NP-MRD: Showing NP-Card for 3beta-Isodihydrocadambine 4-oxide (NP0138774)

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Record Information

Version

2.0

Created at

2022-06-29 18:35:34 UTC

Updated at

2022-06-29 18:35:34 UTC

NP-MRD ID

NP0138774

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3beta-Isodihydrocadambine 4-oxide

Description

3Beta-Isodihydrocadambine 4-oxide belongs to the class of organic compounds known as yohimbine alkaloids. These are alkaloids containing the pentacyclic yohimban skeleton. The Yohimbinoid alkaloids contain a carbocyclic ring E arising through C-17 to C-18 bond formation in a corynantheine precursor. It was first documented in 1993 (PMID: 35862567). Based on a literature review a significant number of articles have been published on 3Beta-Isodihydrocadambine 4-oxide (PMID: 35863886) (PMID: 35863885) (PMID: 35863884) (PMID: 35863883).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652306292220352D          

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    4.0348    2.9027    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3069    2.1239    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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  9 18  1  0  0  0  0
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  8 29  1  1  0  0  0
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 33 38  1  6  0  0  0
 32 39  1  1  0  0  0
 31 40  1  6  0  0  0
M  CHG  2  17   1  21  -1
M  END

     RDKit          3D

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 31 66  1  0
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 28 63  1  0
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M  CHG  2  36   1  37  -1
M  END


  Mrv1652306292220352D          

 40 45  0  0  1  0            999 V2000
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    8.3714   -3.0102    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1820   -3.1640    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.4483   -1.7601    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9040   -0.2024    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2829    0.1050    0.0000 O   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  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  9  8  1  6  0  0  0
  9 10  1  0  0  0  0
 10  5  1  6  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  6  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 12 17  1  0  0  0  0
 17 18  1  0  0  0  0
  9 18  1  0  0  0  0
 18 19  1  6  0  0  0
 19 20  1  0  0  0  0
 17 21  1  0  0  0  0
 14 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 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
 22 27  1  0  0  0  0
 27 28  1  0  0  0  0
 13 28  1  0  0  0  0
  8 29  1  1  0  0  0
 30 29  1  1  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 30 35  1  0  0  0  0
 34 36  1  1  0  0  0
 36 37  1  0  0  0  0
 33 38  1  6  0  0  0
 32 39  1  1  0  0  0
 31 40  1  6  0  0  0
M  CHG  2  17   1  21  -1
M  END
> <DATABASE_ID>
NP0138774

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C1=CO[C@@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H]2[C@@H]1C[C@H]1C3=C(CC[N+]1([O-])[C@H]2CO)C1=CC=CC=C1N3

> <INCHI_IDENTIFIER>
InChI=1S/C27H34N2O11/c1-37-25(35)15-11-38-26(40-27-24(34)23(33)22(32)19(10-31)39-27)20-14(15)8-17-21-13(6-7-29(17,36)18(20)9-30)12-4-2-3-5-16(12)28-21/h2-5,11,14,17-20,22-24,26-28,30-34H,6-10H2,1H3/t14-,17+,18+,19-,20+,22-,23+,24-,26+,27+,29?/m1/s1

> <INCHI_KEY>
NVUHVENKCFNJQW-GDPYHQKMSA-N

> <FORMULA>
C27H34N2O11

> <MOLECULAR_WEIGHT>
562.572

> <EXACT_MASS>
562.216259923

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
56.51343515601657

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,14R,15S,16S,20S)-14-(hydroxymethyl)-19-(methoxycarbonyl)-16-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0^{2,10}.0^{4,9}.0^{15,20}]henicosa-2(10),4,6,8,18-pentaen-13-ium-13-olate

> <ALOGPS_LOGP>
0.01

> <JCHEM_LOGP>
-1.6484466553333328

> <ALOGPS_LOGS>
-2.73

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.019941983212547

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.18154290040337

> <JCHEM_PKA_STRONGEST_BASIC>
2.640545411399644

> <JCHEM_POLAR_SURFACE_AREA>
193.98999999999998

> <JCHEM_REFRACTIVITY>
136.66140000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.05e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,14R,15S,16S,20S)-14-(hydroxymethyl)-19-(methoxycarbonyl)-16-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0^{2,10}.0^{4,9}.0^{15,20}]henicosa-2(10),4,6,8,18-pentaen-13-ium-13-olate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-JUN-22         0                                  
HETATM    1  C   UNK     0       7.532   5.418   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       8.040   3.965   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       9.553   3.678   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      10.558   4.844   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      10.061   2.224   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      11.574   1.937   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      12.082   0.483   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      11.077  -0.684   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.564  -0.397   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.056   1.057   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.543   1.344   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.538   0.177   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.025   0.464   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.019  -0.703   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.527  -2.157   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.041  -2.444   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       7.046  -1.277   0.000  0.00  0.00           N+1
HETATM   18  C   UNK     0       8.559  -1.564   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       9.067  -3.017   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      10.580  -3.304   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       7.554  -2.731   0.000  0.00  0.00           O-1
HETATM   22  C   UNK     0       2.599  -0.108   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.206  -0.765   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -0.059   0.113   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.068   1.648   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       1.461   2.305   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       2.726   1.427   0.000  0.00  0.00           C+0
HETATM   28  N   UNK     0       4.225   1.780   0.000  0.00  0.00           N+0
HETATM   29  O   UNK     0      11.585  -2.138   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      13.098  -2.425   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      14.103  -1.258   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      15.616  -1.545   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      16.124  -2.998   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      15.119  -4.165   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      13.606  -3.878   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      15.627  -5.619   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      17.140  -5.906   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0      17.637  -3.285   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0      16.621  -0.378   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0      13.595   0.196   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   29                                                  
CONECT    9    8   10   18                                                  
CONECT   10    9    5   11                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   17                                                  
CONECT   13   12   14   28                                                  
CONECT   14   13   15   22                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   12   18   21                                             
CONECT   18   17    9   19                                                  
CONECT   19   18   20                                                       
CONECT   20   19                                                            
CONECT   21   17                                                            
CONECT   22   14   23   27                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   22   28                                                  
CONECT   28   27   13                                                       
CONECT   29    8   30                                                       
CONECT   30   29   31   35                                                  
CONECT   31   30   32   40                                                  
CONECT   32   31   33   39                                                  
CONECT   33   32   34   38                                                  
CONECT   34   33   35   36                                                  
CONECT   35   34   30                                                       
CONECT   36   34   37                                                       
CONECT   37   36                                                            
CONECT   38   33                                                            
CONECT   39   32                                                            
CONECT   40   31                                                            
MASTER        0    0    0    0    0    0    0    0   40    0   90    0
END

View in JSmol

Synonyms

Value	Source
3b-Isodihydrocadambine 4-oxide	Generator
3Β-isodihydrocadambine 4-oxide	Generator

Chemical Formula

C₂₇H₃₄N₂O₁₁

Average Mass

562.5720 Da

Monoisotopic Mass

562.21626 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

1092371-18-0

SMILES

COC(=O)C1=CO[C@@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H]2[C@@H]1C[C@H]1C3=C(CC[N+]1([O-])[C@H]2CO)C1=CC=CC=C1N3

InChI Identifier

InChI=1S/C27H34N2O11/c1-37-25(35)15-11-38-26(40-27-24(34)23(33)22(32)19(10-31)39-27)20-14(15)8-17-21-13(6-7-29(17,36)18(20)9-30)12-4-2-3-5-16(12)28-21/h2-5,11,14,17-20,22-24,26-28,30-34H,6-10H2,1H3/t14-,17+,18+,19-,20+,22-,23+,24-,26+,27+,29?/m1/s1

InChI Key

NVUHVENKCFNJQW-GDPYHQKMSA-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 yohimbine alkaloids. These are alkaloids containing the pentacyclic yohimban skeleton. The Yohimbinoid alkaloids contain a carbocyclic ring E arising through C-17 to C-18 bond formation in a corynantheine precursor.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Yohimbine alkaloids

Sub Class

Not Available

Direct Parent

Yohimbine alkaloids

Alternative Parents

Substituents

18-oxayohimban
Yohimbine alkaloid
Beta-carboline
Pyridoindole
Hexose monosaccharide
Glycosyl compound
O-glycosyl compound
3-alkylindole
Indole
Indole or derivatives
Monosaccharide
Oxane
Piperidine
Benzenoid
Trialkyl amine oxide
Heteroaromatic compound
Pyrrole
Vinylogous ester
Methyl ester
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Secondary alcohol
Carboxylic acid ester
Carboxylic acid derivative
Trisubstituted n-oxide
N-oxide
Acetal
Monocarboxylic acid or derivatives
Oxacycle
Azacycle
Polyol
Organoheterocyclic compound
Organic zwitterion
Organic nitrogen compound
Organic oxide
Organopnictogen compound
Hydrocarbon derivative
Alcohol
Organonitrogen compound
Organooxygen compound
Organic salt
Carbonyl group
Primary alcohol
Organic oxygen 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

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

102004692

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Morales Corado JA, Lee CU, Enns GM: Carnitine-Acylcarnitine Translocase Deficiency. 1993. [PubMed:35862567 ]
Kaorop W, Maneechote C, Kumfu S, Chattipakorn SC, Chattipakorn N: Mitochondrial-derived peptides as a novel intervention for obesity and cardiac diseases: bench evidence for potential bedside application. J Clin Pathol. 2022 Jul 21. pii: jcp-2022-208321. doi: 10.1136/jcp-2022-208321. [PubMed:35863886 ]
Zheng T, Zheng S, Wang K, Quan H, Bai Q, Li S, Qi R, Zhao Y, Cui X, Gao X: Automatic CD30 scoring method for whole slide images of primary cutaneous CD30(+) lymphoproliferative diseases. J Clin Pathol. 2022 Jul 21. pii: jcp-2022-208344. doi: 10.1136/jcp-2022-208344. [PubMed:35863885 ]
Humphreys H, Burke L, O'Connell K, Keogan M: Answering Ireland's call: pathology during the COVID-19 pandemic. J Clin Pathol. 2022 Nov;75(11):721-723. doi: 10.1136/jclinpath-2022-208323. Epub 2022 Jul 21. [PubMed:35863884 ]
Albin C, Berkowitz AL: Engaging teaching strategies in neurology: the flipped classroom and simulation training. Pract Neurol. 2022 Jul 21. pii: pn-2022-003371. doi: 10.1136/pn-2022-003371. [PubMed:35863883 ]

Showing NP-Card for 3beta-Isodihydrocadambine 4-oxide (NP0138774)

MOL for NP0138774 (3beta-Isodihydrocadambine 4-oxide)

3D MOL for NP0138774 (3beta-Isodihydrocadambine 4-oxide)

3D SDF for NP0138774 (3beta-Isodihydrocadambine 4-oxide)

3D-SDF for NP0138774 (3beta-Isodihydrocadambine 4-oxide)

PDB for NP0138774 (3beta-Isodihydrocadambine 4-oxide)

3D PDB for NP0138774 (3beta-Isodihydrocadambine 4-oxide)

SMILES for NP0138774 (3beta-Isodihydrocadambine 4-oxide)

INCHI for NP0138774 (3beta-Isodihydrocadambine 4-oxide)

Structure for NP0138774 (3beta-Isodihydrocadambine 4-oxide)

3D Structure for NP0138774 (3beta-Isodihydrocadambine 4-oxide)