NP-MRD: Showing NP-Card for (3r,6r)-6-[(1r,3as,7ar)-4-{2-[(5s)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-hexahydro-1h-inden-1-yl]-2-methylheptane-2,3-diol (NP0237440)

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Record Information

Version

2.0

Created at

2022-09-06 20:34:20 UTC

Updated at

2022-09-06 20:34:20 UTC

NP-MRD ID

NP0237440

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3r,6r)-6-[(1r,3as,7ar)-4-{2-[(5s)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-hexahydro-1h-inden-1-yl]-2-methylheptane-2,3-diol

Description

55721-11-4 Belongs to the class of organic compounds known as vitamin d and derivatives. Vitamin D and derivatives are compounds containing a secosteroid backbone, usually secoergostane or secocholestane. (3r,6r)-6-[(1r,3as,7ar)-4-{2-[(5s)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-hexahydro-1h-inden-1-yl]-2-methylheptane-2,3-diol is found in Homo sapiens. Based on a literature review very few articles have been published on 55721-11-4.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309062222342D          

 30 32  0  0  1  0            999 V2000
    1.1355    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8500    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8500    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    4.5375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.9934    4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4782   -0.8205    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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    1.2949    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  8  9  2  0  0  0  0
  9 10  1  4  0  0  0
 10 11  2  0  0  0  0
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 11 17  1  0  0  0  0
 17 18  1  1  0  0  0
 18 19  1  0  0  0  0
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 21 22  1  6  0  0  0
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 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  1  0  0  0  0
 27 30  1  0  0  0  0
M  END

     RDKit          3D

 74 76  0  0  0  0  0  0  0  0999 V2000
    5.0670    1.2886    2.2668 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.5023    0.3995    0.0995 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4426   -0.7978    0.0674 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9954   -0.9587   -1.2877 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4621   -0.5336    1.1274 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5107   -1.4866    1.4348 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5749   -1.9219    0.5348 C   0  0  1  0  0  0  0  0  0  0  0  0
   -6.3166   -2.8910    1.3731 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6190   -0.9124    0.1387 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.6378   -1.7024   -0.4982 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.1621   -0.1120   -2.8590 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.1906   -1.6444    0.2456 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END


  Mrv1652309062222342D          

 30 32  0  0  1  0            999 V2000
    1.1355    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.2789    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.2789   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 27 30  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0237440

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H](CC[C@@H](O)C(C)(C)O)[C@H]1CC[C@H]2C(CCC[C@]12C)=CC=C1C[C@@H](O)CCC1=C

> <INCHI_IDENTIFIER>
InChI=1S/C27H44O3/c1-18-8-12-22(28)17-21(18)11-10-20-7-6-16-27(5)23(13-14-24(20)27)19(2)9-15-25(29)26(3,4)30/h10-11,19,22-25,28-30H,1,6-9,12-17H2,2-5H3/t19-,22+,23-,24+,25-,27-/m1/s1

> <INCHI_KEY>
FCKJYANJHNLEEP-SUUCIXNTSA-N

> <FORMULA>
C27H44O3

> <MOLECULAR_WEIGHT>
416.646

> <EXACT_MASS>
416.329045277

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
50.99937603848609

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,6R)-6-[(1R,3aS,7aR)-4-{2-[(5S)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-octahydro-1H-inden-1-yl]-2-methylheptane-2,3-diol

> <JCHEM_LOGP>
4.579442462666668

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.325111733971049

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.849642780244135

> <JCHEM_PKA_STRONGEST_BASIC>
-1.3184890847799178

> <JCHEM_POLAR_SURFACE_AREA>
60.69

> <JCHEM_REFRACTIVITY>
126.42209999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3R,6R)-6-[(1R,3aS,7aR)-4-{2-[(5S)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-hexahydro-1H-inden-1-yl]-2-methylheptane-2,3-diol

> <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       2.120   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.453   6.930   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.453   8.470   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.787   9.240   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.121   8.470   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       7.454   9.240   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       6.121   6.930   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.787   6.160   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.787   4.620   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.121   3.850   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.454   1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.454   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.121  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.626  -1.532   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.322   2.016   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.322  -0.476   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.846  -1.941   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       3.877  -3.085   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.340  -2.261   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.864  -3.725   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -0.642  -4.046   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -1.673  -2.901   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -1.118  -5.510   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -1.594  -6.975   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -2.583  -5.034   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       0.347  -5.986   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    2    9                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   17                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17   20                                             
CONECT   16   15                                                            
CONECT   17   15   11   18                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   15   21                                                  
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   29   30                                             
CONECT   28   27                                                            
CONECT   29   27                                                            
CONECT   30   27                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   64    0
END

View in JSmol

Synonyms

Value	Source
(24R)-24,25-Dihydroxyvitamin D3	MeSH
24,25 Dihydroxycholecalciferol	MeSH
24,25-Dihydroxycholecalciferol	MeSH
24,25-Dihydroxyvitamin D 3	MeSH
24,25-Dihydroxyvitamin D3	MeSH
24R,25 Dihydroxycholecalciferol	MeSH
Dihydroxyvitamin D3, 24,25	MeSH
24,25 Dihydroxyvitamin D 3	MeSH
24R,25-Dihydroxycholecalciferol	MeSH
24,25 Dihydroxyvitamin D3	MeSH
24,25-Dihydroxyvitamin D 3, (3beta,5Z,7E,24R)-isomer	MeSH

Chemical Formula

C₂₇H₄₄O₃

Average Mass

416.6460 Da

Monoisotopic Mass

416.32905 Da

IUPAC Name

(3R,6R)-6-[(1R,3aS,7aR)-4-{2-[(5S)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-octahydro-1H-inden-1-yl]-2-methylheptane-2,3-diol

Traditional Name

(3R,6R)-6-[(1R,3aS,7aR)-4-{2-[(5S)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-hexahydro-1H-inden-1-yl]-2-methylheptane-2,3-diol

CAS Registry Number

Not Available

SMILES

C[C@H](CC[C@@H](O)C(C)(C)O)[C@H]1CC[C@H]2C(CCC[C@]12C)=CC=C1C[C@@H](O)CCC1=C

InChI Identifier

InChI=1S/C27H44O3/c1-18-8-12-22(28)17-21(18)11-10-20-7-6-16-27(5)23(13-14-24(20)27)19(2)9-15-25(29)26(3,4)30/h10-11,19,22-25,28-30H,1,6-9,12-17H2,2-5H3/t19-,22+,23-,24+,25-,27-/m1/s1

InChI Key

FCKJYANJHNLEEP-SUUCIXNTSA-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
Homo sapiens	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as vitamin d and derivatives. Vitamin D and derivatives are compounds containing a secosteroid backbone, usually secoergostane or secocholestane.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Vitamin D and derivatives

Direct Parent

Vitamin D and derivatives

Alternative Parents

Substituents

Triterpenoid
Tertiary alcohol
Cyclic alcohol
Secondary alcohol
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
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	4.58	ChemAxon
pKa (Strongest Acidic)	13.85	ChemAxon
pKa (Strongest Basic)	-1.3	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	6	ChemAxon
Refractivity	126.42 m³·mol⁻¹	ChemAxon
Polarizability	51 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

426587

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

486588

PDB ID

Not Available

ChEBI ID

108603

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (3r,6r)-6-[(1r,3as,7ar)-4-{2-[(5s)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-hexahydro-1h-inden-1-yl]-2-methylheptane-2,3-diol (NP0237440)

MOL for NP0237440 ((3r,6r)-6-[(1r,3as,7ar)-4-{2-[(5s)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-hexahydro-1h-inden-1-yl]-2-methylheptane-2,3-diol)

3D MOL for NP0237440 ((3r,6r)-6-[(1r,3as,7ar)-4-{2-[(5s)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-hexahydro-1h-inden-1-yl]-2-methylheptane-2,3-diol)

3D SDF for NP0237440 ((3r,6r)-6-[(1r,3as,7ar)-4-{2-[(5s)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-hexahydro-1h-inden-1-yl]-2-methylheptane-2,3-diol)

3D-SDF for NP0237440 ((3r,6r)-6-[(1r,3as,7ar)-4-{2-[(5s)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-hexahydro-1h-inden-1-yl]-2-methylheptane-2,3-diol)

PDB for NP0237440 ((3r,6r)-6-[(1r,3as,7ar)-4-{2-[(5s)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-hexahydro-1h-inden-1-yl]-2-methylheptane-2,3-diol)

3D PDB for NP0237440 ((3r,6r)-6-[(1r,3as,7ar)-4-{2-[(5s)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-hexahydro-1h-inden-1-yl]-2-methylheptane-2,3-diol)

SMILES for NP0237440 ((3r,6r)-6-[(1r,3as,7ar)-4-{2-[(5s)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-hexahydro-1h-inden-1-yl]-2-methylheptane-2,3-diol)

INCHI for NP0237440 ((3r,6r)-6-[(1r,3as,7ar)-4-{2-[(5s)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-hexahydro-1h-inden-1-yl]-2-methylheptane-2,3-diol)

Structure for NP0237440 ((3r,6r)-6-[(1r,3as,7ar)-4-{2-[(5s)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-hexahydro-1h-inden-1-yl]-2-methylheptane-2,3-diol)

3D Structure for NP0237440 ((3r,6r)-6-[(1r,3as,7ar)-4-{2-[(5s)-5-hydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyl-hexahydro-1h-inden-1-yl]-2-methylheptane-2,3-diol)