NP-MRD: Showing NP-Card for Tenacigenin D (NP0331754)

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Record Information

Version

1.0

Created at

2023-08-01 08:42:46 UTC

Updated at

2024-05-09 01:52:14 UTC

NP-MRD ID

NP0331754

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Tenacigenin D

Description

Not Available

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 08012308422D          

 27 32  0  0  1  0            999 V2000
   -2.9533   -0.7634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1524   -0.5652    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5804   -1.1597    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9236    0.2275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1228    0.4256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5507   -0.1688    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3305    0.6262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7795   -0.9615    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2600   -1.6273    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6165   -1.4126    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0577   -0.5838    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2922    0.0591    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2574    0.8834    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1933   -0.4471    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1788   -1.2681    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7009    0.5000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4063    1.2706    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5932    0.1759    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0499    0.8630    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9242   -0.1824    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5011    0.4074    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6813   -0.8513    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8292   -0.1547    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0855   -0.8227    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1688   -1.4283    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7021   -1.3104    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3422   -2.2349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  6  5  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  3  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 11 10  1  0  0  0  0
 12 11  1  0  0  0  0
 12  6  1  0  0  0  0
 12 13  1  1  0  0  0
 12 14  1  0  0  0  0
 14 15  1  1  0  0  0
 14 16  1  0  0  0  0
 16 17  1  6  0  0  0
 16 18  1  0  0  0  0
 18 19  1  6  0  0  0
 20 18  1  0  0  0  0
 11 20  1  0  0  0  0
 20 21  1  1  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 24 23  1  1  0  0  0
 18 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 15  1  0  0  0  0
 25 26  1  0  0  0  0
 11 26  1  6  0  0  0
 25 27  1  6  0  0  0
M  END


  Mrv2104 08012308422D          

 27 32  0  0  1  0            999 V2000
   -2.9533   -0.7634    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1524   -0.5652    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5804   -1.1597    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9236    0.2275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1228    0.4256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5507   -0.1688    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3305    0.6262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7795   -0.9615    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2600   -1.6273    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6165   -1.4126    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0577   -0.5838    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2922    0.0591    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2574    0.8834    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1933   -0.4471    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1788   -1.2681    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7009    0.5000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4063    1.2706    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5932    0.1759    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0499    0.8630    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9242   -0.1824    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5011    0.4074    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6813   -0.8513    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8292   -0.1547    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0855   -0.8227    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1688   -1.4283    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7021   -1.3104    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3422   -2.2349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  6  5  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  3  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 11 10  1  0  0  0  0
 12 11  1  0  0  0  0
 12  6  1  0  0  0  0
 12 13  1  1  0  0  0
 12 14  1  0  0  0  0
 14 15  1  1  0  0  0
 14 16  1  0  0  0  0
 16 17  1  6  0  0  0
 16 18  1  0  0  0  0
 18 19  1  6  0  0  0
 20 18  1  0  0  0  0
 11 20  1  0  0  0  0
 20 21  1  1  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 24 23  1  1  0  0  0
 18 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 15  1  0  0  0  0
 25 26  1  0  0  0  0
 11 26  1  6  0  0  0
 25 27  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0331754

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]12[C@@H]3O[C@]4(C)O[C@@]1(CC=C1C[C@@H](O)CC[C@]21C)[C@@]1(O)CC[C@@H]4[C@@]1(C)[C@H]3O

> <INCHI_IDENTIFIER>
InChI=1S/C21H30O5/c1-17-7-5-12(22)10-11(17)4-8-20-15(17)14-16(23)18(2)13(6-9-21(18,20)24)19(3,25-14)26-20/h4,12-16,22-24H,5-10H2,1-3H3/t12-,13+,14-,15+,16-,17-,18-,19+,20+,21+/m0/s1

> <INCHI_KEY>
BPUBQTDRARUSNM-OSDPWTDDSA-N

> <FORMULA>
C21H30O5

> <MOLECULAR_WEIGHT>
362.466

> <EXACT_MASS>
362.209324066

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
56

> <JCHEM_AVERAGE_POLARIZABILITY>
38.855151575364374

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,2S,3R,6S,11R,13R,14R,17R,18S,19R)-3,13,18-trimethyl-12,20-dioxahexacyclo[11.6.1.0^{2,11}.0^{3,8}.0^{11,17}.0^{14,18}]icos-8-ene-6,17,19-triol

> <JCHEM_LOGP>
0.7012815349999993

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.871809921476235

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.086029620623115

> <JCHEM_PKA_STRONGEST_BASIC>
-1.3963656308423846

> <JCHEM_POLAR_SURFACE_AREA>
79.15

> <JCHEM_REFRACTIVITY>
95.05610000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,3R,6S,11R,13R,14R,17R,18S,19R)-3,13,18-trimethyl-12,20-dioxahexacyclo[11.6.1.0^{2,11}.0^{3,8}.0^{11,17}.0^{14,18}]icos-8-ene-6,17,19-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 01-AUG-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   01-AUG-23         0                                  
HETATM    1  O   UNK     0      -5.513  -1.425   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -4.018  -1.055   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.950  -2.165   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.591   0.425   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.096   0.794   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.028  -0.315   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.617   1.169   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.455  -1.795   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.485  -3.038   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.151  -2.637   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.974  -1.090   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.545   0.110   0.000  0.00  0.00           C+0
HETATM   13  H   UNK     0       0.480   1.649   0.000  0.00  0.00           H+0
HETATM   14  C   UNK     0       0.361  -0.835   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       0.334  -2.367   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       1.308   0.933   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       0.758   2.372   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       2.974   0.328   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.827   1.611   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.592  -0.340   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       4.669   0.760   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       5.005  -1.589   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.281  -0.289   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       3.893  -1.536   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.182  -2.666   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       3.177  -2.446   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       2.505  -4.172   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2    8                                                       
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8   12                                             
CONECT    7    6                                                            
CONECT    8    6    3    9                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   20   26                                             
CONECT   12   11    6   13   14                                             
CONECT   13   12                                                            
CONECT   14   12   15   16                                                  
CONECT   15   14   25                                                       
CONECT   16   14   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19   20   24                                             
CONECT   19   18                                                            
CONECT   20   18   11   21   22                                             
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   18   25                                                  
CONECT   25   24   15   26   27                                             
CONECT   26   25   11                                                       
CONECT   27   25                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   64    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₁H₃₀O₅

Average Mass

362.4660 Da

Monoisotopic Mass

362.20932 Da

IUPAC Name

(1S,2S,3R,6S,11R,13R,14R,17R,18S,19R)-3,13,18-trimethyl-12,20-dioxahexacyclo[11.6.1.0^{2,11}.0^{3,8}.0^{11,17}.0^{14,18}]icos-8-ene-6,17,19-triol

Traditional Name

(1S,2S,3R,6S,11R,13R,14R,17R,18S,19R)-3,13,18-trimethyl-12,20-dioxahexacyclo[11.6.1.0^{2,11}.0^{3,8}.0^{11,17}.0^{14,18}]icos-8-ene-6,17,19-triol

CAS Registry Number

Not Available

SMILES

[H][C@]12[C@@H]3O[C@]4(C)O[C@@]1(CC=C1C[C@@H](O)CC[C@]21C)[C@@]1(O)CC[C@@H]4[C@@]1(C)[C@H]3O

InChI Identifier

InChI=1S/C21H30O5/c1-17-7-5-12(22)10-11(17)4-8-20-15(17)14-16(23)18(2)13(6-9-21(18,20)24)19(3,25-14)26-20/h4,12-16,22-24H,5-10H2,1-3H3/t12-,13+,14-,15+,16-,17-,18-,19+,20+,21+/m0/s1

InChI Key

BPUBQTDRARUSNM-OSDPWTDDSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D_DEPT NMR	¹³C NMR Spectrum (1D, 101 MHz, CD3OD, experimental)	xht8710@163.com	Not Available	Not Available	2024-05-09	View Spectrum
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 400 MHz, CD3OD, experimental)	xht8710@163.com	Not Available	Not Available	2023-08-01	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 400 MHz, CD3OD, experimental)	xht8710@163.com	Not Available	Not Available	2023-08-01	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 400 MHz, CD3OD, experimental)	xht8710@163.com	Not Available	Not Available	2023-08-01	View Spectrum
1D NMR	[¹H, ] NMR Spectrum (2D, 400 MHz, CD3OD, experimental)	xht8710@163.com	Not Available	Not Available	2023-08-01	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 400 MHz, CD3OD, experimental)	xht8710@163.com	Not Available	Not Available	2023-08-01	View Spectrum
1D NMR	[¹³C, ] NMR Spectrum (2D, 101 MHz, CD3OD, experimental)	xht8710@163.com	Not Available	Not Available	2023-08-01	View Spectrum
1D NMR	[¹H, ] NMR Spectrum (2D, 400 MHz, CD3OD, experimental)	xht8710@163.com	Not Available	Not Available	2023-08-01	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 400, CD₃OD, simulated)	Not Available	Not Available	Not Available	2024-05-09	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
tenacissima		Not Available

Chemical Taxonomy

Classification

Not classified

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	0.7	ChemAxon
pKa (Strongest Acidic)	13.09	ChemAxon
pKa (Strongest Basic)	-1.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	79.15 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	95.06 m³·mol⁻¹	ChemAxon
Polarizability	38.86 Å³	ChemAxon
Number of Rings	6	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

Not Available

References

General References

Liu JL, Xu HT, Mu DD, Han X, Du TT, Wang YL, Wei XH, Chou GX: C(21) steroids from the roots of Marsdenia tenacissima. Phytochemistry. 2023 Sep;213:113782. doi: 10.1016/j.phytochem.2023.113782. Epub 2023 Jul 13. [PubMed:37451564 ]

Showing NP-Card for Tenacigenin D (NP0331754)

MOL for NP0331754 (Tenacigenin D)

3D MOL for NP0331754 (Tenacigenin D)

3D SDF for NP0331754 (Tenacigenin D)

3D-SDF for NP0331754 (Tenacigenin D)

PDB for NP0331754 (Tenacigenin D)

3D PDB for NP0331754 (Tenacigenin D)

SMILES for NP0331754 (Tenacigenin D)

INCHI for NP0331754 (Tenacigenin D)

Structure for NP0331754 (Tenacigenin D)

3D Structure for NP0331754 (Tenacigenin D)