NP-MRD: Showing NP-Card for (1r,7s,8r)-1-[(2s,3r,4r)-3,4-dihydroxy-6-methyl-5-methylideneheptan-2-yl]-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-5-one (NP0234549)

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Record Information

Version

2.0

Created at

2022-09-06 16:38:49 UTC

Updated at

2022-09-06 16:38:49 UTC

NP-MRD ID

NP0234549

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,7s,8r)-1-[(2s,3r,4r)-3,4-dihydroxy-6-methyl-5-methylideneheptan-2-yl]-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-5-one

Description

Dolichosterone belongs to the class of organic compounds known as tetrahydroxy bile acids, alcohols and derivatives. These are prenol lipids structurally characterized by a bile acid or alcohol which bears four hydroxyl groups. (1r,7s,8r)-1-[(2s,3r,4r)-3,4-dihydroxy-6-methyl-5-methylideneheptan-2-yl]-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-5-one is found in Equisetum arvense, Phaseolus vulgaris and Vicia faba. (1r,7s,8r)-1-[(2s,3r,4r)-3,4-dihydroxy-6-methyl-5-methylideneheptan-2-yl]-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-5-one was first documented in 2005 (PMID: 15994910). Based on a literature review a small amount of articles have been published on Dolichosterone (PMID: 29432595) (PMID: 25092597).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309062218382D          

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M  END


  Mrv1652309062218382D          

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  3  5  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  0  0  0  0
  8  9  1  6  0  0  0
  8 10  1  0  0  0  0
 10 11  1  6  0  0  0
 12 10  1  1  0  0  0
 12 13  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
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  6  0  0  0
 22 24  1  0  0  0  0
 24 25  1  6  0  0  0
 24 26  1  0  0  0  0
 26 27  1  0  0  0  0
 20 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  1  0  0  0  0
 16 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 15 32  1  0  0  0  0
 12 32  1  0  0  0  0
 32 33  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0234549

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)C(=C)[C@@H](O)[C@H](O)[C@@H](C)[C@H]1CCC2C3CC(=O)C4C[C@H](O)[C@H](O)CC4(C)C3CCC12C

> <INCHI_IDENTIFIER>
InChI=1S/C28H46O5/c1-14(2)15(3)25(32)26(33)16(4)18-7-8-19-17-11-22(29)21-12-23(30)24(31)13-28(21,6)20(17)9-10-27(18,19)5/h14,16-21,23-26,30-33H,3,7-13H2,1-2,4-6H3/t16-,17?,18+,19?,20?,21?,23-,24+,25+,26+,27?,28?/m0/s1

> <INCHI_KEY>
CYPKCRFYMBXYBU-HXOLDDPBSA-N

> <FORMULA>
C28H46O5

> <MOLECULAR_WEIGHT>
462.671

> <EXACT_MASS>
462.334524581

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
79

> <JCHEM_AVERAGE_POLARIZABILITY>
53.18326489645122

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4R,5S,14R)-14-[(2S,3R,4R)-3,4-dihydroxy-6-methyl-5-methylideneheptan-2-yl]-4,5-dihydroxy-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-8-one

> <JCHEM_LOGP>
3.231926703000001

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.973368297020265

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.305617015583547

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1530299910083173

> <JCHEM_POLAR_SURFACE_AREA>
97.99000000000001

> <JCHEM_REFRACTIVITY>
128.92139999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(4R,5S,14R)-14-[(2S,3R,4R)-3,4-dihydroxy-6-methyl-5-methylideneheptan-2-yl]-4,5-dihydroxy-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-8-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  C   UNK     0      15.726  -2.359   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      15.726  -3.899   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      14.393  -4.669   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      13.059  -3.899   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      14.393  -6.209   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      17.060  -4.669   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      17.060  -6.209   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      18.394  -3.899   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      18.394  -2.359   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      19.728  -4.669   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      19.728  -6.209   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      21.061  -3.899   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      21.222  -2.367   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      22.729  -2.047   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      23.499  -3.381   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      25.005  -3.701   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      26.035  -2.556   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      27.542  -2.877   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      28.572  -1.732   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      28.018  -4.341   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      29.524  -4.661   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      30.000  -6.126   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      31.506  -6.446   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      28.969  -7.271   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      29.445  -8.735   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      27.463  -6.950   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      26.987  -5.486   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      25.957  -6.630   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      25.481  -5.166   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      24.450  -6.310   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      22.944  -5.990   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      22.468  -4.525   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      21.324  -5.556   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    2    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   32                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   32                                                  
CONECT   16   15   17   29                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   27                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   26   20   28   29                                             
CONECT   28   27                                                            
CONECT   29   27   16   30                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   15   12   33                                             
CONECT   33   32                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   72    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₄₆O₅

Average Mass

462.6710 Da

Monoisotopic Mass

462.33452 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CC(C)C(=C)[C@@H](O)[C@H](O)[C@@H](C)[C@H]1CCC2C3CC(=O)C4C[C@H](O)[C@H](O)CC4(C)C3CCC12C

InChI Identifier

InChI=1S/C28H46O5/c1-14(2)15(3)25(32)26(33)16(4)18-7-8-19-17-11-22(29)21-12-23(30)24(31)13-28(21,6)20(17)9-10-27(18,19)5/h14,16-21,23-26,30-33H,3,7-13H2,1-2,4-6H3/t16-,17?,18+,19?,20?,21?,23-,24+,25+,26+,27?,28?/m0/s1

InChI Key

CYPKCRFYMBXYBU-HXOLDDPBSA-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
Equisetum arvense	LOTUS Database	35616633
Phaseolus vulgaris	LOTUS Database	35616633
Vicia faba	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tetrahydroxy bile acids, alcohols and derivatives. These are prenol lipids structurally characterized by a bile acid or alcohol which bears four hydroxyl groups.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Bile acids, alcohols and derivatives

Direct Parent

Tetrahydroxy bile acids, alcohols and derivatives

Alternative Parents

Substituents

Ergostane-skeleton
Ergosterol-skeleton
Tetrahydroxy bile acid, alcohol, or derivatives
Ecdysteroid
23-hydroxysteroid
22-hydroxysteroid
6-oxosteroid
3-alpha-hydroxysteroid
Oxosteroid
Hydroxysteroid
2-hydroxysteroid
3-hydroxysteroid
Cyclic alcohol
Secondary alcohol
Ketone
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00000192

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

101587911

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Youn JH, Kim TW, Joo SH, Son SH, Roh J, Kim S, Kim TW, Kim SK: Function and molecular regulation of DWARF1 as a C-24 reductase in brassinosteroid biosynthesis in Arabidopsis. J Exp Bot. 2018 Apr 9;69(8):1873-1886. doi: 10.1093/jxb/ery038. [PubMed:29432595 ]
Wang L, Duan C, Wu D, Guan Y: Quantification of endogenous brassinosteroids in sub-gram plant tissues by in-line matrix solid-phase dispersion-tandem solid phase extraction coupled with high performance liquid chromatography-tandem mass spectrometry. J Chromatogr A. 2014 Sep 12;1359:44-51. doi: 10.1016/j.chroma.2014.07.037. Epub 2014 Jul 23. [PubMed:25092597 ]
Hong Z, Ueguchi-Tanaka M, Fujioka S, Takatsuto S, Yoshida S, Hasegawa Y, Ashikari M, Kitano H, Matsuoka M: The Rice brassinosteroid-deficient dwarf2 mutant, defective in the rice homolog of Arabidopsis DIMINUTO/DWARF1, is rescued by the endogenously accumulated alternative bioactive brassinosteroid, dolichosterone. Plant Cell. 2005 Aug;17(8):2243-54. doi: 10.1105/tpc.105.030973. Epub 2005 Jul 1. [PubMed:15994910 ]
LOTUS database [Link]

Showing NP-Card for (1r,7s,8r)-1-[(2s,3r,4r)-3,4-dihydroxy-6-methyl-5-methylideneheptan-2-yl]-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-5-one (NP0234549)

MOL for NP0234549 ((1r,7s,8r)-1-[(2s,3r,4r)-3,4-dihydroxy-6-methyl-5-methylideneheptan-2-yl]-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-5-one)

3D MOL for NP0234549 ((1r,7s,8r)-1-[(2s,3r,4r)-3,4-dihydroxy-6-methyl-5-methylideneheptan-2-yl]-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-5-one)

3D SDF for NP0234549 ((1r,7s,8r)-1-[(2s,3r,4r)-3,4-dihydroxy-6-methyl-5-methylideneheptan-2-yl]-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-5-one)

3D-SDF for NP0234549 ((1r,7s,8r)-1-[(2s,3r,4r)-3,4-dihydroxy-6-methyl-5-methylideneheptan-2-yl]-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-5-one)

PDB for NP0234549 ((1r,7s,8r)-1-[(2s,3r,4r)-3,4-dihydroxy-6-methyl-5-methylideneheptan-2-yl]-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-5-one)

3D PDB for NP0234549 ((1r,7s,8r)-1-[(2s,3r,4r)-3,4-dihydroxy-6-methyl-5-methylideneheptan-2-yl]-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-5-one)

SMILES for NP0234549 ((1r,7s,8r)-1-[(2s,3r,4r)-3,4-dihydroxy-6-methyl-5-methylideneheptan-2-yl]-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-5-one)

INCHI for NP0234549 ((1r,7s,8r)-1-[(2s,3r,4r)-3,4-dihydroxy-6-methyl-5-methylideneheptan-2-yl]-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-5-one)

Structure for NP0234549 ((1r,7s,8r)-1-[(2s,3r,4r)-3,4-dihydroxy-6-methyl-5-methylideneheptan-2-yl]-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-5-one)

3D Structure for NP0234549 ((1r,7s,8r)-1-[(2s,3r,4r)-3,4-dihydroxy-6-methyl-5-methylideneheptan-2-yl]-7,8-dihydroxy-9a,11a-dimethyl-tetradecahydrocyclopenta[a]phenanthren-5-one)