NP-MRD: Showing NP-Card for 3a-(hydroxymethyl)-5a,5b,8,8,11a-pentamethyl-1-(prop-1-en-2-yl)-hexadecahydrocyclopenta[a]chrysene-9,10-diol (NP0269643)

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Record Information

Version

1.0

Created at

2022-09-08 15:12:35 UTC

Updated at

2022-09-08 15:12:35 UTC

NP-MRD ID

NP0269643

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3a-(hydroxymethyl)-5a,5b,8,8,11a-pentamethyl-1-(prop-1-en-2-yl)-hexadecahydrocyclopenta[a]chrysene-9,10-diol

Description

(2Alpha,3beta)-20(29)-Lupene-2,3,28-triol belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units (2alpha,3beta)-20(29)-Lupene-2,3,28-triol is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, (2alpha,3beta)-20(29)-lupene-2,3,28-triol has been detected, but not quantified in, green vegetables. 3a-(hydroxymethyl)-5a,5b,8,8,11a-pentamethyl-1-(prop-1-en-2-yl)-hexadecahydrocyclopenta[a]chrysene-9,10-diol is found in Rheum rhabarbarum. It was first documented in 2000 (PMID: 11413487). This could make (2alpha,3beta)-20(29)-lupene-2,3,28-triol a potential biomarker for the consumption of these foods (PMID: 16902246) (PMID: 17374880) (PMID: 20044567).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 05061312272D          

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  Mrv0541 05061312272D          

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   -2.1388   -2.2310    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6094   -2.8621    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8539   -1.8184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5689   -2.2310    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0006   -0.1644    0.0000 C   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
  1 29  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4 13  1  0  0  0  0
  4 26  1  0  0  0  0
  4 33  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6 13  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 31  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 11 18  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 26  1  0  0  0  0
 17 18  1  0  0  0  0
 17 21  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 24  1  0  0  0  0
 22 23  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 29 31  1  0  0  0  0
 31 32  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0269643

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=C)C1CCC2(CO)CCC3(C)C(CCC4C5(C)CC(O)C(O)C(C)(C)C5CCC34C)C12

> <INCHI_IDENTIFIER>
InChI=1S/C30H50O3/c1-18(2)19-10-13-30(17-31)15-14-28(6)20(24(19)30)8-9-23-27(5)16-21(32)25(33)26(3,4)22(27)11-12-29(23,28)7/h19-25,31-33H,1,8-17H2,2-7H3

> <INCHI_KEY>
YTLCVRQYWKFDSE-UHFFFAOYSA-N

> <FORMULA>
C30H50O3

> <MOLECULAR_WEIGHT>
458.7162

> <EXACT_MASS>
458.375995466

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
55.75946441316199

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-(hydroxymethyl)-1,2,14,18,18-pentamethyl-8-(prop-1-en-2-yl)pentacyclo[11.8.0.0²,¹⁰.0⁵,⁹.0¹⁴,¹⁹]henicosane-16,17-diol

> <ALOGPS_LOGP>
4.57

> <JCHEM_LOGP>
5.092371717333333

> <ALOGPS_LOGS>
-5.52

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.15581299250422

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.627318408158253

> <JCHEM_PKA_STRONGEST_BASIC>
-1.1149820300621665

> <JCHEM_POLAR_SURFACE_AREA>
60.69

> <JCHEM_REFRACTIVITY>
134.0445

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.39e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-(hydroxymethyl)-1,2,14,18,18-pentamethyl-8-(prop-1-en-2-yl)pentacyclo[11.8.0.0²,¹⁰.0⁵,⁹.0¹⁴,¹⁹]henicosane-16,17-diol

> <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      -2.660  -3.394   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.326  -4.165   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.006  -3.394   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.006  -1.854   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.660  -0.314   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.660  -1.854   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.992  -1.084   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -5.327  -1.854   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -6.662  -1.084   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.440   5.343   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.965   3.877   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.458   3.556   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.326  -1.084   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.326   0.455   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.006   1.226   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.341   0.455   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.676   1.226   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.994   2.732   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.526   2.894   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.153   1.487   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.008   0.455   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.414  -0.171   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       6.662   0.735   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       4.008  -1.084   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.676  -1.854   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       1.341  -1.084   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.341  -2.624   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -4.983  -5.343   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -3.992  -4.165   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -3.004  -5.343   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -5.327  -3.394   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -6.662  -4.165   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      -0.001  -0.307   0.000  0.00  0.00           C+0
CONECT    1    2    6   29                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3   13   26   33                                             
CONECT    5    6                                                            
CONECT    6    1    5    7   13                                             
CONECT    7    6    8                                                       
CONECT    8    7    9   31                                                  
CONECT    9    8                                                            
CONECT   10   11                                                            
CONECT   11   10   12   18                                                  
CONECT   12   11                                                            
CONECT   13    4    6   14                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   26                                                  
CONECT   17   16   18   21                                                  
CONECT   18   11   17   19                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   17   20   22   24                                             
CONECT   22   21   23                                                       
CONECT   23   22                                                            
CONECT   24   21   25                                                       
CONECT   25   24   26                                                       
CONECT   26    4   16   25   27                                             
CONECT   27   26                                                            
CONECT   28   29                                                            
CONECT   29    1   28   30   31                                             
CONECT   30   29                                                            
CONECT   31    8   29   32                                                  
CONECT   32   31                                                            
CONECT   33    4                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   74    0
END

View in JSmol

Synonyms

Value	Source
(2a,3b)-20(29)-Lupene-2,3,28-triol	Generator
(2Α,3β)-20(29)-lupene-2,3,28-triol	Generator

Chemical Formula

C₃₀H₅₀O₃

Average Mass

458.7162 Da

Monoisotopic Mass

458.37600 Da

IUPAC Name

5-(hydroxymethyl)-1,2,14,18,18-pentamethyl-8-(prop-1-en-2-yl)pentacyclo[11.8.0.0²,¹⁰.0⁵,⁹.0¹⁴,¹⁹]henicosane-16,17-diol

Traditional Name

5-(hydroxymethyl)-1,2,14,18,18-pentamethyl-8-(prop-1-en-2-yl)pentacyclo[11.8.0.0²,¹⁰.0⁵,⁹.0¹⁴,¹⁹]henicosane-16,17-diol

CAS Registry Number

Not Available

SMILES

CC(=C)C1CCC2(CO)CCC3(C)C(CCC4C5(C)CC(O)C(O)C(C)(C)C5CCC34C)C12

InChI Identifier

InChI=1S/C30H50O3/c1-18(2)19-10-13-30(17-31)15-14-28(6)20(24(19)30)8-9-23-27(5)16-21(32)25(33)26(3,4)22(27)11-12-29(23,28)7/h19-25,31-33H,1,8-17H2,2-7H3

InChI Key

YTLCVRQYWKFDSE-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
Rheum rhabarbarum	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

Not Available

Substituents

Not Available

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	4.57	ALOGPS
logP	5.09	ChemAxon
logS	-5.5	ALOGPS
pKa (Strongest Acidic)	13.63	ChemAxon
pKa (Strongest Basic)	-1.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	60.69 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	134.04 m³·mol⁻¹	ChemAxon
Polarizability	55.76 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0041183

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB021079

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

74976566

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
LOTUS database [Link]

Showing NP-Card for 3a-(hydroxymethyl)-5a,5b,8,8,11a-pentamethyl-1-(prop-1-en-2-yl)-hexadecahydrocyclopenta[a]chrysene-9,10-diol (NP0269643)

MOL for NP0269643 (3a-(hydroxymethyl)-5a,5b,8,8,11a-pentamethyl-1-(prop-1-en-2-yl)-hexadecahydrocyclopenta[a]chrysene-9,10-diol)

3D MOL for NP0269643 (3a-(hydroxymethyl)-5a,5b,8,8,11a-pentamethyl-1-(prop-1-en-2-yl)-hexadecahydrocyclopenta[a]chrysene-9,10-diol)

3D SDF for NP0269643 (3a-(hydroxymethyl)-5a,5b,8,8,11a-pentamethyl-1-(prop-1-en-2-yl)-hexadecahydrocyclopenta[a]chrysene-9,10-diol)

3D-SDF for NP0269643 (3a-(hydroxymethyl)-5a,5b,8,8,11a-pentamethyl-1-(prop-1-en-2-yl)-hexadecahydrocyclopenta[a]chrysene-9,10-diol)

PDB for NP0269643 (3a-(hydroxymethyl)-5a,5b,8,8,11a-pentamethyl-1-(prop-1-en-2-yl)-hexadecahydrocyclopenta[a]chrysene-9,10-diol)

3D PDB for NP0269643 (3a-(hydroxymethyl)-5a,5b,8,8,11a-pentamethyl-1-(prop-1-en-2-yl)-hexadecahydrocyclopenta[a]chrysene-9,10-diol)

SMILES for NP0269643 (3a-(hydroxymethyl)-5a,5b,8,8,11a-pentamethyl-1-(prop-1-en-2-yl)-hexadecahydrocyclopenta[a]chrysene-9,10-diol)

INCHI for NP0269643 (3a-(hydroxymethyl)-5a,5b,8,8,11a-pentamethyl-1-(prop-1-en-2-yl)-hexadecahydrocyclopenta[a]chrysene-9,10-diol)

Structure for NP0269643 (3a-(hydroxymethyl)-5a,5b,8,8,11a-pentamethyl-1-(prop-1-en-2-yl)-hexadecahydrocyclopenta[a]chrysene-9,10-diol)

3D Structure for NP0269643 (3a-(hydroxymethyl)-5a,5b,8,8,11a-pentamethyl-1-(prop-1-en-2-yl)-hexadecahydrocyclopenta[a]chrysene-9,10-diol)