NP-MRD: Showing NP-Card for (+)-3-Deoxymethylnimbidate (NP0082146)

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Record Information

Version

1.0

Created at

2022-04-29 03:12:09 UTC

Updated at

2022-04-29 03:12:09 UTC

NP-MRD ID

NP0082146

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-3-Deoxymethylnimbidate

Description

Methyl 2-[(1R,2S,4R,6R,9R,10R,11R,12S,15R,18S)-6-(furan-3-yl)-12-hydroxy-7,9,11,15-tetramethyl-3,17-dioxapentacyclo[9.6.1.0²,⁹.0⁴,⁸.0¹⁵,¹⁸]Octadec-7-en-10-yl]acetate 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. (+)-3-Deoxymethylnimbidate is found in Azadirachta excelsa. It was first documented in 2022 (PMID: 35490355). Based on a literature review a significant number of articles have been published on methyl 2-[(1R,2S,4R,6R,9R,10R,11R,12S,15R,18S)-6-(furan-3-yl)-12-hydroxy-7,9,11,15-tetramethyl-3,17-dioxapentacyclo[9.6.1.0²,⁹.0⁴,⁸.0¹⁵,¹⁸]Octadec-7-en-10-yl]acetate (PMID: 35490354) (PMID: 35490353) (PMID: 35490352) (PMID: 35490351).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292205122D          

 33 38  0  0  1  0            999 V2000
    3.6536   -1.0792    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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    2.4394    0.0381    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2592   -0.7670    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8663   -1.3256    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5226   -2.0756    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7031   -1.9805    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
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 27 31  2  0  0  0  0
 22 32  1  0  0  0  0
  2 33  1  1  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304292205122D          

 33 38  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
NP0082146

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C[C@H]1[C@@]2(C)[C@H](O[C@@H]3C[C@H](C(C)=C23)C2=COC=C2)[C@@H]2OC[C@]3(C)CC[C@H](O)[C@@]1(C)[C@@H]23

> <INCHI_IDENTIFIER>
InChI=1S/C27H36O6/c1-14-16(15-7-9-31-12-15)10-17-21(14)27(4)18(11-20(29)30-5)26(3)19(28)6-8-25(2)13-32-22(23(25)26)24(27)33-17/h7,9,12,16-19,22-24,28H,6,8,10-11,13H2,1-5H3/t16-,17-,18-,19+,22-,23+,24-,25+,26+,27-/m1/s1

> <INCHI_KEY>
NAXSSFQPEXJWGN-FEEXMUEUSA-N

> <FORMULA>
C27H36O6

> <MOLECULAR_WEIGHT>
456.579

> <EXACT_MASS>
456.251188879

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
49.160636290673565

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl 2-[(1R,2S,4R,6R,9R,10R,11R,12S,15R,18S)-6-(furan-3-yl)-12-hydroxy-7,9,11,15-tetramethyl-3,17-dioxapentacyclo[9.6.1.0^{2,9}.0^{4,8}.0^{15,18}]octadec-7-en-10-yl]acetate

> <ALOGPS_LOGP>
3.39

> <JCHEM_LOGP>
2.607383693333333

> <ALOGPS_LOGS>
-4.06

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.685982241826952

> <JCHEM_PKA_STRONGEST_BASIC>
-2.838775168083638

> <JCHEM_POLAR_SURFACE_AREA>
78.13000000000001

> <JCHEM_REFRACTIVITY>
121.6335

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.95e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl [(1R,2S,4R,6R,9R,10R,11R,12S,15R,18S)-6-(furan-3-yl)-12-hydroxy-7,9,11,15-tetramethyl-3,17-dioxapentacyclo[9.6.1.0^{2,9}.0^{4,8}.0^{15,18}]octadec-7-en-10-yl]acetate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0       6.820  -2.014   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.157  -0.512   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.023   0.531   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.554   0.071   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.217  -1.432   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.350  -2.474   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.709  -3.874   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       3.179  -3.697   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.875  -2.187   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.550  -1.403   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.567   0.137   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.909   0.893   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.870   2.432   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       1.620  -3.079   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.677   1.606   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.360   2.034   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.227   3.077   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       3.757   2.617   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       5.563   4.580   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       4.430   5.622   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.690  -0.367   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       9.845   0.651   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      11.171  -0.134   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      10.834  -1.636   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       9.301  -1.781   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       8.145  -2.799   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      12.584   0.478   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      12.921   1.980   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      14.454   2.125   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      15.065   0.711   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      13.909  -0.307   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       9.701   2.184   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       7.648   0.948   0.000  0.00  0.00           C+0
CONECT    1    2    6   26                                                  
CONECT    2    1    3   21   33                                             
CONECT    3    2    4   16                                                  
CONECT    4    3    5   12   15                                             
CONECT    5    4    6    9                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    5   10   14                                             
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11    4   13                                                  
CONECT   13   12                                                            
CONECT   14    9                                                            
CONECT   15    4                                                            
CONECT   16    3   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19                                                            
CONECT   21    2   22   25                                                  
CONECT   22   21   23   32                                                  
CONECT   23   22   24   27                                                  
CONECT   24   23   25                                                       
CONECT   25   24   21   26                                                  
CONECT   26   25    1                                                       
CONECT   27   23   28   31                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   27                                                       
CONECT   32   22                                                            
CONECT   33    2                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   76    0
END

View in JSmol

Synonyms

Value	Source
Methyl 2-[(1R,2S,4R,6R,9R,10R,11R,12S,15R,18S)-6-(furan-3-yl)-12-hydroxy-7,9,11,15-tetramethyl-3,17-dioxapentacyclo[9.6.1.0,.0,.0,]octadec-7-en-10-yl]acetic acid	Generator

Chemical Formula

C₂₇H₃₆O₆

Average Mass

456.5790 Da

Monoisotopic Mass

456.25119 Da

IUPAC Name

methyl 2-[(1R,2S,4R,6R,9R,10R,11R,12S,15R,18S)-6-(furan-3-yl)-12-hydroxy-7,9,11,15-tetramethyl-3,17-dioxapentacyclo[9.6.1.0^{2,9}.0^{4,8}.0^{15,18}]octadec-7-en-10-yl]acetate

Traditional Name

methyl [(1R,2S,4R,6R,9R,10R,11R,12S,15R,18S)-6-(furan-3-yl)-12-hydroxy-7,9,11,15-tetramethyl-3,17-dioxapentacyclo[9.6.1.0^{2,9}.0^{4,8}.0^{15,18}]octadec-7-en-10-yl]acetate

CAS Registry Number

Not Available

SMILES

COC(=O)C[C@H]1[C@@]2(C)[C@H](O[C@@H]3C[C@H](C(C)=C23)C2=COC=C2)[C@@H]2OC[C@]3(C)CC[C@H](O)[C@@]1(C)[C@@H]23

InChI Identifier

InChI=1S/C27H36O6/c1-14-16(15-7-9-31-12-15)10-17-21(14)27(4)18(11-20(29)30-5)26(3)19(28)6-8-25(2)13-32-22(23(25)26)24(27)33-17/h7,9,12,16-19,22-24,28H,6,8,10-11,13H2,1-5H3/t16-,17-,18-,19+,22-,23+,24-,25+,26+,27-/m1/s1

InChI Key

NAXSSFQPEXJWGN-FEEXMUEUSA-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 excelsa	Plant	KNApSAcK

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
Naphthofuran
Heteroaromatic compound
Methyl ester
Tetrahydrofuran
Furan
Cyclic alcohol
Secondary alcohol
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Ether
Dialkyl ether
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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	3.39	ALOGPS
logP	2.61	ChemAxon
logS	-4.1	ALOGPS
pKa (Strongest Acidic)	14.69	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	78.13 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	121.63 m³·mol⁻¹	ChemAxon
Polarizability	49.16 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

8893963

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10718624

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Baumbusch J, Blakey EP, Carapellotti AM, Dohmen M, Fick DM, Kagan SH, Melendez-Torres GJ, Morgan BE, Munsterman E, Resnick B, Young HM: Nurses and the decade of healthy ageing: An unprecedented opportunity. Int J Older People Nurs. 2022 May;17(3):e12469. doi: 10.1111/opn.12469. [PubMed:35490355 ]
Hill NL, Bratlee-Whitaker E, Wion RK, Madrigal C, Bhargava S, Mogle J: Factors that influence the emotional impact of memory problems in older adults: A qualitative descriptive study. Int J Older People Nurs. 2022 May;17(3):e12439. doi: 10.1111/opn.12439. Epub 2021 Dec 8. [PubMed:35490354 ]
Polastri M, Loforte A, Swol J: "Racing team" or "orchestra" approach? Two different perspectives on providing care in emergency and critical settings. Artif Organs. 2022 May 1. doi: 10.1111/aor.14274. [PubMed:35490353 ]
Wei YF, Wang L, Xia ZY, Gou M, Sun ZY, Lv WF, Tang YQ: Microbial communities in crude oil phase and filter-graded aqueous phase from a Daqing oilfield after polymer flooding. J Appl Microbiol. 2022 May 1. doi: 10.1111/jam.15603. [PubMed:35490352 ]
Authors unspecified: CORRIGENDUM. Transbound Emerg Dis. 2022 May 1. doi: 10.1111/tbed.14572. [PubMed:35490351 ]

Showing NP-Card for (+)-3-Deoxymethylnimbidate (NP0082146)

MOL for NP0082146 ((+)-3-Deoxymethylnimbidate)

3D MOL for NP0082146 ((+)-3-Deoxymethylnimbidate)

3D SDF for NP0082146 ((+)-3-Deoxymethylnimbidate)

3D-SDF for NP0082146 ((+)-3-Deoxymethylnimbidate)

PDB for NP0082146 ((+)-3-Deoxymethylnimbidate)

3D PDB for NP0082146 ((+)-3-Deoxymethylnimbidate)

SMILES for NP0082146 ((+)-3-Deoxymethylnimbidate)

INCHI for NP0082146 ((+)-3-Deoxymethylnimbidate)

Structure for NP0082146 ((+)-3-Deoxymethylnimbidate)

3D Structure for NP0082146 ((+)-3-Deoxymethylnimbidate)