NP-MRD: Showing NP-Card for n-[(2s,3r)-6-(aminomethyl)-2-{[(1r,2s,3s,4r,6s)-4,6-diamino-3-{[(2r,3r,4r,5r)-3,5-dihydroxy-5-methyl-4-(methylamino)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-3,4-dihydro-2h-pyran-3-yl]carboximidic acid (NP0229947)

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Record Information

Version

2.0

Created at

2022-09-06 10:13:46 UTC

Updated at

2022-09-06 10:13:46 UTC

NP-MRD ID

NP0229947

Secondary Accession Numbers

None

Natural Product Identification

Common Name

n-[(2s,3r)-6-(aminomethyl)-2-{[(1r,2s,3s,4r,6s)-4,6-diamino-3-{[(2r,3r,4r,5r)-3,5-dihydroxy-5-methyl-4-(methylamino)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-3,4-dihydro-2h-pyran-3-yl]carboximidic acid

Description

76647-54-6, Also known as g-367 S(1), 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. n-[(2s,3r)-6-(aminomethyl)-2-{[(1r,2s,3s,4r,6s)-4,6-diamino-3-{[(2r,3r,4r,5r)-3,5-dihydroxy-5-methyl-4-(methylamino)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-3,4-dihydro-2h-pyran-3-yl]carboximidic acid is found in Dactylosporangium thailandense. Based on a literature review very few articles have been published on 76647-54-6.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309062212132D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309062212132D          

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 30 31  1  0  0  0  0
  3 31  1  0  0  0  0
 31 32  1  1  0  0  0
 31 33  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0229947

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN[C@@H]1[C@@H](O)[C@@H](O[C@H]2[C@H](N)C[C@H](N)[C@@H](O[C@H]3OC(CN)=CC[C@H]3N=CO)[C@@H]2O)OC[C@]1(C)O

> <INCHI_IDENTIFIER>
InChI=1S/C20H37N5O8/c1-20(29)7-30-19(14(28)17(20)24-2)33-16-11(23)5-10(22)15(13(16)27)32-18-12(25-8-26)4-3-9(6-21)31-18/h3,8,10-19,24,27-29H,4-7,21-23H2,1-2H3,(H,25,26)/t10-,11+,12+,13-,14+,15+,16-,17+,18+,19+,20-/m0/s1

> <INCHI_KEY>
CEKWVQNWPXXMIU-QFPUGEGSSA-N

> <FORMULA>
C20H37N5O8

> <MOLECULAR_WEIGHT>
475.543

> <EXACT_MASS>
475.264213171

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
70

> <JCHEM_AVERAGE_POLARIZABILITY>
48.65169698390471

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-[(2S,3R)-6-(aminomethyl)-2-{[(1R,2S,3S,4R,6S)-4,6-diamino-3-{[(2R,3R,4R,5R)-3,5-dihydroxy-5-methyl-4-(methylamino)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-3,4-dihydro-2H-pyran-3-yl]carboximidic acid

> <JCHEM_LOGP>
-6.526971331991101

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
4

> <JCHEM_PKA>
12.59281816940663

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.34860418752844

> <JCHEM_PKA_STRONGEST_BASIC>
9.659456634958984

> <JCHEM_POLAR_SURFACE_AREA>
220.29

> <JCHEM_REFRACTIVITY>
115.7957

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
N-[(2S,3R)-6-(aminomethyl)-2-{[(1R,2S,3S,4R,6S)-4,6-diamino-3-{[(2R,3R,4R,5R)-3,5-dihydroxy-5-methyl-4-(methylamino)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-3,4-dihydro-2H-pyran-3-yl]carboximidic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      -4.001  -2.310   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -4.001  -5.390   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -6.668  -5.390   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -6.668  -6.930   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -8.002  -7.700   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -8.002  -9.240   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -6.668 -10.010   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -9.336 -10.010   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -9.336 -11.550   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -8.002 -12.320   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -6.668 -11.550   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -5.335 -12.320   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -4.001 -11.550   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0      -4.001 -10.010   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0      -5.335 -13.860   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -6.668 -14.630   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -8.002 -13.860   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0      -9.336 -14.630   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0      -9.336 -16.170   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -8.002 -16.940   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0     -10.669  -9.240   0.000  0.00  0.00           C+0
HETATM   25  N   UNK     0     -12.003 -10.010   0.000  0.00  0.00           N+0
HETATM   26  C   UNK     0     -10.669  -7.700   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -9.336  -6.930   0.000  0.00  0.00           C+0
HETATM   28  N   UNK     0      -9.336  -5.390   0.000  0.00  0.00           N+0
HETATM   29  O   UNK     0      -8.002  -4.620   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -7.391  -0.950   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -5.945  -0.950   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   31                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   29                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   27                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   24                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   20                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   18                                                  
CONECT   16   15   17                                                       
CONECT   17   16                                                            
CONECT   18   15   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   13   21                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22                                                            
CONECT   24   11   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   26    8   28                                                  
CONECT   28   27                                                            
CONECT   29    6   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30    3   32   33                                             
CONECT   32   31                                                            
CONECT   33   31                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   70    0
END

View in JSmol

Synonyms

Value	Source
2'-N-Formylsisomycin	MeSH
g-367 S(1)	MeSH

Chemical Formula

C₂₀H₃₇N₅O₈

Average Mass

475.5430 Da

Monoisotopic Mass

475.26421 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CN[C@@H]1[C@@H](O)[C@@H](O[C@H]2[C@H](N)C[C@H](N)[C@@H](O[C@H]3OC(CN)=CC[C@H]3N=CO)[C@@H]2O)OC[C@]1(C)O

InChI Identifier

InChI=1S/C20H37N5O8/c1-20(29)7-30-19(14(28)17(20)24-2)33-16-11(23)5-10(22)15(13(16)27)32-18-12(25-8-26)4-3-9(6-21)31-18/h3,8,10-19,24,27-29H,4-7,21-23H2,1-2H3,(H,25,26)/t10-,11+,12+,13-,14+,15+,16-,17+,18+,19+,20-/m0/s1

InChI Key

CEKWVQNWPXXMIU-QFPUGEGSSA-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
Dactylosporangium thailandense	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
O-glycosyl compound
Glycosyl compound
Aminocyclitol or derivatives
Cyclohexylamine
Cyclohexanol
Oxane
Monosaccharide
Cyclitol or derivatives
Tertiary alcohol
Cyclic alcohol
Secondary carboxylic acid amide
Secondary alcohol
Carboxamide group
Amino acid or derivatives
1,2-aminoalcohol
Oxacycle
Organoheterocyclic compound
Secondary amine
Secondary aliphatic amine
Carboxylic acid derivative
Acetal
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Organonitrogen compound
Primary aliphatic amine
Carbonyl group
Amine
Alcohol
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

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

12889386

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for n-[(2s,3r)-6-(aminomethyl)-2-{[(1r,2s,3s,4r,6s)-4,6-diamino-3-{[(2r,3r,4r,5r)-3,5-dihydroxy-5-methyl-4-(methylamino)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-3,4-dihydro-2h-pyran-3-yl]carboximidic acid (NP0229947)

MOL for NP0229947 (n-[(2s,3r)-6-(aminomethyl)-2-{[(1r,2s,3s,4r,6s)-4,6-diamino-3-{[(2r,3r,4r,5r)-3,5-dihydroxy-5-methyl-4-(methylamino)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-3,4-dihydro-2h-pyran-3-yl]carboximidic acid)

3D MOL for NP0229947 (n-[(2s,3r)-6-(aminomethyl)-2-{[(1r,2s,3s,4r,6s)-4,6-diamino-3-{[(2r,3r,4r,5r)-3,5-dihydroxy-5-methyl-4-(methylamino)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-3,4-dihydro-2h-pyran-3-yl]carboximidic acid)

3D SDF for NP0229947 (n-[(2s,3r)-6-(aminomethyl)-2-{[(1r,2s,3s,4r,6s)-4,6-diamino-3-{[(2r,3r,4r,5r)-3,5-dihydroxy-5-methyl-4-(methylamino)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-3,4-dihydro-2h-pyran-3-yl]carboximidic acid)

3D-SDF for NP0229947 (n-[(2s,3r)-6-(aminomethyl)-2-{[(1r,2s,3s,4r,6s)-4,6-diamino-3-{[(2r,3r,4r,5r)-3,5-dihydroxy-5-methyl-4-(methylamino)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-3,4-dihydro-2h-pyran-3-yl]carboximidic acid)

PDB for NP0229947 (n-[(2s,3r)-6-(aminomethyl)-2-{[(1r,2s,3s,4r,6s)-4,6-diamino-3-{[(2r,3r,4r,5r)-3,5-dihydroxy-5-methyl-4-(methylamino)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-3,4-dihydro-2h-pyran-3-yl]carboximidic acid)

3D PDB for NP0229947 (n-[(2s,3r)-6-(aminomethyl)-2-{[(1r,2s,3s,4r,6s)-4,6-diamino-3-{[(2r,3r,4r,5r)-3,5-dihydroxy-5-methyl-4-(methylamino)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-3,4-dihydro-2h-pyran-3-yl]carboximidic acid)

SMILES for NP0229947 (n-[(2s,3r)-6-(aminomethyl)-2-{[(1r,2s,3s,4r,6s)-4,6-diamino-3-{[(2r,3r,4r,5r)-3,5-dihydroxy-5-methyl-4-(methylamino)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-3,4-dihydro-2h-pyran-3-yl]carboximidic acid)

INCHI for NP0229947 (n-[(2s,3r)-6-(aminomethyl)-2-{[(1r,2s,3s,4r,6s)-4,6-diamino-3-{[(2r,3r,4r,5r)-3,5-dihydroxy-5-methyl-4-(methylamino)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-3,4-dihydro-2h-pyran-3-yl]carboximidic acid)

Structure for NP0229947 (n-[(2s,3r)-6-(aminomethyl)-2-{[(1r,2s,3s,4r,6s)-4,6-diamino-3-{[(2r,3r,4r,5r)-3,5-dihydroxy-5-methyl-4-(methylamino)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-3,4-dihydro-2h-pyran-3-yl]carboximidic acid)

3D Structure for NP0229947 (n-[(2s,3r)-6-(aminomethyl)-2-{[(1r,2s,3s,4r,6s)-4,6-diamino-3-{[(2r,3r,4r,5r)-3,5-dihydroxy-5-methyl-4-(methylamino)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-3,4-dihydro-2h-pyran-3-yl]carboximidic acid)