NP-MRD: Showing NP-Card for Deacetylvindoline (NP0066877)

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Record Information

Version

2.0

Created at

2022-04-28 11:06:37 UTC

Updated at

2022-04-28 11:06:37 UTC

NP-MRD ID

NP0066877

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Deacetylvindoline

Description

Deacetylvindoline is found in Apis cerana and Catharanthus roseus .

Structure

MOL 3D MOL SDF PDB SMILES InChI

 
  Mrv1533006081517302D          
 
 32 36  0  0  1  0            999 V2000
   16.4521   -9.2530    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.1525   -8.8371    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   16.4521  -10.0760    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.0217   -9.2530    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8570   -8.5830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8896   -9.2495    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.1561   -8.0463    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.1748  -10.4954    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.7373  -10.4954    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.0217  -10.0760    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3069   -8.8443    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3093   -7.9040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8933  -10.0796    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   18.6123   -8.8264    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5908   -9.6537    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8825   -7.5768    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5720  -11.1959    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.5567  -11.5466    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.3974  -11.4741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3069  -10.4990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5986   -9.2530    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5908  -10.4661    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.6158   -7.9882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.2984   -9.2459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.3878  -11.1996    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.1640  -11.8964    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.5986  -10.0760    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.7965  -11.9115    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8909  -10.4846    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.1826  -10.0725    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.1525   -9.6537    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.4486  -10.8927    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
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 21 27  1  0  0  0  0
  2 31  1  6  0  0  0
  3 32  1  1  0  0  0
M  END

     RDKit          3D

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M  END

 
  Mrv1533006081517302D          
 
 32 36  0  0  1  0            999 V2000
   16.4521   -9.2530    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.1525   -8.8371    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   16.4521  -10.0760    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.0217   -9.2530    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8570   -8.5830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8896   -9.2495    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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   17.1748  -10.4954    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0066877

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]12N3CC[C@@]11C4=C(C=C(OC)C=C4)N(C)[C@@]1([H])[C@](O)([C@H](O)[C@]2(CC)C=CC3)C(=O)OC

> <INCHI_IDENTIFIER>
InChI=1S/C23H30N2O5/c1-5-21-9-6-11-25-12-10-22(17(21)25)15-8-7-14(29-3)13-16(15)24(2)18(22)23(28,19(21)26)20(27)30-4/h6-9,13,17-19,26,28H,5,10-12H2,1-4H3/t17-,18+,19+,21+,22+,23-/m0/s1

> <INCHI_KEY>
ZDKMPOJNYNVYLA-PEGGBQQISA-N

> <FORMULA>
C23H30N2O5

> <MOLECULAR_WEIGHT>
414.502

> <EXACT_MASS>
414.215472074

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
60

> <JCHEM_AVERAGE_POLARIZABILITY>
43.52605236535252

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl (1R,9R,10S,11R,12R,19R)-12-ethyl-10,11-dihydroxy-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>
1.83

> <JCHEM_LOGP>
1.4415120440000004

> <ALOGPS_LOGS>
-2.21

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
13.973693692888471

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.898378697120217

> <JCHEM_PKA_STRONGEST_BASIC>
8.457105661742656

> <JCHEM_POLAR_SURFACE_AREA>
82.47000000000001

> <JCHEM_REFRACTIVITY>
113.1466

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.57e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl (1R,9R,10S,11R,12R,19R)-12-ethyl-10,11-dihydroxy-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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-JUN-15         0                                  
HETATM    1  C   UNK     0      30.711 -17.272   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      32.018 -16.496   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      30.711 -18.809   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      28.041 -17.272   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      29.600 -16.022   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      33.394 -17.266   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      32.025 -15.020   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      32.060 -19.591   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      29.376 -19.591   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      28.041 -18.809   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      26.706 -16.509   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      30.444 -14.754   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      33.401 -18.815   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      34.743 -16.476   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      34.703 -18.020   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      33.381 -14.143   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      32.801 -20.899   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      30.906 -21.554   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      28.742 -21.418   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      26.706 -19.598   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      25.384 -17.272   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      34.703 -19.537   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      34.750 -14.911   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      36.024 -17.259   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      34.324 -20.906   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      32.039 -22.207   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      25.384 -18.809   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      35.087 -22.235   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      24.063 -19.571   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      22.741 -18.802   0.000  0.00  0.00           C+0
HETATM   31  H   UNK     0      32.018 -18.020   0.000  0.00  0.00           H+0
HETATM   32  H   UNK     0      30.704 -20.333   0.000  0.00  0.00           H+0
CONECT    1    2    3    4    5                                             
CONECT    2    1    6    7   31                                             
CONECT    3    1    8    9   32                                             
CONECT    4    1   10   11                                                  
CONECT    5    1   12                                                       
CONECT    6    2   13   14   15                                             
CONECT    7    2   16   12                                                  
CONECT    8    3   17   18   13                                             
CONECT    9    3   19   10                                                  
CONECT   10    4   20    9                                                  
CONECT   11    4   21                                                       
CONECT   12    5    7                                                       
CONECT   13    6   22    8                                                  
CONECT   14    6   23                                                       
CONECT   15    6   24                                                       
CONECT   16    7   23                                                       
CONECT   17    8   25   26                                                  
CONECT   18    8                                                            
CONECT   19    9                                                            
CONECT   20   10   27                                                       
CONECT   21   11   27                                                       
CONECT   22   13                                                            
CONECT   23   14   16                                                       
CONECT   24   15                                                            
CONECT   25   17   28                                                       
CONECT   26   17                                                            
CONECT   27   20   29   21                                                  
CONECT   28   25                                                            
CONECT   29   27   30                                                       
CONECT   30   29                                                            
CONECT   31    2                                                            
CONECT   32    3                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   72    0
END

View in JSmol

Synonyms

Value	Source
17-O-Deacetylvindoline	Kegg
Desacetylvindoline	Kegg

Chemical Formula

C₂₃H₃₀N₂O₅

Average Mass

414.5020 Da

Monoisotopic Mass

414.21547 Da

IUPAC Name

methyl (1R,9R,10S,11R,12R,19R)-12-ethyl-10,11-dihydroxy-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

methyl (1R,9R,10S,11R,12R,19R)-12-ethyl-10,11-dihydroxy-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

CAS Registry Number

Not Available

SMILES

[H][C@@]12N3CC[C@@]11C4=C(C=C(OC)C=C4)N(C)[C@@]1([H])[C@](O)([C@H](O)[C@]2(CC)C=CC3)C(=O)OC

InChI Identifier

InChI=1S/C23H30N2O5/c1-5-21-9-6-11-25-12-10-22(17(21)25)15-8-7-14(29-3)13-16(15)24(2)18(22)23(28,19(21)26)20(27)30-4/h6-9,13,17-19,26,28H,5,10-12H2,1-4H3/t17-,18+,19+,21+,22+,23-/m0/s1

InChI Key

ZDKMPOJNYNVYLA-PEGGBQQISA-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 roseus	Plant	KNApSAcK

Chemical Taxonomy

Description

This compound 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
Dialkylarylamine
Anisole
Aralkylamine
Tetrahydropyridine
Beta-hydroxy acid
Alkyl aryl ether
Benzenoid
N-alkylpyrrolidine
Hydroxy acid
Methyl ester
Tertiary alcohol
Pyrrolidine
Cyclic alcohol
Tertiary aliphatic amine
Tertiary amine
Secondary alcohol
Carboxylic acid ester
Amino acid or derivatives
1,2-diol
Azacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Ether
Carboxylic acid derivative
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Amine
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Indole alkaloids (C01091 )

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	1.83	ALOGPS
logP	1.44	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	10.9	ChemAxon
pKa (Strongest Basic)	8.46	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	82.47 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	113.15 m³·mol⁻¹	ChemAxon
Polarizability	43.53 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	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

228679

KEGG Compound ID

C01091

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Deacetylvindoline

METLIN ID

Not Available

PubChem Compound

260534

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Deacetylvindoline (NP0066877)

MOL for NP0066877 (Deacetylvindoline)

3D MOL for NP0066877 (Deacetylvindoline)

3D SDF for NP0066877 (Deacetylvindoline)

3D-SDF for NP0066877 (Deacetylvindoline)

PDB for NP0066877 (Deacetylvindoline)

3D PDB for NP0066877 (Deacetylvindoline)

SMILES for NP0066877 (Deacetylvindoline)

INCHI for NP0066877 (Deacetylvindoline)

Structure for NP0066877 (Deacetylvindoline)

3D Structure for NP0066877 (Deacetylvindoline)