NP-MRD: Showing NP-Card for Nimbanal (NP0084254)

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Record Information

Version

2.0

Created at

2022-04-29 05:02:45 UTC

Updated at

2022-04-29 05:02:45 UTC

NP-MRD ID

NP0084254

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Nimbanal

Description

Nimbanal 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. Nimbanal is found in Azadirachta indica . Nimbanal was first documented in 2021 (PMID: 34075339). Based on a literature review very few articles have been published on Nimbanal.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292207022D          

 41 45  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652304292207022D          

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    0.4161    2.0353    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8950    3.3816    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0129   -1.2103    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  1  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
  8 12  1  0  0  0  0
  7 13  1  6  0  0  0
  7 14  1  0  0  0  0
 14 15  1  0  0  0  0
  4 15  1  0  0  0  0
 15 16  1  1  0  0  0
 15 17  1  0  0  0  0
  2 17  1  0  0  0  0
  3 18  1  6  0  0  0
  3 19  1  0  0  0  0
 19 20  1  6  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 21 24  2  0  0  0  0
 19 25  1  0  0  0  0
 25 26  1  6  0  0  0
 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  1  0  0  0
 31 32  2  0  0  0  0
 30 33  1  6  0  0  0
 30 34  1  0  0  0  0
 25 34  1  0  0  0  0
 34 35  1  1  0  0  0
 34 36  1  0  0  0  0
  2 36  1  0  0  0  0
 36 37  1  1  0  0  0
 37 38  1  0  0  0  0
 38 39  1  0  0  0  0
 38 40  2  0  0  0  0
 27 41  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0084254

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]12C[C@]([H])(C(C)=C1[C@@]1(C)[C@H](CC(=O)OC)[C@@]3(C)C(=O)C=C[C@@](C)(C=O)[C@]3([H])[C@@H](OC(C)=O)[C@@]1([H])O2)C1=COC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C29H34O8/c1-15-18(17-8-10-35-13-17)11-19-23(15)29(5)20(12-22(33)34-6)28(4)21(32)7-9-27(3,14-30)25(28)24(26(29)37-19)36-16(2)31/h7-10,13-14,18-20,24-26H,11-12H2,1-6H3/t18-,19-,20-,24-,25+,26-,27+,28+,29-/m1/s1

> <INCHI_KEY>
KTZMJZLZKQMODA-AGKCECBESA-N

> <FORMULA>
C29H34O8

> <MOLECULAR_WEIGHT>
510.583

> <EXACT_MASS>
510.225368055

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
71

> <JCHEM_AVERAGE_POLARIZABILITY>
52.73095807798195

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl 2-[(1S,2R,3S,4R,8R,9S,10R,13R,15R)-2-(acetyloxy)-4-formyl-13-(furan-3-yl)-4,8,10,12-tetramethyl-7-oxo-16-oxatetracyclo[8.6.0.0^{3,8}.0^{11,15}]hexadeca-5,11-dien-9-yl]acetate

> <ALOGPS_LOGP>
3.57

> <JCHEM_LOGP>
2.7620042299999987

> <ALOGPS_LOGS>
-4.26

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-2.858571515122437

> <JCHEM_POLAR_SURFACE_AREA>
109.11000000000001

> <JCHEM_REFRACTIVITY>
133.5832

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.83e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl [(1S,2R,3S,4R,8R,9S,10R,13R,15R)-2-(acetyloxy)-4-formyl-13-(furan-3-yl)-4,8,10,12-tetramethyl-7-oxo-16-oxatetracyclo[8.6.0.0^{3,8}.0^{11,15}]hexadeca-5,11-dien-9-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  H   UNK     0       5.011   3.786   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0       5.129   2.251   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.408   0.736   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.935   0.533   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.050  -0.529   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.847  -2.055   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.405   0.204   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.794  -0.461   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      11.072  -1.975   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      12.599  -2.178   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      13.264  -0.789   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      12.148   0.272   0.000  0.00  0.00           C+0
HETATM   13  H   UNK     0      10.628   1.140   0.000  0.00  0.00           H+0
HETATM   14  C   UNK     0       9.126   1.719   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.599   1.922   0.000  0.00  0.00           C+0
HETATM   16  H   UNK     0       8.264   3.311   0.000  0.00  0.00           H+0
HETATM   17  O   UNK     0       6.484   2.984   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       5.843  -0.741   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.236  -0.262   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.514  -1.777   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.965  -2.293   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       6.243  -3.808   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       7.694  -4.324   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       7.137  -1.294   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       2.785   0.254   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       3.063  -1.261   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.612  -0.745   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       0.161  -0.228   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -0.117   1.286   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       1.055   2.285   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -0.132   3.266   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -1.575   2.729   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       1.815   3.624   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       2.506   1.768   0.000  0.00  0.00           C+0
HETATM   35  H   UNK     0       2.228   3.283   0.000  0.00  0.00           H+0
HETATM   36  C   UNK     0       3.679   2.767   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       3.400   4.282   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0       1.949   4.798   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       0.777   3.799   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0       1.671   6.312   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0       1.891  -2.259   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   17   36                                             
CONECT    3    2    4   18   19                                             
CONECT    4    3    5   15                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   13   14                                             
CONECT    8    7    9   12                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11    8                                                       
CONECT   13    7                                                            
CONECT   14    7   15                                                       
CONECT   15   14    4   16   17                                             
CONECT   16   15                                                            
CONECT   17   15    2                                                       
CONECT   18    3                                                            
CONECT   19    3   20   25                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   24                                                  
CONECT   22   21   23                                                       
CONECT   23   22                                                            
CONECT   24   21                                                            
CONECT   25   19   26   27   34                                             
CONECT   26   25                                                            
CONECT   27   25   28   41                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   33   34                                             
CONECT   31   30   32                                                       
CONECT   32   31                                                            
CONECT   33   30                                                            
CONECT   34   30   25   35   36                                             
CONECT   35   34                                                            
CONECT   36   34    2   37                                                  
CONECT   37   36   38                                                       
CONECT   38   37   39   40                                                  
CONECT   39   38                                                            
CONECT   40   38                                                            
CONECT   41   27                                                            
MASTER        0    0    0    0    0    0    0    0   41    0   90    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₃₄O₈

Average Mass

510.5830 Da

Monoisotopic Mass

510.22537 Da

IUPAC Name

methyl 2-[(1S,2R,3S,4R,8R,9S,10R,13R,15R)-2-(acetyloxy)-4-formyl-13-(furan-3-yl)-4,8,10,12-tetramethyl-7-oxo-16-oxatetracyclo[8.6.0.0^{3,8}.0^{11,15}]hexadeca-5,11-dien-9-yl]acetate

Traditional Name

methyl [(1S,2R,3S,4R,8R,9S,10R,13R,15R)-2-(acetyloxy)-4-formyl-13-(furan-3-yl)-4,8,10,12-tetramethyl-7-oxo-16-oxatetracyclo[8.6.0.0^{3,8}.0^{11,15}]hexadeca-5,11-dien-9-yl]acetate

CAS Registry Number

Not Available

SMILES

[H][C@@]12C[C@]([H])(C(C)=C1[C@@]1(C)[C@H](CC(=O)OC)[C@@]3(C)C(=O)C=C[C@@](C)(C=O)[C@]3([H])[C@@H](OC(C)=O)[C@@]1([H])O2)C1=COC=C1

InChI Identifier

InChI=1S/C29H34O8/c1-15-18(17-8-10-35-13-17)11-19-23(15)29(5)20(12-22(33)34-6)28(4)21(32)7-9-27(3,14-30)25(28)24(26(29)37-19)36-16(2)31/h7-10,13-14,18-20,24-26H,11-12H2,1-6H3/t18-,19-,20-,24-,25+,26-,27+,28+,29-/m1/s1

InChI Key

KTZMJZLZKQMODA-AGKCECBESA-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	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
Cyclohexenone
Dicarboxylic acid or derivatives
Furan
Heteroaromatic compound
Methyl ester
Tetrahydrofuran
Carboxylic acid ester
Ketone
Carboxylic acid derivative
Dialkyl ether
Ether
Oxacycle
Organoheterocyclic compound
Organic oxide
Carbonyl group
Hydrocarbon derivative
Aldehyde
Organic oxygen compound
Organooxygen compound
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	3.57	ALOGPS
logP	2.76	ChemAxon
logS	-4.3	ALOGPS
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	109.11 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	133.58 m³·mol⁻¹	ChemAxon
Polarizability	52.73 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

C00053551

Chemspider ID

10320664

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14194023

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Adegbola AE, Fadahunsi OS, Alausa A, Abijo AZ, Balogun TA, Aderibigbe TS, Semire B, Adegbola PI: Computational prediction of nimbanal as potential antagonist of respiratory syndrome coronavirus. Inform Med Unlocked. 2021;24:100617. doi: 10.1016/j.imu.2021.100617. Epub 2021 May 28. [PubMed:34075339 ]

Showing NP-Card for Nimbanal (NP0084254)

MOL for NP0084254 (Nimbanal)

3D MOL for NP0084254 (Nimbanal)

3D SDF for NP0084254 (Nimbanal)

3D-SDF for NP0084254 (Nimbanal)

PDB for NP0084254 (Nimbanal)

3D PDB for NP0084254 (Nimbanal)

SMILES for NP0084254 (Nimbanal)

INCHI for NP0084254 (Nimbanal)

Structure for NP0084254 (Nimbanal)

3D Structure for NP0084254 (Nimbanal)