NP-MRD: Showing NP-Card for n-(2-{[(3r,4s,5s,7r,9e,11s,12r)-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-2,8-dioxo-1-oxacyclododec-9-en-4-yl]oxy}-3-hydroxy-6-methyloxan-4-yl)-n-methylmethanamine oxide (NP0280137)

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Record Information

Version

2.0

Created at

2022-09-09 05:46:03 UTC

Updated at

2022-09-09 05:46:03 UTC

NP-MRD ID

NP0280137

Secondary Accession Numbers

None

Natural Product Identification

Common Name

n-(2-{[(3r,4s,5s,7r,9e,11s,12r)-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-2,8-dioxo-1-oxacyclododec-9-en-4-yl]oxy}-3-hydroxy-6-methyloxan-4-yl)-n-methylmethanamine oxide

Description

N-(2-{[(3R,4S,5S,7R,11S,12R)-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-2,8-dioxo-1-oxacyclododec-9-en-4-yl]oxy}-3-hydroxy-6-methyloxan-4-yl)-N-methylmethanamine oxide belongs to the class of organic compounds known as macrolides and analogues. These are organic compounds containing a lactone ring of at least twelve members. n-(2-{[(3r,4s,5s,7r,9e,11s,12r)-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-2,8-dioxo-1-oxacyclododec-9-en-4-yl]oxy}-3-hydroxy-6-methyloxan-4-yl)-n-methylmethanamine oxide is found in Streptomyces venezuelae. Based on a literature review very few articles have been published on N-(2-{[(3R,4S,5S,7R,11S,12R)-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-2,8-dioxo-1-oxacyclododec-9-en-4-yl]oxy}-3-hydroxy-6-methyloxan-4-yl)-N-methylmethanamine oxide.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309092207462D          

 34 35  0  0  1  0            999 V2000
    3.5724    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  9 23  1  0  0  0  0
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  3 32  1  0  0  0  0
 32 33  1  1  0  0  0
 32 34  1  6  0  0  0
M  CHG  2  17   1  20  -1
M  END

     RDKit          3D

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M  CHG  2  17   1  20  -1
M  END


  Mrv1652309092207462D          

 34 35  0  0  1  0            999 V2000
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  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  9 10  1  1  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 17 20  1  0  0  0  0
 16 21  1  0  0  0  0
 11 21  1  0  0  0  0
 21 22  1  0  0  0  0
  9 23  1  0  0  0  0
 23 24  1  6  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  1  0  0  0
 26 28  1  0  0  0  0
 28 29  2  0  0  0  0
 28 30  1  0  0  0  0
 30 31  2  0  0  0  0
 31 32  1  0  0  0  0
  3 32  1  0  0  0  0
 32 33  1  1  0  0  0
 32 34  1  6  0  0  0
M  CHG  2  17   1  20  -1
M  END
> <DATABASE_ID>
NP0280137

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC[C@H]1OC(=O)[C@H](C)[C@@H](OC2OC(C)CC(C2O)[N+](C)(C)[O-])[C@@H](C)C[C@@H](C)C(=O)\C=C\[C@]1(C)O

> <INCHI_IDENTIFIER>
InChI=1S/C25H43NO8/c1-9-20-25(6,30)11-10-19(27)14(2)12-15(3)22(17(5)23(29)33-20)34-24-21(28)18(26(7,8)31)13-16(4)32-24/h10-11,14-18,20-22,24,28,30H,9,12-13H2,1-8H3/b11-10+/t14-,15+,16?,17-,18?,20-,21?,22+,24?,25+/m1/s1

> <INCHI_KEY>
PAPFNCSFPKDFRE-WEFAVHQDSA-N

> <FORMULA>
C25H43NO8

> <MOLECULAR_WEIGHT>
485.618

> <EXACT_MASS>
485.298867349

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
77

> <JCHEM_AVERAGE_POLARIZABILITY>
52.50775144000198

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-(2-{[(3R,4S,5S,7R,9E,11S,12R)-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-2,8-dioxo-1-oxacyclododec-9-en-4-yl]oxy}-3-hydroxy-6-methyloxan-4-yl)-N-methylmethanamine oxide

> <JCHEM_LOGP>
2.1516903349999987

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.616382007860345

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.545596570132084

> <JCHEM_PKA_STRONGEST_BASIC>
3.816130436054807

> <JCHEM_POLAR_SURFACE_AREA>
125.35000000000001

> <JCHEM_REFRACTIVITY>
127.7186

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
N-(2-{[(3R,4S,5S,7R,9E,11S,12R)-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-2,8-dioxo-1-oxacyclododec-9-en-4-yl]oxy}-3-hydroxy-6-methyloxan-4-yl)-N-methylmethanamine oxide

> <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       6.668  11.550   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.335  10.780   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001  11.550   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.667  10.780   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       2.667   9.240   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       4.001   8.470   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       1.334   8.470   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  C   UNK     0      -0.000   9.240   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.334   8.470   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -1.334   6.930   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -0.000   6.160   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -0.000   4.620   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -2.667   4.620   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0      -4.001   3.850   0.000  0.00  0.00           N+1
HETATM   18  C   UNK     0      -5.335   3.080   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -4.771   5.184   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -3.231   2.516   0.000  0.00  0.00           O-1
HETATM   21  C   UNK     0      -2.667   6.160   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -4.001   6.930   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -0.000  10.780   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       1.334  11.550   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -1.334  11.550   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -1.334  13.090   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -2.667  13.860   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       0.000  13.860   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       0.000  15.400   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       1.334  13.090   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       2.667  13.860   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       4.001  13.090   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       4.817  14.396   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       5.540  13.144   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   32                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   23                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   21                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17   21                                                  
CONECT   17   16   18   19   20                                             
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   17                                                            
CONECT   21   16   11   22                                                  
CONECT   22   21                                                            
CONECT   23    9   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31    3   33   34                                             
CONECT   33   32                                                            
CONECT   34   32                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   70    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₄₃NO₈

Average Mass

485.6180 Da

Monoisotopic Mass

485.29887 Da

IUPAC Name

N-(2-{[(3R,4S,5S,7R,9E,11S,12R)-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-2,8-dioxo-1-oxacyclododec-9-en-4-yl]oxy}-3-hydroxy-6-methyloxan-4-yl)-N-methylmethanamine oxide

Traditional Name

N-(2-{[(3R,4S,5S,7R,9E,11S,12R)-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-2,8-dioxo-1-oxacyclododec-9-en-4-yl]oxy}-3-hydroxy-6-methyloxan-4-yl)-N-methylmethanamine oxide

CAS Registry Number

Not Available

SMILES

CC[C@H]1OC(=O)[C@H](C)[C@@H](OC2OC(C)CC(C2O)[N+](C)(C)[O-])[C@@H](C)C[C@@H](C)C(=O)\C=C\[C@]1(C)O

InChI Identifier

InChI=1S/C25H43NO8/c1-9-20-25(6,30)11-10-19(27)14(2)12-15(3)22(17(5)23(29)33-20)34-24-21(28)18(26(7,8)31)13-16(4)32-24/h10-11,14-18,20-22,24,28,30H,9,12-13H2,1-8H3/b11-10+/t14-,15+,16?,17-,18?,20-,21?,22+,24?,25+/m1/s1

InChI Key

PAPFNCSFPKDFRE-WEFAVHQDSA-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 venezuelae	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as macrolides and analogues. These are organic compounds containing a lactone ring of at least twelve members.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Macrolides and analogues

Sub Class

Not Available

Direct Parent

Macrolides and analogues

Alternative Parents

Substituents

Macrolide
Amino saccharide
Oxane
Trialkyl amine oxide
Tertiary alcohol
Cyclic ketone
Secondary alcohol
Lactone
Ketone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Trisubstituted n-oxide
Monocarboxylic acid or derivatives
Carboxylic acid derivative
N-oxide
Acetal
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organic zwitterion
Organooxygen compound
Organonitrogen compound
Carbonyl group
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
logP	2.15	ChemAxon
pKa (Strongest Acidic)	11.55	ChemAxon
pKa (Strongest Basic)	3.82	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	125.35 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	127.72 m³·mol⁻¹	ChemAxon
Polarizability	52.51 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

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

163186692

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for n-(2-{[(3r,4s,5s,7r,9e,11s,12r)-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-2,8-dioxo-1-oxacyclododec-9-en-4-yl]oxy}-3-hydroxy-6-methyloxan-4-yl)-n-methylmethanamine oxide (NP0280137)

MOL for NP0280137 (n-(2-{[(3r,4s,5s,7r,9e,11s,12r)-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-2,8-dioxo-1-oxacyclododec-9-en-4-yl]oxy}-3-hydroxy-6-methyloxan-4-yl)-n-methylmethanamine oxide)

3D MOL for NP0280137 (n-(2-{[(3r,4s,5s,7r,9e,11s,12r)-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-2,8-dioxo-1-oxacyclododec-9-en-4-yl]oxy}-3-hydroxy-6-methyloxan-4-yl)-n-methylmethanamine oxide)

3D SDF for NP0280137 (n-(2-{[(3r,4s,5s,7r,9e,11s,12r)-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-2,8-dioxo-1-oxacyclododec-9-en-4-yl]oxy}-3-hydroxy-6-methyloxan-4-yl)-n-methylmethanamine oxide)

3D-SDF for NP0280137 (n-(2-{[(3r,4s,5s,7r,9e,11s,12r)-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-2,8-dioxo-1-oxacyclododec-9-en-4-yl]oxy}-3-hydroxy-6-methyloxan-4-yl)-n-methylmethanamine oxide)

PDB for NP0280137 (n-(2-{[(3r,4s,5s,7r,9e,11s,12r)-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-2,8-dioxo-1-oxacyclododec-9-en-4-yl]oxy}-3-hydroxy-6-methyloxan-4-yl)-n-methylmethanamine oxide)

3D PDB for NP0280137 (n-(2-{[(3r,4s,5s,7r,9e,11s,12r)-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-2,8-dioxo-1-oxacyclododec-9-en-4-yl]oxy}-3-hydroxy-6-methyloxan-4-yl)-n-methylmethanamine oxide)

SMILES for NP0280137 (n-(2-{[(3r,4s,5s,7r,9e,11s,12r)-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-2,8-dioxo-1-oxacyclododec-9-en-4-yl]oxy}-3-hydroxy-6-methyloxan-4-yl)-n-methylmethanamine oxide)

INCHI for NP0280137 (n-(2-{[(3r,4s,5s,7r,9e,11s,12r)-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-2,8-dioxo-1-oxacyclododec-9-en-4-yl]oxy}-3-hydroxy-6-methyloxan-4-yl)-n-methylmethanamine oxide)

Structure for NP0280137 (n-(2-{[(3r,4s,5s,7r,9e,11s,12r)-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-2,8-dioxo-1-oxacyclododec-9-en-4-yl]oxy}-3-hydroxy-6-methyloxan-4-yl)-n-methylmethanamine oxide)

3D Structure for NP0280137 (n-(2-{[(3r,4s,5s,7r,9e,11s,12r)-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-2,8-dioxo-1-oxacyclododec-9-en-4-yl]oxy}-3-hydroxy-6-methyloxan-4-yl)-n-methylmethanamine oxide)