NP-MRD: Showing NP-Card for Echinulin (NP0057995)

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Record Information

Version

2.0

Created at

2022-04-28 03:20:08 UTC

Updated at

2025-02-11 15:45:55 UTC

NP-MRD ID

NP0057995

Natural Product DOI

https://doi.org/10.57994/0601

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Echinulin

Description

Echinulin belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof. Echinulin is found in Eurotium amstelodami, Eurotium chevalieri, Aspergillus variecolor, Cymbidium aloifolium, Dendrobium fimbriatum, Erythrophleum fordii, Eurotium echinulatum and Penicillium griseofulvum. Echinulin was first documented in 2019 (PMID: 31878044). Based on a literature review a significant number of articles have been published on echinulin (PMID: 35323462) (PMID: 33983974) (PMID: 33381959) (PMID: 31494811) (PMID: 37097072).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282205202D          

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M  END

     RDKit          3D

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  Mrv1652304282205202D          

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M  END
> <DATABASE_ID>
NP0057995

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1NC(=O)[C@H](CC2=C(NC3=C(CC=C(C)C)C=C(CC=C(C)C)C=C23)C(C)(C)C=C)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C29H39N3O2/c1-9-29(7,8)26-23(16-24-28(34)30-19(6)27(33)31-24)22-15-20(12-10-17(2)3)14-21(25(22)32-26)13-11-18(4)5/h9-11,14-15,19,24,32H,1,12-13,16H2,2-8H3,(H,30,34)(H,31,33)/t19-,24-/m0/s1

> <INCHI_KEY>
DIKMWTRJIZQJMY-CYFREDJKSA-N

> <FORMULA>
C29H39N3O2

> <MOLECULAR_WEIGHT>
461.65

> <EXACT_MASS>
461.304227508

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
73

> <JCHEM_AVERAGE_POLARIZABILITY>
52.825114255976814

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,6S)-3-{[5,7-bis(3-methylbut-2-en-1-yl)-2-(2-methylbut-3-en-2-yl)-1H-indol-3-yl]methyl}-6-methylpiperazine-2,5-dione

> <ALOGPS_LOGP>
5.17

> <JCHEM_LOGP>
5.744822437666667

> <ALOGPS_LOGS>
-5.56

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.339734678220406

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.117331339091612

> <JCHEM_PKA_STRONGEST_BASIC>
-4.383635296003452

> <JCHEM_POLAR_SURFACE_AREA>
73.99000000000001

> <JCHEM_REFRACTIVITY>
141.9744

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.27e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S,6S)-3-{[5,7-bis(3-methylbut-2-en-1-yl)-2-(2-methylbut-3-en-2-yl)-1H-indol-3-yl]methyl}-6-methylpiperazine-2,5-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       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.000   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.465   2.016   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.370   0.770   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      -1.465  -0.476   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0      -3.910   0.770   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -3.910  -0.770   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -3.910   2.310   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -5.450   0.770   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -6.220   2.104   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -1.941   3.481   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -0.910   4.625   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0       0.596   4.305   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0       1.627   5.449   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       3.133   5.129   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       1.151   6.914   0.000  0.00  0.00           C+0
HETATM   26  N   UNK     0      -0.355   7.234   0.000  0.00  0.00           N+0
HETATM   27  C   UNK     0      -1.386   6.090   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -2.892   6.410   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       2.181   8.058   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
CONECT    1    2    6   30                                                  
CONECT    2    1    3   14                                                  
CONECT    3    2    4   12                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    3   13   20                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13    2                                                       
CONECT   15   13   16   17   18                                             
CONECT   16   15                                                            
CONECT   17   15                                                            
CONECT   18   15   19                                                       
CONECT   19   18                                                            
CONECT   20   12   21                                                       
CONECT   21   20   22   27                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26   29                                                  
CONECT   26   25   27                                                       
CONECT   27   26   21   28                                                  
CONECT   28   27                                                            
CONECT   29   25                                                            
CONECT   30    1   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   72    0
END

View in JSmol

Synonyms

Value	Source
Echinuline	MeSH

Chemical Formula

C₂₉H₃₉N₃O₂

Average Mass

461.6500 Da

Monoisotopic Mass

461.30423 Da

IUPAC Name

(3S,6S)-3-{[5,7-bis(3-methylbut-2-en-1-yl)-2-(2-methylbut-3-en-2-yl)-1H-indol-3-yl]methyl}-6-methylpiperazine-2,5-dione

Traditional Name

(3S,6S)-3-{[5,7-bis(3-methylbut-2-en-1-yl)-2-(2-methylbut-3-en-2-yl)-1H-indol-3-yl]methyl}-6-methylpiperazine-2,5-dione

CAS Registry Number

Not Available

SMILES

C[C@@H]1NC(=O)[C@H](CC2=C(NC3=C(CC=C(C)C)C=C(CC=C(C)C)C=C23)C(C)(C)C=C)NC1=O

InChI Identifier

InChI=1S/C29H39N3O2/c1-9-29(7,8)26-23(16-24-28(34)30-19(6)27(33)31-24)22-15-20(12-10-17(2)3)14-21(25(22)32-26)13-11-18(4)5/h9-11,14-15,19,24,32H,1,12-13,16H2,2-8H3,(H,30,34)(H,31,33)/t19-,24-/m0/s1

InChI Key

DIKMWTRJIZQJMY-CYFREDJKSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View

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

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 400, CDCl₃, simulated)	[email protected]	guangzhou university of Chinese medicine	zhangcuixian	2024-05-11	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Aspergillus amstelodami	Fungi	KNApSAcK
Aspergillus chevalieri	Fungi	KNApSAcK
Aspergillus stellatus	Fungi	KNApSAcK
Aspergillus versicolor CGF 9-1-2		Not Available
Cymbidium aloifolium	LOTUS Database	35616633
Dendrobium fimbriatum	LOTUS Database	35616633
Erythrophleum fordii	LOTUS Database	35616633
Eurotium echinulatum	Fungi	KNApSAcK
Penicillium griseofulvum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids and derivatives

Alternative Parents

Substituents

Alpha-amino acid or derivatives
3-alkylindole
Indole
Indole or derivatives
Dioxopiperazine
2,5-dioxopiperazine
1,4-diazinane
Piperazine
Benzenoid
Substituted pyrrole
Heteroaromatic compound
Pyrrole
Carboxamide group
Lactam
Secondary carboxylic acid amide
Azacycle
Organoheterocyclic compound
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Carbonyl group
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	5.17	ALOGPS
logP	5.74	ChemAxon
logS	-5.6	ALOGPS
pKa (Strongest Acidic)	11.12	ChemAxon
pKa (Strongest Basic)	-4.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	73.99 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	141.97 m³·mol⁻¹	ChemAxon
Polarizability	52.83 Å³	ChemAxon
Number of Rings	3	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

C00011273

Chemspider ID

103122

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

115252

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Alhadrami HA, Burgio G, Thissera B, Orfali R, Jiffri SE, Yaseen M, Sayed AM, Rateb ME: Neoechinulin A as a Promising SARS-CoV-2 M(pro) Inhibitor: In Vitro and In Silico Study Showing the Ability of Simulations in Discerning Active from Inactive Enzyme Inhibitors. Mar Drugs. 2022 Feb 24;20(3). pii: md20030163. doi: 10.3390/md20030163. [PubMed:35323462 ]
Calado MDL, Silva J, Alves C, Susano P, Santos D, Alves J, Martins A, Gaspar H, Pedrosa R, Campos MJ: Marine endophytic fungi associated with Halopteris scoparia (Linnaeus) Sauvageau as producers of bioactive secondary metabolites with potential dermocosmetic application. PLoS One. 2021 May 13;16(5):e0250954. doi: 10.1371/journal.pone.0250954. eCollection 2021. [PubMed:33983974 ]
Nies J, Li SM: Prenylation and Dehydrogenation of a C2-Reversely Prenylated Diketopiperazine as a Branching Point in the Biosynthesis of Echinulin Family Alkaloids in Aspergillus ruber. ACS Chem Biol. 2021 Jan 15;16(1):185-192. doi: 10.1021/acschembio.0c00874. Epub 2020 Dec 31. [PubMed:33381959 ]
Smetanina OF, Yurchenko AN, Girich Ivanets EV, Trinh PTH, Antonov AS, Dyshlovoy SA, von Amsberg G, Kim NY, Chingizova EA, Pislyagin EA, Menchinskaya ES, Yurchenko EA, Van TTT, Afiyatullov SS: Biologically Active Echinulin-Related Indolediketopiperazines from the Marine Sediment-Derived Fungus Aspergillus niveoglaucus. Molecules. 2019 Dec 23;25(1). pii: molecules25010061. doi: 10.3390/molecules25010061. [PubMed:31878044 ]
Bovio E, Fauchon M, Toueix Y, Mehiri M, Varese GC, Hellio C: The Sponge-Associated Fungus Eurotium chevalieri MUT 2316 and its Bioactive Molecules: Potential Applications in the Field of Antifouling. Mar Biotechnol (NY). 2019 Dec;21(6):743-752. doi: 10.1007/s10126-019-09920-y. Epub 2019 Sep 7. [PubMed:31494811 ]
Hu JS, He YP, Zhou FG, Wu PP, Chen LY, Ni C, Zhang ZK, Xiao XJ, An LK, He XX, Zhang CX: New Indole Diketopiperazine Alkaloids from Soft Coral-Associated Epiphytic Fungus Aspergillus versicolor CGF 9-1-2. Chem Biodivers. 2023 Jun;20(6):e202300301. doi: 10.1002/cbdv.202300301. Epub 2023 May 17. [PubMed:37097072 ]
DOI: 10.1002/cbdv.202300301

Showing NP-Card for Echinulin (NP0057995)

MOL for NP0057995 (Echinulin)

3D MOL for NP0057995 (Echinulin)

3D SDF for NP0057995 (Echinulin)

3D-SDF for NP0057995 (Echinulin)

PDB for NP0057995 (Echinulin)

3D PDB for NP0057995 (Echinulin)

SMILES for NP0057995 (Echinulin)

INCHI for NP0057995 (Echinulin)

Structure for NP0057995 (Echinulin)

3D Structure for NP0057995 (Echinulin)