NP-MRD: Showing NP-Card for (3r)-3,6-dihydroxy-3-({[(2s,3s,6r)-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]oxy}carbonyl)-6-methylheptanoic acid (NP0205951)

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Record Information

Version

2.0

Created at

2022-09-05 02:00:29 UTC

Updated at

2022-09-05 02:00:30 UTC

NP-MRD ID

NP0205951

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3r)-3,6-dihydroxy-3-({[(2s,3s,6r)-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]oxy}carbonyl)-6-methylheptanoic acid

Description

CHEMBL4174530 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. Based on a literature review very few articles have been published on CHEMBL4174530.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052204002D          

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M  END

     RDKit          3D

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  Mrv1652309052204002D          

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  5  9  1  6  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 12 17  1  0  0  0  0
 18 17  1  6  0  0  0
  5 18  1  0  0  0  0
 18 19  1  0  0  0  0
  3 19  1  0  0  0  0
 19 20  1  6  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 23 21  1  6  0  0  0
 23 24  1  6  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  1  0  0  0  0
 27 30  1  0  0  0  0
 23 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
 15 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 14 37  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0205951

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C[C@]23CCCN2CCC2=CC4=C(OCO4)C=C2[C@@H]3[C@@H]1OC(=O)[C@@](O)(CCC(C)(C)O)CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C27H35NO9/c1-25(2,32)7-8-27(33,14-21(29)30)24(31)37-23-20(34-3)13-26-6-4-9-28(26)10-5-16-11-18-19(36-15-35-18)12-17(16)22(23)26/h11-13,22-23,32-33H,4-10,14-15H2,1-3H3,(H,29,30)/t22-,23-,26+,27-/m1/s1

> <INCHI_KEY>
GSBQSICGIBSDBW-JUIYCPNDSA-N

> <FORMULA>
C27H35NO9

> <MOLECULAR_WEIGHT>
517.575

> <EXACT_MASS>
517.231181711

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_POLARIZABILITY>
53.348341490439395

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R)-3,6-dihydroxy-3-[(2S,3S,6R)-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 carboxy]-6-methylheptanoic acid

> <JCHEM_LOGP>
-1.4378280396957626

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.370521958375914

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.6115091223783238

> <JCHEM_PKA_STRONGEST_BASIC>
9.418235652264332

> <JCHEM_POLAR_SURFACE_AREA>
134.99

> <JCHEM_REFRACTIVITY>
132.70479999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(3R)-3,6-dihydroxy-3-[(2S,3S,6R)-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 carboxy]-6-methylheptanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0      -1.048  -5.884   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       0.475  -5.652   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       1.036  -4.218   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.246  -3.135   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.181  -1.730   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.077  -2.619   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.310  -1.696   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.814  -0.238   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       0.726  -0.259   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       1.591   1.014   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.127   1.131   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.176   0.004   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.609   0.568   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.814  -0.391   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.586  -1.914   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.154  -2.478   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.948  -1.520   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.616  -2.291   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.526  -3.829   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       3.716  -4.805   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       3.466  -6.325   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       2.025  -6.868   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       4.657  -7.301   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       5.848  -8.278   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       5.633  -6.110   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       7.153  -6.361   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       8.130  -5.170   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       9.106  -3.979   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       6.939  -4.193   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       9.320  -6.146   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       3.680  -8.492   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       4.223  -9.933   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       5.743 -10.183   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       3.247 -11.124   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0       7.965  -2.601   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       9.044  -1.502   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       8.333  -0.136   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   19                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    9   18                                             
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    5   10                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   17                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   37                                                  
CONECT   15   14   16   35                                                  
CONECT   16   15   17                                                       
CONECT   17   16   12   18                                                  
CONECT   18   17    5   19                                                  
CONECT   19   18    3   20                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   25   31                                             
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   29   30                                             
CONECT   28   27                                                            
CONECT   29   27                                                            
CONECT   30   27                                                            
CONECT   31   23   32                                                       
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32                                                            
CONECT   35   15   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   14                                                       
MASTER        0    0    0    0    0    0    0    0   37    0   82    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₃₅NO₉

Average Mass

517.5750 Da

Monoisotopic Mass

517.23118 Da

IUPAC Name

(3R)-3,6-dihydroxy-3-[(2S,3S,6R)-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 carboxy]-6-methylheptanoic acid

Traditional Name

(3R)-3,6-dihydroxy-3-[(2S,3S,6R)-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 carboxy]-6-methylheptanoic acid

CAS Registry Number

Not Available

SMILES

COC1=C[C@]23CCCN2CCC2=CC4=C(OCO4)C=C2[C@@H]3[C@@H]1OC(=O)[C@@](O)(CCC(C)(C)O)CC(O)=O

InChI Identifier

InChI=1S/C27H35NO9/c1-25(2,32)7-8-27(33,14-21(29)30)24(31)37-23-20(34-3)13-26-6-4-9-28(26)10-5-16-11-18-19(36-15-35-18)12-17(16)22(23)26/h11-13,22-23,32-33H,4-10,14-15H2,1-3H3,(H,29,30)/t22-,23-,26+,27-/m1/s1

InChI Key

GSBQSICGIBSDBW-JUIYCPNDSA-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

Not Available

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
Azepine
Fatty acid ester
Aralkylamine
Dicarboxylic acid or derivatives
N-alkylpyrrolidine
Benzenoid
Fatty acyl
Pyrrolidine
Tertiary alcohol
Tertiary aliphatic amine
Tertiary amine
Amino acid or derivatives
Amino acid
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Acetal
Azacycle
Carboxylic acid derivative
Carboxylic acid
Alcohol
Organic oxide
Hydrocarbon derivative
Carbonyl group
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Organonitrogen compound
Amine
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	-1.4	ChemAxon
pKa (Strongest Acidic)	3.61	ChemAxon
pKa (Strongest Basic)	9.42	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	134.99 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	132.7 m³·mol⁻¹	ChemAxon
Polarizability	53.35 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

8705291

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10529895

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (3r)-3,6-dihydroxy-3-({[(2s,3s,6r)-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]oxy}carbonyl)-6-methylheptanoic acid (NP0205951)

MOL for NP0205951 ((3r)-3,6-dihydroxy-3-({[(2s,3s,6r)-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]oxy}carbonyl)-6-methylheptanoic acid)

3D MOL for NP0205951 ((3r)-3,6-dihydroxy-3-({[(2s,3s,6r)-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]oxy}carbonyl)-6-methylheptanoic acid)

3D SDF for NP0205951 ((3r)-3,6-dihydroxy-3-({[(2s,3s,6r)-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]oxy}carbonyl)-6-methylheptanoic acid)

3D-SDF for NP0205951 ((3r)-3,6-dihydroxy-3-({[(2s,3s,6r)-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]oxy}carbonyl)-6-methylheptanoic acid)

PDB for NP0205951 ((3r)-3,6-dihydroxy-3-({[(2s,3s,6r)-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]oxy}carbonyl)-6-methylheptanoic acid)

3D PDB for NP0205951 ((3r)-3,6-dihydroxy-3-({[(2s,3s,6r)-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]oxy}carbonyl)-6-methylheptanoic acid)

SMILES for NP0205951 ((3r)-3,6-dihydroxy-3-({[(2s,3s,6r)-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]oxy}carbonyl)-6-methylheptanoic acid)

INCHI for NP0205951 ((3r)-3,6-dihydroxy-3-({[(2s,3s,6r)-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]oxy}carbonyl)-6-methylheptanoic acid)

Structure for NP0205951 ((3r)-3,6-dihydroxy-3-({[(2s,3s,6r)-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]oxy}carbonyl)-6-methylheptanoic acid)

3D Structure for NP0205951 ((3r)-3,6-dihydroxy-3-({[(2s,3s,6r)-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]oxy}carbonyl)-6-methylheptanoic acid)