NP-MRD: Showing NP-Card for 4-amino-n-{1-[(2r,5s,6r)-5-{[(2r,3r,4s,5s,6r)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide (NP0209451)

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Record Information

Version

2.0

Created at

2022-09-05 06:51:55 UTC

Updated at

2022-09-05 06:51:55 UTC

NP-MRD ID

NP0209451

Secondary Accession Numbers

None

Natural Product Identification

Common Name

4-amino-n-{1-[(2r,5s,6r)-5-{[(2r,3r,4s,5s,6r)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide

Description

R-285 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-[(2r,5s,6r)-5-{[(2r,3r,4s,5s,6r)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide is found in Streptomyces plicatus. Based on a literature review a small amount of articles have been published on R-285.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052208512D          

 37 40  0  0  1  0            999 V2000
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M  END

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M  END


  Mrv1652309052208512D          

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  9 10  1  4  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 17 18  2  0  0  0  0
 12 18  1  0  0  0  0
  8 19  1  0  0  0  0
 19 20  2  0  0  0  0
  5 20  1  0  0  0  0
 20 21  1  0  0  0  0
  4 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
  2 24  1  0  0  0  0
 24 25  1  1  0  0  0
 26 25  1  1  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  6  0  0  0
 28 30  1  0  0  0  0
 30 31  1  1  0  0  0
 31 32  1  0  0  0  0
 31 33  1  0  0  0  0
 30 34  1  0  0  0  0
 34 35  1  6  0  0  0
 34 36  1  0  0  0  0
 26 36  1  0  0  0  0
 36 37  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0209451

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1O[C@H](CC[C@@H]1O[C@H]1O[C@H](C)[C@H]([C@H](O)[C@H]1O)N(C)C)N1C=CC(=NC(=O)C2=CC=C(N)C=C2)N=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C25H35N5O7/c1-13-17(37-24-22(32)21(31)20(29(3)4)14(2)36-24)9-10-19(35-13)30-12-11-18(28-25(30)34)27-23(33)15-5-7-16(26)8-6-15/h5-8,11-14,17,19-22,24,31-32H,9-10,26H2,1-4H3,(H,27,28,33,34)/t13-,14-,17+,19-,20-,21+,22-,24-/m1/s1

> <INCHI_KEY>
NFOMJDXALJABQF-DDNYSEEGSA-N

> <FORMULA>
C25H35N5O7

> <MOLECULAR_WEIGHT>
517.583

> <EXACT_MASS>
517.253648487

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_POLARIZABILITY>
55.5933047484526

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-amino-N-{1-[(2R,5S,6R)-5-{[(2R,3R,4S,5S,6R)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-6-methyloxan-2-yl]-2-hydroxy-1,4-dihydropyrimidin-4-ylidene}benzamide

> <JCHEM_LOGP>
-1.6061087357614652

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
12.362131086522187

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.700711579947863

> <JCHEM_PKA_STRONGEST_BASIC>
8.229251710208562

> <JCHEM_POLAR_SURFACE_AREA>
162.66999999999996

> <JCHEM_REFRACTIVITY>
134.98979999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
4-amino-N-{1-[(2R,5S,6R)-5-{[(2R,3R,4S,5S,6R)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       1.334  -5.390   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -2.667  -7.700   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      -2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.334 -10.010   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -4.001 -11.550   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -5.335 -12.320   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -6.668 -11.550   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0      -8.002 -12.320   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0      -6.668 -10.010   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -5.335  -9.240   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0      -1.334  -5.390   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       9.336  -2.310   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      12.003  -2.310   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   31  N   UNK     0      12.003  -5.390   0.000  0.00  0.00           N+0
HETATM   32  C   UNK     0      13.337  -4.620   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      12.003  -6.930   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       9.336  -6.930   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       6.668  -5.390   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   24                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   22                                                  
CONECT    5    4    6   20                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   19                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   18                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   12                                                       
CONECT   19    8   20                                                       
CONECT   20   19    5   21                                                  
CONECT   21   20                                                            
CONECT   22    4   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23    2   25                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   36                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31   34                                                  
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31                                                            
CONECT   34   30   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   26   37                                                  
CONECT   37   36                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₃₅N₅O₇

Average Mass

517.5830 Da

Monoisotopic Mass

517.25365 Da

IUPAC Name

4-amino-N-{1-[(2R,5S,6R)-5-{[(2R,3R,4S,5S,6R)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-6-methyloxan-2-yl]-2-hydroxy-1,4-dihydropyrimidin-4-ylidene}benzamide

Traditional Name

4-amino-N-{1-[(2R,5S,6R)-5-{[(2R,3R,4S,5S,6R)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide

CAS Registry Number

Not Available

SMILES

C[C@H]1O[C@H](CC[C@@H]1O[C@H]1O[C@H](C)[C@H]([C@H](O)[C@H]1O)N(C)C)N1C=CC(=NC(=O)C2=CC=C(N)C=C2)N=C1O

InChI Identifier

InChI=1S/C25H35N5O7/c1-13-17(37-24-22(32)21(31)20(29(3)4)14(2)36-24)9-10-19(35-13)30-12-11-18(28-25(30)34)27-23(33)15-5-7-16(26)8-6-15/h5-8,11-14,17,19-22,24,31-32H,9-10,26H2,1-4H3,(H,27,28,33,34)/t13-,14-,17+,19-,20-,21+,22-,24-/m1/s1

InChI Key

NFOMJDXALJABQF-DDNYSEEGSA-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
Benzamide
Benzoic acid or derivatives
Benzoyl
Aniline or substituted anilines
Pyrimidone
Monocyclic benzene moiety
Hydropyrimidine
Monosaccharide
Oxane
Primary aromatic amine
Pyrimidine
Benzenoid
Imidolactam
Heteroaromatic compound
Tertiary aliphatic amine
Amino acid or derivatives
Tertiary amine
Secondary carboxylic acid amide
Secondary alcohol
1,2-aminoalcohol
1,2-diol
Carboxamide group
Azacycle
Organoheterocyclic compound
Oxacycle
Acetal
Carboxylic acid derivative
Alcohol
Primary amine
Amine
Organic oxide
Organonitrogen compound
Hydrocarbon derivative
Organic nitrogen compound
Organopnictogen compound
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	-1.6	ChemAxon
pKa (Strongest Acidic)	5.7	ChemAxon
pKa (Strongest Basic)	8.23	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	162.67 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	134.99 m³·mol⁻¹	ChemAxon
Polarizability	55.59 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	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

8657099

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

285

METLIN ID

Not Available

PubChem Compound

10481692

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-[(2r,5s,6r)-5-{[(2r,3r,4s,5s,6r)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide (NP0209451)

MOL for NP0209451 (4-amino-n-{1-[(2r,5s,6r)-5-{[(2r,3r,4s,5s,6r)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide)

3D MOL for NP0209451 (4-amino-n-{1-[(2r,5s,6r)-5-{[(2r,3r,4s,5s,6r)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide)

3D SDF for NP0209451 (4-amino-n-{1-[(2r,5s,6r)-5-{[(2r,3r,4s,5s,6r)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide)

3D-SDF for NP0209451 (4-amino-n-{1-[(2r,5s,6r)-5-{[(2r,3r,4s,5s,6r)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide)

PDB for NP0209451 (4-amino-n-{1-[(2r,5s,6r)-5-{[(2r,3r,4s,5s,6r)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide)

3D PDB for NP0209451 (4-amino-n-{1-[(2r,5s,6r)-5-{[(2r,3r,4s,5s,6r)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide)

SMILES for NP0209451 (4-amino-n-{1-[(2r,5s,6r)-5-{[(2r,3r,4s,5s,6r)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide)

INCHI for NP0209451 (4-amino-n-{1-[(2r,5s,6r)-5-{[(2r,3r,4s,5s,6r)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide)

Structure for NP0209451 (4-amino-n-{1-[(2r,5s,6r)-5-{[(2r,3r,4s,5s,6r)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide)

3D Structure for NP0209451 (4-amino-n-{1-[(2r,5s,6r)-5-{[(2r,3r,4s,5s,6r)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}benzamide)