NP-MRD: Showing NP-Card for (-)-Vindoline (NP0050920)

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Record Information

Version

2.0

Created at

2022-04-27 22:23:11 UTC

Updated at

2022-04-27 22:23:12 UTC

NP-MRD ID

NP0050920

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Vindoline

Description

Vindoline belongs to the class of organic compounds known as plumeran-type alkaloids. These are alkaloids with a structure based on the plumeran skeleton. Plumeran is a pentacyclic compound that consists of a pyrrolidine ring shed to the quinoline moiety of pyrido[3,2-c]carbazole ring system. Vindoline is a very strong basic compound (based on its pKa). Vindoline is a chemical precursor to vinblastine. (-)-Vindoline is found in Apis cerana, Catharanthus longifolius, Catharanthus ovalis, Catharanthus pusillus, Catharanthus roseus , Melodinus fusiformis and Vinca pusilla . Vindoline is a potentially toxic compound.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 08291400582D          

 36 40  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv0541 08291400582D          

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M  END
> <DATABASE_ID>
NP0050920

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]12N(C)C3=C(C=CC(OC)=C3)[C@@]11CCN3CC=C[C@](CC)([C@@]13[H])[C@@]([H])(OC(C)=O)[C@]2(O)C(=O)OC

> <INCHI_IDENTIFIER>
InChI=1S/C25H32N2O6/c1-6-23-10-7-12-27-13-11-24(19(23)27)17-9-8-16(31-4)14-18(17)26(3)20(24)25(30,22(29)32-5)21(23)33-15(2)28/h7-10,14,19-21,30H,6,11-13H2,1-5H3/t19-,20+,21+,23+,24+,25-/m0/s1

> <INCHI_KEY>
CXBGOBGJHGGWIE-ACSXSLCXSA-N

> <FORMULA>
C25H32N2O6

> <MOLECULAR_WEIGHT>
456.5314

> <EXACT_MASS>
456.226036766

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
47.71757479788246

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl (1R,9R,10S,11R,12R,19R)-11-(acetyloxy)-12-ethyl-10-hydroxy-5-methoxy-8-methyl-8,16-diazapentacyclo[10.6.1.0¹,⁹.0²,⁷.0¹⁶,¹⁹]nonadeca-2(7),3,5,13-tetraene-10-carboxylate

> <ALOGPS_LOGP>
2.53

> <JCHEM_LOGP>
1.8826374543333317

> <ALOGPS_LOGS>
-3.07

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.868158007477678

> <JCHEM_PKA_STRONGEST_BASIC>
8.673438058558657

> <JCHEM_POLAR_SURFACE_AREA>
88.54000000000002

> <JCHEM_REFRACTIVITY>
122.29809999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.92e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
vindolin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-AUG-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-AUG-14         0                                  
HETATM    1  C   UNK     0      -2.392  -3.481   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.664  -8.043   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.341  -5.772   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.106   0.748   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.308  -7.400   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.953  -4.031   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.438  -0.990   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.132  -0.052   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.645  -0.452   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.196  -2.510   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.844  -1.443   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.243  -0.019   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.004  -0.152   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.825  -2.628   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.468  -7.073   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.222  -1.140   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.248  -1.940   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.338  -3.028   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.438  -2.090   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.119  -4.162   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.485  -4.582   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.851  -6.361   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.243  -3.061   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.877  -2.641   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       1.923  -5.132   0.000  0.00  0.00           C+0
HETATM   26  N   UNK     0       4.640  -4.401   0.000  0.00  0.00           N+0
HETATM   27  N   UNK     0       1.196  -0.570   0.000  0.00  0.00           N+0
HETATM   28  O   UNK     0       0.970  -7.623   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       2.251  -7.779   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       1.423  -6.589   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       8.709  -0.740   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       4.380  -6.172   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      -0.711  -5.552   0.000  0.00  0.00           O+0
HETATM   34  H   UNK     0       0.000  -1.540   0.000  0.00  0.00           H+0
HETATM   35  H   UNK     0       3.519  -5.649   0.000  0.00  0.00           H+0
HETATM   36  H   UNK     0       1.681  -3.611   0.000  0.00  0.00           H+0
CONECT    1    6                                                            
CONECT    2   15                                                            
CONECT    3   26                                                            
CONECT    4   31                                                            
CONECT    5   32                                                            
CONECT    6    1   23                                                       
CONECT    7   10   12                                                       
CONECT    8    9   16                                                       
CONECT    9    8   17                                                       
CONECT   10    7   23                                                       
CONECT   11   13   24                                                       
CONECT   12    7   27                                                       
CONECT   13   11   27                                                       
CONECT   14   16   18                                                       
CONECT   15    2   28   33                                                  
CONECT   16    8   14   31                                                  
CONECT   17    9   18   24                                                  
CONECT   18   14   17   26                                                  
CONECT   19   23   24   27   34                                             
CONECT   20   24   25   26   35                                             
CONECT   21   23   25   33   36                                             
CONECT   22   25   29   32                                                  
CONECT   23    6   10   19   21                                             
CONECT   24   11   17   19   20                                             
CONECT   25   20   21   22   30                                             
CONECT   26    3   18   20                                                  
CONECT   27   12   13   19                                                  
CONECT   28   15                                                            
CONECT   29   22                                                            
CONECT   30   25                                                            
CONECT   31    4   16                                                       
CONECT   32    5   22                                                       
CONECT   33   15   21                                                       
CONECT   34   19                                                            
CONECT   35   20                                                            
CONECT   36   21                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   80    0
END

View in JSmol

Synonyms

Value	Source
Vindoline, citrate, (2beta,3beta,4beta,5alpha,12beta,19alpha)-isomer	MeSH
Vindoline, monohydrochloride, (2beta,3beta,4beta,5alpha,12beta,19alpha)-isomer	MeSH

Chemical Formula

C₂₅H₃₂N₂O₆

Average Mass

456.5314 Da

Monoisotopic Mass

456.22604 Da

IUPAC Name

methyl (1R,9R,10S,11R,12R,19R)-11-(acetyloxy)-12-ethyl-10-hydroxy-5-methoxy-8-methyl-8,16-diazapentacyclo[10.6.1.0¹,⁹.0²,⁷.0¹⁶,¹⁹]nonadeca-2(7),3,5,13-tetraene-10-carboxylate

Traditional Name

vindolin

CAS Registry Number

Not Available

SMILES

[H][C@@]12N(C)C3=C(C=CC(OC)=C3)[C@@]11CCN3CC=C[C@](CC)([C@@]13[H])[C@@]([H])(OC(C)=O)[C@]2(O)C(=O)OC

InChI Identifier

InChI=1S/C25H32N2O6/c1-6-23-10-7-12-27-13-11-24(19(23)27)17-9-8-16(31-4)14-18(17)26(3)20(24)25(30,22(29)32-5)21(23)33-15(2)28/h7-10,14,19-21,30H,6,11-13H2,1-5H3/t19-,20+,21+,23+,24+,25-/m0/s1

InChI Key

CXBGOBGJHGGWIE-ACSXSLCXSA-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
Apis cerana	LOTUS Database	35616633
Catharanthus longifolius	Plant	KNApSAcK
Catharanthus ovalis	Plant	KNApSAcK
Catharanthus pusillus	Plant	KNApSAcK
Catharanthus roseus	Plant	KNApSAcK
Melodinus fusiformis	Plant	KNApSAcK
Vinca pusilla	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as plumeran-type alkaloids. These are alkaloids with a structure based on the plumeran skeleton. Plumeran is a pentacyclic compound that consists of a pyrrolidine ring shed to the quinoline moiety of pyrido[3,2-c]carbazole ring system.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Plumeran-type alkaloids

Sub Class

Not Available

Direct Parent

Plumeran-type alkaloids

Alternative Parents

Substituents

Plumeran-type alkaloid
Carbazole
Indole or derivatives
Anisole
Tertiary aliphatic/aromatic amine
Dialkylarylamine
Alkyl aryl ether
Aralkylamine
N-alkylpyrrolidine
Benzenoid
Dicarboxylic acid or derivatives
Methyl ester
Cyclic alcohol
Tertiary alcohol
Pyrrolidine
Tertiary aliphatic amine
Tertiary amine
Amino acid or derivatives
Carboxylic acid ester
Carboxylic acid derivative
Azacycle
Organoheterocyclic compound
Ether
Organic nitrogen compound
Hydrocarbon derivative
Alcohol
Carbonyl group
Organic oxide
Organopnictogen compound
Amine
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Indole alkaloids (C01626 )

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	2.53	ALOGPS
logP	1.88	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	10.87	ChemAxon
pKa (Strongest Basic)	8.67	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	88.54 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	122.3 m³·mol⁻¹	ChemAxon
Polarizability	47.72 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

C00024613

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Vindoline

METLIN ID

Not Available

PubChem Compound

260535

PDB ID

Not Available

ChEBI ID

16380

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (-)-Vindoline (NP0050920)

MOL for NP0050920 ((-)-Vindoline)

3D MOL for NP0050920 ((-)-Vindoline)

3D SDF for NP0050920 ((-)-Vindoline)

3D-SDF for NP0050920 ((-)-Vindoline)

PDB for NP0050920 ((-)-Vindoline)

3D PDB for NP0050920 ((-)-Vindoline)

SMILES for NP0050920 ((-)-Vindoline)

INCHI for NP0050920 ((-)-Vindoline)

Structure for NP0050920 ((-)-Vindoline)

3D Structure for NP0050920 ((-)-Vindoline)