NP-MRD: Showing NP-Card for paromomycin ii (NP0255146)

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Record Information

Version

2.0

Created at

2022-09-07 19:32:16 UTC

Updated at

2022-09-07 19:32:16 UTC

NP-MRD ID

NP0255146

Secondary Accession Numbers

None

Natural Product Identification

Common Name

paromomycin ii

Description

Neomycin F belongs to the class of organic compounds known as 4,5-disubstituted 2-deoxystreptamines. These are 2-deoxystreptamine aminoglycosides that are glycosidically linked to a pyranose of furanose unit at the C4- and C5-positions. Neomycin F is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. paromomycin ii is found in Streptomyces fradiae. Based on a literature review very few articles have been published on Neomycin F.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072221322D          

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M  END

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M  END


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    1.9275   -5.6203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4425   -4.9529    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6221   -5.0391    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7781   -4.1992    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2932   -3.5318    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4727   -3.6180    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1371   -4.3717    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6833   -4.4579    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0189   -5.2116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5340   -5.8790    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1683   -3.7905    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.9888   -3.8767    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8327   -3.0368    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3176   -2.3694    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0122   -2.9506    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3233   -2.1969    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7041   -1.9072    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4888   -1.6523    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    0.6402    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0367    1.0527    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4656    1.0527    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.4656    1.8777    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1801    0.6402    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.8946    1.0527    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  6  0  0  0
  7  6  1  1  0  0  0
  7  8  1  0  0  0  0
  8  9  1  6  0  0  0
  9 10  1  0  0  0  0
  8 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  6  0  0  0
 14 13  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  1  1  0  0  0
 15 17  1  0  0  0  0
 17 18  1  6  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  6  0  0  0
 20 22  1  0  0  0  0
 14 22  1  0  0  0  0
 22 23  1  1  0  0  0
 24 23  1  1  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  6  0  0  0
 27 28  1  0  0  0  0
 26 29  1  0  0  0  0
 29 30  1  1  0  0  0
 29 31  1  0  0  0  0
 31 32  1  6  0  0  0
 31 33  1  0  0  0  0
 24 33  1  0  0  0  0
 33 34  1  1  0  0  0
 12 35  1  0  0  0  0
  7 35  1  0  0  0  0
 35 36  1  1  0  0  0
  5 37  1  0  0  0  0
 37 38  1  6  0  0  0
 37 39  1  0  0  0  0
 39 40  1  1  0  0  0
 39 41  1  0  0  0  0
  3 41  1  0  0  0  0
 41 42  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0255146

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC[C@H]1O[C@H](O[C@@H]2[C@@H](CO)O[C@@H](O[C@@H]3[C@@H](O)[C@H](N)C[C@H](N)[C@H]3O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3N)[C@@H]2O)[C@H](N)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C23H45N5O14/c24-2-7-13(32)15(34)10(27)21(37-7)41-19-9(4-30)39-23(17(19)36)42-20-12(31)5(25)1-6(26)18(20)40-22-11(28)16(35)14(33)8(3-29)38-22/h5-23,29-36H,1-4,24-28H2/t5-,6+,7-,8-,9-,10-,11-,12+,13-,14-,15-,16-,17-,18-,19-,20-,21-,22-,23+/m1/s1

> <INCHI_KEY>
UOZODPSAJZTQNH-VZXHOKRSSA-N

> <FORMULA>
C23H45N5O14

> <MOLECULAR_WEIGHT>
615.634

> <EXACT_MASS>
615.296301149

> <JCHEM_ACCEPTOR_COUNT>
19

> <JCHEM_ATOM_COUNT>
87

> <JCHEM_AVERAGE_POLARIZABILITY>
60.52370388330229

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
13

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-{[(2R,3S,4R,5S)-5-{[(1R,2R,3S,5R,6S)-3,5-diamino-2-{[(2S,3R,4R,5S,6R)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-6-hydroxycyclohexyl]oxy}-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy}oxane-3,4-diol

> <JCHEM_LOGP>
-8.308295949333333

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
5

> <JCHEM_PKA>
12.902366318365829

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.226663013739758

> <JCHEM_PKA_STRONGEST_BASIC>
9.681358573994746

> <JCHEM_POLAR_SURFACE_AREA>
347.32000000000005

> <JCHEM_REFRACTIVITY>
134.24279999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-{[(2R,3S,4R,5S)-5-{[(1R,2R,3S,5R,6S)-3,5-diamino-2-{[(2S,3R,4R,5S,6R)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-6-hydroxycyclohexyl]oxy}-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy}oxane-3,4-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  N   UNK     0      10.470  -0.345   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       9.137  -1.115   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.803  -0.345   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       6.469  -1.115   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       5.136  -0.345   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       3.802  -1.115   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       3.802  -2.655   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.556  -3.560   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.091  -3.084   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       0.771  -1.578   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       3.032  -5.025   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       4.572  -5.025   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       5.477  -6.271   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       4.851  -7.678   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.756  -8.923   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       7.287  -8.762   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       5.129 -10.330   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0       6.035 -11.576   0.000  0.00  0.00           N+0
HETATM   19  C   UNK     0       3.598 -10.491   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.693  -9.245   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0       1.161  -9.406   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0       3.319  -7.839   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       2.414  -6.593   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       0.882  -6.754   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       0.256  -8.160   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      -1.276  -8.321   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -1.902  -9.728   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -0.997 -10.974   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -2.181  -7.076   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -3.712  -7.237   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -1.554  -5.669   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -2.460  -4.423   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      -0.023  -5.508   0.000  0.00  0.00           C+0
HETATM   34  N   UNK     0       0.604  -4.101   0.000  0.00  0.00           N+0
HETATM   35  C   UNK     0       5.048  -3.560   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       6.512  -3.084   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       5.136   1.195   0.000  0.00  0.00           C+0
HETATM   38  N   UNK     0       3.802   1.965   0.000  0.00  0.00           N+0
HETATM   39  C   UNK     0       6.469   1.965   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0       6.469   3.505   0.000  0.00  0.00           O+0
HETATM   41  C   UNK     0       7.803   1.195   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0       9.137   1.965   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   41                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   37                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   35                                                  
CONECT    8    7    9   11                                                  
CONECT    9    8   10                                                       
CONECT   10    9                                                            
CONECT   11    8   12                                                       
CONECT   12   11   13   35                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   22                                                  
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   14   23                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   33                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   29                                                  
CONECT   27   26   28                                                       
CONECT   28   27                                                            
CONECT   29   26   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   24   34                                                  
CONECT   34   33                                                            
CONECT   35   12    7   36                                                  
CONECT   36   35                                                            
CONECT   37    5   38   39                                                  
CONECT   38   37                                                            
CONECT   39   37   40   41                                                  
CONECT   40   39                                                            
CONECT   41   39    3   42                                                  
CONECT   42   41                                                            
MASTER        0    0    0    0    0    0    0    0   42    0   90    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₃H₄₅N₅O₁₄

Average Mass

615.6340 Da

Monoisotopic Mass

615.29630 Da

IUPAC Name

(2R,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-{[(2R,3S,4R,5S)-5-{[(1R,2R,3S,5R,6S)-3,5-diamino-2-{[(2S,3R,4R,5S,6R)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-6-hydroxycyclohexyl]oxy}-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy}oxane-3,4-diol

Traditional Name

CAS Registry Number

Not Available

SMILES

NC[C@H]1O[C@H](O[C@@H]2[C@@H](CO)O[C@@H](O[C@@H]3[C@@H](O)[C@H](N)C[C@H](N)[C@H]3O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3N)[C@@H]2O)[C@H](N)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C23H45N5O14/c24-2-7-13(32)15(34)10(27)21(37-7)41-19-9(4-30)39-23(17(19)36)42-20-12(31)5(25)1-6(26)18(20)40-22-11(28)16(35)14(33)8(3-29)38-22/h5-23,29-36H,1-4,24-28H2/t5-,6+,7-,8-,9-,10-,11-,12+,13-,14-,15-,16-,17-,18-,19-,20-,21-,22-,23+/m1/s1

InChI Key

UOZODPSAJZTQNH-VZXHOKRSSA-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 fradiae	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 4,5-disubstituted 2-deoxystreptamines. These are 2-deoxystreptamine aminoglycosides that are glycosidically linked to a pyranose of furanose unit at the C4- and C5-positions.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

4,5-disubstituted 2-deoxystreptamines

Alternative Parents

Substituents

4,5-disubstituted 2-deoxystreptamine
Disaccharide
Glycosyl compound
O-glycosyl compound
Aminocyclitol or derivatives
Cyclohexanol
Cyclohexylamine
Cyclitol or derivatives
Oxane
Tetrahydrofuran
Cyclic alcohol
Secondary alcohol
1,2-aminoalcohol
Acetal
Organoheterocyclic compound
Oxacycle
Primary alcohol
Hydrocarbon derivative
Organopnictogen compound
Primary aliphatic amine
Organonitrogen compound
Organic nitrogen compound
Amine
Alcohol
Primary amine
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

amino oligosaccharide (CHEBI:81287 )

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	-8.3	ChemAxon
pKa (Strongest Acidic)	12.23	ChemAxon
pKa (Strongest Basic)	9.68	ChemAxon
Physiological Charge	5	ChemAxon
Hydrogen Acceptor Count	19	ChemAxon
Hydrogen Donor Count	13	ChemAxon
Polar Surface Area	347.32 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	134.24 m³·mol⁻¹	ChemAxon
Polarizability	60.52 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	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

2303594

KEGG Compound ID

C17712

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

3040200

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for paromomycin ii (NP0255146)

MOL for NP0255146 (paromomycin ii)

3D MOL for NP0255146 (paromomycin ii)

3D SDF for NP0255146 (paromomycin ii)

3D-SDF for NP0255146 (paromomycin ii)

PDB for NP0255146 (paromomycin ii)

3D PDB for NP0255146 (paromomycin ii)

SMILES for NP0255146 (paromomycin ii)

INCHI for NP0255146 (paromomycin ii)

Structure for NP0255146 (paromomycin ii)

3D Structure for NP0255146 (paromomycin ii)