NP-MRD: Showing NP-Card for (3e)-11-ethyl-2,21,28-trihydroxy-10-methyl-14-oxa-22,27-diazahexacyclo[24.2.1.0⁵,¹⁷.0⁷,¹⁶.0⁸,¹².0¹³,¹⁵]nonacosa-1,3,19,21,27-pentaen-29-one (NP0307622)

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Record Information

Version

2.0

Created at

2022-09-11 00:52:31 UTC

Updated at

2022-09-11 00:52:31 UTC

NP-MRD ID

NP0307622

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3e)-11-ethyl-2,21,28-trihydroxy-10-methyl-14-oxa-22,27-diazahexacyclo[24.2.1.0⁵,¹⁷.0⁷,¹⁶.0⁸,¹².0¹³,¹⁵]nonacosa-1,3,19,21,27-pentaen-29-one

Description

Ikarugamycin epoxide belongs to the class of organic compounds known as iridoids and derivatives. These are monoterpenes containing a skeleton structurally characterized by the presence of a cylopentane fused to a pyran ( forming a 4,7-dimethylcyclopenta[c]pyran), or a derivative where the pentane moiety is open. (3e)-11-ethyl-2,21,28-trihydroxy-10-methyl-14-oxa-22,27-diazahexacyclo[24.2.1.0⁵,¹⁷.0⁷,¹⁶.0⁸,¹².0¹³,¹⁵]nonacosa-1,3,19,21,27-pentaen-29-one was first documented in 2003 (PMID: 12817810). Based on a literature review very few articles have been published on Ikarugamycin epoxide.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309112202522D          

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M  END

     RDKit          3D

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M  END


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  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  4  0  0  0
 13 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 16 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 22 21  1  4  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 25 23  1  4  0  0  0
 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 10 28  1  0  0  0  0
 28 29  1  0  0  0  0
  8 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
 30 32  1  0  0  0  0
 32 33  1  0  0  0  0
  3 33  1  0  0  0  0
  7 33  1  0  0  0  0
 18 34  1  0  0  0  0
 34 35  2  0  0  0  0
 15 35  1  0  0  0  0
 35 36  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0307622

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC1C(C)CC2C3CC4\C=C\C(O)=C5C(O)=NC(CCCN=C(O)C=CCC4C3C3OC3C12)C5=O

> <INCHI_IDENTIFIER>
InChI=1S/C29H38N2O5/c1-3-16-14(2)12-18-19-13-15-9-10-21(32)25-26(34)20(31-29(25)35)7-5-11-30-22(33)8-4-6-17(15)24(19)28-27(36-28)23(16)18/h4,8-10,14-20,23-24,27-28,32H,3,5-7,11-13H2,1-2H3,(H,30,33)(H,31,35)/b8-4?,10-9+,25-21?

> <INCHI_KEY>
XVOOQLPJKAEVAZ-KRWLBPITSA-N

> <FORMULA>
C29H38N2O5

> <MOLECULAR_WEIGHT>
494.632

> <EXACT_MASS>
494.278072332

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
54.18554220337203

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3E)-11-ethyl-2,21,28-trihydroxy-10-methyl-14-oxa-22,27-diazahexacyclo[24.2.1.0^{5,17}.0^{7,16}.0^{8,12}.0^{13,15}]nonacosa-1,3,19,21,27-pentaen-29-one

> <JCHEM_LOGP>
2.680078480693085

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.857519200355898

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.825430636069579

> <JCHEM_PKA_STRONGEST_BASIC>
6.68215889834087

> <JCHEM_POLAR_SURFACE_AREA>
115.01

> <JCHEM_REFRACTIVITY>
139.1274

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3E)-11-ethyl-2,21,28-trihydroxy-10-methyl-14-oxa-22,27-diazahexacyclo[24.2.1.0^{5,17}.0^{7,16}.0^{8,12}.0^{13,15}]nonacosa-1,3,19,21,27-pentaen-29-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0      -3.967  -8.298   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.587  -8.981   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.306  -8.127   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.243  -6.588   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.452  -5.633   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.239  -6.172   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.093  -7.453   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.617  -7.676   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.802  -6.692   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.104  -7.516   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.586  -7.099   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.967  -5.607   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.450  -5.191   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       8.831  -3.699   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       9.552  -6.267   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.171  -7.759   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       7.688  -8.175   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      10.273  -8.835   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       9.892 -10.327   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      10.994 -11.403   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      10.613 -12.895   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0       9.131 -13.311   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0       8.029 -12.235   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       8.409 -10.743   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       6.546 -12.652   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       5.444 -11.576   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       5.825 -10.084   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.723  -9.008   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       3.186  -9.107   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       2.231 -10.315   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       1.277 -11.523   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       0.708 -10.092   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       0.139  -8.661   0.000  0.00  0.00           C+0
HETATM   34  N   UNK     0      11.507  -7.811   0.000  0.00  0.00           N+0
HETATM   35  C   UNK     0      11.091  -6.329   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      12.045  -5.121   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   33                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8   33                                                  
CONECT    8    7    9   29                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   28                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   35                                                  
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19   34                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   10   29                                                  
CONECT   29   28    8   30                                                  
CONECT   30   29   31   32                                                  
CONECT   31   30   32                                                       
CONECT   32   31   30   33                                                  
CONECT   33   32    3    7                                                  
CONECT   34   18   35                                                       
CONECT   35   34   15   36                                                  
CONECT   36   35                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   82    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₃₈N₂O₅

Average Mass

494.6320 Da

Monoisotopic Mass

494.27807 Da

IUPAC Name

(3E)-11-ethyl-2,21,28-trihydroxy-10-methyl-14-oxa-22,27-diazahexacyclo[24.2.1.0^{5,17}.0^{7,16}.0^{8,12}.0^{13,15}]nonacosa-1,3,19,21,27-pentaen-29-one

Traditional Name

(3E)-11-ethyl-2,21,28-trihydroxy-10-methyl-14-oxa-22,27-diazahexacyclo[24.2.1.0^{5,17}.0^{7,16}.0^{8,12}.0^{13,15}]nonacosa-1,3,19,21,27-pentaen-29-one

CAS Registry Number

Not Available

SMILES

CCC1C(C)CC2C3CC4\C=C\C(O)=C5C(O)=NC(CCCN=C(O)C=CCC4C3C3OC3C12)C5=O

InChI Identifier

InChI=1S/C29H38N2O5/c1-3-16-14(2)12-18-19-13-15-9-10-21(32)25-26(34)20(31-29(25)35)7-5-11-30-22(33)8-4-6-17(15)24(19)28-27(36-28)23(16)18/h4,8-10,14-20,23-24,27-28,32H,3,5-7,11-13H2,1-2H3,(H,30,33)(H,31,35)/b8-4?,10-9+,25-21?

InChI Key

XVOOQLPJKAEVAZ-KRWLBPITSA-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 iridoids and derivatives. These are monoterpenes containing a skeleton structurally characterized by the presence of a cylopentane fused to a pyran ( forming a 4,7-dimethylcyclopenta[c]pyran), or a derivative where the pentane moiety is open.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Monoterpenoids

Direct Parent

Iridoids and derivatives

Alternative Parents

Substituents

11-noriridane monoterpenoid
Oxepane
Vinylogous acid
Cyclic carboximidic acid
Pyrroline
Ketone
Oxacycle
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Polyol
Ether
Oxirane
Enol
Dialkyl ether
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic 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	2.68	ChemAxon
pKa (Strongest Acidic)	3.83	ChemAxon
pKa (Strongest Basic)	6.68	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	115.01 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	139.13 m³·mol⁻¹	ChemAxon
Polarizability	54.19 Å³	ChemAxon
Number of Rings	6	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

C00014916

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

139588417

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Bertasso M, Holzenkampfer M, Zeeck A, Stackebrandt E, Beil W, Fiedler HP: Ripromycin and other polycyclic macrolactams from Streptomyces sp. Tu 6239: taxonomy, fermentation, isolation and biological properties. J Antibiot (Tokyo). 2003 Apr;56(4):364-71. doi: 10.7164/antibiotics.56.364. [PubMed:12817810 ]
LOTUS database [Link]

Showing NP-Card for (3e)-11-ethyl-2,21,28-trihydroxy-10-methyl-14-oxa-22,27-diazahexacyclo[24.2.1.0⁵,¹⁷.0⁷,¹⁶.0⁸,¹².0¹³,¹⁵]nonacosa-1,3,19,21,27-pentaen-29-one (NP0307622)

MOL for NP0307622 ((3e)-11-ethyl-2,21,28-trihydroxy-10-methyl-14-oxa-22,27-diazahexacyclo[24.2.1.0⁵,¹⁷.0⁷,¹⁶.0⁸,¹².0¹³,¹⁵]nonacosa-1,3,19,21,27-pentaen-29-one)

3D MOL for NP0307622 ((3e)-11-ethyl-2,21,28-trihydroxy-10-methyl-14-oxa-22,27-diazahexacyclo[24.2.1.0⁵,¹⁷.0⁷,¹⁶.0⁸,¹².0¹³,¹⁵]nonacosa-1,3,19,21,27-pentaen-29-one)

3D SDF for NP0307622 ((3e)-11-ethyl-2,21,28-trihydroxy-10-methyl-14-oxa-22,27-diazahexacyclo[24.2.1.0⁵,¹⁷.0⁷,¹⁶.0⁸,¹².0¹³,¹⁵]nonacosa-1,3,19,21,27-pentaen-29-one)

3D-SDF for NP0307622 ((3e)-11-ethyl-2,21,28-trihydroxy-10-methyl-14-oxa-22,27-diazahexacyclo[24.2.1.0⁵,¹⁷.0⁷,¹⁶.0⁸,¹².0¹³,¹⁵]nonacosa-1,3,19,21,27-pentaen-29-one)

PDB for NP0307622 ((3e)-11-ethyl-2,21,28-trihydroxy-10-methyl-14-oxa-22,27-diazahexacyclo[24.2.1.0⁵,¹⁷.0⁷,¹⁶.0⁸,¹².0¹³,¹⁵]nonacosa-1,3,19,21,27-pentaen-29-one)

3D PDB for NP0307622 ((3e)-11-ethyl-2,21,28-trihydroxy-10-methyl-14-oxa-22,27-diazahexacyclo[24.2.1.0⁵,¹⁷.0⁷,¹⁶.0⁸,¹².0¹³,¹⁵]nonacosa-1,3,19,21,27-pentaen-29-one)

SMILES for NP0307622 ((3e)-11-ethyl-2,21,28-trihydroxy-10-methyl-14-oxa-22,27-diazahexacyclo[24.2.1.0⁵,¹⁷.0⁷,¹⁶.0⁸,¹².0¹³,¹⁵]nonacosa-1,3,19,21,27-pentaen-29-one)

INCHI for NP0307622 ((3e)-11-ethyl-2,21,28-trihydroxy-10-methyl-14-oxa-22,27-diazahexacyclo[24.2.1.0⁵,¹⁷.0⁷,¹⁶.0⁸,¹².0¹³,¹⁵]nonacosa-1,3,19,21,27-pentaen-29-one)

Structure for NP0307622 ((3e)-11-ethyl-2,21,28-trihydroxy-10-methyl-14-oxa-22,27-diazahexacyclo[24.2.1.0⁵,¹⁷.0⁷,¹⁶.0⁸,¹².0¹³,¹⁵]nonacosa-1,3,19,21,27-pentaen-29-one)

3D Structure for NP0307622 ((3e)-11-ethyl-2,21,28-trihydroxy-10-methyl-14-oxa-22,27-diazahexacyclo[24.2.1.0⁵,¹⁷.0⁷,¹⁶.0⁸,¹².0¹³,¹⁵]nonacosa-1,3,19,21,27-pentaen-29-one)