NP-MRD: Showing NP-Card for Homoharringtonine (NP0137259)

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Record Information

Version

2.0

Created at

2022-05-30 16:46:55 UTC

Updated at

2022-05-30 16:46:55 UTC

NP-MRD ID

NP0137259

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Homoharringtonine

Description

Homoharringtonine, also known as omacetaxine or ceflatonin, 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. Females that are using HHT should avoid to becoming pregnant and also Advise females to avoid nursing while receiving HHT.Omacetaxine is a protein translation inhibitor. In June 2009, results of a long-term open label Phase II study were published, which investigated the use of omacetaxine infusions in CML patients. It interacts with the ribosomal A-site and prevents the correct positioning of amino acid side chains of incoming aminoacyl-tRNAs. Homoharringtonine is a very strong basic compound (based on its pKa). Omacetaxine mepesuccinate (INN, trade names Synribo ), formerly named as homoharringtonine or HHT, is a pharmaceutical drug substance that is indicated for treatment of chronic myeloid leukemia (CML). HHT and related compound esters of cephalotaxine were described first in 1970, and were the subject of intensive research efforts by Chinese investigators to clarify their role as anticancer and antileukemic agents from the 1970s until the present. Omacetaxine acts only on the initial step of protein translation and does not inhibit protein synthesis from mRNAs that have already commenced translation. Patients with solid tumors did not benefit from omacetaxine. After twelve months of treatment, about one third of patients showed a cytogenetic response. Phase I studies including a small number of patients have shown benefit in treating myelodysplastic syndrome (MDS, 25 patients) and acute myelogenous leukaemia (AML, 76 patients). Homoharringtonine is found in Cephalotaxus fortunei and Cephalotaxus harringtonia. HHT is a natural plant alkaloid derived from Cephalotoxus fortune.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 04121512132D          

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M  END

     RDKit          3D

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M  END


  Mrv0541 04121512132D          

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    4.4357   -0.8834    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8711   -1.4850    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0488   -1.4186    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5880   -0.7342    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7630   -0.7418    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5009    0.0404    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0940    0.4380    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8357    0.0527    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3154    0.6929    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7636    1.3856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4666    2.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6515    2.2830    0.0000 C   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  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 11 14  1  0  0  0  0
  6 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  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  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 22 26  2  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 20 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  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
 19 35  1  0  0  0  0
 31 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  2  0  0  0  0
 18 37  1  0  0  0  0
 37 38  1  0  0  0  0
 38 39  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0137259

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)CC(O)(CCCC(C)(C)O)C(=O)OC1C2C3=CC4=C(OCO4)C=C3CCN3CCCC23C=C1OC

> <INCHI_IDENTIFIER>
InChI=1S/C29H39NO9/c1-27(2,33)8-5-10-29(34,16-23(31)36-4)26(32)39-25-22(35-3)15-28-9-6-11-30(28)12-7-18-13-20-21(38-17-37-20)14-19(18)24(25)28/h13-15,24-25,33-34H,5-12,16-17H2,1-4H3

> <INCHI_KEY>
HYFHYPWGAURHIV-UHFFFAOYSA-N

> <FORMULA>
C29H39NO9

> <MOLECULAR_WEIGHT>
545.629

> <EXACT_MASS>
545.26248184

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
78

> <JCHEM_AVERAGE_POLARIZABILITY>
57.9180473966083

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-methoxy-16,18-dioxa-10-azapentacyclo[11.7.0.0²,⁶.0⁶,¹⁰.0¹⁵,¹⁹]icosa-1(20),4,13,15(19)-tetraen-3-yl 1-methyl 3-hydroxy-3-(4-hydroxy-4-methylpentyl)butanedioate

> <ALOGPS_LOGP>
2.09

> <JCHEM_LOGP>
1.8846706793333348

> <ALOGPS_LOGS>
-3.70

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
18.53070408521904

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.090441034596882

> <JCHEM_PKA_STRONGEST_BASIC>
9.417794628939516

> <JCHEM_POLAR_SURFACE_AREA>
123.99000000000002

> <JCHEM_REFRACTIVITY>
142.07489999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.08e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
homoharringtonine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-APR-15         0                                  
HETATM    1  C   UNK     0      13.356   6.384   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      11.835   6.141   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      11.285   4.702   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      12.257   3.507   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       9.765   4.458   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.794   5.653   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       7.822   6.849   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       9.989   6.625   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.745   8.145   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      10.940   9.117   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.697  10.637   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.453  12.158   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.176  10.394   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      12.218  10.881   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       7.599   4.682   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       6.160   5.232   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       7.842   3.162   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       6.647   2.190   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       6.730   0.653   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.059  -0.125   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       9.269   0.828   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      10.699   0.257   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      12.080   0.938   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      13.155  -0.165   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      12.438  -1.528   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      10.920  -1.267   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       9.710  -2.220   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       8.280  -1.649   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       7.226  -2.772   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.691  -2.648   0.000  0.00  0.00           C+0
HETATM   31  N   UNK     0       4.831  -1.371   0.000  0.00  0.00           N+0
HETATM   32  C   UNK     0       3.291  -1.385   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       2.802   0.075   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       3.909   0.818   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       5.293   0.098   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       4.322   1.294   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       5.159   2.586   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0       4.604   4.023   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0       3.083   4.262   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7    8   15                                             
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13   14                                             
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   11                                                            
CONECT   15    6   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   19   37                                                  
CONECT   19   18   20   35                                                  
CONECT   20   19   21   28                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23   26                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   22   27                                                  
CONECT   27   26   28                                                       
CONECT   28   27   20   29                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32   35                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   19   31   36                                             
CONECT   36   35   37                                                       
CONECT   37   36   18   38                                                  
CONECT   38   37   39                                                       
CONECT   39   38                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   86    0
END

View in JSmol

Synonyms

Value	Source
Omacetaxine mepesuccinate	MeSH
Omacetaxine	MeSH
Ceflatonin	MeSH
Cephalotaxine	MeSH
Homoharringtonine (3(R))-isomer	MeSH
Synribo	MeSH
Homoharringtonine, 3H-labeled, (3(R))-isomer	MeSH
4-Methoxy-16,18-dioxa-10-azapentacyclo[11.7.0.0²,⁶.0⁶,¹⁰.0¹⁵,¹⁹]icosa-1(20),4,13,15(19)-tetraen-3-yl 1-methyl 3-hydroxy-3-(4-hydroxy-4-methylpentyl)butanedioic acid	Generator
4-Methoxy-16,18-dioxa-10-azapentacyclo[11.7.0.0,.0,.0,]icosa-1(20),4,13,15(19)-tetraen-3-yl 1-methyl 3-hydroxy-3-(4-hydroxy-4-methylpentyl)butanedioic acid	Generator

Chemical Formula

C₂₉H₃₉NO₉

Average Mass

545.6290 Da

Monoisotopic Mass

545.26248 Da

IUPAC Name

4-methoxy-16,18-dioxa-10-azapentacyclo[11.7.0.0²,⁶.0⁶,¹⁰.0¹⁵,¹⁹]icosa-1(20),4,13,15(19)-tetraen-3-yl 1-methyl 3-hydroxy-3-(4-hydroxy-4-methylpentyl)butanedioate

Traditional Name

homoharringtonine

CAS Registry Number

Not Available

SMILES

COC(=O)CC(O)(CCCC(C)(C)O)C(=O)OC1C2C3=CC4=C(OCO4)C=C3CCN3CCCC23C=C1OC

InChI Identifier

InChI=1S/C29H39NO9/c1-27(2,33)8-5-10-29(34,16-23(31)36-4)26(32)39-25-22(35-3)15-28-9-6-11-30(28)12-7-18-13-20-21(38-17-37-20)14-19(18)24(25)28/h13-15,24-25,33-34H,5-12,16-17H2,1-4H3

InChI Key

HYFHYPWGAURHIV-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
Cephalotaxus fortunei	LOTUS Database	35616633
Cephalotaxus harringtonia	LOTUS Database	35616633

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
Fatty acid methyl ester
Azepine
Fatty acid ester
Aralkylamine
N-alkylpyrrolidine
Benzenoid
Dicarboxylic acid or derivatives
Fatty acyl
Pyrrolidine
Methyl ester
Tertiary alcohol
Amino acid or derivatives
Carboxylic acid ester
Tertiary amine
Tertiary aliphatic amine
Acetal
Carboxylic acid derivative
Oxacycle
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Alcohol
Carbonyl group
Organic oxide
Organopnictogen compound
Organic oxygen compound
Amine
Organic nitrogen compound
Organonitrogen compound
Organooxygen 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
logP	2.09	ALOGPS
logP	1.88	ChemAxon
logS	-3.7	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	11	ChemAxon
Refractivity	142.07 m³·mol⁻¹	ChemAxon
Polarizability	57.92 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	No	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

Omacetaxine mepesuccinate

METLIN ID

Not Available

PubChem Compound

3628

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Homoharringtonine (NP0137259)

MOL for NP0137259 (Homoharringtonine)

3D MOL for NP0137259 (Homoharringtonine)

3D SDF for NP0137259 (Homoharringtonine)

3D-SDF for NP0137259 (Homoharringtonine)

PDB for NP0137259 (Homoharringtonine)

3D PDB for NP0137259 (Homoharringtonine)

SMILES for NP0137259 (Homoharringtonine)

INCHI for NP0137259 (Homoharringtonine)

Structure for NP0137259 (Homoharringtonine)

3D Structure for NP0137259 (Homoharringtonine)