NP-MRD: Showing NP-Card for (-)-Ipobscurine C (NP0068707)

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Record Information

Version

2.0

Created at

2022-04-28 13:58:14 UTC

Updated at

2022-04-28 13:58:14 UTC

NP-MRD ID

NP0068707

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Ipobscurine C

Description

(3S,4R,15Z)-3-(hydroxymethyl)-7-methoxy-2,10-dioxa-18,23-diazapentacyclo[19.5.2.2¹¹,¹⁴.1⁵,⁹.0²⁴,²⁸]Hentriaconta-1(27),5,7,9(31),11,13,15,17,21,24(28),25,29-dodecaene-4,8,17-triol belongs to the class of organic compounds known as macrolactams. These are cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring. They are nitrogen analogues (the a nitrogen atom replacing the o atom of the cyclic carboxylic acid group ) of the naturally occurring macrolides. (-)-Ipobscurine C is found in Ipomoea obscura . Based on a literature review very few articles have been published on (3S,4R,15Z)-3-(hydroxymethyl)-7-methoxy-2,10-dioxa-18,23-diazapentacyclo[19.5.2.2¹¹,¹⁴.1⁵,⁹.0²⁴,²⁸]Hentriaconta-1(27),5,7,9(31),11,13,15,17,21,24(28),25,29-dodecaene-4,8,17-triol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282215582D          

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M  END

     RDKit          3D

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M  END


  Mrv1652304282215582D          

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 22 23  2  0  0  0  0
 22 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 29 30  1  0  0  0  0
  3 30  1  0  0  0  0
 29 31  1  0  0  0  0
 31 32  2  0  0  0  0
 26 32  1  0  0  0  0
  8 33  1  6  0  0  0
 33 34  1  0  0  0  0
  7 35  1  1  0  0  0
  2 36  1  0  0  0  0
  1 37  1  0  0  0  0
 37 38  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0068707

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C(O)C2=CC(=C1)[C@@H](O)[C@H](CO)OC1=CC=C3NC=C(CCNC(=O)\C=C/C4=CC=C(O2)C=C4)C3=C1

> <INCHI_IDENTIFIER>
InChI=1S/C29H28N2O7/c1-36-24-12-19-13-25(29(24)35)37-20-5-2-17(3-6-20)4-9-27(33)30-11-10-18-15-31-23-8-7-21(14-22(18)23)38-26(16-32)28(19)34/h2-9,12-15,26,28,31-32,34-35H,10-11,16H2,1H3,(H,30,33)/b9-4-/t26-,28+/m0/s1

> <INCHI_KEY>
RYKHLLTYMPMIRA-IOCRKHGWSA-N

> <FORMULA>
C29H28N2O7

> <MOLECULAR_WEIGHT>
516.55

> <EXACT_MASS>
516.18965125

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
53.37339387382417

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,4R,15E)-4,8-dihydroxy-3-(hydroxymethyl)-7-methoxy-2,10-dioxa-18,23-diazapentacyclo[19.5.2.2^{11,14}.1^{5,9}.0^{24,28}]hentriaconta-1(26),5,7,9(31),11,13,15,21,24,27,29-undecaen-17-one

> <ALOGPS_LOGP>
3.14

> <JCHEM_LOGP>
3.036652774666666

> <ALOGPS_LOGS>
-4.68

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.365465162433061

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.987234403617423

> <JCHEM_PKA_STRONGEST_BASIC>
-0.387323552361717

> <JCHEM_POLAR_SURFACE_AREA>
133.27

> <JCHEM_REFRACTIVITY>
141.8606

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.09e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S,4R,15E)-4,8-dihydroxy-3-(hydroxymethyl)-7-methoxy-2,10-dioxa-18,23-diazapentacyclo[19.5.2.2^{11,14}.1^{5,9}.0^{24,28}]hentriaconta-1(26),5,7,9(31),11,13,15,21,24,27,29-undecaen-17-one

> <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      19.703   5.511   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      19.628   7.070   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      18.215   7.817   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      16.910   6.924   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      16.995   5.352   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      18.402   4.669   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      15.758   4.360   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      14.325   3.701   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      12.736   3.653   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      11.175   4.068   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.710   5.577   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.188   6.039   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.092   4.918   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.511   3.408   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      10.013   3.012   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       6.668   5.597   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       6.865   7.131   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       8.401   7.434   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.461   9.019   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.610  10.584   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0       9.363  11.972   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0      10.524  13.069   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       9.656  14.341   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      11.973  13.751   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      13.558  13.964   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      15.077  13.356   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      16.648  13.651   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      17.706  12.494   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      17.268  10.965   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      17.786   9.402   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      15.729  10.701   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      14.680  11.835   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      14.676   2.202   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      13.554   1.147   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      16.568   3.050   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      20.927   7.897   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0      21.073   4.809   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      22.367   5.644   0.000  0.00  0.00           C+0
CONECT    1    2    6   37                                                  
CONECT    2    1    3   36                                                  
CONECT    3    2    4   30                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8   35                                                  
CONECT    8    7    9   33                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   18                                                  
CONECT   13   12   14   16                                                  
CONECT   14   13   15                                                       
CONECT   15   14   10                                                       
CONECT   16   13   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   12   19                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   32                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29    3                                                       
CONECT   31   29   32                                                       
CONECT   32   31   26                                                       
CONECT   33    8   34                                                       
CONECT   34   33                                                            
CONECT   35    7                                                            
CONECT   36    2                                                            
CONECT   37    1   38                                                       
CONECT   38   37                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   84    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₂₈N₂O₇

Average Mass

516.5500 Da

Monoisotopic Mass

516.18965 Da

IUPAC Name

(3S,4R,15E)-4,8-dihydroxy-3-(hydroxymethyl)-7-methoxy-2,10-dioxa-18,23-diazapentacyclo[19.5.2.2^{11,14}.1^{5,9}.0^{24,28}]hentriaconta-1(26),5,7,9(31),11,13,15,21,24,27,29-undecaen-17-one

Traditional Name

(3S,4R,15E)-4,8-dihydroxy-3-(hydroxymethyl)-7-methoxy-2,10-dioxa-18,23-diazapentacyclo[19.5.2.2^{11,14}.1^{5,9}.0^{24,28}]hentriaconta-1(26),5,7,9(31),11,13,15,21,24,27,29-undecaen-17-one

CAS Registry Number

Not Available

SMILES

COC1=C(O)C2=CC(=C1)[C@@H](O)[C@H](CO)OC1=CC=C3NC=C(CCNC(=O)\C=C/C4=CC=C(O2)C=C4)C3=C1

InChI Identifier

InChI=1S/C29H28N2O7/c1-36-24-12-19-13-25(29(24)35)37-20-5-2-17(3-6-20)4-9-27(33)30-11-10-18-15-31-23-8-7-21(14-22(18)23)38-26(16-32)28(19)34/h2-9,12-15,26,28,31-32,34-35H,10-11,16H2,1H3,(H,30,33)/b9-4-/t26-,28+/m0/s1

InChI Key

RYKHLLTYMPMIRA-IOCRKHGWSA-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
Ipomoea obscura	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as macrolactams. These are cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring. They are nitrogen analogues (the a nitrogen atom replacing the o atom of the cyclic carboxylic acid group ) of the naturally occurring macrolides.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Macrolactams

Sub Class

Not Available

Direct Parent

Macrolactams

Alternative Parents

Substituents

Macrolactam
Diaryl ether
3-alkylindole
Indole
Indole or derivatives
Anisole
Phenol ether
Phenol
Alkyl aryl ether
Benzenoid
Heteroaromatic compound
Pyrrole
Carboxamide group
Secondary carboxylic acid amide
Secondary alcohol
Lactam
Oxacycle
Azacycle
Organoheterocyclic compound
Carboxylic acid derivative
Ether
Organic oxygen compound
Carbonyl group
Organic nitrogen compound
Alcohol
Organic oxide
Primary alcohol
Hydrocarbon derivative
Organonitrogen compound
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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	3.14	ALOGPS
logP	3.04	ChemAxon
logS	-4.7	ALOGPS
pKa (Strongest Acidic)	8.99	ChemAxon
pKa (Strongest Basic)	-0.39	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	133.27 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	141.86 m³·mol⁻¹	ChemAxon
Polarizability	53.37 Å³	ChemAxon
Number of Rings	5	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

4477030

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5318461

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (-)-Ipobscurine C (NP0068707)

MOL for NP0068707 ((-)-Ipobscurine C)

3D MOL for NP0068707 ((-)-Ipobscurine C)

3D SDF for NP0068707 ((-)-Ipobscurine C)

3D-SDF for NP0068707 ((-)-Ipobscurine C)

PDB for NP0068707 ((-)-Ipobscurine C)

3D PDB for NP0068707 ((-)-Ipobscurine C)

SMILES for NP0068707 ((-)-Ipobscurine C)

INCHI for NP0068707 ((-)-Ipobscurine C)

Structure for NP0068707 ((-)-Ipobscurine C)

3D Structure for NP0068707 ((-)-Ipobscurine C)