NP-MRD: Showing NP-Card for 3,10-dihydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,3,4,5,6,7,8,8a,10,11,12,12b,13,14b-tetradecahydropicene-4a-carboxylic acid (NP0290628)

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Record Information

Version

2.0

Created at

2022-09-09 21:23:46 UTC

Updated at

2022-09-09 21:23:46 UTC

NP-MRD ID

NP0290628

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3,10-dihydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,3,4,5,6,7,8,8a,10,11,12,12b,13,14b-tetradecahydropicene-4a-carboxylic acid

Description

21Beta-Hydroxyhederagenin belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. 21Beta-Hydroxyhederagenin is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, 21beta-Hydroxyhederagenin has been detected, but not quantified in, fruits. 3,10-dihydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,3,4,5,6,7,8,8a,10,11,12,12b,13,14b-tetradecahydropicene-4a-carboxylic acid is found in Nigella glandulifera. This could make 21beta-hydroxyhederagenin a potential biomarker for the consumption of these foods.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 02241210582D          

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M  END

     RDKit          3D

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M  END


  Mrv0541 02241210582D          

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    3.5643    2.4203    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8559    0.3638    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8559   -0.4631    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5726    0.7774    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7152   -0.8725    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0027    0.3694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4266    0.3694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5726   -1.6981    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  6  1  0  0  0  0
  2  3  1  0  0  0  0
  2 35  1  0  0  0  0
  3  4  1  0  0  0  0
  3 23  1  0  0  0  0
  3 24  1  0  0  0  0
  4  5  1  0  0  0  0
  4  7  1  0  0  0  0
  5  6  1  0  0  0  0
  5 10  1  0  0  0  0
  5 34  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
  9 33  1  0  0  0  0
 10 14  1  0  0  0  0
 11 12  1  0  0  0  0
 11 15  1  0  0  0  0
 11 32  1  0  0  0  0
 12 13  2  0  0  0  0
 12 18  1  0  0  0  0
 13 14  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 17 29  1  0  0  0  0
 18 22  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 28  1  0  0  0  0
 21 22  1  0  0  0  0
 21 26  1  0  0  0  0
 21 27  1  0  0  0  0
 24 25  1  0  0  0  0
 29 30  2  0  0  0  0
 29 31  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0290628

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1(C)CC2C3=CCC4C5(C)CCC(O)C(C)(CO)C5CCC4(C)C3(C)CCC2(CC1O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C30H48O5/c1-25(2)15-19-18-7-8-21-26(3)11-10-22(32)27(4,17-31)20(26)9-12-29(21,6)28(18,5)13-14-30(19,24(34)35)16-23(25)33/h7,19-23,31-33H,8-17H2,1-6H3,(H,34,35)

> <INCHI_KEY>
SQDDCZCCYJZMCV-UHFFFAOYSA-N

> <FORMULA>
C30H48O5

> <MOLECULAR_WEIGHT>
488.6991

> <EXACT_MASS>
488.350174646

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
56.98245216323162

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3,10-dihydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,12b,13,14b-icosahydropicene-4a-carboxylic acid

> <ALOGPS_LOGP>
5.00

> <JCHEM_LOGP>
4.083251209666667

> <ALOGPS_LOGS>
-4.73

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.28197332586332

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.6435779385659455

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7854425934406057

> <JCHEM_POLAR_SURFACE_AREA>
97.99000000000001

> <JCHEM_REFRACTIVITY>
136.91469999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.06e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3,10-dihydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,3,4,5,6,7,8,8a,10,11,12,12b,13,14b-tetradecahydropicene-4a-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -5.331  -0.854   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.331  -2.398   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.996  -3.170   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.663  -2.398   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.663  -0.854   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.996  -0.085   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.328  -3.170   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.005  -2.398   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.005  -0.854   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.328  -0.085   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.335  -0.085   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.335   1.451   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.005   2.218   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.328   1.451   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.665  -0.852   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.993  -0.085   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.993   1.451   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.665   2.215   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.318   2.215   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.318   3.746   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       3.993   4.507   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.665   3.746   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -4.767  -4.508   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -3.224  -4.508   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -3.996  -5.846   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       3.221   5.846   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       4.765   5.846   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       6.653   4.518   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       5.331   0.679   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       5.331  -0.864   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       6.669   1.451   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       1.335  -1.629   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       0.005   0.690   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -2.663   0.690   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -6.669  -3.170   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3   35                                                  
CONECT    3    2    4   23   24                                             
CONECT    4    3    5    7                                                  
CONECT    5    4    6   10   34                                             
CONECT    6    1    5                                                       
CONECT    7    4    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11   33                                             
CONECT   10    5    9   14                                                  
CONECT   11    9   12   15   32                                             
CONECT   12   11   13   18                                                  
CONECT   13   12   14                                                       
CONECT   14   10   13                                                       
CONECT   15   11   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19   29                                             
CONECT   18   12   17   22                                                  
CONECT   19   17   20                                                       
CONECT   20   19   21   28                                                  
CONECT   21   20   22   26   27                                             
CONECT   22   18   21                                                       
CONECT   23    3                                                            
CONECT   24    3   25                                                       
CONECT   25   24                                                            
CONECT   26   21                                                            
CONECT   27   21                                                            
CONECT   28   20                                                            
CONECT   29   17   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29                                                            
CONECT   32   11                                                            
CONECT   33    9                                                            
CONECT   34    5                                                            
CONECT   35    2                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   78    0
END

View in JSmol

Synonyms

Value	Source
21b-Hydroxyhederagenin	Generator
21Β-hydroxyhederagenin	Generator
3,10-Dihydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,12b,13,14b-icosahydropicene-4a-carboxylate	Generator

Chemical Formula

C₃₀H₄₈O₅

Average Mass

488.6991 Da

Monoisotopic Mass

488.35017 Da

IUPAC Name

3,10-dihydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,2,3,4,4a,5,6,6a,6b,7,8,8a,9,10,11,12,12a,12b,13,14b-icosahydropicene-4a-carboxylic acid

Traditional Name

3,10-dihydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,3,4,5,6,7,8,8a,10,11,12,12b,13,14b-tetradecahydropicene-4a-carboxylic acid

CAS Registry Number

Not Available

SMILES

CC1(C)CC2C3=CCC4C5(C)CCC(O)C(C)(CO)C5CCC4(C)C3(C)CCC2(CC1O)C(O)=O

InChI Identifier

InChI=1S/C30H48O5/c1-25(2)15-19-18-7-8-21-26(3)11-10-22(32)27(4,17-31)20(26)9-12-29(21,6)28(18,5)13-14-30(19,24(34)35)16-23(25)33/h7,19-23,31-33H,8-17H2,1-6H3,(H,34,35)

InChI Key

SQDDCZCCYJZMCV-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

Species Name	Source	Reference
Nigella glandulifera	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Triterpenoids

Direct Parent

Triterpenoids

Alternative Parents

Substituents

Triterpenoid
Steroid
Cyclic alcohol
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic 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	5	ALOGPS
logP	4.08	ChemAxon
logS	-4.7	ALOGPS
pKa (Strongest Acidic)	4.64	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	97.99 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	136.91 m³·mol⁻¹	ChemAxon
Polarizability	56.98 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0041039

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB020911

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

14158843

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 3,10-dihydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,3,4,5,6,7,8,8a,10,11,12,12b,13,14b-tetradecahydropicene-4a-carboxylic acid (NP0290628)

MOL for NP0290628 (3,10-dihydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,3,4,5,6,7,8,8a,10,11,12,12b,13,14b-tetradecahydropicene-4a-carboxylic acid)

3D MOL for NP0290628 (3,10-dihydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,3,4,5,6,7,8,8a,10,11,12,12b,13,14b-tetradecahydropicene-4a-carboxylic acid)

3D SDF for NP0290628 (3,10-dihydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,3,4,5,6,7,8,8a,10,11,12,12b,13,14b-tetradecahydropicene-4a-carboxylic acid)

3D-SDF for NP0290628 (3,10-dihydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,3,4,5,6,7,8,8a,10,11,12,12b,13,14b-tetradecahydropicene-4a-carboxylic acid)

PDB for NP0290628 (3,10-dihydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,3,4,5,6,7,8,8a,10,11,12,12b,13,14b-tetradecahydropicene-4a-carboxylic acid)

3D PDB for NP0290628 (3,10-dihydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,3,4,5,6,7,8,8a,10,11,12,12b,13,14b-tetradecahydropicene-4a-carboxylic acid)

SMILES for NP0290628 (3,10-dihydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,3,4,5,6,7,8,8a,10,11,12,12b,13,14b-tetradecahydropicene-4a-carboxylic acid)

INCHI for NP0290628 (3,10-dihydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,3,4,5,6,7,8,8a,10,11,12,12b,13,14b-tetradecahydropicene-4a-carboxylic acid)

Structure for NP0290628 (3,10-dihydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,3,4,5,6,7,8,8a,10,11,12,12b,13,14b-tetradecahydropicene-4a-carboxylic acid)

3D Structure for NP0290628 (3,10-dihydroxy-9-(hydroxymethyl)-2,2,6a,6b,9,12a-hexamethyl-1,3,4,5,6,7,8,8a,10,11,12,12b,13,14b-tetradecahydropicene-4a-carboxylic acid)