NP-MRD: Showing NP-Card for (-)-11alpha-Hydroxydeoxyharringtonine (NP0069280)

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Record Information

Version

2.0

Created at

2022-04-28 14:37:48 UTC

Updated at

2022-04-28 14:37:49 UTC

NP-MRD ID

NP0069280

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-11alpha-Hydroxydeoxyharringtonine

Description

(2S,3S,6S,12R)-12-hydroxy-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 (3S)-3-hydroxy-3-(3-methylbutyl)butanedioate 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. (-)-11alpha-Hydroxydeoxyharringtonine is found in Cephalotaxus harringtonia. Based on a literature review very few articles have been published on (2S,3S,6S,12R)-12-hydroxy-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 (3S)-3-hydroxy-3-(3-methylbutyl)butanedioate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282216372D          

 38 42  0  0  1  0            999 V2000
    4.7730    1.4926    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652304282216372D          

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    1.5018   -0.5149    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6863   -0.6401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7072    2.4461    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0892    1.7149    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5119    1.1256    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  7  5  1  6  0  0  0
  7  8  1  0  0  0  0
  8  9  1  1  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  4 11  1  0  0  0  0
 11 12  1  6  0  0  0
  9 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
  8 15  1  0  0  0  0
  8 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
  7 18  1  0  0  0  0
 18 19  1  6  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 22 20  1  6  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 24 26  1  0  0  0  0
 26 27  1  0  0  0  0
 22 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
 30 32  1  0  0  0  0
 22 33  1  1  0  0  0
 17 34  1  0  0  0  0
 34 35  1  0  0  0  0
  2 36  1  0  0  0  0
 36 37  1  0  0  0  0
 37 38  1  0  0  0  0
  1 38  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0069280

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C[C@@](O)(CCC(C)C)C(=O)O[C@H]1[C@H]2C3=CC4=C(OCO4)C=C3[C@@H](O)CN3CCC[C@@]23C=C1OC

> <INCHI_IDENTIFIER>
InChI=1S/C28H37NO9/c1-16(2)6-8-28(33,13-23(31)35-4)26(32)38-25-22(34-3)12-27-7-5-9-29(27)14-19(30)17-10-20-21(37-15-36-20)11-18(17)24(25)27/h10-12,16,19,24-25,30,33H,5-9,13-15H2,1-4H3/t19-,24+,25+,27+,28-/m0/s1

> <INCHI_KEY>
MUYLHTHAOBTAIZ-UBXQZGGWSA-N

> <FORMULA>
C28H37NO9

> <MOLECULAR_WEIGHT>
531.602

> <EXACT_MASS>
531.246831775

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
75

> <JCHEM_AVERAGE_POLARIZABILITY>
55.99525009786419

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S,6S,12R)-12-hydroxy-4-methoxy-16,18-dioxa-10-azapentacyclo[11.7.0.0^{2,6}.0^{6,10}.0^{15,19}]icosa-1(20),4,13,15(19)-tetraen-3-yl 1-methyl (3S)-3-hydroxy-3-(3-methylbutyl)butanedioate

> <ALOGPS_LOGP>
2.16

> <JCHEM_LOGP>
1.992220552333333

> <ALOGPS_LOGS>
-3.26

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
14.00345345459873

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.08416749341065

> <JCHEM_PKA_STRONGEST_BASIC>
8.925883120883293

> <JCHEM_POLAR_SURFACE_AREA>
123.99000000000002

> <JCHEM_REFRACTIVITY>
136.84529999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.95e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S,6S,12R)-12-hydroxy-4-methoxy-16,18-dioxa-10-azapentacyclo[11.7.0.0^{2,6}.0^{6,10}.0^{15,19}]icosa-1(20),4,13,15(19)-tetraen-3-yl 1-methyl (3S)-3-hydroxy-3-(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       8.910   2.786   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.135   4.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.928   5.267   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.496   4.700   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.271   3.177   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.478   2.220   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.939   2.403   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.504   2.962   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       3.046   4.432   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       3.910   5.707   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.446   5.826   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       6.004   7.261   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       1.506   4.451   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.013   2.992   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.037   2.128   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.529   1.770   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.362   0.474   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.851   0.865   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       6.044  -0.109   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       5.796  -1.629   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       4.355  -2.174   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       6.988  -2.604   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.180  -3.579   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       7.932  -5.099   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       6.491  -5.644   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       9.124  -6.074   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       8.876  -7.593   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       7.963  -1.412   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       9.482  -1.660   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      10.027  -3.100   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       9.053  -4.293   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      11.547  -3.348   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       6.013  -3.796   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       2.803  -0.961   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       1.281  -1.195   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    6   38                                                  
CONECT    2    1    3   36                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   11                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8   18                                                  
CONECT    8    7    9   15   16                                             
CONECT    9    8   10   13                                                  
CONECT   10    9   11                                                       
CONECT   11   10    4   12                                                  
CONECT   12   11                                                            
CONECT   13    9   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14    8                                                       
CONECT   16    8   17                                                       
CONECT   17   16   18   34                                                  
CONECT   18   17    7   19                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   28   33                                             
CONECT   23   22   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   26                                                            
CONECT   28   22   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30                                                            
CONECT   33   22                                                            
CONECT   34   17   35                                                       
CONECT   35   34                                                            
CONECT   36    2   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37    1                                                       
MASTER        0    0    0    0    0    0    0    0   38    0   84    0
END

View in JSmol

Synonyms

Value	Source
(2S,3S,6S,12R)-12-Hydroxy-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 (3S)-3-hydroxy-3-(3-methylbutyl)butanedioic acid	Generator

Chemical Formula

C₂₈H₃₇NO₉

Average Mass

531.6020 Da

Monoisotopic Mass

531.24683 Da

IUPAC Name

(2S,3S,6S,12R)-12-hydroxy-4-methoxy-16,18-dioxa-10-azapentacyclo[11.7.0.0^{2,6}.0^{6,10}.0^{15,19}]icosa-1(20),4,13,15(19)-tetraen-3-yl 1-methyl (3S)-3-hydroxy-3-(3-methylbutyl)butanedioate

Traditional Name

(2S,3S,6S,12R)-12-hydroxy-4-methoxy-16,18-dioxa-10-azapentacyclo[11.7.0.0^{2,6}.0^{6,10}.0^{15,19}]icosa-1(20),4,13,15(19)-tetraen-3-yl 1-methyl (3S)-3-hydroxy-3-(3-methylbutyl)butanedioate

CAS Registry Number

Not Available

SMILES

COC(=O)C[C@@](O)(CCC(C)C)C(=O)O[C@H]1[C@H]2C3=CC4=C(OCO4)C=C3[C@@H](O)CN3CCC[C@@]23C=C1OC

InChI Identifier

InChI=1S/C28H37NO9/c1-16(2)6-8-28(33,13-23(31)35-4)26(32)38-25-22(34-3)12-27-7-5-9-29(27)14-19(30)17-10-20-21(37-15-36-20)11-18(17)24(25)27/h10-12,16,19,24-25,30,33H,5-9,13-15H2,1-4H3/t19-,24+,25+,27+,28-/m0/s1

InChI Key

MUYLHTHAOBTAIZ-UBXQZGGWSA-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 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
Secondary alcohol
Carboxylic acid ester
Amino acid or derivatives
1,2-aminoalcohol
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	2.16	ALOGPS
logP	1.99	ChemAxon
logS	-3.3	ALOGPS
pKa (Strongest Acidic)	12.08	ChemAxon
pKa (Strongest Basic)	8.93	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	136.85 m³·mol⁻¹	ChemAxon
Polarizability	56 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

163105105

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (-)-11alpha-Hydroxydeoxyharringtonine (NP0069280)

MOL for NP0069280 ((-)-11alpha-Hydroxydeoxyharringtonine)

3D MOL for NP0069280 ((-)-11alpha-Hydroxydeoxyharringtonine)

3D SDF for NP0069280 ((-)-11alpha-Hydroxydeoxyharringtonine)

3D-SDF for NP0069280 ((-)-11alpha-Hydroxydeoxyharringtonine)

PDB for NP0069280 ((-)-11alpha-Hydroxydeoxyharringtonine)

3D PDB for NP0069280 ((-)-11alpha-Hydroxydeoxyharringtonine)

SMILES for NP0069280 ((-)-11alpha-Hydroxydeoxyharringtonine)

INCHI for NP0069280 ((-)-11alpha-Hydroxydeoxyharringtonine)

Structure for NP0069280 ((-)-11alpha-Hydroxydeoxyharringtonine)

3D Structure for NP0069280 ((-)-11alpha-Hydroxydeoxyharringtonine)