NP-MRD: Showing NP-Card for 4-amino-n-[1-(5-{[3,4-dihydroxy-6-methyl-5-(methylamino)oxan-2-yl]oxy}-6-methyloxan-2-yl)-2-hydroxypyrimidin-4-ylidene]benzamide (NP0331076)

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Record Information

Version

1.0

Created at

2022-09-12 17:03:58 UTC

Updated at

2022-09-12 17:03:58 UTC

NP-MRD ID

NP0331076

Secondary Accession Numbers

None

Natural Product Identification

Common Name

4-amino-n-[1-(5-{[3,4-dihydroxy-6-methyl-5-(methylamino)oxan-2-yl]oxy}-6-methyloxan-2-yl)-2-hydroxypyrimidin-4-ylidene]benzamide

Description

4-Amino-N-[1-(5-{[3,4-dihydroxy-6-methyl-5-(methylamino)oxan-2-yl]oxy}-6-methyloxan-2-yl)-2-hydroxy-1,4-dihydropyrimidin-4-ylidene]benzamide belongs to the class of organic compounds known as aminoglycosides. These are molecules or a portion of a molecule composed of amino-modified sugars. 4-amino-n-[1-(5-{[3,4-dihydroxy-6-methyl-5-(methylamino)oxan-2-yl]oxy}-6-methyloxan-2-yl)-2-hydroxypyrimidin-4-ylidene]benzamide is found in Streptomyces plicatus. 4-Amino-N-[1-(5-{[3,4-dihydroxy-6-methyl-5-(methylamino)oxan-2-yl]oxy}-6-methyloxan-2-yl)-2-hydroxy-1,4-dihydropyrimidin-4-ylidene]benzamide is a very strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004161507182D          

 36 39  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1533004161507182D          

 36 39  0  0  0  0            999 V2000
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 20 21  1  0  0  0  0
 16 21  1  0  0  0  0
 21 22  2  0  0  0  0
 19 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 24 26  1  0  0  0  0
 26 27  2  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 29 30  1  0  0  0  0
 29 31  1  0  0  0  0
 31 32  2  0  0  0  0
 26 32  1  0  0  0  0
  7 33  1  0  0  0  0
 33 34  1  0  0  0  0
 33 35  1  0  0  0  0
  3 35  1  0  0  0  0
 35 36  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0331076

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CNC1C(C)OC(OC2CCC(OC2C)N2C=CC(NC(=O)C3=CC=C(N)C=C3)=NC2=O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C24H33N5O7/c1-12-16(36-23-21(31)20(30)19(26-3)13(2)35-23)8-9-18(34-12)29-11-10-17(28-24(29)33)27-22(32)14-4-6-15(25)7-5-14/h4-7,10-13,16,18-21,23,26,30-31H,8-9,25H2,1-3H3,(H,27,28,32,33)

> <INCHI_KEY>
HJFXGPLQIPLHSS-UHFFFAOYSA-N

> <FORMULA>
C24H33N5O7

> <MOLECULAR_WEIGHT>
503.556

> <EXACT_MASS>
503.237998423

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
53.80564064298653

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-amino-N-[1-(5-{[3,4-dihydroxy-6-methyl-5-(methylamino)oxan-2-yl]oxy}-6-methyloxan-2-yl)-2-oxo-1,2-dihydropyrimidin-4-yl]benzamide

> <ALOGPS_LOGP>
0.11

> <JCHEM_LOGP>
-0.21318839033333462

> <ALOGPS_LOGS>
-3.06

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
13.607358094140281

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.34375757347238

> <JCHEM_PKA_STRONGEST_BASIC>
8.940920644462276

> <JCHEM_POLAR_SURFACE_AREA>
167.97

> <JCHEM_REFRACTIVITY>
128.7754

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.39e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-amino-N-[1-(5-{[3,4-dihydroxy-6-methyl-5-(methylamino)oxan-2-yl]oxy}-6-methyloxan-2-yl)-2-oxopyrimidin-4-yl]benzamide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         0                                  
HETATM    1  C   UNK     0       6.668 -11.550   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       5.335 -12.320   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       5.335 -13.860   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.001 -14.630   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667 -13.860   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       4.001 -16.170   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       5.335 -16.940   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       5.335 -18.480   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       4.001 -19.250   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001 -20.790   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667 -21.560   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.334 -20.790   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       1.334 -19.250   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       2.667 -18.480   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.667 -16.940   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       0.000 -21.560   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       0.000 -23.100   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -1.334 -23.870   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -2.667 -23.100   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0      -2.667 -21.560   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0      -1.334 -20.790   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -1.334 -19.250   0.000  0.00  0.00           O+0
HETATM   23  N   UNK     0      -4.001 -23.870   0.000  0.00  0.00           N+0
HETATM   24  C   UNK     0      -4.001 -25.410   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -2.667 -26.180   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      -5.335 -26.180   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -5.335 -27.720   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -6.668 -28.490   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -8.002 -27.720   0.000  0.00  0.00           C+0
HETATM   30  N   UNK     0      -9.336 -28.490   0.000  0.00  0.00           N+0
HETATM   31  C   UNK     0      -8.002 -26.180   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -6.668 -25.410   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       6.668 -16.170   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       8.002 -16.940   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       6.668 -14.630   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       8.002 -13.860   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   35                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8   33                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   14                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   16                                                  
CONECT   13   12   14                                                       
CONECT   14   13    9   15                                                  
CONECT   15   14                                                            
CONECT   16   12   17   21                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   23                                                  
CONECT   20   19   21                                                       
CONECT   21   20   16   22                                                  
CONECT   22   21                                                            
CONECT   23   19   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27   32                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32                                                       
CONECT   32   31   26                                                       
CONECT   33    7   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33    3   36                                                  
CONECT   36   35                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₃₃N₅O₇

Average Mass

503.5560 Da

Monoisotopic Mass

503.23800 Da

IUPAC Name

4-amino-N-[1-(5-{[3,4-dihydroxy-6-methyl-5-(methylamino)oxan-2-yl]oxy}-6-methyloxan-2-yl)-2-oxo-1,2-dihydropyrimidin-4-yl]benzamide

Traditional Name

4-amino-N-[1-(5-{[3,4-dihydroxy-6-methyl-5-(methylamino)oxan-2-yl]oxy}-6-methyloxan-2-yl)-2-oxopyrimidin-4-yl]benzamide

CAS Registry Number

Not Available

SMILES

CNC1C(C)OC(OC2CCC(OC2C)N2C=CC(NC(=O)C3=CC=C(N)C=C3)=NC2=O)C(O)C1O

InChI Identifier

InChI=1S/C24H33N5O7/c1-12-16(36-23-21(31)20(30)19(26-3)13(2)35-23)8-9-18(34-12)29-11-10-17(28-24(29)33)27-22(32)14-4-6-15(25)7-5-14/h4-7,10-13,16,18-21,23,26,30-31H,8-9,25H2,1-3H3,(H,27,28,32,33)

InChI Key

HJFXGPLQIPLHSS-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

Species Name	Source	Reference
Streptomyces plicatus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aminoglycosides. These are molecules or a portion of a molecule composed of amino-modified sugars.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Aminoglycosides

Alternative Parents

Substituents

Aminoglycoside core
Aminobenzoic acid or derivatives
Benzoic acid or derivatives
Benzoyl
Aniline or substituted anilines
Hydroxypyrimidine
Monocyclic benzene moiety
Hydropyrimidine
Monosaccharide
Oxane
Primary aromatic amine
Pyrimidine
Benzenoid
Heteroaromatic compound
Amino acid or derivatives
Secondary alcohol
1,2-aminoalcohol
1,2-diol
Oxacycle
Azacycle
Organoheterocyclic compound
Secondary amine
Carboxylic acid derivative
Secondary aliphatic amine
Acetal
Organopnictogen compound
Alcohol
Organic oxide
Hydrocarbon derivative
Organic nitrogen compound
Amine
Organonitrogen compound
Primary amine
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	0.11	ALOGPS
logP	-0.21	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	12.34	ChemAxon
pKa (Strongest Basic)	8.94	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	167.97 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	128.78 m³·mol⁻¹	ChemAxon
Polarizability	53.81 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

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

78173663

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 4-amino-n-[1-(5-{[3,4-dihydroxy-6-methyl-5-(methylamino)oxan-2-yl]oxy}-6-methyloxan-2-yl)-2-hydroxypyrimidin-4-ylidene]benzamide (NP0331076)

MOL for NP0331076 (4-amino-n-[1-(5-{[3,4-dihydroxy-6-methyl-5-(methylamino)oxan-2-yl]oxy}-6-methyloxan-2-yl)-2-hydroxypyrimidin-4-ylidene]benzamide)

3D MOL for NP0331076 (4-amino-n-[1-(5-{[3,4-dihydroxy-6-methyl-5-(methylamino)oxan-2-yl]oxy}-6-methyloxan-2-yl)-2-hydroxypyrimidin-4-ylidene]benzamide)

3D SDF for NP0331076 (4-amino-n-[1-(5-{[3,4-dihydroxy-6-methyl-5-(methylamino)oxan-2-yl]oxy}-6-methyloxan-2-yl)-2-hydroxypyrimidin-4-ylidene]benzamide)

3D-SDF for NP0331076 (4-amino-n-[1-(5-{[3,4-dihydroxy-6-methyl-5-(methylamino)oxan-2-yl]oxy}-6-methyloxan-2-yl)-2-hydroxypyrimidin-4-ylidene]benzamide)

PDB for NP0331076 (4-amino-n-[1-(5-{[3,4-dihydroxy-6-methyl-5-(methylamino)oxan-2-yl]oxy}-6-methyloxan-2-yl)-2-hydroxypyrimidin-4-ylidene]benzamide)

3D PDB for NP0331076 (4-amino-n-[1-(5-{[3,4-dihydroxy-6-methyl-5-(methylamino)oxan-2-yl]oxy}-6-methyloxan-2-yl)-2-hydroxypyrimidin-4-ylidene]benzamide)

SMILES for NP0331076 (4-amino-n-[1-(5-{[3,4-dihydroxy-6-methyl-5-(methylamino)oxan-2-yl]oxy}-6-methyloxan-2-yl)-2-hydroxypyrimidin-4-ylidene]benzamide)

INCHI for NP0331076 (4-amino-n-[1-(5-{[3,4-dihydroxy-6-methyl-5-(methylamino)oxan-2-yl]oxy}-6-methyloxan-2-yl)-2-hydroxypyrimidin-4-ylidene]benzamide)

Structure for NP0331076 (4-amino-n-[1-(5-{[3,4-dihydroxy-6-methyl-5-(methylamino)oxan-2-yl]oxy}-6-methyloxan-2-yl)-2-hydroxypyrimidin-4-ylidene]benzamide)

3D Structure for NP0331076 (4-amino-n-[1-(5-{[3,4-dihydroxy-6-methyl-5-(methylamino)oxan-2-yl]oxy}-6-methyloxan-2-yl)-2-hydroxypyrimidin-4-ylidene]benzamide)