NP-MRD: Showing NP-Card for 2-{[4,6-diamino-3-({3-amino-6-[(methylamino)methyl]-3,4-dihydro-2h-pyran-2-yl}oxy)-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol (NP0281925)

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Record Information

Version

2.0

Created at

2022-09-09 08:33:23 UTC

Updated at

2022-09-09 08:33:23 UTC

NP-MRD ID

NP0281925

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-{[4,6-diamino-3-({3-amino-6-[(methylamino)methyl]-3,4-dihydro-2h-pyran-2-yl}oxy)-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol

Description

Antibiotic G-52 belongs to the class of organic compounds known as aminocyclitol glycosides. These are organic compounds containing an amicocyclitol moiety glycosidically linked to a carbohydrate moiety. There are two major classes of aminoglycosides containing a 2-streptamine core. They are called 4,5- and 4,6-disubstituted 2-deoxystreptamines. 2-{[4,6-diamino-3-({3-amino-6-[(methylamino)methyl]-3,4-dihydro-2h-pyran-2-yl}oxy)-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol is found in Micromonospora zionensis. 2-{[4,6-diamino-3-({3-amino-6-[(methylamino)methyl]-3,4-dihydro-2h-pyran-2-yl}oxy)-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol was first documented in 1996 (PMID: 8808941). Based on a literature review very few articles have been published on Antibiotic G-52.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309092210332D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309092210332D          

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M  END
> <DATABASE_ID>
NP0281925

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CNCC1=CCC(N)C(OC2C(N)CC(N)C(OC3OCC(C)(O)C(NC)C3O)C2O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C20H39N5O7/c1-20(28)8-29-19(14(27)17(20)25-3)32-16-12(23)6-11(22)15(13(16)26)31-18-10(21)5-4-9(30-18)7-24-2/h4,10-19,24-28H,5-8,21-23H2,1-3H3

> <INCHI_KEY>
ARCVBMPERJRMKB-UHFFFAOYSA-N

> <FORMULA>
C20H39N5O7

> <MOLECULAR_WEIGHT>
461.56

> <EXACT_MASS>
461.284948616

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
71

> <JCHEM_AVERAGE_POLARIZABILITY>
48.52298680057513

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-{[4,6-diamino-3-({3-amino-6-[(methylamino)methyl]-3,4-dihydro-2H-pyran-2-yl}oxy)-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol

> <JCHEM_LOGP>
-3.8859871569999997

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
5

> <JCHEM_PKA>
13.159158671374126

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.548262951206336

> <JCHEM_PKA_STRONGEST_BASIC>
9.747564291635788

> <JCHEM_POLAR_SURFACE_AREA>
199.72999999999996

> <JCHEM_REFRACTIVITY>
115.0953

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
2-{[4,6-diamino-3-({3-amino-6-[(methylamino)methyl]-3,4-dihydro-2H-pyran-2-yl}oxy)-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      -5.335  -0.000   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      -6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -6.668  -2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -6.668  -5.390   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      -6.668  -6.930   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      -8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -9.336  -5.390   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0     -10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0     -10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0      -9.336  -2.310   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0     -12.003  -2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0     -13.337  -3.080   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0     -14.670  -2.310   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0     -13.337  -4.620   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0     -14.670  -5.390   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0     -14.670  -6.930   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0     -13.337  -7.700   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0     -13.337  -9.240   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0     -14.670 -10.010   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0     -13.681 -11.190   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0     -15.660 -11.190   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0     -16.004  -9.240   0.000  0.00  0.00           C+0
HETATM   26  N   UNK     0     -17.338 -10.010   0.000  0.00  0.00           N+0
HETATM   27  C   UNK     0     -18.672  -9.240   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0     -16.004  -7.700   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0     -17.338  -6.930   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0     -12.003  -5.390   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0     -12.003  -6.930   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -8.002  -3.080   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   32                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   32                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   30                                                  
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   30                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   28                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24   25                                             
CONECT   23   22                                                            
CONECT   24   22                                                            
CONECT   25   22   26   28                                                  
CONECT   26   25   27                                                       
CONECT   27   26                                                            
CONECT   28   25   19   29                                                  
CONECT   29   28                                                            
CONECT   30   17   11   31                                                  
CONECT   31   30                                                            
CONECT   32    9    4                                                       
MASTER        0    0    0    0    0    0    0    0   32    0   68    0
END

View in JSmol

Synonyms

Value	Source
6'-N-Methylsisomicin	MeSH

Chemical Formula

C₂₀H₃₉N₅O₇

Average Mass

461.5600 Da

Monoisotopic Mass

461.28495 Da

IUPAC Name

2-{[4,6-diamino-3-({3-amino-6-[(methylamino)methyl]-3,4-dihydro-2H-pyran-2-yl}oxy)-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol

Traditional Name

2-{[4,6-diamino-3-({3-amino-6-[(methylamino)methyl]-3,4-dihydro-2H-pyran-2-yl}oxy)-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol

CAS Registry Number

Not Available

SMILES

CNCC1=CCC(N)C(OC2C(N)CC(N)C(OC3OCC(C)(O)C(NC)C3O)C2O)O1

InChI Identifier

InChI=1S/C20H39N5O7/c1-20(28)8-29-19(14(27)17(20)25-3)32-16-12(23)6-11(22)15(13(16)26)31-18-10(21)5-4-9(30-18)7-24-2/h4,10-19,24-28H,5-8,21-23H2,1-3H3

InChI Key

ARCVBMPERJRMKB-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
Micromonospora zionensis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aminocyclitol glycosides. These are organic compounds containing an amicocyclitol moiety glycosidically linked to a carbohydrate moiety. There are two major classes of aminoglycosides containing a 2-streptamine core. They are called 4,5- and 4,6-disubstituted 2-deoxystreptamines.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Aminocyclitol glycosides

Alternative Parents

Substituents

Amino cyclitol glycoside
Glycosyl compound
O-glycosyl compound
Aminocyclitol or derivatives
Cyclohexanol
Cyclohexylamine
Cyclitol or derivatives
Monosaccharide
Oxane
Cyclic alcohol
Tertiary alcohol
1,2-aminoalcohol
Secondary alcohol
Acetal
Secondary aliphatic amine
Secondary amine
Organoheterocyclic compound
Oxacycle
Primary aliphatic amine
Hydrocarbon derivative
Organopnictogen compound
Organic nitrogen compound
Amine
Alcohol
Primary amine
Organonitrogen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic 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	-3.9	ChemAxon
pKa (Strongest Acidic)	12.55	ChemAxon
pKa (Strongest Basic)	9.75	ChemAxon
Physiological Charge	5	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	199.73 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	115.1 m³·mol⁻¹	ChemAxon
Polarizability	48.52 Å³	ChemAxon
Number of Rings	3	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

149572

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

171087

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Kojic M, Topisirovic L, Vasiljevic B: Translational autoregulation of the sgm gene from Micromonospora zionensis. J Bacteriol. 1996 Sep;178(18):5493-8. doi: 10.1128/jb.178.18.5493-5498.1996. [PubMed:8808941 ]
LOTUS database [Link]

Showing NP-Card for 2-{[4,6-diamino-3-({3-amino-6-[(methylamino)methyl]-3,4-dihydro-2h-pyran-2-yl}oxy)-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol (NP0281925)

MOL for NP0281925 (2-{[4,6-diamino-3-({3-amino-6-[(methylamino)methyl]-3,4-dihydro-2h-pyran-2-yl}oxy)-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol)

3D MOL for NP0281925 (2-{[4,6-diamino-3-({3-amino-6-[(methylamino)methyl]-3,4-dihydro-2h-pyran-2-yl}oxy)-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol)

3D SDF for NP0281925 (2-{[4,6-diamino-3-({3-amino-6-[(methylamino)methyl]-3,4-dihydro-2h-pyran-2-yl}oxy)-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol)

3D-SDF for NP0281925 (2-{[4,6-diamino-3-({3-amino-6-[(methylamino)methyl]-3,4-dihydro-2h-pyran-2-yl}oxy)-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol)

PDB for NP0281925 (2-{[4,6-diamino-3-({3-amino-6-[(methylamino)methyl]-3,4-dihydro-2h-pyran-2-yl}oxy)-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol)

3D PDB for NP0281925 (2-{[4,6-diamino-3-({3-amino-6-[(methylamino)methyl]-3,4-dihydro-2h-pyran-2-yl}oxy)-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol)

SMILES for NP0281925 (2-{[4,6-diamino-3-({3-amino-6-[(methylamino)methyl]-3,4-dihydro-2h-pyran-2-yl}oxy)-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol)

INCHI for NP0281925 (2-{[4,6-diamino-3-({3-amino-6-[(methylamino)methyl]-3,4-dihydro-2h-pyran-2-yl}oxy)-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol)

Structure for NP0281925 (2-{[4,6-diamino-3-({3-amino-6-[(methylamino)methyl]-3,4-dihydro-2h-pyran-2-yl}oxy)-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol)

3D Structure for NP0281925 (2-{[4,6-diamino-3-({3-amino-6-[(methylamino)methyl]-3,4-dihydro-2h-pyran-2-yl}oxy)-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol)