NP-MRD: Showing NP-Card for (+)-7-Deacetylgedunin (NP0076089)

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Record Information

Version

2.0

Created at

2022-04-28 21:15:51 UTC

Updated at

2022-04-28 21:15:51 UTC

NP-MRD ID

NP0076089

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-7-Deacetylgedunin

Description

7-Deacetylgedunin belongs to the class of organic compounds known as limonoids. These are highly oxygenated, modified terpenoids with a prototypical structure either containing or derived from a precursor with a 4,4,8-trimethyl-17-furanylsteroid skeleton. All naturally occurring citrus limonoids contain a furan ring attached to the D-ring, at C-17, as well as oxygen containing functional groups at C-3, C-4, C-7, C-16 and C-17. (+)-7-Deacetylgedunin is found in Azadirachta indica, Cedrela odorata, Pseudocedrela kotschyi , Toona sinensis, Xylocarpus granatum and Xylocarpus moluccensis. (+)-7-Deacetylgedunin was first documented in 2015 (PMID: 25714725). Based on a literature review a small amount of articles have been published on 7-deacetylgedunin (PMID: 34948062) (PMID: 32277328) (PMID: 28903401) (PMID: 28145090).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282223152D          

 32 37  0  0  1  0            999 V2000
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    4.2251    1.1921    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.9550   -0.2111    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.7651   -0.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3052    0.2566    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1154    0.1007    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    2.6048   -0.6789    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3347    0.1007    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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    2.6048    1.5039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7946    1.6598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652304282223152D          

 32 37  0  0  1  0            999 V2000
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    3.9550   -0.2111    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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    2.0647   -1.3025    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  2  0  0  0  0
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  3 32  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0076089

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1(C)[C@@H]2C[C@@H](O)[C@]3(C)[C@H](CC[C@@]4(C)[C@@H](OC(=O)[C@H]5O[C@@]345)C3=COC=C3)[C@@]2(C)C=CC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C26H32O6/c1-22(2)16-12-18(28)25(5)15(23(16,3)9-7-17(22)27)6-10-24(4)19(14-8-11-30-13-14)31-21(29)20-26(24,25)32-20/h7-9,11,13,15-16,18-20,28H,6,10,12H2,1-5H3/t15-,16+,18-,19+,20-,23-,24+,25+,26-/m1/s1

> <INCHI_KEY>
HCEYJYMNIQHPPK-DXTZDJJUSA-N

> <FORMULA>
C26H32O6

> <MOLECULAR_WEIGHT>
440.536

> <EXACT_MASS>
440.21988875

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
46.70044502682621

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,2R,4S,7R,8S,11R,12R,17R,19R)-7-(furan-3-yl)-19-hydroxy-1,8,12,16,16-pentamethyl-3,6-dioxapentacyclo[9.8.0.0^{2,4}.0^{2,8}.0^{12,17}]nonadec-13-ene-5,15-dione

> <ALOGPS_LOGP>
3.84

> <JCHEM_LOGP>
3.858858902666666

> <ALOGPS_LOGS>
-4.27

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.595237684480637

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8698490767599094

> <JCHEM_POLAR_SURFACE_AREA>
89.27000000000001

> <JCHEM_REFRACTIVITY>
115.8415

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.38e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2R,4S,7R,8S,11R,12R,17R,19R)-7-(furan-3-yl)-19-hydroxy-1,8,12,16,16-pentamethyl-3,6-dioxapentacyclo[9.8.0.0^{2,4}.0^{2,8}.0^{12,17}]nonadec-13-ene-5,15-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       9.399   1.934   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.887   2.225   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.879   1.061   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.383  -0.394   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.895  -0.685   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.903   0.479   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      11.415   0.188   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      10.023  -1.733   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.657  -2.207   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.375  -1.558   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.862  -1.267   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.358   0.188   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.366   1.352   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.862   2.807   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.350   3.098   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.342   1.934   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.846   0.479   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.838  -0.685   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.326  -0.394   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -0.683  -1.558   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -0.179   1.061   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       0.830   2.225   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.326   3.680   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -1.148   4.128   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -1.178   5.668   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       0.277   6.172   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.206   4.943   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       3.350  -0.976   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       1.838   3.389   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       4.227  -1.346   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       3.854  -2.431   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       6.375   2.516   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   13   32                                             
CONECT    4    3    5   10                                                  
CONECT    5    4    6    8    9                                             
CONECT    6    5    1    7                                                  
CONECT    7    6                                                            
CONECT    8    5                                                            
CONECT    9    5                                                            
CONECT   10    4   11                                                       
CONECT   11   10   12   31                                                  
CONECT   12   11   13   17   30                                             
CONECT   13   12    3   14                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   22   29                                             
CONECT   17   16   12   18   28                                             
CONECT   18   17   19   28                                                  
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   16   23                                                  
CONECT   23   22   24   27                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   23                                                       
CONECT   28   18   17                                                       
CONECT   29   16                                                            
CONECT   30   12                                                            
CONECT   31   11                                                            
CONECT   32    3                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   74    0
END

View in JSmol

Synonyms

Value	Source
(5alpha,7alpha,13alpha,14beta,15beta,17Aalpha)-14,15:21,23-diepoxy-7-hydroxy-4,4,8-trimethyl-D-homo-24-nor-17-oxachlola-1,20-,22-triene-3,16-dione	ChEBI
7-Deacetoxy-7alpha-hydroxygedunin	ChEBI
Deacetylgedunin	ChEBI
(5a,7a,13a,14b,15b,17Aalpha)-14,15:21,23-diepoxy-7-hydroxy-4,4,8-trimethyl-D-homo-24-nor-17-oxachlola-1,20-,22-triene-3,16-dione	Generator
(5Α,7α,13α,14β,15β,17aalpha)-14,15:21,23-diepoxy-7-hydroxy-4,4,8-trimethyl-D-homo-24-nor-17-oxachlola-1,20-,22-triene-3,16-dione	Generator
7-Deacetoxy-7a-hydroxygedunin	Generator
7-Deacetoxy-7α-hydroxygedunin	Generator

Chemical Formula

C₂₆H₃₂O₆

Average Mass

440.5360 Da

Monoisotopic Mass

440.21989 Da

IUPAC Name

(1S,2R,4S,7R,8S,11R,12R,17R,19R)-7-(furan-3-yl)-19-hydroxy-1,8,12,16,16-pentamethyl-3,6-dioxapentacyclo[9.8.0.0^{2,4}.0^{2,8}.0^{12,17}]nonadec-13-ene-5,15-dione

Traditional Name

(1S,2R,4S,7R,8S,11R,12R,17R,19R)-7-(furan-3-yl)-19-hydroxy-1,8,12,16,16-pentamethyl-3,6-dioxapentacyclo[9.8.0.0^{2,4}.0^{2,8}.0^{12,17}]nonadec-13-ene-5,15-dione

CAS Registry Number

Not Available

SMILES

CC1(C)[C@@H]2C[C@@H](O)[C@]3(C)[C@H](CC[C@@]4(C)[C@@H](OC(=O)[C@H]5O[C@@]345)C3=COC=C3)[C@@]2(C)C=CC1=O

InChI Identifier

InChI=1S/C26H32O6/c1-22(2)16-12-18(28)25(5)15(23(16,3)9-7-17(22)27)6-10-24(4)19(14-8-11-30-13-14)31-21(29)20-26(24,25)32-20/h7-9,11,13,15-16,18-20,28H,6,10,12H2,1-5H3/t15-,16+,18-,19+,20-,23-,24+,25+,26-/m1/s1

InChI Key

HCEYJYMNIQHPPK-DXTZDJJUSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Azadirachta indica	LOTUS Database	35616633
Cedrela odorata	LOTUS Database	35616633
Pseudocedrela kotschyi	Plant	KNApSAcK
Toona sinensis	LOTUS Database	35616633
Xylocarpus granatum	LOTUS Database	35616633
Xylocarpus moluccensis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as limonoids. These are highly oxygenated, modified terpenoids with a prototypical structure either containing or derived from a precursor with a 4,4,8-trimethyl-17-furanylsteroid skeleton. All naturally occurring citrus limonoids contain a furan ring attached to the D-ring, at C-17, as well as oxygen containing functional groups at C-3, C-4, C-7, C-16 and C-17.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Triterpenoids

Direct Parent

Limonoids

Alternative Parents

Substituents

Limonoid skeleton
Naphthopyran
Naphthalene
1,4-dioxepane
Cyclohexenone
Delta valerolactone
Dioxepane
Delta_valerolactone
Pyran
Oxane
Cyclic alcohol
Heteroaromatic compound
Furan
Carboxylic acid ester
Ketone
Cyclic ketone
Lactone
Secondary alcohol
Organoheterocyclic compound
Ether
Oxirane
Oxacycle
Dialkyl ether
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Alcohol
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Carbonyl group
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

epoxide (CHEBI:67296 )
enone (CHEBI:67296 )
furans (CHEBI:67296 )
delta-lactone (CHEBI:67296 )
pentacyclic triterpenoid (CHEBI:67296 )
cyclic terpene ketone (CHEBI:67296 )
limonoid (CHEBI:67296 )

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	3.84	ALOGPS
logP	3.86	ChemAxon
logS	-4.3	ALOGPS
pKa (Strongest Acidic)	14.6	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	89.27 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	115.84 m³·mol⁻¹	ChemAxon
Polarizability	46.7 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

C00038317

Chemspider ID

2298629

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

3034112

PDB ID

Not Available

ChEBI ID

67296

Good Scents ID

Not Available

References

General References

Lin M, Yang S, Huang J, Zhou L: Insecticidal Triterpenes in Meliaceae: Plant Species, Molecules and Activities: Part (Aphanamixis-Chukrasia). Int J Mol Sci. 2021 Dec 9;22(24). pii: ijms222413262. doi: 10.3390/ijms222413262. [PubMed:34948062 ]
Steverding D, Sidjui LS, Ferreira ER, Ngameni B, Folefoc GN, Mahiou-Leddet V, Ollivier E, Stephenson GR, Storr TE, Tyler KM: Trypanocidal and leishmanicidal activity of six limonoids. J Nat Med. 2020 Jun;74(3):606-611. doi: 10.1007/s11418-020-01408-7. Epub 2020 Apr 10. [PubMed:32277328 ]
Chen JY, Zhu GY, Su XH, Wang R, Liu J, Liao K, Ren R, Li T, Liu L: 7-deacetylgedunin suppresses inflammatory responses through activation of Keap1/Nrf2/HO-1 signaling. Oncotarget. 2017 Jul 5;8(33):55051-55063. doi: 10.18632/oncotarget.19017. eCollection 2017 Aug 15. [PubMed:28903401 ]
Akihisa T, Nishimoto Y, Ogihara E, Matsumoto M, Zhang J, Abe M: Nitric Oxide Production-Inhibitory Activity of Limonoids from Azadirachta indica and Melia azedarach. Chem Biodivers. 2017 Jun;14(6). doi: 10.1002/cbdv.201600468. Epub 2017 May 23. [PubMed:28145090 ]
Sarigaputi C, Sangpech N, Palaga T, Pudhom K: Suppression of inducible nitric oxide synthase pathway by 7-deacetylgedunin, a limonoid from Xylocarpus sp. Planta Med. 2015 Mar;81(4):312-9. doi: 10.1055/s-0034-1396308. Epub 2015 Feb 25. [PubMed:25714725 ]

Showing NP-Card for (+)-7-Deacetylgedunin (NP0076089)

MOL for NP0076089 ((+)-7-Deacetylgedunin)

3D MOL for NP0076089 ((+)-7-Deacetylgedunin)

3D SDF for NP0076089 ((+)-7-Deacetylgedunin)

3D-SDF for NP0076089 ((+)-7-Deacetylgedunin)

PDB for NP0076089 ((+)-7-Deacetylgedunin)

3D PDB for NP0076089 ((+)-7-Deacetylgedunin)

SMILES for NP0076089 ((+)-7-Deacetylgedunin)

INCHI for NP0076089 ((+)-7-Deacetylgedunin)

Structure for NP0076089 ((+)-7-Deacetylgedunin)

3D Structure for NP0076089 ((+)-7-Deacetylgedunin)