NP-MRD: Showing NP-Card for (2e)-n-{1-[(2s,4s,5r,6r)-5-{[(2s,3r,4s,5r,6s)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}-3-(methylsulfanyl)prop-2-enamide (NP0176507)

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Record Information

Version

2.0

Created at

2022-09-03 14:10:57 UTC

Updated at

2022-09-03 14:10:57 UTC

NP-MRD ID

NP0176507

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2e)-n-{1-[(2s,4s,5r,6r)-5-{[(2s,3r,4s,5r,6s)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}-3-(methylsulfanyl)prop-2-enamide

Description

(2E)-N-{1-[(2S,4S,5R,6R)-5-{[(2S,3R,4S,5R,6S)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxy-1,4-dihydropyrimidin-4-ylidene}-3-(methylsulfanyl)prop-2-enamide belongs to the class of organic compounds known as aminoglycosides. These are molecules or a portion of a molecule composed of amino-modified sugars. (2e)-n-{1-[(2s,4s,5r,6r)-5-{[(2s,3r,4s,5r,6s)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}-3-(methylsulfanyl)prop-2-enamide is found in Streptomyces amakusaensis. Based on a literature review very few articles have been published on (2E)-N-{1-[(2S,4S,5R,6R)-5-{[(2S,3R,4S,5R,6S)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxy-1,4-dihydropyrimidin-4-ylidene}-3-(methylsulfanyl)prop-2-enamide.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309032216102D          

 35 37  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309032216102D          

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 14 15  1  1  0  0  0
 14 16  1  0  0  0  0
 16 17  1  6  0  0  0
 18 17  1  6  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  1  0  0  0
 20 22  1  0  0  0  0
 22 23  1  6  0  0  0
 23 24  1  0  0  0  0
 23 25  1  0  0  0  0
 22 26  1  0  0  0  0
 26 27  1  6  0  0  0
 26 28  1  0  0  0  0
 18 28  1  0  0  0  0
 28 29  1  1  0  0  0
 16 30  1  0  0  0  0
 30 31  1  6  0  0  0
 30 32  1  0  0  0  0
 12 32  1  0  0  0  0
 11 33  1  0  0  0  0
 33 34  1  0  0  0  0
 33 35  2  0  0  0  0
  8 35  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0176507

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CS\C=C\C(=O)N=C1C=CN([C@@H]2C[C@H](O)[C@@H](O[C@@H]3O[C@@H](C)[C@@H]([C@H](O)[C@H]3O)N(C)C)[C@@H](C)O2)C(O)=N1

> <INCHI_IDENTIFIER>
InChI=1S/C22H34N4O8S/c1-11-17(25(3)4)18(29)19(30)21(33-11)34-20-12(2)32-16(10-13(20)27)26-8-6-14(24-22(26)31)23-15(28)7-9-35-5/h6-9,11-13,16-21,27,29-30H,10H2,1-5H3,(H,23,24,28,31)/b9-7+/t11-,12+,13-,16-,17-,18-,19+,20-,21-/m0/s1

> <INCHI_KEY>
OEIFFRHFKRNPAL-DWROEDOGSA-N

> <FORMULA>
C22H34N4O8S

> <MOLECULAR_WEIGHT>
514.59

> <EXACT_MASS>
514.209735245

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
53.99685808318981

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-2.30775005783964

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.351675281359412

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.772899126890416

> <JCHEM_PKA_STRONGEST_BASIC>
8.229484906745078

> <JCHEM_POLAR_SURFACE_AREA>
156.88

> <JCHEM_REFRACTIVITY>
127.9096

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2E)-N-{1-[(2S,4S,5R,6R)-5-{[(2S,3R,4S,5R,6S)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}-3-(methylsulfanyl)prop-2-enamide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM    2  S   UNK     0      -5.335   1.540   0.000  0.00  0.00           S+0
HETATM    3  C   UNK     0      -5.335   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -6.668  -2.310   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -8.002  -3.080   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0      -5.335  -3.080   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      -5.335  -7.700   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0      -5.335  -9.240   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -6.668 -10.010   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -6.668 -11.550   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -8.002 -12.320   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -5.335 -12.320   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -5.335 -13.860   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      -4.001 -14.630   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -2.667 -13.860   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      -1.334 -14.630   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -0.000 -13.860   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -1.334 -16.170   0.000  0.00  0.00           C+0
HETATM   23  N   UNK     0      -0.000 -16.940   0.000  0.00  0.00           N+0
HETATM   24  C   UNK     0       1.334 -16.170   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -0.000 -18.480   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -2.667 -16.940   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -2.667 -18.480   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -4.001 -16.170   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -5.335 -16.940   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -4.001 -11.550   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -2.667 -12.320   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -4.001 -10.010   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      -6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -8.002  -7.700   0.000  0.00  0.00           O+0
HETATM   35  N   UNK     0      -6.668  -5.390   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   35                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   33                                                  
CONECT   12   11   13   32                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   30                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   28                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   26                                                  
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23                                                            
CONECT   26   22   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   18   29                                                  
CONECT   29   28                                                            
CONECT   30   16   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   12                                                       
CONECT   33   11   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33    8                                                       
MASTER        0    0    0    0    0    0    0    0   35    0   74    0
END

View in JSmol

Synonyms

Value	Source
(2E)-N-{1-[(2S,4S,5R,6R)-5-{[(2S,3R,4S,5R,6S)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxy-1,4-dihydropyrimidin-4-ylidene}-3-(methylsulphanyl)prop-2-enamide	Generator

Chemical Formula

C₂₂H₃₄N₄O₈S

Average Mass

514.5900 Da

Monoisotopic Mass

514.20974 Da

IUPAC Name

Traditional Name

(2E)-N-{1-[(2S,4S,5R,6R)-5-{[(2S,3R,4S,5R,6S)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}-3-(methylsulfanyl)prop-2-enamide

CAS Registry Number

Not Available

SMILES

CS\C=C\C(=O)N=C1C=CN([C@@H]2C[C@H](O)[C@@H](O[C@@H]3O[C@@H](C)[C@@H]([C@H](O)[C@H]3O)N(C)C)[C@@H](C)O2)C(O)=N1

InChI Identifier

InChI=1S/C22H34N4O8S/c1-11-17(25(3)4)18(29)19(30)21(33-11)34-20-12(2)32-16(10-13(20)27)26-8-6-14(24-22(26)31)23-15(28)7-9-35-5/h6-9,11-13,16-21,27,29-30H,10H2,1-5H3,(H,23,24,28,31)/b9-7+/t11-,12+,13-,16-,17-,18-,19+,20-,21-/m0/s1

InChI Key

OEIFFRHFKRNPAL-DWROEDOGSA-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 aMAKUSAENSIS	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
Pyrimidone
Vinylogous thioester
Pyrimidine
Oxane
Monosaccharide
Hydropyrimidine
Acrylic acid or derivatives
Heteroaromatic compound
N-acylimine
Urea
Tertiary aliphatic amine
Thioenolether
Tertiary amine
Secondary alcohol
Amino acid or derivatives
1,2-aminoalcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Sulfenyl compound
Carboxylic acid derivative
Acetal
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organosulfur compound
Organonitrogen compound
Carbonyl group
Amine
Alcohol
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	-2.3	ChemAxon
pKa (Strongest Acidic)	5.77	ChemAxon
pKa (Strongest Basic)	8.23	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	156.88 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	127.91 m³·mol⁻¹	ChemAxon
Polarizability	54 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

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

162981987

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2e)-n-{1-[(2s,4s,5r,6r)-5-{[(2s,3r,4s,5r,6s)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}-3-(methylsulfanyl)prop-2-enamide (NP0176507)

MOL for NP0176507 ((2e)-n-{1-[(2s,4s,5r,6r)-5-{[(2s,3r,4s,5r,6s)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}-3-(methylsulfanyl)prop-2-enamide)

3D MOL for NP0176507 ((2e)-n-{1-[(2s,4s,5r,6r)-5-{[(2s,3r,4s,5r,6s)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}-3-(methylsulfanyl)prop-2-enamide)

3D SDF for NP0176507 ((2e)-n-{1-[(2s,4s,5r,6r)-5-{[(2s,3r,4s,5r,6s)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}-3-(methylsulfanyl)prop-2-enamide)

3D-SDF for NP0176507 ((2e)-n-{1-[(2s,4s,5r,6r)-5-{[(2s,3r,4s,5r,6s)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}-3-(methylsulfanyl)prop-2-enamide)

PDB for NP0176507 ((2e)-n-{1-[(2s,4s,5r,6r)-5-{[(2s,3r,4s,5r,6s)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}-3-(methylsulfanyl)prop-2-enamide)

3D PDB for NP0176507 ((2e)-n-{1-[(2s,4s,5r,6r)-5-{[(2s,3r,4s,5r,6s)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}-3-(methylsulfanyl)prop-2-enamide)

SMILES for NP0176507 ((2e)-n-{1-[(2s,4s,5r,6r)-5-{[(2s,3r,4s,5r,6s)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}-3-(methylsulfanyl)prop-2-enamide)

INCHI for NP0176507 ((2e)-n-{1-[(2s,4s,5r,6r)-5-{[(2s,3r,4s,5r,6s)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}-3-(methylsulfanyl)prop-2-enamide)

Structure for NP0176507 ((2e)-n-{1-[(2s,4s,5r,6r)-5-{[(2s,3r,4s,5r,6s)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}-3-(methylsulfanyl)prop-2-enamide)

3D Structure for NP0176507 ((2e)-n-{1-[(2s,4s,5r,6r)-5-{[(2s,3r,4s,5r,6s)-5-(dimethylamino)-3,4-dihydroxy-6-methyloxan-2-yl]oxy}-4-hydroxy-6-methyloxan-2-yl]-2-hydroxypyrimidin-4-ylidene}-3-(methylsulfanyl)prop-2-enamide)