NP-MRD: Showing NP-Card for (3s,6z)-3-methyl-6-{[6-(3-methylbut-2-en-1-yl)-2-(2-methylbut-3-en-2-yl)-1h-indol-3-yl]methylidene}-3h-pyrazine-2,5-diol (NP0247528)

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Record Information

Version

2.0

Created at

2022-09-07 09:24:48 UTC

Updated at

2022-09-07 09:24:48 UTC

NP-MRD ID

NP0247528

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3s,6z)-3-methyl-6-{[6-(3-methylbut-2-en-1-yl)-2-(2-methylbut-3-en-2-yl)-1h-indol-3-yl]methylidene}-3h-pyrazine-2,5-diol

Description

Neoechinulin D 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. (3s,6z)-3-methyl-6-{[6-(3-methylbut-2-en-1-yl)-2-(2-methylbut-3-en-2-yl)-1h-indol-3-yl]methylidene}-3h-pyrazine-2,5-diol was first documented in 2019 (PMID: 31075485). Based on a literature review very few articles have been published on Neoechinulin D (PMID: 30978942).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309072211242D          

 29 31  0  0  1  0            999 V2000
   -1.4087   -1.4124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9962   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7812   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7812   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4957   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4358   -2.7631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2428   -2.5916    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7948   -3.2047    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6018   -3.0331    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5399   -3.9893    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0919   -4.6024    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7329   -4.1608    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1809   -3.5477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3739   -3.7192    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  3  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  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  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 10 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
  8 18  1  0  0  0  0
 18 19  1  0  0  0  0
  6 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 23 25  1  0  0  0  0
 25 26  1  6  0  0  0
 25 27  1  0  0  0  0
 27 28  2  0  0  0  0
 21 28  1  0  0  0  0
 28 29  1  0  0  0  0
M  END


  Mrv1652309072211242D          

 29 31  0  0  1  0            999 V2000
   -1.4087   -1.4124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9962   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7812   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7812   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4957   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4358   -2.7631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2428   -2.5916    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7948   -3.2047    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6018   -3.0331    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5399   -3.9893    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0919   -4.6024    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7329   -4.1608    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1809   -3.5477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3739   -3.7192    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  3  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  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  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 10 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
  8 18  1  0  0  0  0
 18 19  1  0  0  0  0
  6 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 23 25  1  0  0  0  0
 25 26  1  6  0  0  0
 25 27  1  0  0  0  0
 27 28  2  0  0  0  0
 21 28  1  0  0  0  0
 28 29  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0247528

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1N=C(O)\C(=C\C2=C(NC3=CC(CC=C(C)C)=CC=C23)C(C)(C)C=C)N=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C24H29N3O2/c1-7-24(5,6)21-18(13-20-23(29)25-15(4)22(28)27-20)17-11-10-16(9-8-14(2)3)12-19(17)26-21/h7-8,10-13,15,26H,1,9H2,2-6H3,(H,25,29)(H,27,28)/b20-13-/t15-/m0/s1

> <INCHI_KEY>
YCCLECFRSYOPML-HYTQYMIGSA-N

> <FORMULA>
C24H29N3O2

> <MOLECULAR_WEIGHT>
391.515

> <EXACT_MASS>
391.225977186

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
58

> <JCHEM_AVERAGE_POLARIZABILITY>
45.66453656664152

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3S,6Z)-3-methyl-6-{[6-(3-methylbut-2-en-1-yl)-2-(2-methylbut-3-en-2-yl)-1H-indol-3-yl]methylidene}-3,6-dihydropyrazine-2,5-diol

> <JCHEM_LOGP>
4.859170735544034

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
7.89056210821553

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.375547272541376

> <JCHEM_PKA_STRONGEST_BASIC>
3.4219930499238354

> <JCHEM_POLAR_SURFACE_AREA>
80.97

> <JCHEM_REFRACTIVITY>
120.34349999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3S,6Z)-3-methyl-6-{[6-(3-methylbut-2-en-1-yl)-2-(2-methylbut-3-en-2-yl)-1H-indol-3-yl]methylidene}-3H-pyrazine-2,5-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0      -2.630  -2.637   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.860  -1.303   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.320  -1.303   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.320  -2.843   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.320   0.237   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.591   0.237   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.925  -0.533   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.925  -2.073   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      10.259  -2.843   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.591  -2.843   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.650  -4.013   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.680  -5.158   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0       4.187  -4.838   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0       5.217  -5.982   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       6.723  -5.662   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       4.741  -7.447   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       5.772  -8.591   0.000  0.00  0.00           C+0
HETATM   27  N   UNK     0       3.235  -7.767   0.000  0.00  0.00           N+0
HETATM   28  C   UNK     0       2.204  -6.622   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       0.698  -6.943   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5    6                                             
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    3    7   19                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   18                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   16                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16   10   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17    8   19                                                  
CONECT   19   18    6   20                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   28                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28                                                       
CONECT   28   27   21   29                                                  
CONECT   29   28                                                            
MASTER        0    0    0    0    0    0    0    0   29    0   62    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₂₉N₃O₂

Average Mass

391.5150 Da

Monoisotopic Mass

391.22598 Da

IUPAC Name

(3S,6Z)-3-methyl-6-{[6-(3-methylbut-2-en-1-yl)-2-(2-methylbut-3-en-2-yl)-1H-indol-3-yl]methylidene}-3,6-dihydropyrazine-2,5-diol

Traditional Name

(3S,6Z)-3-methyl-6-{[6-(3-methylbut-2-en-1-yl)-2-(2-methylbut-3-en-2-yl)-1H-indol-3-yl]methylidene}-3H-pyrazine-2,5-diol

CAS Registry Number

Not Available

SMILES

C[C@@H]1N=C(O)\C(=C\C2=C(NC3=CC(CC=C(C)C)=CC=C23)C(C)(C)C=C)N=C1O

InChI Identifier

InChI=1S/C24H29N3O2/c1-7-24(5,6)21-18(13-20-23(29)25-15(4)22(28)27-20)17-11-10-16(9-8-14(2)3)12-19(17)26-21/h7-8,10-13,15,26H,1,9H2,2-6H3,(H,25,29)(H,27,28)/b20-13-/t15-/m0/s1

InChI Key

YCCLECFRSYOPML-HYTQYMIGSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

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
Indole
Indole or derivatives
Dioxopiperazine
2,5-dioxopiperazine
1,4-diazinane
Piperazine
Substituted pyrrole
Benzenoid
Heteroaromatic compound
Pyrrole
Lactam
Carboxamide group
Secondary carboxylic acid amide
Azacycle
Organoheterocyclic compound
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen 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	4.86	ChemAxon
pKa (Strongest Acidic)	4.38	ChemAxon
pKa (Strongest Basic)	3.42	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	80.97 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	120.34 m³·mol⁻¹	ChemAxon
Polarizability	45.66 Å³	ChemAxon
Number of Rings	3	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

C00011287

Chemspider ID

34997054

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

92468099

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Zhao C, Zhang C, He F, Zhang W, Leng A, Ying X: Two new alkaloids from Portulaca oleracea L. and their bioactivities. Fitoterapia. 2019 Jul;136:104166. doi: 10.1016/j.fitote.2019.05.005. Epub 2019 May 7. [PubMed:31075485 ]
Bovio E, Garzoli L, Poli A, Luganini A, Villa P, Musumeci R, McCormack GP, Cocuzza CE, Gribaudo G, Mehiri M, Varese GC: Marine Fungi from the Sponge Grantia compressa: Biodiversity, Chemodiversity, and Biotechnological Potential. Mar Drugs. 2019 Apr 11;17(4):220. doi: 10.3390/md17040220. [PubMed:30978942 ]
LOTUS database [Link]

Showing NP-Card for (3s,6z)-3-methyl-6-{[6-(3-methylbut-2-en-1-yl)-2-(2-methylbut-3-en-2-yl)-1h-indol-3-yl]methylidene}-3h-pyrazine-2,5-diol (NP0247528)

MOL for NP0247528 ((3s,6z)-3-methyl-6-{[6-(3-methylbut-2-en-1-yl)-2-(2-methylbut-3-en-2-yl)-1h-indol-3-yl]methylidene}-3h-pyrazine-2,5-diol)

3D MOL for NP0247528 ((3s,6z)-3-methyl-6-{[6-(3-methylbut-2-en-1-yl)-2-(2-methylbut-3-en-2-yl)-1h-indol-3-yl]methylidene}-3h-pyrazine-2,5-diol)

3D SDF for NP0247528 ((3s,6z)-3-methyl-6-{[6-(3-methylbut-2-en-1-yl)-2-(2-methylbut-3-en-2-yl)-1h-indol-3-yl]methylidene}-3h-pyrazine-2,5-diol)

3D-SDF for NP0247528 ((3s,6z)-3-methyl-6-{[6-(3-methylbut-2-en-1-yl)-2-(2-methylbut-3-en-2-yl)-1h-indol-3-yl]methylidene}-3h-pyrazine-2,5-diol)

PDB for NP0247528 ((3s,6z)-3-methyl-6-{[6-(3-methylbut-2-en-1-yl)-2-(2-methylbut-3-en-2-yl)-1h-indol-3-yl]methylidene}-3h-pyrazine-2,5-diol)

3D PDB for NP0247528 ((3s,6z)-3-methyl-6-{[6-(3-methylbut-2-en-1-yl)-2-(2-methylbut-3-en-2-yl)-1h-indol-3-yl]methylidene}-3h-pyrazine-2,5-diol)

SMILES for NP0247528 ((3s,6z)-3-methyl-6-{[6-(3-methylbut-2-en-1-yl)-2-(2-methylbut-3-en-2-yl)-1h-indol-3-yl]methylidene}-3h-pyrazine-2,5-diol)

INCHI for NP0247528 ((3s,6z)-3-methyl-6-{[6-(3-methylbut-2-en-1-yl)-2-(2-methylbut-3-en-2-yl)-1h-indol-3-yl]methylidene}-3h-pyrazine-2,5-diol)

Structure for NP0247528 ((3s,6z)-3-methyl-6-{[6-(3-methylbut-2-en-1-yl)-2-(2-methylbut-3-en-2-yl)-1h-indol-3-yl]methylidene}-3h-pyrazine-2,5-diol)

3D Structure for NP0247528 ((3s,6z)-3-methyl-6-{[6-(3-methylbut-2-en-1-yl)-2-(2-methylbut-3-en-2-yl)-1h-indol-3-yl]methylidene}-3h-pyrazine-2,5-diol)