NP-MRD: Showing NP-Card for didemnidine b (NP0168274)

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Record Information

Version

1.0

Created at

2022-09-03 04:02:35 UTC

Updated at

2022-09-03 04:02:35 UTC

NP-MRD ID

NP0168274

Secondary Accession Numbers

None

Natural Product Identification

Common Name

didemnidine b

Description

Didemnidine B belongs to the class of organic compounds known as indoles. Indoles are compounds containing an indole moiety, which consists of pyrrole ring fused to benzene to form 2,3-benzopyrrole. Based on a literature review very few articles have been published on Didemnidine B.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 47 48  0  0  0  0  0  0  0  0999 V2000
    6.3436    1.1441    1.6876 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.1495    0.8368    0.5480 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7858   -0.4260   -0.1802 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4040   -0.4369   -0.7560 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2926   -0.2839    0.2103 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9818   -0.3293   -0.4047 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6213   -1.6151   -0.9370 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2182   -1.4308   -1.5369 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3379   -0.9973   -0.4088 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0351   -0.7708   -0.8049 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9686   -0.3572    0.1661 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6168   -0.1915    1.3432 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3473   -0.1258   -0.2245 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7021   -0.3018   -1.4351 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3521    0.3033    0.7173 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2429    0.5654    2.0662 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4388    0.9356    2.5246 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3515    0.9345    1.5407 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6978    1.2245    1.4616 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4380    1.1461    0.3022 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.3037    1.5564    0.2335 Br  0  0  0  0  0  0  0  0  0  0  0  0
   -7.7635    0.7507   -0.8329 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4026    0.4514   -0.7835 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6912    0.5412    0.3999 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0420    2.1220    1.6757 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8926    0.9558    2.5753 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0217    1.6921   -0.1873 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2330    0.8683    0.8046 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5164   -0.5010   -1.0435 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9674   -1.3060    0.4806 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2437   -1.4265   -1.2827 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4020    0.3377   -1.5620 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3708   -0.9970    1.0390 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3449    0.7562    0.6521 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7882    0.4642   -1.0180 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2588   -1.9503   -1.7611 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5661   -2.3592   -0.1453 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8959   -2.3824   -2.0124 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2271   -0.6690   -2.3217 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3822   -1.7865    0.3918 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7731   -0.0573   -0.0001 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2661   -0.9287   -1.8066 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3369    0.4891    2.6772 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6822    1.1995    3.5043 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1989    1.5321    2.3697 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3015    0.6755   -1.7625 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9227    0.1478   -1.6955 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 13 14  2  0
 13 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  1  0
 20 22  2  0
 22 23  1  0
 23 24  2  0
 24 15  1  0
 24 18  1  0
  1 25  1  0
  1 26  1  0
  2 27  1  0
  2 28  1  0
  3 29  1  0
  3 30  1  0
  4 31  1  0
  4 32  1  0
  5 33  1  0
  5 34  1  0
  6 35  1  0
  7 36  1  0
  7 37  1  0
  8 38  1  0
  8 39  1  0
  9 40  1  0
  9 41  1  0
 10 42  1  0
 16 43  1  0
 17 44  1  0
 19 45  1  0
 22 46  1  0
 23 47  1  0
M  END


  Mrv1652309032206022D          

 24 25  0  0  0  0            999 V2000
    8.9296   -2.1758    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.6440   -2.5883    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3585   -2.1758    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0730   -2.5883    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7874   -2.1758    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5019   -2.5883    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.2164   -2.1758    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9309   -2.5883    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6453   -2.1758    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.3598   -2.5883    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.0743   -2.1758    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.0743   -1.3508    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.7887   -2.5883    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7887   -3.4133    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.5032   -2.1758    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5894   -1.3554    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.3964   -1.1838    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.8089   -1.8983    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.6159   -2.0698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.8708   -2.8545    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.6778   -3.0260    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
   19.3188   -3.4675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5118   -3.2960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.2569   -2.5114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  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  2  0  0  0  0
 13 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 15 24  1  0  0  0  0
 18 24  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0168274

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NCCCCNCCCNC(=O)C(=O)C1=CNC2=CC(Br)=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C17H23BrN4O2/c18-12-4-5-13-14(11-22-15(13)10-12)16(23)17(24)21-9-3-8-20-7-2-1-6-19/h4-5,10-11,20,22H,1-3,6-9,19H2,(H,21,24)

> <INCHI_KEY>
IAMCWSVWBJVYIO-UHFFFAOYSA-N

> <FORMULA>
C17H23BrN4O2

> <MOLECULAR_WEIGHT>
395.301

> <EXACT_MASS>
394.100439

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
47

> <JCHEM_AVERAGE_POLARIZABILITY>
40.446756439792615

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
N-{3-[(4-aminobutyl)amino]propyl}-2-(6-bromo-1H-indol-3-yl)-2-oxoacetamide

> <ALOGPS_LOGP>
1.85

> <JCHEM_LOGP>
1.0535321962538442

> <ALOGPS_LOGS>
-4.53

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
13.421468353049551

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.029521146624054

> <JCHEM_PKA_STRONGEST_BASIC>
10.589650407953567

> <JCHEM_POLAR_SURFACE_AREA>
100.00999999999999

> <JCHEM_REFRACTIVITY>
98.73350000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.16e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-{3-[(4-aminobutyl)amino]propyl}-2-(6-bromo-1H-indol-3-yl)-2-oxoacetamide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  N   UNK     0      16.669  -4.062   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      18.002  -4.832   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      19.336  -4.062   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      20.670  -4.832   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      22.003  -4.062   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      23.337  -4.832   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      24.671  -4.062   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      26.004  -4.832   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      27.338  -4.062   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      28.672  -4.832   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      30.005  -4.062   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      30.005  -2.522   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      31.339  -4.832   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      31.339  -6.372   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      32.673  -4.062   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      32.834  -2.530   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0      34.340  -2.210   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0      35.110  -3.544   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      36.616  -3.864   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      37.092  -5.328   0.000  0.00  0.00           C+0
HETATM   21 Br   UNK     0      38.599  -5.648   0.000  0.00  0.00          Br+0
HETATM   22  C   UNK     0      36.062  -6.473   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      34.555  -6.153   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      34.080  -4.688   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   24                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   24                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   15   18                                                  
MASTER        0    0    0    0    0    0    0    0   24    0   50    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₇H₂₃BrN₄O₂

Average Mass

395.3010 Da

Monoisotopic Mass

394.10044 Da

IUPAC Name

N-{3-[(4-aminobutyl)amino]propyl}-2-(6-bromo-1H-indol-3-yl)-2-oxoacetamide

Traditional Name

N-{3-[(4-aminobutyl)amino]propyl}-2-(6-bromo-1H-indol-3-yl)-2-oxoacetamide

CAS Registry Number

Not Available

SMILES

NCCCCNCCCNC(=O)C(=O)C1=CNC2=CC(Br)=CC=C12

InChI Identifier

InChI=1S/C17H23BrN4O2/c18-12-4-5-13-14(11-22-15(13)10-12)16(23)17(24)21-9-3-8-20-7-2-1-6-19/h4-5,10-11,20,22H,1-3,6-9,19H2,(H,21,24)

InChI Key

IAMCWSVWBJVYIO-UHFFFAOYSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as indoles. Indoles are compounds containing an indole moiety, which consists of pyrrole ring fused to benzene to form 2,3-benzopyrrole.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Indoles

Direct Parent

Indoles

Alternative Parents

Substituents

Indole
Aryl ketone
Aryl bromide
Aryl halide
Benzenoid
Substituted pyrrole
Heteroaromatic compound
Vinylogous amide
Pyrrole
Amino acid or derivatives
Carboxamide group
Ketone
Secondary carboxylic acid amide
Carboxylic acid derivative
Secondary aliphatic amine
Azacycle
Secondary amine
Organobromide
Organohalogen compound
Primary aliphatic amine
Hydrocarbon derivative
Organic nitrogen compound
Amine
Organic oxide
Carbonyl group
Organopnictogen compound
Organonitrogen compound
Organooxygen compound
Primary amine
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

tryptamines (CHEBI:67325 )

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	1.85	ALOGPS
logP	1.05	ChemAxon
logS	-4.5	ALOGPS
pKa (Strongest Acidic)	12.03	ChemAxon
pKa (Strongest Basic)	10.59	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	100.01 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	98.73 m³·mol⁻¹	ChemAxon
Polarizability	40.45 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

26342833

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

52950926

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for didemnidine b (NP0168274)

MOL for NP0168274 (didemnidine b)

3D MOL for NP0168274 (didemnidine b)

3D SDF for NP0168274 (didemnidine b)

3D-SDF for NP0168274 (didemnidine b)

PDB for NP0168274 (didemnidine b)

3D PDB for NP0168274 (didemnidine b)

SMILES for NP0168274 (didemnidine b)

INCHI for NP0168274 (didemnidine b)

Structure for NP0168274 (didemnidine b)

3D Structure for NP0168274 (didemnidine b)