NP-MRD: Showing NP-Card for Harringtonine (NP0051364)

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Record Information

Version

2.0

Created at

2022-04-27 22:45:33 UTC

Updated at

2022-04-27 22:45:33 UTC

NP-MRD ID

NP0051364

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Harringtonine

Description

ZINC31394501 belongs to the class of organic compounds known as cephalotaxus alkaloids. These are alkaloids with a structure based on the cephalotaxine skeleton, a tetracyclic 1,3-benzodioxole-containing compound which arises from the skeletal rearrangement of the hydroaromatic component of the Erythrina group. Harringtonine is found in Cephalotaxus fortunei, Cephalotaxus hainensis and Cephalotaxus harringtonia. Based on a literature review very few articles have been published on ZINC31394501.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282200452D          

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M  END

     RDKit          3D

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M  END


  Mrv1652304282200452D          

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  6  7  1  0  0  0  0
  1  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  4 10  1  0  0  0  0
  4 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
  3 13  1  0  0  0  0
 13 14  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 17 15  1  1  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 20 23  1  0  0  0  0
 17 24  1  6  0  0  0
 17 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 26 28  1  0  0  0  0
 28 29  1  0  0  0  0
 12 30  1  0  0  0  0
 30 31  1  0  0  0  0
  2 32  1  0  0  0  0
 32 33  2  0  0  0  0
 33 34  1  0  0  0  0
 34 35  2  0  0  0  0
  1 35  1  0  0  0  0
 34 36  1  0  0  0  0
 36 37  1  0  0  0  0
 37 38  1  0  0  0  0
 33 38  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0051364

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C[C@](O)(CCC(C)(C)O)C(=O)O[C@H]1[C@H]2C3=C(CCN4CCC[C@@]24C=C1OC)C=C1OCOC1=C3

> <INCHI_IDENTIFIER>
InChI=1S/C28H37NO9/c1-26(2,32)8-9-28(33,15-22(30)35-4)25(31)38-24-21(34-3)14-27-7-5-10-29(27)11-6-17-12-19-20(37-16-36-19)13-18(17)23(24)27/h12-14,23-24,32-33H,5-11,15-16H2,1-4H3/t23-,24-,27-,28-/m1/s1

> <INCHI_KEY>
HAVJATCHLFRDHY-NFFAYCCRSA-N

> <FORMULA>
C28H37NO9

> <MOLECULAR_WEIGHT>
531.602

> <EXACT_MASS>
531.246831775

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
75

> <JCHEM_AVERAGE_POLARIZABILITY>
55.80066261599205

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S,6S)-4-methoxy-16,18-dioxa-10-azapentacyclo[11.7.0.0^{2,6}.0^{6,10}.0^{15,19}]icosa-1(13),4,14,19-tetraen-3-yl 1-methyl (3R)-3-hydroxy-3-(3-hydroxy-3-methylbutyl)butanedioate

> <ALOGPS_LOGP>
1.85

> <JCHEM_LOGP>
1.4401020143333347

> <ALOGPS_LOGS>
-3.46

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
15.396972120823754

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.085256848125379

> <JCHEM_PKA_STRONGEST_BASIC>
9.417783498555847

> <JCHEM_POLAR_SURFACE_AREA>
123.99000000000001

> <JCHEM_REFRACTIVITY>
137.4739

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.83e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S,6S)-4-methoxy-16,18-dioxa-10-azapentacyclo[11.7.0.0^{2,6}.0^{6,10}.0^{15,19}]icosa-1(13),4,14,19-tetraen-3-yl 1-methyl (3R)-3-hydroxy-3-(3-hydroxy-3-methylbutyl)butanedioate

> <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       6.496   4.700   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.271   3.177   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.939   2.403   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.504   2.962   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       3.046   4.432   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       3.910   5.707   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.446   5.826   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.506   4.451   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.013   2.992   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.037   2.128   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.529   1.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.362   0.474   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.851   0.865   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       6.044  -0.109   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       5.796  -1.629   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       6.988  -2.604   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       4.355  -2.174   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.900  -3.615   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       6.420  -3.863   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.965  -5.303   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       7.510  -6.743   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       8.405  -4.758   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       5.525  -5.848   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       3.810  -0.734   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       2.915  -2.719   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.667  -4.239   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       1.226  -4.784   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       3.859  -5.214   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       3.611  -6.734   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       2.803  -0.961   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       1.281  -1.195   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       7.478   2.220   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       8.910   2.786   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       9.135   4.310   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       7.928   5.267   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      10.653   4.566   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      11.367   3.201   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      10.289   2.101   0.000  0.00  0.00           O+0
CONECT    1    2    7   35                                                  
CONECT    2    1    3   32                                                  
CONECT    3    2    4   13                                                  
CONECT    4    3    5   10   11                                             
CONECT    5    4    6    8                                                  
CONECT    6    5    7                                                       
CONECT    7    6    1                                                       
CONECT    8    5    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    4                                                       
CONECT   11    4   12                                                       
CONECT   12   11   13   30                                                  
CONECT   13   12    3   14                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   24   25                                             
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   22   23                                             
CONECT   21   20                                                            
CONECT   22   20                                                            
CONECT   23   20                                                            
CONECT   24   17                                                            
CONECT   25   17   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28                                                            
CONECT   30   12   31                                                       
CONECT   31   30                                                            
CONECT   32    2   33                                                       
CONECT   33   32   34   38                                                  
CONECT   34   33   35   36                                                  
CONECT   35   34    1                                                       
CONECT   36   34   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   33                                                       
MASTER        0    0    0    0    0    0    0    0   38    0   84    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₃₇NO₉

Average Mass

531.6020 Da

Monoisotopic Mass

531.24683 Da

IUPAC Name

(2S,3S,6S)-4-methoxy-16,18-dioxa-10-azapentacyclo[11.7.0.0^{2,6}.0^{6,10}.0^{15,19}]icosa-1(13),4,14,19-tetraen-3-yl 1-methyl (3R)-3-hydroxy-3-(3-hydroxy-3-methylbutyl)butanedioate

Traditional Name

(2S,3S,6S)-4-methoxy-16,18-dioxa-10-azapentacyclo[11.7.0.0^{2,6}.0^{6,10}.0^{15,19}]icosa-1(13),4,14,19-tetraen-3-yl 1-methyl (3R)-3-hydroxy-3-(3-hydroxy-3-methylbutyl)butanedioate

CAS Registry Number

Not Available

SMILES

COC(=O)C[C@](O)(CCC(C)(C)O)C(=O)O[C@H]1[C@H]2C3=C(CCN4CCC[C@@]24C=C1OC)C=C1OCOC1=C3

InChI Identifier

InChI=1S/C28H37NO9/c1-26(2,32)8-9-28(33,15-22(30)35-4)25(31)38-24-21(34-3)14-27-7-5-10-29(27)11-6-17-12-19-20(37-16-36-19)13-18(17)23(24)27/h12-14,23-24,32-33H,5-11,15-16H2,1-4H3/t23-,24-,27-,28-/m1/s1

InChI Key

HAVJATCHLFRDHY-NFFAYCCRSA-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
Cephalotaxus fortunei	Plant	KNApSAcK
Cephalotaxus hainensis	Plant	KNApSAcK
Cephalotaxus harringtonia	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cephalotaxus alkaloids. These are alkaloids with a structure based on the cephalotaxine skeleton, a tetracyclic 1,3-benzodioxole-containing compound which arises from the skeletal rearrangement of the hydroaromatic component of the Erythrina group.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Cephalotaxus alkaloids

Sub Class

Not Available

Direct Parent

Cephalotaxus alkaloids

Alternative Parents

Substituents

Cephalotaxine
Cephalotaxus alkaloid skeleton
Benzazepine
Benzodioxole
Aralkylamine
Fatty acid methyl ester
Fatty acid ester
Azepine
Fatty acyl
Benzenoid
N-alkylpyrrolidine
Dicarboxylic acid or derivatives
Methyl ester
Tertiary alcohol
Pyrrolidine
Tertiary aliphatic amine
Tertiary amine
Carboxylic acid ester
Amino acid or derivatives
Oxacycle
Azacycle
Organoheterocyclic compound
Carboxylic acid derivative
Acetal
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Amine
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	1.85	ALOGPS
logP	1.44	ChemAxon
logS	-3.5	ALOGPS
pKa (Strongest Acidic)	12.09	ChemAxon
pKa (Strongest Basic)	9.42	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	123.99 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	137.47 m³·mol⁻¹	ChemAxon
Polarizability	55.8 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	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

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

124389641

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Harringtonine (NP0051364)

MOL for NP0051364 (Harringtonine)

3D MOL for NP0051364 (Harringtonine)

3D SDF for NP0051364 (Harringtonine)

3D-SDF for NP0051364 (Harringtonine)

PDB for NP0051364 (Harringtonine)

3D PDB for NP0051364 (Harringtonine)

SMILES for NP0051364 (Harringtonine)

INCHI for NP0051364 (Harringtonine)

Structure for NP0051364 (Harringtonine)

3D Structure for NP0051364 (Harringtonine)