NP-MRD: Showing NP-Card for Withanicandrin (NP0331577)

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Record Information

Version

2.0

Created at

2023-04-04 00:20:15 UTC

Updated at

2024-09-03 04:16:10 UTC

NP-MRD ID

NP0331577

Natural Product DOI

https://doi.org/10.57994/0556

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Withanicandrin

Description

Withanicandrin belongs to the class of organic compounds known as withanolides and derivatives. These are c28 steroids structurally characterized by an ergostane skeleton usually functionalized at carbons 1, 22 and 26 to form a lactone ring. Withanicandrin was first documented in 2010 (PMID: 20580923). Based on a literature review very few articles have been published on Withanicandrin (PMID: 36965582).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052221442D          

 34 39  0  0  1  0            999 V2000
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    0.3056   -1.3868    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4338   -2.2638    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7447   -3.0280    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309052221442D          

 34 39  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
NP0331577

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]([C@H]1CC[C@H]2[C@@H]3[C@@H]4O[C@@H]4[C@@]4(O)CC=CC(=O)[C@]4(C)[C@H]3CC(=O)[C@]12C)[C@@H]1CC(C)=C(C)C(=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C28H36O6/c1-13-11-19(33-25(31)14(13)2)15(3)16-8-9-17-22-18(12-21(30)26(16,17)4)27(5)20(29)7-6-10-28(27,32)24-23(22)34-24/h6-7,15-19,22-24,32H,8-12H2,1-5H3/t15-,16+,17-,18-,19-,22-,23-,24-,26+,27-,28-/m0/s1

> <INCHI_KEY>
UEXBVTCXVKSQTD-DBRLRIMGSA-N

> <FORMULA>
C28H36O6

> <MOLECULAR_WEIGHT>
468.59

> <EXACT_MASS>
468.251188879

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
70

> <JCHEM_AVERAGE_POLARIZABILITY>
50.87189860205787

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,2S,4S,5R,10R,11S,14R,15R,18S)-15-[(1S)-1-[(2S)-4,5-dimethyl-6-oxo-3,6-dihydro-2H-pyran-2-yl]ethyl]-5-hydroxy-10,14-dimethyl-3-oxapentacyclo[9.7.0.0^{2,4}.0^{5,10}.0^{14,18}]octadec-7-ene-9,13-dione

> <JCHEM_LOGP>
4.117508179666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.693558036866502

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.096631985010621

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6202150767549774

> <JCHEM_POLAR_SURFACE_AREA>
93.19999999999999

> <JCHEM_REFRACTIVITY>
126.19019999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,4S,5R,10R,11S,14R,15R,18S)-15-[(1S)-1-[(2S)-4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl]ethyl]-5-hydroxy-10,14-dimethyl-3-oxapentacyclo[9.7.0.0^{2,4}.0^{5,10}.0^{14,18}]octadec-7-ene-9,13-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0      -0.159  -7.873   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.786  -6.657   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.206  -5.231   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.320  -5.020   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.151  -4.015   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.571  -2.589   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       2.676  -4.226   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       3.257  -5.652   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.782  -5.863   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.363  -7.289   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.727  -4.647   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.299  -3.168   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.574  -2.304   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.790  -3.249   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.306  -2.978   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.829  -1.529   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      10.352  -0.081   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      11.345  -1.258   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      12.338  -2.436   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      12.861  -0.987   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      13.854  -2.164   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      14.846  -3.342   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      14.323  -4.790   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      12.807  -5.061   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      12.284  -6.510   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      11.814  -3.884   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      11.291  -5.332   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      10.299  -4.155   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       9.775  -5.603   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       8.259  -5.874   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       7.736  -7.323   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       7.267  -4.697   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       6.595  -6.083   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       2.312  -6.868   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   34                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   34                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   32                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   32                                                  
CONECT   15   14   16   28                                                  
CONECT   16   15   17   18                                                  
CONECT   17   16   18                                                       
CONECT   18   17   16   19                                                  
CONECT   19   18   20   21   26                                             
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   19   27   28                                             
CONECT   27   26                                                            
CONECT   28   26   15   29                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   14   11   33                                             
CONECT   33   32                                                            
CONECT   34    8    2                                                       
MASTER        0    0    0    0    0    0    0    0   34    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₃₆O₆

Average Mass

468.5900 Da

Monoisotopic Mass

468.25119 Da

IUPAC Name

(1S,2S,4S,5R,10R,11S,14R,15R,18S)-15-[(1S)-1-[(2S)-4,5-dimethyl-6-oxo-3,6-dihydro-2H-pyran-2-yl]ethyl]-5-hydroxy-10,14-dimethyl-3-oxapentacyclo[9.7.0.0^{2,4}.0^{5,10}.0^{14,18}]octadec-7-ene-9,13-dione

Traditional Name

(1S,2S,4S,5R,10R,11S,14R,15R,18S)-15-[(1S)-1-[(2S)-4,5-dimethyl-6-oxo-2,3-dihydropyran-2-yl]ethyl]-5-hydroxy-10,14-dimethyl-3-oxapentacyclo[9.7.0.0^{2,4}.0^{5,10}.0^{14,18}]octadec-7-ene-9,13-dione

CAS Registry Number

Not Available

SMILES

C[C@@H]([C@H]1CC[C@H]2[C@@H]3[C@@H]4O[C@@H]4[C@@]4(O)CC=CC(=O)[C@]4(C)[C@H]3CC(=O)[C@]12C)[C@@H]1CC(C)=C(C)C(=O)O1

InChI Identifier

InChI=1S/C28H36O6/c1-13-11-19(33-25(31)14(13)2)15(3)16-8-9-17-22-18(12-21(30)26(16,17)4)27(5)20(29)7-6-10-28(27,32)24-23(22)34-24/h6-7,15-19,22-24,32H,8-12H2,1-5H3/t15-,16+,17-,18-,19-,22-,23-,24-,26+,27-,28-/m0/s1

InChI Key

UEXBVTCXVKSQTD-DBRLRIMGSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D_DEPT NMR	¹³C NMR Spectrum (1D, 151 MHz, CDCl3, experimental)	kibrom.gebreheiwot@aau.edu.et	Not Available	Not Available	2024-05-11	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 601 MHz, CDCl3, experimental)	kibrom.gebreheiwot@aau.edu.et	Not Available	Not Available	2023-04-04	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 601 MHz, CDCl3, experimental)	kibrom.gebreheiwot@aau.edu.et	Not Available	Not Available	2023-04-04	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 601 MHz, CDCl3, experimental)	kibrom.gebreheiwot@aau.edu.et	Not Available	Not Available	2023-04-04	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, CDCl3, experimental)	kibrom.gebreheiwot@aau.edu.et	Not Available	Not Available	2023-04-04	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 601 MHz, CDCl3, experimental)	kibrom.gebreheiwot@aau.edu.et	Not Available	Not Available	2023-04-04	View Spectrum

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
penninervium		Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as withanolides and derivatives. These are c28 steroids structurally characterized by an ergostane skeleton usually functionalized at carbons 1, 22 and 26 to form a lactone ring.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Steroid lactones

Direct Parent

Withanolides and derivatives

Alternative Parents

Substituents

Withanolide-skeleton
Cyclohexenone
Oxepane
Dihydropyranone
Pyran
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Tertiary alcohol
Cyclic alcohol
Lactone
Ketone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Ether
Oxirane
Dialkyl ether
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic 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	4.12	ChemAxon
pKa (Strongest Acidic)	13.1	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	93.2 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	126.19 m³·mol⁻¹	ChemAxon
Polarizability	50.87 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

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

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

91809632

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Suleiman RK, Zarga MA, Sabri SS: New withanolides from Mandragora officinarum: first report of withanolides from the Genus Mandragora. Fitoterapia. 2010 Oct;81(7):864-8. doi: 10.1016/j.fitote.2010.05.013. Epub 2010 May 23. [PubMed:20580923 ]
Bedane KG, Desta MA, Spiteller P: Withanolides from Discopodium penninervium. Fitoterapia. 2023 Jun;167:105478. doi: 10.1016/j.fitote.2023.105478. Epub 2023 Mar 24. [PubMed:36965582 ]

Showing NP-Card for Withanicandrin (NP0331577)

MOL for NP0331577 (Withanicandrin)

3D MOL for NP0331577 (Withanicandrin)

3D SDF for NP0331577 (Withanicandrin)

3D-SDF for NP0331577 (Withanicandrin)

PDB for NP0331577 (Withanicandrin)

3D PDB for NP0331577 (Withanicandrin)

SMILES for NP0331577 (Withanicandrin)

INCHI for NP0331577 (Withanicandrin)

Structure for NP0331577 (Withanicandrin)

3D Structure for NP0331577 (Withanicandrin)