NP-MRD: Showing NP-Card for 1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-({[(2e)-3-methyl-5-[(2r,3r)-3-methyl-3-(4-methylpent-3-en-1-yl)oxiran-2-yl]pent-2-en-1-yl]oxy}methyl)oxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one (NP0213030)

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Record Information

Version

2.0

Created at

2022-09-05 11:52:54 UTC

Updated at

2022-09-05 11:52:54 UTC

NP-MRD ID

NP0213030

Secondary Accession Numbers

None

Natural Product Identification

Common Name

1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-({[(2e)-3-methyl-5-[(2r,3r)-3-methyl-3-(4-methylpent-3-en-1-yl)oxiran-2-yl]pent-2-en-1-yl]oxy}methyl)oxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one

Description

CHEMBL2419630 belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety. Based on a literature review very few articles have been published on CHEMBL2419630.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052213522D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309052213522D          

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M  END
> <DATABASE_ID>
NP0213030

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CCC[C@@]1(C)O[C@@H]1CC\C(C)=C\COC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1CCC(O)=NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C24H38N2O7/c1-15(2)6-5-11-24(4)18(33-24)8-7-16(3)10-13-31-14-17-20(28)21(29)22(32-17)26-12-9-19(27)25-23(26)30/h6,10,17-18,20-22,28-29H,5,7-9,11-14H2,1-4H3,(H,25,27,30)/b16-10+/t17-,18-,20-,21-,22-,24-/m1/s1

> <INCHI_KEY>
PMYKSEMADATAMV-WKIHLUAGSA-N

> <FORMULA>
C24H38N2O7

> <MOLECULAR_WEIGHT>
466.575

> <EXACT_MASS>
466.267901572

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
71

> <JCHEM_AVERAGE_POLARIZABILITY>
50.741466853973535

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-({[(2E)-3-methyl-5-[(2R,3R)-3-methyl-3-(4-methylpent-3-en-1-yl)oxiran-2-yl]pent-2-en-1-yl]oxy}methyl)oxolan-2-yl]-4-hydroxy-1,2,5,6-tetrahydropyrimidin-2-one

> <JCHEM_LOGP>
2.0173615663333324

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.564657694491085

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.154495601956056

> <JCHEM_PKA_STRONGEST_BASIC>
-1.5733039262421697

> <JCHEM_POLAR_SURFACE_AREA>
124.35

> <JCHEM_REFRACTIVITY>
122.89859999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-({[(2E)-3-methyl-5-[(2R,3R)-3-methyl-3-(4-methylpent-3-en-1-yl)oxiran-2-yl]pent-2-en-1-yl]oxy}methyl)oxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one

> <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       6.243 -13.298   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.064 -14.288   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.331 -15.804   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.617 -13.761   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.437 -14.751   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.990 -14.224   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.190 -15.214   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.370 -14.224   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       0.580 -16.548   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -0.960 -16.548   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.294 -17.318   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -3.627 -16.548   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -4.961 -17.318   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -4.961 -18.858   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -6.295 -16.548   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -7.628 -17.318   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -8.962 -16.548   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0     -10.296 -17.318   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0     -11.629 -16.548   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0     -13.036 -17.174   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0     -14.067 -16.030   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0     -15.598 -16.191   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0     -16.225 -17.597   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0     -17.756 -17.758   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0     -18.661 -16.512   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0     -20.193 -16.673   0.000  0.00  0.00           O+0
HETATM   27  N   UNK     0     -18.035 -15.106   0.000  0.00  0.00           N+0
HETATM   28  C   UNK     0     -16.503 -14.945   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0     -15.877 -13.538   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0     -13.297 -14.696   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0     -13.923 -13.289   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0     -11.790 -15.016   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0     -10.646 -13.986   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9   10                                             
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9    7   11                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   32                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   30                                                  
CONECT   22   21   23   28                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28                                                       
CONECT   28   27   22   29                                                  
CONECT   29   28                                                            
CONECT   30   21   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   19   33                                                  
CONECT   33   32                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   70    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₃₈N₂O₇

Average Mass

466.5750 Da

Monoisotopic Mass

466.26790 Da

IUPAC Name

1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-({[(2E)-3-methyl-5-[(2R,3R)-3-methyl-3-(4-methylpent-3-en-1-yl)oxiran-2-yl]pent-2-en-1-yl]oxy}methyl)oxolan-2-yl]-4-hydroxy-1,2,5,6-tetrahydropyrimidin-2-one

Traditional Name

1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-({[(2E)-3-methyl-5-[(2R,3R)-3-methyl-3-(4-methylpent-3-en-1-yl)oxiran-2-yl]pent-2-en-1-yl]oxy}methyl)oxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one

CAS Registry Number

Not Available

SMILES

CC(C)=CCC[C@@]1(C)O[C@@H]1CC\C(C)=C\COC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1CCC(O)=NC1=O

InChI Identifier

InChI=1S/C24H38N2O7/c1-15(2)6-5-11-24(4)18(33-24)8-7-16(3)10-13-31-14-17-20(28)21(29)22(32-17)26-12-9-19(27)25-23(26)30/h6,10,17-18,20-22,28-29H,5,7-9,11-14H2,1-4H3,(H,25,27,30)/b16-10+/t17-,18-,20-,21-,22-,24-/m1/s1

InChI Key

PMYKSEMADATAMV-WKIHLUAGSA-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 pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Not Available

Direct Parent

Pyrimidine nucleosides

Alternative Parents

Substituents

Pyrimidine nucleoside
Sesquiterpenoid
Glycosyl compound
N-glycosyl compound
Pentose monosaccharide
N-acyl urea
Pyrimidone
Ureide
1,3-diazinane
Monosaccharide
Pyrimidine
Tetrahydrofuran
Dicarboximide
Urea
Secondary alcohol
Carbonic acid derivative
1,2-diol
Organoheterocyclic compound
Carboxylic acid derivative
Dialkyl ether
Oxacycle
Azacycle
Oxirane
Ether
Hydrocarbon derivative
Organic nitrogen compound
Organic oxygen compound
Organonitrogen compound
Organooxygen compound
Organopnictogen compound
Organic oxide
Carbonyl group
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic 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	2.02	ChemAxon
pKa (Strongest Acidic)	4.15	ChemAxon
pKa (Strongest Basic)	-1.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	124.35 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	122.9 m³·mol⁻¹	ChemAxon
Polarizability	50.74 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

30771244

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

73355244

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-({[(2e)-3-methyl-5-[(2r,3r)-3-methyl-3-(4-methylpent-3-en-1-yl)oxiran-2-yl]pent-2-en-1-yl]oxy}methyl)oxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one (NP0213030)

MOL for NP0213030 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-({[(2e)-3-methyl-5-[(2r,3r)-3-methyl-3-(4-methylpent-3-en-1-yl)oxiran-2-yl]pent-2-en-1-yl]oxy}methyl)oxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one)

3D MOL for NP0213030 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-({[(2e)-3-methyl-5-[(2r,3r)-3-methyl-3-(4-methylpent-3-en-1-yl)oxiran-2-yl]pent-2-en-1-yl]oxy}methyl)oxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one)

3D SDF for NP0213030 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-({[(2e)-3-methyl-5-[(2r,3r)-3-methyl-3-(4-methylpent-3-en-1-yl)oxiran-2-yl]pent-2-en-1-yl]oxy}methyl)oxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one)

3D-SDF for NP0213030 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-({[(2e)-3-methyl-5-[(2r,3r)-3-methyl-3-(4-methylpent-3-en-1-yl)oxiran-2-yl]pent-2-en-1-yl]oxy}methyl)oxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one)

PDB for NP0213030 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-({[(2e)-3-methyl-5-[(2r,3r)-3-methyl-3-(4-methylpent-3-en-1-yl)oxiran-2-yl]pent-2-en-1-yl]oxy}methyl)oxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one)

3D PDB for NP0213030 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-({[(2e)-3-methyl-5-[(2r,3r)-3-methyl-3-(4-methylpent-3-en-1-yl)oxiran-2-yl]pent-2-en-1-yl]oxy}methyl)oxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one)

SMILES for NP0213030 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-({[(2e)-3-methyl-5-[(2r,3r)-3-methyl-3-(4-methylpent-3-en-1-yl)oxiran-2-yl]pent-2-en-1-yl]oxy}methyl)oxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one)

INCHI for NP0213030 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-({[(2e)-3-methyl-5-[(2r,3r)-3-methyl-3-(4-methylpent-3-en-1-yl)oxiran-2-yl]pent-2-en-1-yl]oxy}methyl)oxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one)

Structure for NP0213030 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-({[(2e)-3-methyl-5-[(2r,3r)-3-methyl-3-(4-methylpent-3-en-1-yl)oxiran-2-yl]pent-2-en-1-yl]oxy}methyl)oxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one)

3D Structure for NP0213030 (1-[(2r,3r,4s,5r)-3,4-dihydroxy-5-({[(2e)-3-methyl-5-[(2r,3r)-3-methyl-3-(4-methylpent-3-en-1-yl)oxiran-2-yl]pent-2-en-1-yl]oxy}methyl)oxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one)