NP-MRD: Showing NP-Card for boydine E (NP0350838)

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Record Information

Version

2.0

Created at

2025-03-14 03:56:29 UTC

Updated at

2025-03-16 00:03:43 UTC

NP-MRD ID

NP0350838

Natural Product DOI

https://doi.org/10.57994/3823

Secondary Accession Numbers

None

Natural Product Identification

Common Name

boydine E

Description

Boydine E 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. boydine E was first documented in 2025 (PMID: 40062959). Based on a literature review very few articles have been published on boydine E.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 06112304032D          

 29 32  0  0  1  0            999 V2000
    3.5206    0.7526    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9075    0.2006    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.0790   -0.6064    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7464   -0.1215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4139   -0.6064    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2208   -0.4349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7729   -1.0479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5179   -1.8326    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7110   -2.0041    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.4560   -2.7887    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1589   -1.3910    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8234   -2.1447    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3339   -1.3910    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7819   -2.0041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9749   -1.8326    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7200   -1.0479    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2720   -0.4349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0171    0.3498    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7753   -2.6331    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9823   -2.8605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7827   -3.6610    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3762   -4.2340    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0103   -3.8884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6038   -3.3153    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4042   -2.5148    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3888   -2.2874    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1997   -2.1147    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.5677   -1.5844    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0368   -2.7887    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  9  8  1  0  0  0  0
  9 10  1  6  0  0  0
  9 11  1  0  0  0  0
 11  5  1  0  0  0  0
 11 12  1  6  0  0  0
  3 13  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 15 14  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
  3 17  1  0  0  0  0
 17 18  2  0  0  0  0
 15 19  1  6  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 20 26  1  0  0  0  0
 15 27  1  1  0  0  0
 27 28  1  0  0  0  0
 14 29  2  0  0  0  0
M  END


  Mrv2104 06112304032D          

 29 32  0  0  1  0            999 V2000
    3.5206    0.7526    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9075    0.2006    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.0790   -0.6064    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7464   -0.1215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4139   -0.6064    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2208   -0.4349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7729   -1.0479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5179   -1.8326    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7110   -2.0041    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.4560   -2.7887    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1589   -1.3910    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8234   -2.1447    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3339   -1.3910    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7819   -2.0041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9749   -1.8326    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7200   -1.0479    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2720   -0.4349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0171    0.3498    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7753   -2.6331    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9823   -2.8605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7827   -3.6610    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3762   -4.2340    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0103   -3.8884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6038   -3.3153    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4042   -2.5148    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3888   -2.2874    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1997   -2.1147    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.5677   -1.5844    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0368   -2.7887    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  9  8  1  0  0  0  0
  9 10  1  6  0  0  0
  9 11  1  0  0  0  0
 11  5  1  0  0  0  0
 11 12  1  6  0  0  0
  3 13  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 15 14  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
  3 17  1  0  0  0  0
 17 18  2  0  0  0  0
 15 19  1  6  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 20 26  1  0  0  0  0
 15 27  1  1  0  0  0
 27 28  1  0  0  0  0
 14 29  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0350838

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]12[C@@H](O)C=CC=C1C[C@]1(SC)N2C(=O)[C@](CC2=C(O)C=CC=C2)(NC1=O)SC

> <INCHI_IDENTIFIER>
InChI=1S/C20H22N2O4S2/c1-27-19(10-12-6-3-4-8-14(12)23)18(26)22-16-13(7-5-9-15(16)24)11-20(22,28-2)17(25)21-19/h3-9,15-16,23-24H,10-11H2,1-2H3,(H,21,25)/t15-,16-,19+,20+/m0/s1

> <INCHI_KEY>
UYQAICBKGNCBMM-XAMWDVODSA-N

> <FORMULA>
C20H22N2O4S2

> <MOLECULAR_WEIGHT>
418.53

> <EXACT_MASS>
418.102099544

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
50

> <JCHEM_AVERAGE_POLARIZABILITY>
41.264390458717926

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3R,5aS,6S,10aR)-6-hydroxy-3-[(2-hydroxyphenyl)methyl]-3,10a-bis(methylsulfanyl)-1H,2H,3H,4H,5aH,6H,10H,10aH-pyrazino[1,2-a]indole-1,4-dione

> <JCHEM_LOGP>
2.5580108570000006

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.600270581676718

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.297019964386044

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1815183699831873

> <JCHEM_POLAR_SURFACE_AREA>
89.87

> <JCHEM_REFRACTIVITY>
113.05569999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3R,5aS,6S,10aR)-6-hydroxy-3-[(2-hydroxyphenyl)methyl]-3,10a-bis(methylsulfanyl)-2H,5aH,6H,10H-pyrazino[1,2-a]indole-1,4-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-JUN-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-JUN-23         0                                  
HETATM    1  C   UNK     0       6.572   1.405   0.000  0.00  0.00           C+0
HETATM    2  S   UNK     0       5.427   0.374   0.000  0.00  0.00           S+0
HETATM    3  C   UNK     0       5.747  -1.132   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.993  -0.227   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.239  -1.132   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.746  -0.812   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.776  -1.956   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.300  -3.421   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.794  -3.741   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       8.318  -5.206   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       7.763  -2.597   0.000  0.00  0.00           C+0
HETATM   12  H   UNK     0       7.137  -4.003   0.000  0.00  0.00           H+0
HETATM   13  N   UNK     0       6.223  -2.597   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       5.193  -3.741   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.687  -3.421   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       3.211  -1.956   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       4.241  -0.812   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       3.765   0.653   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       3.314  -4.915   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.834  -5.340   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.461  -6.834   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       2.569  -7.904   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -0.019  -7.258   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -1.127  -6.188   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -0.754  -4.694   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       0.726  -4.270   0.000  0.00  0.00           C+0
HETATM   27  S   UNK     0       2.239  -3.948   0.000  0.00  0.00           S+0
HETATM   28  C   UNK     0       1.060  -2.958   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       5.669  -5.206   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   13   17                                             
CONECT    4    3    5                                                       
CONECT    5    4    6   11                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9    5   12   13                                             
CONECT   12   11                                                            
CONECT   13    3   11   14                                                  
CONECT   14   13   15   29                                                  
CONECT   15   14   16   19   27                                             
CONECT   16   15   17                                                       
CONECT   17   16    3   18                                                  
CONECT   18   17                                                            
CONECT   19   15   20                                                       
CONECT   20   19   21   26                                                  
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   20                                                       
CONECT   27   15   28                                                       
CONECT   28   27                                                            
CONECT   29   14                                                            
MASTER        0    0    0    0    0    0    0    0   29    0   64    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₀H₂₂N₂O₄S₂

Average Mass

418.5300 Da

Monoisotopic Mass

418.10210 Da

IUPAC Name

(3R,5aS,6S,10aR)-6-hydroxy-3-[(2-hydroxyphenyl)methyl]-3,10a-bis(methylsulfanyl)-1H,2H,3H,4H,5aH,6H,10H,10aH-pyrazino[1,2-a]indole-1,4-dione

Traditional Name

(3R,5aS,6S,10aR)-6-hydroxy-3-[(2-hydroxyphenyl)methyl]-3,10a-bis(methylsulfanyl)-2H,5aH,6H,10H-pyrazino[1,2-a]indole-1,4-dione

CAS Registry Number

Not Available

SMILES

[H][C@@]12[C@@H](O)C=CC=C1C[C@]1(SC)N2C(=O)[C@](CC2=C(O)C=CC=C2)(NC1=O)SC

InChI Identifier

InChI=1S/C20H22N2O4S2/c1-27-19(10-12-6-3-4-8-14(12)23)18(26)22-16-13(7-5-9-15(16)24)11-20(22,28-2)17(25)21-19/h3-9,15-16,23-24H,10-11H2,1-2H3,(H,21,25)/t15-,16-,19+,20+/m0/s1

InChI Key

UYQAICBKGNCBMM-XAMWDVODSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
ROESY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	zhanganxin19950802@163.com	chinese academy of science	Zhang Anxin	2025-03-14	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	zhanganxin19950802@163.com	chinese academy of science	Zhang Anxin	2025-03-14	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	zhanganxin19950802@163.com	chinese academy of science	Zhang Anxin	2025-03-14	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	zhanganxin19950802@163.com	chinese academy of science	Zhang Anxin	2025-03-14	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CD3OD, experimental)	zhanganxin19950802@163.com	chinese academy of science	Zhang Anxin	2025-03-14	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, CD3OD, experimental)	zhanganxin19950802@163.com	chinese academy of science	Zhang Anxin	2025-03-14	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 125.751504144 MHz, CD₃OD, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 125.751504144, CD₃OD, simulated)	zhanganxin19950802@163.com	chinese academy of science	Zhang Anxin	2025-03-14	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Epicoccum dendrobii		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
Thiodioxopiperazine
Indole or derivatives
2,5-dioxopiperazine
Dioxopiperazine
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
N-alkylpiperazine
Phenol
Benzenoid
Piperazine
1,4-diazinane
Monocyclic benzene moiety
Tertiary carboxylic acid amide
Pyrrolidine
Secondary carboxylic acid amide
Secondary alcohol
Lactam
Carboxamide group
Azacycle
Organoheterocyclic compound
Dialkylthioether
Sulfenyl compound
Hemithioaminal
Thioether
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organosulfur compound
Organooxygen compound
Organonitrogen 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	2.56	ChemAxon
pKa (Strongest Acidic)	9.3	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	89.87 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	113.06 m³·mol⁻¹	ChemAxon
Polarizability	41.26 Å³	ChemAxon
Number of Rings	4	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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

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METLIN ID

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PubChem Compound

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PDB ID

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ChEBI ID

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Good Scents ID

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References

General References

Zhang A, Xu X, Yin WB: Genome Mining of Epicoccum dendrobii Reveals Diverse Antimicrobial Natural Products. J Agric Food Chem. 2025 Mar 10. doi: 10.1021/acs.jafc.4c11808. [PubMed:40062959 ]
DOI: 10.1021/acs.jafc.4c11808
PMID: 40062959

Showing NP-Card for boydine E (NP0350838)

MOL for NP0350838 (boydine E)

3D MOL for NP0350838 (boydine E)

3D SDF for NP0350838 (boydine E)

3D-SDF for NP0350838 (boydine E)

PDB for NP0350838 (boydine E)

3D PDB for NP0350838 (boydine E)

SMILES for NP0350838 (boydine E)

INCHI for NP0350838 (boydine E)

Structure for NP0350838 (boydine E)

3D Structure for NP0350838 (boydine E)