NP-MRD: Showing NP-Card for 5-O-Desosaminylplatenolide I (NP0062065)

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Record Information

Version

2.0

Created at

2022-04-28 06:44:35 UTC

Updated at

2022-04-28 06:44:35 UTC

NP-MRD ID

NP0062065

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5-O-Desosaminylplatenolide I

Description

(4R,5S,6S,7S,9R,11E,13E,16R)-6-{[(2S,3S,4R,6S)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy}-7-ethyl-4-hydroxy-5-methoxy-9,16-dimethyl-1-oxacyclohexadeca-11,13-diene-2,10-dione belongs to the class of organic compounds known as aminoglycosides. These are molecules or a portion of a molecule composed of amino-modified sugars. 5-O-Desosaminylplatenolide I is found in Streptomyces narabonesis ISP 5016. Based on a literature review very few articles have been published on (4R,5S,6S,7S,9R,11E,13E,16R)-6-{[(2S,3S,4R,6S)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy}-7-ethyl-4-hydroxy-5-methoxy-9,16-dimethyl-1-oxacyclohexadeca-11,13-diene-2,10-dione.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282208442D          

 37 38  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652304282208442D          

 37 38  0  0  1  0            999 V2000
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   -1.4289   -4.1250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  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  2  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
  1 18  1  0  0  0  0
 18 19  1  1  0  0  0
 20 19  1  6  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 20 25  1  0  0  0  0
 24 26  1  1  0  0  0
 22 27  1  1  0  0  0
 27 28  1  0  0  0  0
 27 29  1  0  0  0  0
 21 30  1  6  0  0  0
 17 31  1  6  0  0  0
 31 32  1  0  0  0  0
 16 33  1  6  0  0  0
 11 34  1  1  0  0  0
  3 35  1  1  0  0  0
  1 36  1  6  0  0  0
 36 37  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0062065

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C28H47NO8/c1-8-20-14-17(2)22(30)13-11-9-10-12-18(3)35-24(32)16-23(31)27(34-7)26(20)37-28-25(33)21(29(5)6)15-19(4)36-28/h9-11,13,17-21,23,25-28,31,33H,8,12,14-16H2,1-7H3/b10-9+,13-11+/t17-,18-,19+,20+,21-,23-,25+,26+,27+,28+/m1/s1

> <INCHI_KEY>
PKRBCWQDXCULFS-XGTVNSMKSA-N

> <FORMULA>
C28H47NO8

> <MOLECULAR_WEIGHT>
525.683

> <EXACT_MASS>
525.330167477

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
84

> <JCHEM_AVERAGE_POLARIZABILITY>
57.509787283133576

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4R,5S,6S,7S,9R,11E,13E,16R)-6-{[(2S,3S,4R,6S)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy}-7-ethyl-4-hydroxy-5-methoxy-9,16-dimethyl-1-oxacyclohexadeca-11,13-diene-2,10-dione

> <ALOGPS_LOGP>
2.43

> <JCHEM_LOGP>
3.2032172816666664

> <ALOGPS_LOGS>
-3.45

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
13.89127109513473

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.792293983213082

> <JCHEM_PKA_STRONGEST_BASIC>
8.380996069890601

> <JCHEM_POLAR_SURFACE_AREA>
114.76000000000002

> <JCHEM_REFRACTIVITY>
142.3253

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.88e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4R,5S,6S,7S,9R,11E,13E,16R)-6-{[(2S,3S,4R,6S)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy}-7-ethyl-4-hydroxy-5-methoxy-9,16-dimethyl-1-oxacyclohexadeca-11,13-diene-2,10-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.000   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       6.668  -0.770   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      -0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   27  N   UNK     0      -2.667  -7.700   0.000  0.00  0.00           N+0
HETATM   28  C   UNK     0      -4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -0.000  -1.540   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
CONECT    1    2   18   36                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4   35                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   34                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17   33                                                  
CONECT   17   16   18   31                                                  
CONECT   18   17    1   19                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   25                                                  
CONECT   21   20   22   30                                                  
CONECT   22   21   23   27                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24   20                                                       
CONECT   26   24                                                            
CONECT   27   22   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27                                                            
CONECT   30   21                                                            
CONECT   31   17   32                                                       
CONECT   32   31                                                            
CONECT   33   16                                                            
CONECT   34   11                                                            
CONECT   35    3                                                            
CONECT   36    1   37                                                       
CONECT   37   36                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₄₇NO₈

Average Mass

525.6830 Da

Monoisotopic Mass

525.33017 Da

IUPAC Name

(4R,5S,6S,7S,9R,11E,13E,16R)-6-{[(2S,3S,4R,6S)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy}-7-ethyl-4-hydroxy-5-methoxy-9,16-dimethyl-1-oxacyclohexadeca-11,13-diene-2,10-dione

Traditional Name

(4R,5S,6S,7S,9R,11E,13E,16R)-6-{[(2S,3S,4R,6S)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy}-7-ethyl-4-hydroxy-5-methoxy-9,16-dimethyl-1-oxacyclohexadeca-11,13-diene-2,10-dione

CAS Registry Number

Not Available

SMILES

CC[C@H]1C[C@@H](C)C(=O)\C=C\C=C\C[C@@H](C)OC(=O)C[C@@H](O)[C@H](OC)[C@H]1O[C@@H]1O[C@@H](C)C[C@H]([C@@H]1O)N(C)C

InChI Identifier

InChI=1S/C28H47NO8/c1-8-20-14-17(2)22(30)13-11-9-10-12-18(3)35-24(32)16-23(31)27(34-7)26(20)37-28-25(33)21(29(5)6)15-19(4)36-28/h9-11,13,17-21,23,25-28,31,33H,8,12,14-16H2,1-7H3/b10-9+,13-11+/t17-,18-,19+,20+,21-,23-,25+,26+,27+,28+/m1/s1

InChI Key

PKRBCWQDXCULFS-XGTVNSMKSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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 narabonesis ISP 5016	Bacteria	KNApSAcK

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
Macrolide
Oxane
Cyclic ketone
Tertiary aliphatic amine
Tertiary amine
Secondary alcohol
Lactone
Ketone
Carboxylic acid ester
Amino acid or derivatives
1,2-aminoalcohol
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Ether
Dialkyl ether
Carboxylic acid derivative
Acetal
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organonitrogen compound
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
logP	2.43	ALOGPS
logP	3.2	ChemAxon
logS	-3.4	ALOGPS
pKa (Strongest Acidic)	12.79	ChemAxon
pKa (Strongest Basic)	8.38	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	114.76 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	142.33 m³·mol⁻¹	ChemAxon
Polarizability	57.51 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

163056929

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for 5-O-Desosaminylplatenolide I (NP0062065)

MOL for NP0062065 (5-O-Desosaminylplatenolide I)

3D MOL for NP0062065 (5-O-Desosaminylplatenolide I)

3D SDF for NP0062065 (5-O-Desosaminylplatenolide I)

3D-SDF for NP0062065 (5-O-Desosaminylplatenolide I)

PDB for NP0062065 (5-O-Desosaminylplatenolide I)

3D PDB for NP0062065 (5-O-Desosaminylplatenolide I)

SMILES for NP0062065 (5-O-Desosaminylplatenolide I)

INCHI for NP0062065 (5-O-Desosaminylplatenolide I)

Structure for NP0062065 (5-O-Desosaminylplatenolide I)

3D Structure for NP0062065 (5-O-Desosaminylplatenolide I)