NP-MRD: Showing NP-Card for (-)-Ipobscurine B (NP0068706)

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Record Information

Version

2.0

Created at

2022-04-28 13:58:11 UTC

Updated at

2022-04-28 13:58:11 UTC

NP-MRD ID

NP0068706

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Ipobscurine B

Description

Ipobscurine B belongs to the class of organic compounds known as lignans, neolignans and related compounds. These are plant products of low molecular weight formed primarily from oxidative coupling of two p-propylphenol moieties. They can also be described as micromolecules with two phenylpropanoid units coupled together. They can be attached in various manners, like C5-C5', C8-C8'. Most known natural lignans are oxidized at C9 and C9´ and, based upon the way in which oxygen is incorporated into the skeleton and on the cyclization patterns, a wide range of lignans of very different structural types can be formed. (-)-Ipobscurine B is found in Ipomoea obscura . (-)-Ipobscurine B was first documented in 2003 (PMID: 12648548). Based on a literature review very few articles have been published on Ipobscurine B.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282215582D          

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M  END

     RDKit          3D

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  2 24  1  0  0  0  0
 25 24  1  6  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 27 32  1  0  0  0  0
 30 33  1  0  0  0  0
 29 34  1  0  0  0  0
 34 35  1  0  0  0  0
 26 36  1  1  0  0  0
 25 37  1  0  0  0  0
 37 38  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0068706

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C(O)C=CC(=C1)[C@@H](O)[C@H](CO)OC1=CC=C2NC=C(CCNC(=O)\C=C\C3=CC=C(O)C=C3)C2=C1

> <INCHI_IDENTIFIER>
InChI=1S/C29H30N2O7/c1-37-26-14-19(5-10-25(26)34)29(36)27(17-32)38-22-8-9-24-23(15-22)20(16-31-24)12-13-30-28(35)11-4-18-2-6-21(33)7-3-18/h2-11,14-16,27,29,31-34,36H,12-13,17H2,1H3,(H,30,35)/b11-4+/t27-,29+/m0/s1

> <INCHI_KEY>
LMWMSKRQOYZVFO-SWBAOWADSA-N

> <FORMULA>
C29H30N2O7

> <MOLECULAR_WEIGHT>
518.566

> <EXACT_MASS>
518.205301314

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
54.54129914505506

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2E)-N-[2-(5-{[(1R,2S)-1,3-dihydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-2-yl]oxy}-1H-indol-3-yl)ethyl]-3-(4-hydroxyphenyl)prop-2-enamide

> <ALOGPS_LOGP>
3.22

> <JCHEM_LOGP>
3.206046086

> <ALOGPS_LOGS>
-5.06

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.030751129654199

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.297977945886235

> <JCHEM_PKA_STRONGEST_BASIC>
-0.38746877490364107

> <JCHEM_POLAR_SURFACE_AREA>
144.27

> <JCHEM_REFRACTIVITY>
143.6587

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.49e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2E)-N-[2-(5-{[(1R,2S)-1,3-dihydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-2-yl]oxy}-1H-indol-3-yl)ethyl]-3-(4-hydroxyphenyl)prop-2-enamide

> <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       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       2.126   4.089   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.126   1.597   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.650   0.132   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.143  -0.188   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      -0.333  -1.652   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0      -1.839  -1.973   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -2.869  -0.828   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -2.315  -3.437   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -1.284  -4.582   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.760  -6.046   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -0.730  -7.191   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -1.206  -8.655   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -2.712  -8.976   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -3.742  -7.831   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -3.267  -6.367   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -3.188 -10.440   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       7.591   1.303   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       7.591  -0.237   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       8.925  -1.007   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      10.259  -0.237   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      10.259   1.303   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      11.592   2.073   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      12.926   1.303   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      12.926  -0.237   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      11.592  -1.007   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      14.260   2.073   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      11.592   3.613   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0      12.926   4.383   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       8.925  -2.547   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       6.258  -1.007   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0       6.258  -2.547   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3   24                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    4   10                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   22                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   23                                                  
CONECT   21   20   22                                                       
CONECT   22   21   17                                                       
CONECT   23   20                                                            
CONECT   24    2   25                                                       
CONECT   25   24   26   37                                                  
CONECT   26   25   27   36                                                  
CONECT   27   26   28   32                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30   34                                                  
CONECT   30   29   31   33                                                  
CONECT   31   30   32                                                       
CONECT   32   31   27                                                       
CONECT   33   30                                                            
CONECT   34   29   35                                                       
CONECT   35   34                                                            
CONECT   36   26                                                            
CONECT   37   25   38                                                       
CONECT   38   37                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   82    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₃₀N₂O₇

Average Mass

518.5660 Da

Monoisotopic Mass

518.20530 Da

IUPAC Name

(2E)-N-[2-(5-{[(1R,2S)-1,3-dihydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-2-yl]oxy}-1H-indol-3-yl)ethyl]-3-(4-hydroxyphenyl)prop-2-enamide

Traditional Name

(2E)-N-[2-(5-{[(1R,2S)-1,3-dihydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-2-yl]oxy}-1H-indol-3-yl)ethyl]-3-(4-hydroxyphenyl)prop-2-enamide

CAS Registry Number

Not Available

SMILES

COC1=C(O)C=CC(=C1)[C@@H](O)[C@H](CO)OC1=CC=C2NC=C(CCNC(=O)\C=C\C3=CC=C(O)C=C3)C2=C1

InChI Identifier

InChI=1S/C29H30N2O7/c1-37-26-14-19(5-10-25(26)34)29(36)27(17-32)38-22-8-9-24-23(15-22)20(16-31-24)12-13-30-28(35)11-4-18-2-6-21(33)7-3-18/h2-11,14-16,27,29,31-34,36H,12-13,17H2,1H3,(H,30,35)/b11-4+/t27-,29+/m0/s1

InChI Key

LMWMSKRQOYZVFO-SWBAOWADSA-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 lignans, neolignans and related compounds. These are plant products of low molecular weight formed primarily from oxidative coupling of two p-propylphenol moieties. They can also be described as micromolecules with two phenylpropanoid units coupled together. They can be attached in various manners, like C5-C5', C8-C8'. Most known natural lignans are oxidized at C9 and C9´ and, based upon the way in which oxygen is incorporated into the skeleton and on the cyclization patterns, a wide range of lignans of very different structural types can be formed.

Kingdom

Organic compounds

Super Class

Lignans, neolignans and related compounds

Class

Not Available

Sub Class

Not Available

Direct Parent

Lignans, neolignans and related compounds

Alternative Parents

Substituents

Neolignan skeleton
Cinnamic acid amide
Cinnamic acid or derivatives
Coumaric acid or derivatives
Hydroxycinnamic acid or derivatives
Methoxyphenol
3-alkylindole
Indole
Indole or derivatives
Anisole
Phenoxy compound
Methoxybenzene
Phenol ether
Styrene
Alkyl aryl ether
1-hydroxy-2-unsubstituted benzenoid
Phenol
Substituted pyrrole
Monocyclic benzene moiety
Benzenoid
Pyrrole
Heteroaromatic compound
Secondary carboxylic acid amide
Secondary alcohol
Carboxamide group
Carboxylic acid derivative
Ether
Organoheterocyclic compound
Azacycle
Organic oxide
Organic oxygen compound
Alcohol
Primary alcohol
Organonitrogen compound
Carbonyl group
Organooxygen compound
Organic nitrogen compound
Hydrocarbon derivative
Aromatic alcohol
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	3.22	ALOGPS
logP	3.21	ChemAxon
logS	-5.1	ALOGPS
pKa (Strongest Acidic)	9.3	ChemAxon
pKa (Strongest Basic)	-0.39	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	144.27 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	143.66 m³·mol⁻¹	ChemAxon
Polarizability	54.54 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00026741

Chemspider ID

4477029

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5318459

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Jenett-Siems K, Weigl R, Kaloga M, Schulz J, Eich E: Ipobscurines C and D: macrolactam-type indole alkaloids from the seeds of Ipomoea obscura. Phytochemistry. 2003 Apr;62(8):1257-63. doi: 10.1016/s0031-9422(02)00756-2. [PubMed:12648548 ]

Showing NP-Card for (-)-Ipobscurine B (NP0068706)

MOL for NP0068706 ((-)-Ipobscurine B)

3D MOL for NP0068706 ((-)-Ipobscurine B)

3D SDF for NP0068706 ((-)-Ipobscurine B)

3D-SDF for NP0068706 ((-)-Ipobscurine B)

PDB for NP0068706 ((-)-Ipobscurine B)

3D PDB for NP0068706 ((-)-Ipobscurine B)

SMILES for NP0068706 ((-)-Ipobscurine B)

INCHI for NP0068706 ((-)-Ipobscurine B)

Structure for NP0068706 ((-)-Ipobscurine B)

3D Structure for NP0068706 ((-)-Ipobscurine B)