NP-MRD: Showing NP-Card for Hymenocardine (NP0051098)

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Record Information

Version

2.0

Created at

2022-04-27 22:31:50 UTC

Updated at

2022-04-27 22:31:50 UTC

NP-MRD ID

NP0051098

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Hymenocardine

Description

Hymenocardine 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. Hymenocardine is found in Hymenocardia acida . Hymenocardine was first documented in 2016 (PMID: 27351950). Based on a literature review very few articles have been published on Hymenocardine (PMID: 28152554).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282200312D          

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M  END

     RDKit          3D

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 30 74  1  0
 31 75  1  0
 31 76  1  0
 35 77  1  0
 36 78  1  0
 42 81  1  0
 42 82  1  0
 42 83  1  0
 43 84  1  0
 43 85  1  0
 43 86  1  0
 38 79  1  0
 39 80  1  0
M  END


  Mrv1652304282200312D          

 49 52  0  0  1  0            999 V2000
    0.6792   -4.9951    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2504   -5.7231    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5784   -5.7153    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0593   -5.0268    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6206   -4.3307    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2022   -4.3107    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8007   -4.5777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3690   -5.1758    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2826   -3.8668    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2602   -3.0014    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8000   -2.2653    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3721   -1.6709    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0575   -1.8395    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2261   -1.7874    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5466   -2.0965    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0142   -1.4168    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1125   -2.7086    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3618   -3.5116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2629   -4.3529    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0829   -3.1108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1440   -3.7737    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8269   -2.2961    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5414   -2.7086    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5414   -3.5336    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2559   -2.2961    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2559   -1.4711    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9703   -1.0586    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5414   -1.0586    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9703   -2.7086    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.6848   -2.2961    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6848   -1.4711    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3993   -2.7086    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.1137   -2.2961    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.8282   -2.7086    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5427   -2.2961    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1137   -1.4711    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3993   -3.5336    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.1137   -3.9461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6848   -3.9461    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2947   -1.0493    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0976   -0.8597    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4160   -0.0986    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2383   -0.1663    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4279   -0.9692    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7229   -1.3977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7415   -2.2225    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4651   -2.6188    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1701   -2.1903    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1515   -1.3655    0.0000 C   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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  4  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
  1 19  1  0  0  0  0
 18 20  1  0  0  0  0
 18 21  1  0  0  0  0
 17 22  1  1  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  1  0  0  0  0
 25 29  1  6  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 30 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 33 36  1  1  0  0  0
 32 37  1  6  0  0  0
 37 38  1  0  0  0  0
 37 39  1  0  0  0  0
 13 40  1  6  0  0  0
 40 41  1  0  0  0  0
 41 42  2  0  0  0  0
 42 43  1  0  0  0  0
 43 44  1  0  0  0  0
 44 45  1  0  0  0  0
 41 45  1  0  0  0  0
 45 46  2  0  0  0  0
 46 47  1  0  0  0  0
 47 48  2  0  0  0  0
 48 49  1  0  0  0  0
 44 49  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0051098

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC[C@H](C)[C@H](N(C)C)C(=O)N[C@@H](C(C)C)C(=O)N[C@@H]1C(=O)N[C@@H](CC2=CNC3=CC=CC=C23)C(=O)NCC(=O)C2=CC=C(OC1(C)C)C=C2

> <INCHI_IDENTIFIER>
InChI=1S/C37H50N6O6/c1-9-22(4)31(43(7)8)35(47)41-30(21(2)3)34(46)42-32-36(48)40-28(18-24-19-38-27-13-11-10-12-26(24)27)33(45)39-20-29(44)23-14-16-25(17-15-23)49-37(32,5)6/h10-17,19,21-22,28,30-32,38H,9,18,20H2,1-8H3,(H,39,45)(H,40,48)(H,41,47)(H,42,46)/t22-,28-,30-,31-,32+/m0/s1

> <INCHI_KEY>
ATQXXRJEZULCTG-DLCFQVRISA-N

> <FORMULA>
C37H50N6O6

> <MOLECULAR_WEIGHT>
674.843

> <EXACT_MASS>
674.379183354

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
99

> <JCHEM_AVERAGE_POLARIZABILITY>
72.27769816472839

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S)-2-(dimethylamino)-N-[(1S)-1-{[(4S,7S)-7-[(1H-indol-3-yl)methyl]-3,3-dimethyl-5,8,11-trioxo-2-oxa-6,9-diazabicyclo[10.2.2]hexadeca-1(14),12,15-trien-4-yl]carbamoyl}-2-methylpropyl]-3-methylpentanamide

> <ALOGPS_LOGP>
3.73

> <JCHEM_LOGP>
3.2621108313333336

> <ALOGPS_LOGS>
-5.20

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
11.506326862738645

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.786891426401384

> <JCHEM_PKA_STRONGEST_BASIC>
8.05409867484547

> <JCHEM_POLAR_SURFACE_AREA>
161.73000000000002

> <JCHEM_REFRACTIVITY>
186.17969999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.30e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S)-2-(dimethylamino)-N-[(1S)-1-{[(4S,7S)-7-(1H-indol-3-ylmethyl)-3,3-dimethyl-5,8,11-trioxo-2-oxa-6,9-diazabicyclo[10.2.2]hexadeca-1(14),12,15-trien-4-yl]carbamoyl}-2-methylpropyl]-3-methylpentanamide

> <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       1.268  -9.324   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.467 -10.683   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.080 -10.669   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.977  -9.383   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.158  -8.084   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.377  -8.047   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.361  -8.545   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -4.422  -9.661   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -4.261  -7.218   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      -4.219  -5.603   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      -3.360  -4.228   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -4.428  -3.119   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -1.974  -3.434   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      -0.422  -3.336   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       1.020  -3.913   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       1.893  -2.645   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       2.077  -5.056   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.542  -6.555   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       2.357  -8.125   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       3.888  -5.807   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.002  -7.044   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0       3.410  -4.286   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0       4.744  -5.056   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       4.744  -6.596   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       6.078  -4.286   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       6.078  -2.746   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       7.411  -1.976   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.744  -1.976   0.000  0.00  0.00           C+0
HETATM   29  N   UNK     0       7.411  -5.056   0.000  0.00  0.00           N+0
HETATM   30  C   UNK     0       8.745  -4.286   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       8.745  -2.746   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      10.079  -5.056   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      11.412  -4.286   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      12.746  -5.056   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      14.080  -4.286   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      11.412  -2.746   0.000  0.00  0.00           C+0
HETATM   37  N   UNK     0      10.079  -6.596   0.000  0.00  0.00           N+0
HETATM   38  C   UNK     0      11.412  -7.366   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       8.745  -7.366   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      -2.417  -1.959   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      -3.915  -1.605   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      -4.510  -0.184   0.000  0.00  0.00           C+0
HETATM   43  N   UNK     0      -6.045  -0.310   0.000  0.00  0.00           N+0
HETATM   44  C   UNK     0      -6.399  -1.809   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      -5.083  -2.609   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      -5.118  -4.149   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      -6.468  -4.888   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      -7.784  -4.089   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      -7.750  -2.549   0.000  0.00  0.00           C+0
CONECT    1    2    6   19                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    7                                                  
CONECT    5    4    6                                                       
CONECT    6    5    1                                                       
CONECT    7    4    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   40                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   22                                                  
CONECT   18   17   19   20   21                                             
CONECT   19   18    1                                                       
CONECT   20   18                                                            
CONECT   21   18                                                            
CONECT   22   17   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26   29                                                  
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26                                                            
CONECT   29   25   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33   37                                                  
CONECT   33   32   34   36                                                  
CONECT   34   33   35                                                       
CONECT   35   34                                                            
CONECT   36   33                                                            
CONECT   37   32   38   39                                                  
CONECT   38   37                                                            
CONECT   39   37                                                            
CONECT   40   13   41                                                       
CONECT   41   40   42   45                                                  
CONECT   42   41   43                                                       
CONECT   43   42   44                                                       
CONECT   44   43   45   49                                                  
CONECT   45   44   41   46                                                  
CONECT   46   45   47                                                       
CONECT   47   46   48                                                       
CONECT   48   47   49                                                       
CONECT   49   48   44                                                       
MASTER        0    0    0    0    0    0    0    0   49    0  104    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₇H₅₀N₆O₆

Average Mass

674.8430 Da

Monoisotopic Mass

674.37918 Da

IUPAC Name

(2S,3S)-2-(dimethylamino)-N-[(1S)-1-{[(4S,7S)-7-[(1H-indol-3-yl)methyl]-3,3-dimethyl-5,8,11-trioxo-2-oxa-6,9-diazabicyclo[10.2.2]hexadeca-1(14),12,15-trien-4-yl]carbamoyl}-2-methylpropyl]-3-methylpentanamide

Traditional Name

(2S,3S)-2-(dimethylamino)-N-[(1S)-1-{[(4S,7S)-7-(1H-indol-3-ylmethyl)-3,3-dimethyl-5,8,11-trioxo-2-oxa-6,9-diazabicyclo[10.2.2]hexadeca-1(14),12,15-trien-4-yl]carbamoyl}-2-methylpropyl]-3-methylpentanamide

CAS Registry Number

Not Available

SMILES

CC[C@H](C)[C@H](N(C)C)C(=O)N[C@@H](C(C)C)C(=O)N[C@@H]1C(=O)N[C@@H](CC2=CNC3=CC=CC=C23)C(=O)NCC(=O)C2=CC=C(OC1(C)C)C=C2

InChI Identifier

InChI=1S/C37H50N6O6/c1-9-22(4)31(43(7)8)35(47)41-30(21(2)3)34(46)42-32-36(48)40-28(18-24-19-38-27-13-11-10-12-26(24)27)33(45)39-20-29(44)23-14-16-25(17-15-23)49-37(32,5)6/h10-17,19,21-22,28,30-32,38H,9,18,20H2,1-8H3,(H,39,45)(H,40,48)(H,41,47)(H,42,46)/t22-,28-,30-,31-,32+/m0/s1

InChI Key

ATQXXRJEZULCTG-DLCFQVRISA-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
Hymenocardia acida	Plant	KNApSAcK

Chemical Taxonomy

Description

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
Cyclic alpha peptide
Isoleucine or derivatives
N-acyl-alpha amino acid or derivatives
Valine or derivatives
Macrolactam
Alpha-amino acid amide
N-substituted-alpha-amino acid
Alpha-amino acid or derivatives
3-alkylindole
Indole
Indole or derivatives
Aryl alkyl ketone
Aryl ketone
Alkyl aryl ether
Substituted pyrrole
Benzenoid
Fatty amide
N-acyl-amine
Fatty acyl
Heteroaromatic compound
Pyrrole
Secondary carboxylic acid amide
Amino acid or derivatives
Carboxamide group
Ketone
Lactam
Tertiary aliphatic amine
Tertiary amine
Azacycle
Oxacycle
Ether
Organoheterocyclic compound
Organic nitrogen compound
Hydrocarbon derivative
Organopnictogen compound
Carbonyl group
Organic oxide
Amine
Organic oxygen compound
Organonitrogen compound
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

cyclic peptide (CHEBI:5823 )

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	3.73	ALOGPS
logP	3.26	ChemAxon
logS	-5.2	ALOGPS
pKa (Strongest Acidic)	10.79	ChemAxon
pKa (Strongest Basic)	8.05	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	161.73 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	186.18 m³·mol⁻¹	ChemAxon
Polarizability	72.28 Å³	ChemAxon
Number of Rings	4	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

C00001999

Chemspider ID

390978

KEGG Compound ID

C10004

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

442568

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Tuenter E, Bijttebier S, Foubert K, Breynaert A, Apers S, Hermans N, Pieters L: In Vitro and In Vivo Study of the Gastrointestinal Absorption and Metabolisation of Hymenocardine, a Cyclopeptide Alkaloid. Planta Med. 2017 Jun;83(9):790-796. doi: 10.1055/s-0043-102494. Epub 2017 Feb 2. [PubMed:28152554 ]
Tuenter E, Exarchou V, Balde A, Cos P, Maes L, Apers S, Pieters L: Cyclopeptide Alkaloids from Hymenocardia acida. J Nat Prod. 2016 Jul 22;79(7):1746-51. doi: 10.1021/acs.jnatprod.6b00131. Epub 2016 Jun 28. [PubMed:27351950 ]

Showing NP-Card for Hymenocardine (NP0051098)

MOL for NP0051098 (Hymenocardine)

3D MOL for NP0051098 (Hymenocardine)

3D SDF for NP0051098 (Hymenocardine)

3D-SDF for NP0051098 (Hymenocardine)

PDB for NP0051098 (Hymenocardine)

3D PDB for NP0051098 (Hymenocardine)

SMILES for NP0051098 (Hymenocardine)

INCHI for NP0051098 (Hymenocardine)

Structure for NP0051098 (Hymenocardine)

3D Structure for NP0051098 (Hymenocardine)