NP-MRD: Showing NP-Card for Lucidin (NP0051620)

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Record Information

Version

2.0

Created at

2022-04-27 22:55:21 UTC

Updated at

2022-04-27 22:55:21 UTC

NP-MRD ID

NP0051620

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Lucidin

Description

Lucidin belongs to the class of organic compounds known as hydroxyanthraquinones. Hydroxyanthraquinones are compounds containing a hydroxyanthraquinone moiety, which consists of an anthracene bearing a quinone, and hydroxyl group. Lucidin is found in Asperula odorata , Coelospermum paniculatum, Coelospermum reticulatum, Commitheca liebrechtsiana, Coprosma acerosa, Coprosma lucida, Coprosma rotundifolia, Faramea occidentalis, Galium mollugo, Galium rubioides, Galium spp., Morinda umbellata, Hymenodictyon excelsum , Hymenodictyon orixense, Lindera lucida, Morinda citrifolia , Morinda officinalis , Rubia tinctorum , Rubia wallichiana and Rubia wallichiana DECNE . Lucidin is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 30 32  0  0  0  0  0  0  0  0999 V2000
    1.2767   -2.7971    0.2839 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1545   -1.5625    0.1941 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3135   -0.6845    0.2725 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5792   -1.2089    0.4491 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6563   -0.3780    0.5210 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4847    0.9880    0.4175 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2479    1.5477    0.2420 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1572    0.6838    0.1706 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8014    1.1797   -0.0146 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6820    2.4166   -0.1042 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3800    0.3409   -0.0979 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2124   -1.0413    0.0062 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2917   -1.8938   -0.0646 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5567   -1.3741   -0.2409 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6496   -2.2565   -0.3114 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7760   -0.0235   -0.3489 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1431    0.5245   -0.5385 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1040    1.9150   -0.6195 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6676    0.8258   -0.2746 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9251    2.1406   -0.3847 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7257   -2.2766    0.5314 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6710   -0.7236    0.6580 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3373    1.6678    0.4730 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0705    2.5908    0.1577 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1039   -2.9661    0.0227 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4544   -3.2405   -0.2287 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6225    0.1355   -1.4627 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7672    0.2766    0.3599 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1564    2.2828    0.2979 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3472    2.9110   -0.3661 H   0  0  0  0  0  0  0  0  0  0  0  0
 18 17  1  0
 17 16  1  0
 16 14  2  0
 14 15  1  0
 14 13  1  0
 13 12  2  0
 12  2  1  0
  2  1  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
 11 19  2  0
 19 20  1  0
 19 16  1  0
 11 12  1  0
  8  3  1  0
 18 29  1  0
 17 27  1  0
 17 28  1  0
 15 26  1  0
 13 25  1  0
  4 21  1  0
  5 22  1  0
  6 23  1  0
  7 24  1  0
 20 30  1  0
M  END


  Mrv1533004241517452D          

 20 22  0  0  0  0            999 V2000
    0.7145   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -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
    0.7145   -1.2375    0.0000 O   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 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    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
    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
    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
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    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
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 10 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 16 18  1  0  0  0  0
  7 18  1  0  0  0  0
 18 19  2  0  0  0  0
  3 19  1  0  0  0  0
 19 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0051620

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1=C(O)C=C2C(=O)C3=CC=CC=C3C(=O)C2=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C15H10O5/c16-6-10-11(17)5-9-12(15(10)20)14(19)8-4-2-1-3-7(8)13(9)18/h1-5,16-17,20H,6H2

> <INCHI_KEY>
AMIDUPFSOUCLQB-UHFFFAOYSA-N

> <FORMULA>
C15H10O5

> <MOLECULAR_WEIGHT>
270.24

> <EXACT_MASS>
270.052823422

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
26.486915273876807

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1,3-dihydroxy-2-(hydroxymethyl)-9,10-dihydroanthracene-9,10-dione

> <ALOGPS_LOGP>
2.43

> <JCHEM_LOGP>
2.194225664

> <ALOGPS_LOGS>
-2.87

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.395660974062839

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.780002774417163

> <JCHEM_PKA_STRONGEST_BASIC>
-3.183380440685772

> <JCHEM_POLAR_SURFACE_AREA>
94.83

> <JCHEM_REFRACTIVITY>
71.9287

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.63e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
henine

> <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  O   UNK     0       1.334  -6.930   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       6.668  -0.770   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       6.668  -6.930   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   19                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8   18                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   10   16                                                  
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16    7   19                                                  
CONECT   19   18    3   20                                                  
CONECT   20   19                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

View in JSmol

Synonyms

Value	Source
1,3-Dihydroxy-2-hydroxymethyl-9,10-anthraquinone	MeSH

Chemical Formula

C₁₅H₁₀O₅

Average Mass

270.2400 Da

Monoisotopic Mass

270.05282 Da

IUPAC Name

1,3-dihydroxy-2-(hydroxymethyl)-9,10-dihydroanthracene-9,10-dione

Traditional Name

henine

CAS Registry Number

Not Available

SMILES

OCC1=C(O)C=C2C(=O)C3=CC=CC=C3C(=O)C2=C1O

InChI Identifier

InChI=1S/C15H10O5/c16-6-10-11(17)5-9-12(15(10)20)14(19)8-4-2-1-3-7(8)13(9)18/h1-5,16-17,20H,6H2

InChI Key

AMIDUPFSOUCLQB-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
Asperula odorata	Plant	KNApSAcK
Coelospermum paniculatum	LOTUS Database	35616633
Coelospermum reticulatum	Plant	KNApSAcK
Commitheca liebrechtsiana	-	KNApSAcK
Coprosma acerosa	LOTUS Database	35616633
Coprosma lucida	LOTUS Database	35616633
Coprosma rotundifolia	Plant	KNApSAcK
Faramea occidentalis	LOTUS Database	35616633
Galium mollugo	LOTUS Database	35616633
Galium rubioides	LOTUS Database	35616633
Galium spp.	Plant	KNApSAcK
Gynochthodes umbellata	Plant	KNApSAcK
Hymenodictyon excelsum	Plant	KNApSAcK
Hymenodictyon orixense	LOTUS Database	35616633
Lindera lucida	Plant	KNApSAcK
Morinda citrifolia	Plant	KNApSAcK
Morinda officinalis	Plant	KNApSAcK
Rubia tinctorum	Plant	KNApSAcK
Rubia wallichiana	LOTUS Database	35616633
Rubia wallichiana DECNE	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydroxyanthraquinones. Hydroxyanthraquinones are compounds containing a hydroxyanthraquinone moiety, which consists of an anthracene bearing a quinone, and hydroxyl group.

Kingdom

Super Class

Class

Sub Class

Direct Parent

Hydroxyanthraquinones

Alternative Parents

Substituents

Hydroxyanthraquinone
Aryl ketone
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Vinylogous acid
Ketone
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Aromatic alcohol
Primary alcohol
Organooxygen compound
Alcohol
Aromatic homopolycyclic compound

Molecular Framework

Aromatic homopolycyclic compounds

External Descriptors

hydroxyanthraquinones (CHEBI:6554 )
Anthraquinone type (C10369 )

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	2.43	ALOGPS
logP	2.19	ChemAxon
logS	-2.9	ALOGPS
pKa (Strongest Acidic)	7.78	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	94.83 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	71.93 m³·mol⁻¹	ChemAxon
Polarizability	26.49 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

C00002838

Chemspider ID

Not Available

KEGG Compound ID

C10369

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10163

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Lucidin (NP0051620)

MOL for NP0051620 (Lucidin)

3D MOL for NP0051620 (Lucidin)

3D SDF for NP0051620 (Lucidin)

3D-SDF for NP0051620 (Lucidin)

PDB for NP0051620 (Lucidin)

3D PDB for NP0051620 (Lucidin)

SMILES for NP0051620 (Lucidin)

INCHI for NP0051620 (Lucidin)

Structure for NP0051620 (Lucidin)

3D Structure for NP0051620 (Lucidin)