NP-MRD: Showing NP-Card for Violaceotide D (NP0332297)

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Record Information

Version

2.0

Created at

2024-01-03 04:00:56 UTC

Updated at

2026-02-27 15:01:39 UTC

NP-MRD ID

NP0332297

Natural Product DOI

https://doi.org/10.57994/1499

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Violaceotide D

Description

Violaceotide D belongs to the class of organic compounds known as oligopeptides. These are organic compounds containing a sequence of between three and ten alpha-amino acids joined by peptide bonds. Violaceotide D was first documented in 2024 (PMID: 38276888). Based on a literature review very few articles have been published on Violaceotide D.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 01032404002D          

 34 35  0  0  1  0            999 V2000
    3.7934    2.2836    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7934    1.4586    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0789    1.0461    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2925    0.2492    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    1.0461    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8414    1.7605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8414    0.3316    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539   -0.3829    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539   -1.2079    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5395   -1.6204    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -2.4454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539   -2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539   -3.6829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -4.0954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -4.9204    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -5.3329    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -3.6829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684   -1.6204    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6829   -1.2079    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5079   -1.2079    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.9204   -1.9224    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.7454   -1.9224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5079   -2.6368    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684   -2.4454    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164    0.3316    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5079    1.0461    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.2224    1.4586    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9368    1.0461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6513    1.4586    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9368    0.2211    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5079    0.2211    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.9204   -0.4934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7454   -0.4934    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
  5  3  1  0  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  9  8  1  0  0  0  0
  9 10  1  6  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 14 17  1  0  0  0  0
 17 18  2  0  0  0  0
 11 18  1  0  0  0  0
  9 19  1  0  0  0  0
 19 20  1  0  0  0  0
 21 20  1  0  0  0  0
 21 22  1  6  0  0  0
 22 23  1  6  0  0  0
 22 24  1  0  0  0  0
 19 25  2  0  0  0  0
  7 26  2  0  0  0  0
 27  2  1  0  0  0  0
 27 28  1  6  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 29 31  1  0  0  0  0
 27 32  1  0  0  0  0
 32 33  1  0  0  0  0
 21 33  1  0  0  0  0
 33 34  2  0  0  0  0
M  END


  Mrv2104 01032404002D          

 34 35  0  0  1  0            999 V2000
    3.7934    2.2836    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7934    1.4586    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0789    1.0461    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2925    0.2492    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    1.0461    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8414    1.7605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8414    0.3316    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539   -0.3829    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539   -1.2079    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5395   -1.6204    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -2.4454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539   -2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539   -3.6829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -4.0954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -4.9204    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -5.3329    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -3.6829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684   -1.6204    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6829   -1.2079    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5079   -1.2079    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.9204   -1.9224    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.7454   -1.9224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5079   -2.6368    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684   -2.4454    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164    0.3316    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5079    1.0461    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.2224    1.4586    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9368    1.0461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6513    1.4586    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9368    0.2211    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5079    0.2211    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.9204   -0.4934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7454   -0.4934    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
  5  3  1  0  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  9  8  1  0  0  0  0
  9 10  1  6  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 14 17  1  0  0  0  0
 17 18  2  0  0  0  0
 11 18  1  0  0  0  0
  9 19  1  0  0  0  0
 19 20  1  0  0  0  0
 21 20  1  0  0  0  0
 21 22  1  6  0  0  0
 22 23  1  6  0  0  0
 22 24  1  0  0  0  0
 19 25  2  0  0  0  0
  7 26  2  0  0  0  0
 27  2  1  0  0  0  0
 27 28  1  6  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 29 31  1  0  0  0  0
 27 32  1  0  0  0  0
 32 33  1  0  0  0  0
 21 33  1  0  0  0  0
 33 34  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0332297

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC=C(C[C@@H]2NC(=O)[C@H](C)N(C)C(=O)[C@H](CC(C)C)NC(=O)[C@@H](NC2=O)[C@@H](C)O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C24H36N4O6/c1-13(2)11-19-24(33)28(5)14(3)21(30)25-18(12-16-7-9-17(34-6)10-8-16)22(31)27-20(15(4)29)23(32)26-19/h7-10,13-15,18-20,29H,11-12H2,1-6H3,(H,25,30)(H,26,32)(H,27,31)/t14-,15+,18-,19-,20-/m0/s1

> <INCHI_KEY>
TXTHSIPLLZUHPW-DOKOSKEHSA-N

> <FORMULA>
C24H36N4O6

> <MOLECULAR_WEIGHT>
476.574

> <EXACT_MASS>
476.263484895

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
70

> <JCHEM_AVERAGE_POLARIZABILITY>
49.924336240355586

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3S,6S,9S,12S)-6-[(1R)-1-hydroxyethyl]-9-[(4-methoxyphenyl)methyl]-1,12-dimethyl-3-(2-methylpropyl)-1,4,7,10-tetraazacyclododecane-2,5,8,11-tetrone

> <JCHEM_LOGP>
0.2000303926666663

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.195848413096721

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.591996741805682

> <JCHEM_PKA_STRONGEST_BASIC>
-2.937119481228067

> <JCHEM_POLAR_SURFACE_AREA>
137.07

> <JCHEM_REFRACTIVITY>
124.80459999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3S,6S,9S,12S)-6-[(1R)-1-hydroxyethyl]-9-[(4-methoxyphenyl)methyl]-1,12-dimethyl-3-(2-methylpropyl)-1,4,7,10-tetraazacyclododecane-2,5,8,11-tetrone

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-JAN-24   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-JAN-24         0                                  
HETATM    1  O   UNK     0       7.081   4.263   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       7.081   2.723   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       5.747   1.953   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       6.146   0.465   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.207   1.953   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.437   3.286   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.437   0.619   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       4.207  -0.715   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       4.207  -2.255   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.874  -3.025   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.874  -4.565   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.207  -5.335   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.207  -6.875   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.874  -7.645   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       2.874  -9.185   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       1.540  -9.955   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.540  -6.875   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.540  -5.335   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.541  -3.025   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0       6.875  -2.255   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0       8.415  -2.255   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       9.185  -3.588   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      10.725  -3.588   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       8.415  -4.922   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       5.541  -4.565   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       1.897   0.619   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       8.415   1.953   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       9.748   2.723   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      11.082   1.953   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      12.416   2.723   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      11.082   0.413   0.000  0.00  0.00           C+0
HETATM   32  N   UNK     0       8.415   0.413   0.000  0.00  0.00           N+0
HETATM   33  C   UNK     0       9.185  -0.921   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      10.725  -0.921   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   27                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   26                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   19                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   18                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   17                                                  
CONECT   15   14   16                                                       
CONECT   16   15                                                            
CONECT   17   14   18                                                       
CONECT   18   17   11                                                       
CONECT   19    9   20   25                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   33                                                  
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22                                                            
CONECT   25   19                                                            
CONECT   26    7                                                            
CONECT   27    2   28   32                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29                                                            
CONECT   32   27   33                                                       
CONECT   33   32   21   34                                                  
CONECT   34   33                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   70    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₃₆N₄O₆

Average Mass

476.5740 Da

Monoisotopic Mass

476.26348 Da

IUPAC Name

(3S,6S,9S,12S)-6-[(1R)-1-hydroxyethyl]-9-[(4-methoxyphenyl)methyl]-1,12-dimethyl-3-(2-methylpropyl)-1,4,7,10-tetraazacyclododecane-2,5,8,11-tetrone

Traditional Name

(3S,6S,9S,12S)-6-[(1R)-1-hydroxyethyl]-9-[(4-methoxyphenyl)methyl]-1,12-dimethyl-3-(2-methylpropyl)-1,4,7,10-tetraazacyclododecane-2,5,8,11-tetrone

CAS Registry Number

Not Available

SMILES

COC1=CC=C(C[C@@H]2NC(=O)[C@H](C)N(C)C(=O)[C@H](CC(C)C)NC(=O)[C@@H](NC2=O)[C@@H](C)O)C=C1

InChI Identifier

InChI=1S/C24H36N4O6/c1-13(2)11-19-24(33)28(5)14(3)21(30)25-18(12-16-7-9-17(34-6)10-8-16)22(31)27-20(15(4)29)23(32)26-19/h7-10,13-15,18-20,29H,11-12H2,1-6H3,(H,25,30)(H,26,32)(H,27,31)/t14-,15+,18-,19-,20-/m0/s1

InChI Key

TXTHSIPLLZUHPW-DOKOSKEHSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 700 MHz, C2D6OS, experimental)	[email protected]	Not Available	Not Available	2024-05-03	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, C2D6OS, experimental)	[email protected]	Not Available	Not Available	2024-05-03	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 700.0, Dimethylsulfoxide-d6, simulated)	[email protected]	Not Available	Not Available	2026-02-27	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 150.0, Dimethylsulfoxide-d6, simulated)	[email protected]	Not Available	Not Available	2026-02-27	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Aspergillus insulicola IMB18-072		Not Available
Aspergillus insulicola IMB18-072		Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as oligopeptides. These are organic compounds containing a sequence of between three and ten alpha-amino acids joined by peptide bonds.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Oligopeptides

Alternative Parents

Substituents

Alpha-oligopeptide
Leucine or derivatives
N-acyl-alpha amino acid or derivatives
Alpha-amino acid amide
Alanine or derivatives
Alpha-amino acid or derivatives
N-substituted-alpha-amino acid
Phenoxy compound
Methoxybenzene
Phenol ether
Anisole
Alkyl aryl ether
Fatty acyl
Benzenoid
N-acyl-amine
Fatty amide
Monocyclic benzene moiety
Tertiary carboxylic acid amide
Secondary alcohol
Lactam
Carboxamide group
Azacycle
Organoheterocyclic compound
Ether
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic 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	0.2	ChemAxon
pKa (Strongest Acidic)	10.59	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	137.07 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	124.8 m³·mol⁻¹	ChemAxon
Polarizability	49.92 Å³	ChemAxon
Number of Rings	2	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

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

DOI: 10.1021/acs.jnatprod.3c01115

Showing NP-Card for Violaceotide D (NP0332297)

MOL for NP0332297 (Violaceotide D)

3D MOL for NP0332297 (Violaceotide D)

3D SDF for NP0332297 (Violaceotide D)

3D-SDF for NP0332297 (Violaceotide D)

PDB for NP0332297 (Violaceotide D)

3D PDB for NP0332297 (Violaceotide D)

SMILES for NP0332297 (Violaceotide D)

INCHI for NP0332297 (Violaceotide D)

Structure for NP0332297 (Violaceotide D)

3D Structure for NP0332297 (Violaceotide D)