NP-MRD: Showing NP-Card for (3r,6s,9e)-5,8,13-trihydroxy-14-(2-hydroxyethyl)-3-isopropyl-6-methyl-11-methylidene-15-(octan-2-yl)-1-oxa-4,7,12-triazacyclopentadeca-4,7,9,12-tetraen-2-one (NP0161891)

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Record Information

Version

2.0

Created at

2022-09-02 20:11:19 UTC

Updated at

2022-09-02 20:11:19 UTC

NP-MRD ID

NP0161891

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3r,6s,9e)-5,8,13-trihydroxy-14-(2-hydroxyethyl)-3-isopropyl-6-methyl-11-methylidene-15-(octan-2-yl)-1-oxa-4,7,12-triazacyclopentadeca-4,7,9,12-tetraen-2-one

Description

Vinylamycin belongs to the class of organic compounds known as cyclic depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids) connected in a ring. The residues are commonly but not necessarily regularly alternating. Vinylamycin is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. (3r,6s,9e)-5,8,13-trihydroxy-14-(2-hydroxyethyl)-3-isopropyl-6-methyl-11-methylidene-15-(octan-2-yl)-1-oxa-4,7,12-triazacyclopentadeca-4,7,9,12-tetraen-2-one was first documented in 1999 (PMID: 10604756). Based on a literature review very few articles have been published on vinylamycin (PMID: 22591554).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309022222112D          

 35 35  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309022222112D          

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  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  4  0  0  0
  5  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  1  0  0  0
  8 10  1  0  0  0  0
 10 11  1  4  0  0  0
 10 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  6  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 13 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 20 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 29 33  1  0  0  0  0
 33 34  1  0  0  0  0
 33 35  2  0  0  0  0
 35  2  1  4  0  0  0
M  END
> <DATABASE_ID>
NP0161891

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCCC(C)C1OC(=O)[C@H](N=C(O)[C@H](C)N=C(O)\C=C\C(=C)N=C(O)C1CCO)C(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C26H43N3O6/c1-7-8-9-10-11-17(4)23-20(14-15-30)25(33)27-18(5)12-13-21(31)28-19(6)24(32)29-22(16(2)3)26(34)35-23/h12-13,16-17,19-20,22-23,30H,5,7-11,14-15H2,1-4,6H3,(H,27,33)(H,28,31)(H,29,32)/b13-12+/t17?,19-,20?,22+,23?/m0/s1

> <INCHI_KEY>
ONGSLGFACDWAIV-OIXFFAKGSA-N

> <FORMULA>
C26H43N3O6

> <MOLECULAR_WEIGHT>
493.645

> <EXACT_MASS>
493.315186117

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
78

> <JCHEM_AVERAGE_POLARIZABILITY>
55.16889738670274

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,6S,9E)-5,8,13-trihydroxy-14-(2-hydroxyethyl)-6-methyl-11-methylidene-15-(octan-2-yl)-3-(propan-2-yl)-1-oxa-4,7,12-triazacyclopentadeca-4,7,9,12-tetraen-2-one

> <ALOGPS_LOGP>
3.20

> <JCHEM_LOGP>
-0.1843547228992209

> <ALOGPS_LOGS>
-4.51

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
0.48444662197217214

> <JCHEM_PKA_STRONGEST_ACIDIC>
-2.0375602442080707

> <JCHEM_PKA_STRONGEST_BASIC>
11.51648401526763

> <JCHEM_POLAR_SURFACE_AREA>
144.3

> <JCHEM_REFRACTIVITY>
136.19209999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.54e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R,6S,9E)-5,8,13-trihydroxy-14-(2-hydroxyethyl)-3-isopropyl-6-methyl-11-methylidene-15-(octan-2-yl)-1-oxa-4,7,12-triazacyclopentadeca-4,7,9,12-tetraen-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-SEP-22         0                                  
HETATM    1  C   UNK     0       2.701 -10.780   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.173  -8.462   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.334  -8.782   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.104  -7.448   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -2.635  -7.287   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0      -0.073  -6.304   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      -0.000  -4.620   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.317  -3.821   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.334  -3.850   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   12  N   UNK     0       1.334  -2.310   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       2.667  -1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.001   0.770   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.334   0.770   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       5.335  -1.540   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       4.001  -3.850   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.668  -3.850   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       9.336  -3.850   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      12.003  -3.850   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      13.337  -4.620   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      14.670  -3.850   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       5.335  -6.160   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       8.002  -6.160   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       9.336  -6.930   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       2.667  -6.160   0.000  0.00  0.00           O+0
HETATM   35  N   UNK     0       4.001  -8.470   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3   35                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14   17                                                  
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17   13   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21   29                                                  
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27                                                            
CONECT   29   20   30   33                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31                                                            
CONECT   33   29   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33    2                                                       
MASTER        0    0    0    0    0    0    0    0   35    0   70    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₄₃N₃O₆

Average Mass

493.6450 Da

Monoisotopic Mass

493.31519 Da

IUPAC Name

(3R,6S,9E)-5,8,13-trihydroxy-14-(2-hydroxyethyl)-6-methyl-11-methylidene-15-(octan-2-yl)-3-(propan-2-yl)-1-oxa-4,7,12-triazacyclopentadeca-4,7,9,12-tetraen-2-one

Traditional Name

(3R,6S,9E)-5,8,13-trihydroxy-14-(2-hydroxyethyl)-3-isopropyl-6-methyl-11-methylidene-15-(octan-2-yl)-1-oxa-4,7,12-triazacyclopentadeca-4,7,9,12-tetraen-2-one

CAS Registry Number

Not Available

SMILES

CCCCCCC(C)C1OC(=O)[C@H](N=C(O)[C@H](C)N=C(O)\C=C\C(=C)N=C(O)C1CCO)C(C)C

InChI Identifier

InChI=1S/C26H43N3O6/c1-7-8-9-10-11-17(4)23-20(14-15-30)25(33)27-18(5)12-13-21(31)28-19(6)24(32)29-22(16(2)3)26(34)35-23/h12-13,16-17,19-20,22-23,30H,5,7-11,14-15H2,1-4,6H3,(H,27,33)(H,28,31)(H,29,32)/b13-12+/t17?,19-,20?,22+,23?/m0/s1

InChI Key

ONGSLGFACDWAIV-OIXFFAKGSA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyclic depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids) connected in a ring. The residues are commonly but not necessarily regularly alternating.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Peptidomimetics

Sub Class

Depsipeptides

Direct Parent

Cyclic depsipeptides

Alternative Parents

Substituents

Cyclic depsipeptide
Macrolide lactam
Alpha-amino acid ester
Macrolactam
Macrolide
Alpha-amino acid or derivatives
Carboxamide group
Carboxylic acid ester
Lactam
Lactone
Secondary carboxylic acid amide
Carboxylic acid derivative
Oxacycle
Azacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Alcohol
Organopnictogen compound
Organic oxygen compound
Primary alcohol
Organooxygen compound
Carbonyl group
Organonitrogen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

primary alcohol (CHEBI:66360 )
cyclodepsipeptide (CHEBI:66360 )
macrocycle (CHEBI:66360 )

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	3.2	ALOGPS
logP	-0.18	ChemAxon
logS	-4.5	ALOGPS
pKa (Strongest Acidic)	-2	ChemAxon
pKa (Strongest Basic)	11.52	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	144.3 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	136.19 m³·mol⁻¹	ChemAxon
Polarizability	55.17 Å³	ChemAxon
Number of Rings	1	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

C00015413

Chemspider ID

28533032

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

70678757

PDB ID

Not Available

ChEBI ID

66360

Good Scents ID

Not Available

References

General References

Igarashi M, Shida T, Sasaki Y, Kinoshita N, Naganawa H, Hamada M, Takeuchi T: Vinylamycin, a new depsipeptide antibiotic, from Streptomyces sp. J Antibiot (Tokyo). 1999 Oct;52(10):873-9. doi: 10.7164/antibiotics.52.873. [PubMed:10604756 ]
Carr G, Poulsen M, Klassen JL, Hou Y, Wyche TP, Bugni TS, Currie CR, Clardy J: Microtermolides A and B from termite-associated Streptomyces sp. and structural revision of vinylamycin. Org Lett. 2012 Jun 1;14(11):2822-5. doi: 10.1021/ol301043p. Epub 2012 May 16. [PubMed:22591554 ]
LOTUS database [Link]

Showing NP-Card for (3r,6s,9e)-5,8,13-trihydroxy-14-(2-hydroxyethyl)-3-isopropyl-6-methyl-11-methylidene-15-(octan-2-yl)-1-oxa-4,7,12-triazacyclopentadeca-4,7,9,12-tetraen-2-one (NP0161891)

MOL for NP0161891 ((3r,6s,9e)-5,8,13-trihydroxy-14-(2-hydroxyethyl)-3-isopropyl-6-methyl-11-methylidene-15-(octan-2-yl)-1-oxa-4,7,12-triazacyclopentadeca-4,7,9,12-tetraen-2-one)

3D MOL for NP0161891 ((3r,6s,9e)-5,8,13-trihydroxy-14-(2-hydroxyethyl)-3-isopropyl-6-methyl-11-methylidene-15-(octan-2-yl)-1-oxa-4,7,12-triazacyclopentadeca-4,7,9,12-tetraen-2-one)

3D SDF for NP0161891 ((3r,6s,9e)-5,8,13-trihydroxy-14-(2-hydroxyethyl)-3-isopropyl-6-methyl-11-methylidene-15-(octan-2-yl)-1-oxa-4,7,12-triazacyclopentadeca-4,7,9,12-tetraen-2-one)

3D-SDF for NP0161891 ((3r,6s,9e)-5,8,13-trihydroxy-14-(2-hydroxyethyl)-3-isopropyl-6-methyl-11-methylidene-15-(octan-2-yl)-1-oxa-4,7,12-triazacyclopentadeca-4,7,9,12-tetraen-2-one)

PDB for NP0161891 ((3r,6s,9e)-5,8,13-trihydroxy-14-(2-hydroxyethyl)-3-isopropyl-6-methyl-11-methylidene-15-(octan-2-yl)-1-oxa-4,7,12-triazacyclopentadeca-4,7,9,12-tetraen-2-one)

3D PDB for NP0161891 ((3r,6s,9e)-5,8,13-trihydroxy-14-(2-hydroxyethyl)-3-isopropyl-6-methyl-11-methylidene-15-(octan-2-yl)-1-oxa-4,7,12-triazacyclopentadeca-4,7,9,12-tetraen-2-one)

SMILES for NP0161891 ((3r,6s,9e)-5,8,13-trihydroxy-14-(2-hydroxyethyl)-3-isopropyl-6-methyl-11-methylidene-15-(octan-2-yl)-1-oxa-4,7,12-triazacyclopentadeca-4,7,9,12-tetraen-2-one)

INCHI for NP0161891 ((3r,6s,9e)-5,8,13-trihydroxy-14-(2-hydroxyethyl)-3-isopropyl-6-methyl-11-methylidene-15-(octan-2-yl)-1-oxa-4,7,12-triazacyclopentadeca-4,7,9,12-tetraen-2-one)

Structure for NP0161891 ((3r,6s,9e)-5,8,13-trihydroxy-14-(2-hydroxyethyl)-3-isopropyl-6-methyl-11-methylidene-15-(octan-2-yl)-1-oxa-4,7,12-triazacyclopentadeca-4,7,9,12-tetraen-2-one)

3D Structure for NP0161891 ((3r,6s,9e)-5,8,13-trihydroxy-14-(2-hydroxyethyl)-3-isopropyl-6-methyl-11-methylidene-15-(octan-2-yl)-1-oxa-4,7,12-triazacyclopentadeca-4,7,9,12-tetraen-2-one)