NP-MRD: Showing NP-Card for (-)-Ekeberin C3 (NP0076491)

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Record Information

Version

1.0

Created at

2022-04-28 21:40:01 UTC

Updated at

2022-04-28 21:40:01 UTC

NP-MRD ID

NP0076491

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Ekeberin C3

Description

(AlphaR,4R)-alpha-Acetoxy-4-(3-furyl)-1,4,4a,5,6,6abeta,7,8,9,10,11,12-dodecahydro-4abeta,7,9,9-tetramethyl-2,10,13-trioxo-7beta,11beta-methano-2H-cycloocta[f][2]benzopyran-8beta-acetic acid methyl ester 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. (-)-Ekeberin C3 is found in Ekebergia capensis and Lansium domesticum. It was first documented in 2022 (PMID: 35490355). Based on a literature review a significant number of articles have been published on (alphaR,4R)-alpha-Acetoxy-4-(3-furyl)-1,4,4a,5,6,6abeta,7,8,9,10,11,12-dodecahydro-4abeta,7,9,9-tetramethyl-2,10,13-trioxo-7beta,11beta-methano-2H-cycloocta[f][2]benzopyran-8beta-acetic acid methyl ester (PMID: 35490354) (PMID: 35490353) (PMID: 35490352) (PMID: 35490351).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282223402D          

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M  END

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  Mrv1652304282223402D          

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   -1.3854   -2.3994    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3256   -1.3233    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4989    0.4245    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5480   -0.3036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  6  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  6 11  1  0  0  0  0
  9 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
  8 16  1  0  0  0  0
 12 17  1  1  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 17 21  2  0  0  0  0
  9 22  1  1  0  0  0
  7 23  1  0  0  0  0
 23 24  1  0  0  0  0
  1 24  1  0  0  0  0
 24 25  1  1  0  0  0
  5 25  1  0  0  0  0
 25 26  2  0  0  0  0
  5 27  1  1  0  0  0
  4 28  1  1  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 29 31  1  0  0  0  0
 31 32  1  0  0  0  0
 28 33  1  6  0  0  0
 33 34  1  0  0  0  0
 34 35  2  0  0  0  0
 34 36  1  0  0  0  0
  3 37  1  0  0  0  0
  3 38  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0076491

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)[C@H](OC(C)=O)[C@H]1C(C)(C)C(=O)[C@@H]2CC3=C4CC(=O)O[C@@H](C5=COC=C5)[C@]4(C)CC[C@@H]3[C@@]1(C)C2=O

> <INCHI_IDENTIFIER>
InChI=1S/C29H34O9/c1-14(30)37-21(26(34)35-6)22-27(2,3)23(32)17-11-16-18(29(22,5)24(17)33)7-9-28(4)19(16)12-20(31)38-25(28)15-8-10-36-13-15/h8,10,13,17-18,21-22,25H,7,9,11-12H2,1-6H3/t17-,18-,21+,22-,25-,28+,29+/m0/s1

> <INCHI_KEY>
GXYWZNJCGCCUAH-HMXNUIANSA-N

> <FORMULA>
C29H34O9

> <MOLECULAR_WEIGHT>
526.582

> <EXACT_MASS>
526.220282675

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_POLARIZABILITY>
53.903229764165964

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl (2R)-2-(acetyloxy)-2-[(1R,2S,5R,6R,13S,16S)-6-(furan-3-yl)-1,5,15,15-tetramethyl-8,14,17-trioxo-7-oxatetracyclo[11.3.1.0^{2,11}.0^{5,10}]heptadec-10-en-16-yl]acetate

> <ALOGPS_LOGP>
3.38

> <JCHEM_LOGP>
3.6048045789999996

> <ALOGPS_LOGS>
-4.06

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.336115593101129

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8888511447270924

> <JCHEM_POLAR_SURFACE_AREA>
126.18

> <JCHEM_REFRACTIVITY>
132.6135

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.54e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(R)-(methyl (acetyloxy)[(1R,2S,5R,6R,13S,16S)-6-(furan-3-yl)-1,5,15,15-tetramethyl-8,14,17-trioxo-7-oxatetracyclo[11.3.1.0^{2,11}.0^{5,10}]heptadec-10-en-16-yl]acetate)

> <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       1.085   1.400   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       0.071   2.560   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       0.401   0.020   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.893  -1.439   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.273  -2.123   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.732  -1.631   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.416  -0.251   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.953  -0.153   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.806  -1.435   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.122  -2.815   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.585  -2.913   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.343  -1.338   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       9.027   0.042   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       8.174   1.324   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       8.857   2.704   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       6.637   1.227   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.196  -2.620   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      10.735  -2.683   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      11.150  -4.166   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       9.868  -5.019   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       8.660  -4.063   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       7.659  -2.717   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       3.924   1.208   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.544   1.892   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       1.907  -0.082   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       0.724   0.905   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       2.169  -3.660   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -0.267  -2.453   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       0.031  -3.964   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       1.488  -4.461   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      -1.129  -4.977   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -0.831  -6.488   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -1.724  -1.955   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      -2.884  -2.968   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -2.586  -4.479   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      -4.341  -2.470   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      -0.931   0.792   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      -1.023  -0.567   0.000  0.00  0.00           C+0
CONECT    1    2    3   24                                                  
CONECT    2    1                                                            
CONECT    3    1    4   37   38                                             
CONECT    4    3    5   28                                                  
CONECT    5    4    6   25   27                                             
CONECT    6    5    7   11                                                  
CONECT    7    6    8   23                                                  
CONECT    8    7    9   16                                                  
CONECT    9    8   10   12   22                                             
CONECT   10    9   11                                                       
CONECT   11   10    6                                                       
CONECT   12    9   13   17                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14    8                                                       
CONECT   17   12   18   21                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   17                                                       
CONECT   22    9                                                            
CONECT   23    7   24                                                       
CONECT   24   23    1   25                                                  
CONECT   25   24    5   26                                                  
CONECT   26   25                                                            
CONECT   27    5                                                            
CONECT   28    4   29   33                                                  
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32                                                       
CONECT   32   31                                                            
CONECT   33   28   34                                                       
CONECT   34   33   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34                                                            
CONECT   37    3                                                            
CONECT   38    3                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   84    0
END

View in JSmol

Synonyms

Value	Source
(AlphaR,4R)-a-acetoxy-4-(3-furyl)-1,4,4a,5,6,6abeta,7,8,9,10,11,12-dodecahydro-4abeta,7,9,9-tetramethyl-2,10,13-trioxo-7b,11b-methano-2H-cycloocta[F][2]benzopyran-8b-acetate methyl ester	Generator
(AlphaR,4R)-a-acetoxy-4-(3-furyl)-1,4,4a,5,6,6abeta,7,8,9,10,11,12-dodecahydro-4abeta,7,9,9-tetramethyl-2,10,13-trioxo-7b,11b-methano-2H-cycloocta[F][2]benzopyran-8b-acetic acid methyl ester	Generator
(AlphaR,4R)-alpha-acetoxy-4-(3-furyl)-1,4,4a,5,6,6abeta,7,8,9,10,11,12-dodecahydro-4abeta,7,9,9-tetramethyl-2,10,13-trioxo-7beta,11beta-methano-2H-cycloocta[F][2]benzopyran-8beta-acetate methyl ester	Generator
(AlphaR,4R)-α-acetoxy-4-(3-furyl)-1,4,4a,5,6,6abeta,7,8,9,10,11,12-dodecahydro-4abeta,7,9,9-tetramethyl-2,10,13-trioxo-7β,11β-methano-2H-cycloocta[F][2]benzopyran-8β-acetate methyl ester	Generator
(AlphaR,4R)-α-acetoxy-4-(3-furyl)-1,4,4a,5,6,6abeta,7,8,9,10,11,12-dodecahydro-4abeta,7,9,9-tetramethyl-2,10,13-trioxo-7β,11β-methano-2H-cycloocta[F][2]benzopyran-8β-acetic acid methyl ester	Generator

Chemical Formula

C₂₉H₃₄O₉

Average Mass

526.5820 Da

Monoisotopic Mass

526.22028 Da

IUPAC Name

methyl (2R)-2-(acetyloxy)-2-[(1R,2S,5R,6R,13S,16S)-6-(furan-3-yl)-1,5,15,15-tetramethyl-8,14,17-trioxo-7-oxatetracyclo[11.3.1.0^{2,11}.0^{5,10}]heptadec-10-en-16-yl]acetate

Traditional Name

(R)-(methyl (acetyloxy)[(1R,2S,5R,6R,13S,16S)-6-(furan-3-yl)-1,5,15,15-tetramethyl-8,14,17-trioxo-7-oxatetracyclo[11.3.1.0^{2,11}.0^{5,10}]heptadec-10-en-16-yl]acetate)

CAS Registry Number

Not Available

SMILES

COC(=O)[C@H](OC(C)=O)[C@H]1C(C)(C)C(=O)[C@@H]2CC3=C4CC(=O)O[C@@H](C5=COC=C5)[C@]4(C)CC[C@@H]3[C@@]1(C)C2=O

InChI Identifier

InChI=1S/C29H34O9/c1-14(30)37-21(26(34)35-6)22-27(2,3)23(32)17-11-16-18(29(22,5)24(17)33)7-9-28(4)19(16)12-20(31)38-25(28)15-8-10-36-13-15/h8,10,13,17-18,21-22,25H,7,9,11-12H2,1-6H3/t17-,18-,21+,22-,25-,28+,29+/m0/s1

InChI Key

GXYWZNJCGCCUAH-HMXNUIANSA-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
Ekebergia capensis	Plant	KNApSAcK
Lansium domesticum	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
Mexicanolide
Naphthopyran
Naphthalene
Tricarboxylic acid or derivatives
Delta valerolactone
1,3-diketone
Delta_valerolactone
1,3-dicarbonyl compound
Pyran
Oxane
Furan
Heteroaromatic compound
Methyl ester
Lactone
Ketone
Carboxylic acid ester
Carboxylic acid derivative
Oxacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Carbonyl group
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	3.38	ALOGPS
logP	3.6	ChemAxon
logS	-4.1	ALOGPS
pKa (Strongest Acidic)	11.34	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	126.18 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	132.61 m³·mol⁻¹	ChemAxon
Polarizability	53.9 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

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

101448553

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 (-)-Ekeberin C3 (NP0076491)

MOL for NP0076491 ((-)-Ekeberin C3)

3D MOL for NP0076491 ((-)-Ekeberin C3)

3D SDF for NP0076491 ((-)-Ekeberin C3)

3D-SDF for NP0076491 ((-)-Ekeberin C3)

PDB for NP0076491 ((-)-Ekeberin C3)

3D PDB for NP0076491 ((-)-Ekeberin C3)

SMILES for NP0076491 ((-)-Ekeberin C3)

INCHI for NP0076491 ((-)-Ekeberin C3)

Structure for NP0076491 ((-)-Ekeberin C3)

3D Structure for NP0076491 ((-)-Ekeberin C3)