NP-MRD: Showing NP-Card for Aplicyanin D (NP0081941)

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Record Information

Version

2.0

Created at

2022-04-29 03:00:10 UTC

Updated at

2022-04-29 03:00:10 UTC

NP-MRD ID

NP0081941

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Aplicyanin D

Description

N-[(6S)-6-(5-bromo-1-methoxy-1H-indol-3-yl)-1,4,5,6-tetrahydropyrimidin-2-yl]ethanimidic acid belongs to the class of organic compounds known as 3-alkylindoles. 3-Alkylindoles are compounds containing an indole moiety that carries an alkyl chain at the 3-position. Aplicyanin D is found in Aplidium cyaneum. Based on a literature review very few articles have been published on N-[(6S)-6-(5-bromo-1-methoxy-1H-indol-3-yl)-1,4,5,6-tetrahydropyrimidin-2-yl]ethanimidic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 39 41  0  0  0  0  0  0  0  0999 V2000
   -3.4942    3.1629    1.2087 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5620    2.2576    1.6863 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0616    1.1821    1.0165 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7858    0.7147    0.9838 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6826   -0.3800    0.1582 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5303   -1.0784   -0.3436 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7721   -2.3982    0.3248 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2014   -2.8050    0.5201 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2094   -1.9145    0.1019 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0116   -0.6781   -0.1885 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1356    0.1062   -0.5952 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0939    1.4704   -0.9069 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3129    2.1774   -1.3297 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0154    2.0925   -0.8287 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7014   -0.1960   -0.1006 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9792   -0.6085   -0.3508 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4292   -1.6118   -1.1872 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7985   -1.6443   -1.5088 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3864   -3.0670   -2.6378 Br  0  0  0  0  0  0  0  0  0  0  0  0
   -4.6457   -0.6819   -0.9834 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1423    0.3055   -0.1406 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7761    0.3717    0.2052 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1052    4.2308    1.3461 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5890    3.0565    0.0763 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5222    3.0640    1.6150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0177    1.1758    1.5712 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4291   -1.2186   -1.4188 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2827   -3.2111   -0.3189 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2203   -2.4600    1.2842 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3811   -3.0653    1.6061 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3876   -3.7975   -0.0040 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0878   -0.3578   -0.6375 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0718    2.0588   -0.4911 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1025    3.2586   -1.5255 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7186    1.6947   -2.2438 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5193    0.7703    0.1715 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7260   -2.3081   -1.5510 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6983   -0.7206   -1.2448 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7826    1.0522    0.2557 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  2  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 12 14  2  0
 10 15  1  0
  5 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  1  0
 18 20  2  0
 20 21  1  0
 21 22  2  0
 22  3  1  0
 15  6  1  0
 22 16  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  4 26  1  0
  6 27  1  6
  7 28  1  0
  7 29  1  0
  8 30  1  0
  8 31  1  0
 11 32  1  0
 13 33  1  0
 13 34  1  0
 13 35  1  0
 15 36  1  0
 17 37  1  0
 20 38  1  0
 21 39  1  0
M  END


  Mrv1652304292205002D          

 22 24  0  0  1  0            999 V2000
    3.3523    1.9354    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    0.6979    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
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4358   -0.5422    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1809   -1.3268    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3739   -1.4984    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1781   -0.8853    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768   -0.1006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7329   -1.9399    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4780   -2.7246    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0300   -3.3376    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6710   -2.8961    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    2.9750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768    3.1465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0668    0.6979    0.0000 Br  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
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  4  9  1  0  0  0  0
 10  9  1  1  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
 14 15  1  0  0  0  0
 10 15  1  0  0  0  0
 12 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
  7 20  1  0  0  0  0
 20 21  1  0  0  0  0
  2 22  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0081941

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CON1C=C([C@@H]2CCN=C(NC(C)=O)N2)C2=CC(Br)=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C15H17BrN4O2/c1-9(21)18-15-17-6-5-13(19-15)12-8-20(22-2)14-4-3-10(16)7-11(12)14/h3-4,7-8,13H,5-6H2,1-2H3,(H2,17,18,19,21)/t13-/m0/s1

> <INCHI_KEY>
PNPNLBSBVMICFT-ZDUSSCGKSA-N

> <FORMULA>
C15H17BrN4O2

> <MOLECULAR_WEIGHT>
365.231

> <EXACT_MASS>
364.053489

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
34.003727889842494

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
N-[(6S)-6-(5-bromo-1-methoxy-1H-indol-3-yl)-1,4,5,6-tetrahydropyrimidin-2-yl]acetamide

> <ALOGPS_LOGP>
2.15

> <JCHEM_LOGP>
1.4417333679999993

> <ALOGPS_LOGS>
-3.64

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.563221666802098

> <JCHEM_PKA_STRONGEST_BASIC>
6.621891860603104

> <JCHEM_POLAR_SURFACE_AREA>
67.65

> <JCHEM_REFRACTIVITY>
88.1051

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.42e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-[(4S)-4-(5-bromo-1-methoxyindol-3-yl)-3,4,5,6-tetrahydropyrimidin-2-yl]acetamide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       2.126   4.089   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.126   1.597   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.650   0.132   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       2.680  -1.012   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       2.204  -2.477   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       0.698  -2.797   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      -0.333  -1.652   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.143  -0.188   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       3.235  -3.621   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       2.759  -5.086   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       3.789  -6.230   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       1.253  -5.406   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       1.650   5.553   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       0.143   5.874   0.000  0.00  0.00           C+0
HETATM   22 Br   UNK     0       7.591   1.303   0.000  0.00  0.00          Br+0
CONECT    1    2    6                                                       
CONECT    2    1    3   22                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8   20                                                  
CONECT    8    7    9                                                       
CONECT    9    8    4   10                                                  
CONECT   10    9   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   16                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   10                                                       
CONECT   16   12   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20    7   21                                                       
CONECT   21   20                                                            
CONECT   22    2                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

View in JSmol

Synonyms

Value	Source
N-[(6S)-6-(5-Bromo-1-methoxy-1H-indol-3-yl)-1,4,5,6-tetrahydropyrimidin-2-yl]ethanimidate	Generator

Chemical Formula

C₁₅H₁₇BrN₄O₂

Average Mass

365.2310 Da

Monoisotopic Mass

364.05349 Da

IUPAC Name

N-[(6S)-6-(5-bromo-1-methoxy-1H-indol-3-yl)-1,4,5,6-tetrahydropyrimidin-2-yl]acetamide

Traditional Name

N-[(4S)-4-(5-bromo-1-methoxyindol-3-yl)-3,4,5,6-tetrahydropyrimidin-2-yl]acetamide

CAS Registry Number

Not Available

SMILES

CON1C=C([C@@H]2CCN=C(NC(C)=O)N2)C2=CC(Br)=CC=C12

InChI Identifier

InChI=1S/C15H17BrN4O2/c1-9(21)18-15-17-6-5-13(19-15)12-8-20(22-2)14-4-3-10(16)7-11(12)14/h3-4,7-8,13H,5-6H2,1-2H3,(H2,17,18,19,21)/t13-/m0/s1

InChI Key

PNPNLBSBVMICFT-ZDUSSCGKSA-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
Aplidium cyaneum	Animalia	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 3-alkylindoles. 3-Alkylindoles are compounds containing an indole moiety that carries an alkyl chain at the 3-position.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Indoles

Direct Parent

3-alkylindoles

Alternative Parents

Substituents

3-alkylindole
Aryl bromide
Aryl halide
Hydropyrimidine
1,4,5,6-tetrahydropyrimidine
Substituted pyrrole
Benzenoid
Heteroaromatic compound
Pyrrole
Azacycle
Organic 1,3-dipolar compound
Carboximidamide
Propargyl-type 1,3-dipolar organic compound
Organooxygen compound
Organonitrogen compound
Organobromide
Organohalogen compound
Hydrocarbon derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
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	2.15	ALOGPS
logP	1.44	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	9.56	ChemAxon
pKa (Strongest Basic)	6.62	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	67.65 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	88.11 m³·mol⁻¹	ChemAxon
Polarizability	34 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

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

162874498

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Aplicyanin D (NP0081941)

MOL for NP0081941 (Aplicyanin D)

3D MOL for NP0081941 (Aplicyanin D)

3D SDF for NP0081941 (Aplicyanin D)

3D-SDF for NP0081941 (Aplicyanin D)

PDB for NP0081941 (Aplicyanin D)

3D PDB for NP0081941 (Aplicyanin D)

SMILES for NP0081941 (Aplicyanin D)

INCHI for NP0081941 (Aplicyanin D)

Structure for NP0081941 (Aplicyanin D)

3D Structure for NP0081941 (Aplicyanin D)