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0934    0.5145    1.6091 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4287   -0.6339   -1.2222 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4876    1.0994   -0.7290 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2732    2.0521    0.3764 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7140    2.0008    0.9005 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9144   -0.1120    0.6847 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7504   -2.1980   -0.0440 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3690   -2.1389   -0.5533 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6158    1.9925    0.8125 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2 16  2  0
 16  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
  7  6  2  0
  6  4  1  0
  4  5  1  0
  4  3  2  0
  3  2  1  0
 15 10  1  0
  1 17  1  0
 16 30  1  0
  8 21  1  0
  8 22  1  0
  9 23  1  0
  9 24  1  0
 11 25  1  0
 12 26  1  0
 13 27  1  0
 14 28  1  0
 15 29  1  0
  6 20  1  0
  5 19  1  0
  3 18  1  0
M  END


  Mrv1652309272007322D          

 16 17  0  0  0  0            999 V2000
10000.341610000.5934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.056410000.1815    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.488710000.5934    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9172 9998.1226    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.630510000.1820    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.916010000.5945    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.201510000.1819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.2015 9999.3570    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9159 9998.9445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.6305 9999.3570    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.198410001.4176    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.483910001.8300    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.769410001.4175    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.769310000.5926    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.483810000.1800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10003.198410000.5926    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  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  2  0  0  0  0
 10  5  1  0  0  0  0
 11 12  2  0  0  0  0
 12 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
 16 11  1  0  0  0  0
  2 14  1  0  0  0  0
  1  5  1  0  0  0  0
  7  3  1  0  0  0  0
  9  4  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0051651

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1=CC(CCC2=CC=CC=C2)=CC(O)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C14H14O2/c15-13-8-12(9-14(16)10-13)7-6-11-4-2-1-3-5-11/h1-5,8-10,15-16H,6-7H2

> <INCHI_KEY>
LDBYHULIXFIJAZ-UHFFFAOYSA-N

> <FORMULA>
C14H14O2

> <MOLECULAR_WEIGHT>
214.264

> <EXACT_MASS>
214.099379691

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
23.828532940261844

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-(2-phenylethyl)benzene-1,3-diol

> <ALOGPS_LOGP>
3.06

> <JCHEM_LOGP>
3.9024778646666665

> <ALOGPS_LOGS>
-3.29

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.80335787922153

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.351001563839601

> <JCHEM_PKA_STRONGEST_BASIC>
-5.665352397312362

> <JCHEM_POLAR_SURFACE_AREA>
40.46

> <JCHEM_REFRACTIVITY>
64.35800000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.11e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
dihydropinosylvin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 27-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-SEP-20         0                                  
HETATM    1  C   UNK     0    8667.3048667.774   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8668.6398667.005   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0    8661.9798667.774   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0    8664.6458663.162   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0    8665.9778667.006   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0    8664.6438667.776   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0    8663.3098667.006   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8663.3098665.466   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8664.6438664.696   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8665.9778665.466   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8672.6378669.313   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    8671.3038670.083   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0    8669.9708669.313   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0    8669.9698667.773   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8671.3038667.003   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8672.6378667.773   0.000  0.00  0.00           C+0
CONECT    1    2    5                                                       
CONECT    2    1   14                                                       
CONECT    3    7                                                            
CONECT    4    9                                                            
CONECT    5    6   10    1                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    3                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10    4                                                  
CONECT   10    9    5                                                       
CONECT   11   12   16                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15    2                                                  
CONECT   15   14   16                                                       
CONECT   16   15   11                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

View in JSmol

Synonyms

Value	Source
5-(2-Phenylethyl)resorcinol	ChEBI
5-(2-Phenylethyl)-1,3-benzenediol	PhytoBank
5-Phenethylresorcinol	PhytoBank
5-Phenethylbenzene-1,3-diol	PhytoBank

Chemical Formula

C₁₄H₁₄O₂

Average Mass

214.2640 Da

Monoisotopic Mass

214.09938 Da

IUPAC Name

5-(2-phenylethyl)benzene-1,3-diol

Traditional Name

dihydropinosylvin

CAS Registry Number

Not Available

SMILES

OC1=CC(CCC2=CC=CC=C2)=CC(O)=C1

InChI Identifier

InChI=1S/C14H14O2/c15-13-8-12(9-14(16)10-13)7-6-11-4-2-1-3-5-11/h1-5,8-10,15-16H,6-7H2

InChI Key

LDBYHULIXFIJAZ-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
Bauhinia purpurea	LOTUS Database	35616633
Dioscorea alata	Plant	KNApSAcK
Dioscorea batatas	Plant	KNApSAcK
Dioscorea cayenensis	LOTUS Database	35616633
Dioscorea japonica	LOTUS Database	35616633
Dioscorea mangenotiana	LOTUS Database	35616633
Dioscorea opposita	Plant	KNApSAcK
Dioscorea rotundata	Plant	KNApSAcK
Oroxylum indicum	LOTUS Database	35616633
Pinus albicaulis	Plant	KNApSAcK
Pinus armandii	Plant	KNApSAcK
Pinus ayacahuite	Plant	KNApSAcK
Pinus balfouriana	Plant	KNApSAcK
Pinus cembra	Plant	KNApSAcK
Pinus flexilis	Plant	KNApSAcK
Pinus parviflora	Plant	KNApSAcK
Pinus sibirica	Plant	KNApSAcK
Pinus sylvestris	LOTUS Database	35616633
Pseudomonas cichorii	LOTUS Database	35616633
Stemona cf. pierrei	Plant	KNApSAcK
Stemona cochinchinensis	Plant	KNApSAcK
Stemona collinsiae	Plant	KNApSAcK
Stemona involuta	Plant	KNApSAcK
Stemona japonica	Plant	KNApSAcK
Stemona kerrii	Plant	KNApSAcK
Stemona lucida	Plant	KNApSAcK
Stemona phyllantha	Plant	KNApSAcK
Stemona pierrei	Plant	KNApSAcK
Stemona sessilifolia	Plant	KNApSAcK
Stemona tuberosa	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as stilbenes. These are organic compounds containing a 1,2-diphenylethylene moiety. Stilbenes (C6-C2-C6 ) are derived from the common phenylpropene (C6-C3) skeleton building block. The introduction of one or more hydroxyl groups to a phenyl ring lead to stilbenoids.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Stilbenes

Sub Class

Not Available

Direct Parent

Stilbenes

Alternative Parents

Substituents

Stilbene
Resorcinol
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Benzenoid
Monocyclic benzene moiety
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

resorcinols (CHEBI:4579 )
diphenylethane (CHEBI:4579 )
Diphenyl ethers, biphenyls, dibenzyls and stilbenes (C10254 )
Bibenzyls (C10254 )
Diphenyl ethers, biphenyls, dibenzyls and stilbenes (LMPK13090034 )
a small molecule (CPD-6963 )

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	3.06	ALOGPS
logP	3.9	ChemAxon
logS	-3.3	ALOGPS
pKa (Strongest Acidic)	9.35	ChemAxon
pKa (Strongest Basic)	-5.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	40.46 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	64.36 m³·mol⁻¹	ChemAxon
Polarizability	23.83 Å³	ChemAxon
Number of Rings	2	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

C00002878

Chemspider ID

Not Available

KEGG Compound ID

C10254

BioCyc ID

CPD-6963

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

442700

PDB ID

Not Available

ChEBI ID

4579

Good Scents ID

Not Available

References

General References

Adams M, Pacher T, Greger H, Bauer R: Inhibition of leukotriene biosynthesis by stilbenoids from Stemona species. J Nat Prod. 2005 Jan;68(1):83-5. doi: 10.1021/np0497043. [PubMed:15679323 ]
Fliegmann J, Schroder G, Schanz S, Britsch L, Schroder J: Molecular analysis of chalcone and dihydropinosylvin synthase from Scots pine (Pinus sylvestris), and differential regulation of these and related enzyme activities in stressed plants. Plant Mol Biol. 1992 Feb;18(3):489-503. doi: 10.1007/BF00040665. [PubMed:1536925 ]
Wei XN, Lin BB, Xie GY, Li JW, Qin MJ: [Chemical constitunents of seeds of Oroxylum indicum]. Zhongguo Zhong Yao Za Zhi. 2013 Jan;38(2):204-7. [PubMed:23672042 ]

Showing NP-Card for 3,5-Dihydroxybibenzyl (NP0051651)

MOL for NP0051651 (3,5-Dihydroxybibenzyl)

3D MOL for NP0051651 (3,5-Dihydroxybibenzyl)

3D SDF for NP0051651 (3,5-Dihydroxybibenzyl)

3D-SDF for NP0051651 (3,5-Dihydroxybibenzyl)

PDB for NP0051651 (3,5-Dihydroxybibenzyl)

3D PDB for NP0051651 (3,5-Dihydroxybibenzyl)

SMILES for NP0051651 (3,5-Dihydroxybibenzyl)

INCHI for NP0051651 (3,5-Dihydroxybibenzyl)

Structure for NP0051651 (3,5-Dihydroxybibenzyl)

3D Structure for NP0051651 (3,5-Dihydroxybibenzyl)