NP-MRD: Showing NP-Card for 19-ethenyl-18-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-2(10),4,6,8,15-pentaen-14-one (NP0315792)

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Record Information

Version

2.0

Created at

2022-09-11 14:36:17 UTC

Updated at

2022-09-11 14:36:17 UTC

NP-MRD ID

NP0315792

Secondary Accession Numbers

None

Natural Product Identification

Common Name

19-ethenyl-18-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-2(10),4,6,8,15-pentaen-14-one

Description

Vincosamide belongs to the class of organic compounds known as beta carbolines. Beta carbolines are compounds containing a 9H-pyrido[3,4-b]indole moiety. 19-ethenyl-18-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-2(10),4,6,8,15-pentaen-14-one is found in Camptotheca acuminata, Catharanthus roseus, Cephalanthus occidentalis, Cinnamodendron axillare, Koompassia malaccensis, Mostuea brunonis, Nauclea orientalis, Ophiorrhiza liukiuensis, Ophiorrhiza pumila, Psychotria bahiensis, Rauvolfia serpentina, Sarcocephalus latifolius, Sinoadina racemosa and Uncaria rhynchophylla. Vincosamide is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004161515152D          

 36 41  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1533004161515152D          

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 20 25  1  0  0  0  0
 14 26  1  0  0  0  0
 10 26  1  0  0  0  0
 26 27  2  0  0  0  0
 11 28  1  0  0  0  0
  7 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
  5 31  1  0  0  0  0
 31 32  1  0  0  0  0
 31 33  1  0  0  0  0
 33 34  1  0  0  0  0
 33 35  1  0  0  0  0
  3 35  1  0  0  0  0
 35 36  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0315792

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1OC(OC2OC=C3C(CC4N(CCC5=C4NC4=CC=CC=C54)C3=O)C2C=C)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C26H30N2O8/c1-2-12-15-9-18-20-14(13-5-3-4-6-17(13)27-20)7-8-28(18)24(33)16(15)11-34-25(12)36-26-23(32)22(31)21(30)19(10-29)35-26/h2-6,11-12,15,18-19,21-23,25-27,29-32H,1,7-10H2

> <INCHI_KEY>
LBRPLJCNRZUXLS-UHFFFAOYSA-N

> <FORMULA>
C26H30N2O8

> <MOLECULAR_WEIGHT>
498.532

> <EXACT_MASS>
498.200215934

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
51.992802536654075

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
19-ethenyl-18-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-2(10),4,6,8,15-pentaen-14-one

> <ALOGPS_LOGP>
0.55

> <JCHEM_LOGP>
-0.025120791666666198

> <ALOGPS_LOGS>
-2.61

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.195573720660832

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.20665776487562

> <JCHEM_PKA_STRONGEST_BASIC>
0.04894351832158861

> <JCHEM_POLAR_SURFACE_AREA>
144.71

> <JCHEM_REFRACTIVITY>
126.85090000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.22e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
19-ethenyl-18-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-2(10),4,6,8,15-pentaen-14-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         0                                  
HETATM    1  O   UNK     0      19.128  -3.037   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      17.615  -3.323   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      16.610  -2.157   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      15.097  -2.444   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      14.092  -1.277   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      12.579  -1.564   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      11.574  -0.397   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      12.082   1.057   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      11.077   2.224   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.564   1.937   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.056   0.483   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.543   0.196   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.538   1.363   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       7.046   2.817   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       6.041   3.984   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.527   3.697   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.019   2.243   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.025   1.076   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0       4.225  -0.240   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0       2.726   0.113   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.461  -0.765   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.068  -0.108   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.059   1.427   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       1.206   2.305   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.599   1.648   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       8.559   3.104   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       9.067   4.557   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      10.061  -0.684   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       9.553  -2.138   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      10.558  -3.304   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      14.600   0.177   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      13.595   1.344   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      16.113   0.464   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      16.621   1.918   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0      17.118  -0.703   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      18.631  -0.416   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   35                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   31                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   28                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   26                                                  
CONECT   11   10   12   28                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   18                                                  
CONECT   14   13   15   26                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   25                                                  
CONECT   18   17   13   19                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   25                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   17   20                                                  
CONECT   26   14   10   27                                                  
CONECT   27   26                                                            
CONECT   28   11    7   29                                                  
CONECT   29   28   30                                                       
CONECT   30   29                                                            
CONECT   31    5   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33    3   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

C₂₆H₃₀N₂O₈

Average Mass

498.5320 Da

Monoisotopic Mass

498.20022 Da

IUPAC Name

19-ethenyl-18-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-2(10),4,6,8,15-pentaen-14-one

Traditional Name

19-ethenyl-18-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-2(10),4,6,8,15-pentaen-14-one

CAS Registry Number

Not Available

SMILES

OCC1OC(OC2OC=C3C(CC4N(CCC5=C4NC4=CC=CC=C54)C3=O)C2C=C)C(O)C(O)C1O

InChI Identifier

InChI=1S/C26H30N2O8/c1-2-12-15-9-18-20-14(13-5-3-4-6-17(13)27-20)7-8-28(18)24(33)16(15)11-34-25(12)36-26-23(32)22(31)21(30)19(10-29)35-26/h2-6,11-12,15,18-19,21-23,25-27,29-32H,1,7-10H2

InChI Key

LBRPLJCNRZUXLS-UHFFFAOYSA-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

Species Name	Source	Reference
Camptotheca acuminata	LOTUS Database	35616633
Catharanthus roseus	LOTUS Database	35616633
Cephalanthus occidentalis	LOTUS Database	35616633
Cinnamodendron axillare	LOTUS Database	35616633
Koompassia malaccensis	LOTUS Database	35616633
Mostuea brunonis	LOTUS Database	35616633
Nauclea orientalis	LOTUS Database	35616633
Ophiorrhiza liukiuensis	LOTUS Database	35616633
Ophiorrhiza pumila	LOTUS Database	35616633
Psychotria bahiensis	LOTUS Database	35616633
Rauvolfia serpentina	LOTUS Database	35616633
Sarcocephalus latifolius	LOTUS Database	35616633
Sinoadina racemosa	LOTUS Database	35616633
Uncaria rhynchophylla	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as beta carbolines. Beta carbolines are compounds containing a 9H-pyrido[3,4-b]indole moiety.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Pyridoindoles

Direct Parent

Beta carbolines

Alternative Parents

Substituents

Beta-carboline
Hexose monosaccharide
Glycosyl compound
O-glycosyl compound
3-alkylindole
Indole
Delta-lactam
Piperidinone
Monosaccharide
Oxane
Piperidine
Benzenoid
Vinylogous ester
Pyrrole
Tertiary carboxylic acid amide
Heteroaromatic compound
Secondary alcohol
Carboxamide group
Lactam
Polyol
Acetal
Azacycle
Carboxylic acid derivative
Oxacycle
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Carbonyl group
Primary alcohol
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	0.55	ALOGPS
logP	-0.025	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	12.21	ChemAxon
pKa (Strongest Basic)	0.049	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	144.71 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	126.85 m³·mol⁻¹	ChemAxon
Polarizability	51.99 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

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

5015264

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 19-ethenyl-18-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-2(10),4,6,8,15-pentaen-14-one (NP0315792)

MOL for NP0315792 (19-ethenyl-18-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-2(10),4,6,8,15-pentaen-14-one)

3D MOL for NP0315792 (19-ethenyl-18-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-2(10),4,6,8,15-pentaen-14-one)

3D SDF for NP0315792 (19-ethenyl-18-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-2(10),4,6,8,15-pentaen-14-one)

3D-SDF for NP0315792 (19-ethenyl-18-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-2(10),4,6,8,15-pentaen-14-one)

PDB for NP0315792 (19-ethenyl-18-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-2(10),4,6,8,15-pentaen-14-one)

3D PDB for NP0315792 (19-ethenyl-18-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-2(10),4,6,8,15-pentaen-14-one)

SMILES for NP0315792 (19-ethenyl-18-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-2(10),4,6,8,15-pentaen-14-one)

INCHI for NP0315792 (19-ethenyl-18-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-2(10),4,6,8,15-pentaen-14-one)

Structure for NP0315792 (19-ethenyl-18-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-2(10),4,6,8,15-pentaen-14-one)

3D Structure for NP0315792 (19-ethenyl-18-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-17-oxa-3,13-diazapentacyclo[11.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]henicosa-2(10),4,6,8,15-pentaen-14-one)