NP-MRD: Showing NP-Card for 1-[(2r,3s,5r)-5-({[(2e,6s,7r)-6,7-dihydroxy-3,7,11-trimethyldodeca-2,10-dien-1-yl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one (NP0149096)

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Record Information

Version

2.0

Created at

2022-09-02 04:56:16 UTC

Updated at

2022-09-02 04:56:16 UTC

NP-MRD ID

NP0149096

Secondary Accession Numbers

None

Natural Product Identification

Common Name

1-[(2r,3s,5r)-5-({[(2e,6s,7r)-6,7-dihydroxy-3,7,11-trimethyldodeca-2,10-dien-1-yl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one

Description

1-[(2R,3S,5R)-5-({[(2E,6S,7R)-6,7-dihydroxy-3,7,11-trimethyldodeca-2,10-dien-1-yl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-4-hydroxy-1,2,5,6-tetrahydropyrimidin-2-one belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units. Based on a literature review very few articles have been published on 1-[(2R,3S,5R)-5-({[(2E,6S,7R)-6,7-dihydroxy-3,7,11-trimethyldodeca-2,10-dien-1-yl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-4-hydroxy-1,2,5,6-tetrahydropyrimidin-2-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309022206562D          

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     RDKit          3D

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  Mrv1652309022206562D          

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 21 22  1  0  0  0  0
 22 23  1  1  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  2  0  0  0  0
 28 29  1  0  0  0  0
 23 29  1  0  0  0  0
 29 30  2  0  0  0  0
 22 31  1  0  0  0  0
 31 32  1  1  0  0  0
 31 33  1  0  0  0  0
 20 33  1  0  0  0  0
 33 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0149096

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CCC[C@@](C)(O)[C@@H](O)CC\C(C)=C\COC[C@H]1O[C@H]([C@@H](O)C1O)N1CCC(O)=NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C24H40N2O8/c1-15(2)6-5-11-24(4,32)18(27)8-7-16(3)10-13-33-14-17-20(29)21(30)22(34-17)26-12-9-19(28)25-23(26)31/h6,10,17-18,20-22,27,29-30,32H,5,7-9,11-14H2,1-4H3,(H,25,28,31)/b16-10+/t17-,18+,20?,21+,22-,24-/m1/s1

> <INCHI_KEY>
AHUPOCLKEKMZQR-XMVPZBMOSA-N

> <FORMULA>
C24H40N2O8

> <MOLECULAR_WEIGHT>
484.59

> <EXACT_MASS>
484.278466256

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
52.98048139167132

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(2R,3S,5R)-5-({[(2E,6S,7R)-6,7-dihydroxy-3,7,11-trimethyldodeca-2,10-dien-1-yl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-4-hydroxy-1,2,5,6-tetrahydropyrimidin-2-one

> <ALOGPS_LOGP>
0.76

> <JCHEM_LOGP>
0.855657993999999

> <ALOGPS_LOGS>
-3.18

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.535755615603044

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.154495599944769

> <JCHEM_PKA_STRONGEST_BASIC>
-1.5742771405173084

> <JCHEM_POLAR_SURFACE_AREA>
152.27999999999997

> <JCHEM_REFRACTIVITY>
126.40869999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.19e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-[(2R,3S,5R)-5-({[(2E,6S,7R)-6,7-dihydroxy-3,7,11-trimethyldodeca-2,10-dien-1-yl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-SEP-22         0                                  
HETATM    1  C   UNK     0      -4.001  14.630   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.001  13.090   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.667  12.320   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.335  12.320   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -5.335  10.780   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.001  10.010   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -4.001   8.470   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -5.541   8.470   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.461   8.470   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -4.001   6.930   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -5.335   6.160   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -2.667   6.160   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.667   4.620   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       0.000  -0.000   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       2.580  -3.215   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       2.104  -4.680   0.000  0.00  0.00           C+0
HETATM   23  N   UNK     0       3.009  -5.926   0.000  0.00  0.00           N+0
HETATM   24  C   UNK     0       4.540  -5.765   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       5.446  -7.011   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.819  -8.417   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       5.724  -9.663   0.000  0.00  0.00           O+0
HETATM   28  N   UNK     0       3.288  -8.578   0.000  0.00  0.00           N+0
HETATM   29  C   UNK     0       2.382  -7.333   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       0.851  -7.494   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       0.564  -4.680   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -0.342  -5.926   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       0.088  -3.215   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -1.377  -2.739   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                                                            
CONECT   10    7   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   33                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23   31                                                  
CONECT   23   22   24   29                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28   23   30                                                  
CONECT   30   29                                                            
CONECT   31   22   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   20   34                                                  
CONECT   34   33                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   70    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₄₀N₂O₈

Average Mass

484.5900 Da

Monoisotopic Mass

484.27847 Da

IUPAC Name

1-[(2R,3S,5R)-5-({[(2E,6S,7R)-6,7-dihydroxy-3,7,11-trimethyldodeca-2,10-dien-1-yl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-4-hydroxy-1,2,5,6-tetrahydropyrimidin-2-one

Traditional Name

1-[(2R,3S,5R)-5-({[(2E,6S,7R)-6,7-dihydroxy-3,7,11-trimethyldodeca-2,10-dien-1-yl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one

CAS Registry Number

Not Available

SMILES

CC(C)=CCC[C@@](C)(O)[C@@H](O)CC\C(C)=C\COC[C@H]1O[C@H]([C@@H](O)C1O)N1CCC(O)=NC1=O

InChI Identifier

InChI=1S/C24H40N2O8/c1-15(2)6-5-11-24(4,32)18(27)8-7-16(3)10-13-33-14-17-20(29)21(30)22(34-17)26-12-9-19(28)25-23(26)31/h6,10,17-18,20-22,27,29-30,32H,5,7-9,11-14H2,1-4H3,(H,25,28,31)/b16-10+/t17-,18+,20?,21+,22-,24-/m1/s1

InChI Key

AHUPOCLKEKMZQR-XMVPZBMOSA-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 sesquiterpenoids. These are terpenes with three consecutive isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Sesquiterpenoids

Alternative Parents

Substituents

Farsesane sesquiterpenoid
Sesquiterpenoid
N-glycosyl compound
Glycosyl compound
Pentose monosaccharide
Pyrimidone
Pyrimidine
Monosaccharide
1,2,5,6-tetrahydropyrimidine
Hydropyrimidine
Tetrahydrofuran
Tertiary alcohol
Secondary alcohol
Carbonic acid derivative
Oxacycle
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Ether
Dialkyl ether
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
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	0.76	ALOGPS
logP	0.86	ChemAxon
logS	-3.2	ALOGPS
pKa (Strongest Acidic)	4.15	ChemAxon
pKa (Strongest Basic)	-1.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	152.28 Å²	ChemAxon
Rotatable Bond Count	12	ChemAxon
Refractivity	126.41 m³·mol⁻¹	ChemAxon
Polarizability	52.98 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	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

163017496

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,3s,5r)-5-({[(2e,6s,7r)-6,7-dihydroxy-3,7,11-trimethyldodeca-2,10-dien-1-yl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one (NP0149096)

MOL for NP0149096 (1-[(2r,3s,5r)-5-({[(2e,6s,7r)-6,7-dihydroxy-3,7,11-trimethyldodeca-2,10-dien-1-yl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one)

3D MOL for NP0149096 (1-[(2r,3s,5r)-5-({[(2e,6s,7r)-6,7-dihydroxy-3,7,11-trimethyldodeca-2,10-dien-1-yl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one)

3D SDF for NP0149096 (1-[(2r,3s,5r)-5-({[(2e,6s,7r)-6,7-dihydroxy-3,7,11-trimethyldodeca-2,10-dien-1-yl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one)

3D-SDF for NP0149096 (1-[(2r,3s,5r)-5-({[(2e,6s,7r)-6,7-dihydroxy-3,7,11-trimethyldodeca-2,10-dien-1-yl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one)

PDB for NP0149096 (1-[(2r,3s,5r)-5-({[(2e,6s,7r)-6,7-dihydroxy-3,7,11-trimethyldodeca-2,10-dien-1-yl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one)

3D PDB for NP0149096 (1-[(2r,3s,5r)-5-({[(2e,6s,7r)-6,7-dihydroxy-3,7,11-trimethyldodeca-2,10-dien-1-yl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one)

SMILES for NP0149096 (1-[(2r,3s,5r)-5-({[(2e,6s,7r)-6,7-dihydroxy-3,7,11-trimethyldodeca-2,10-dien-1-yl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one)

INCHI for NP0149096 (1-[(2r,3s,5r)-5-({[(2e,6s,7r)-6,7-dihydroxy-3,7,11-trimethyldodeca-2,10-dien-1-yl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one)

Structure for NP0149096 (1-[(2r,3s,5r)-5-({[(2e,6s,7r)-6,7-dihydroxy-3,7,11-trimethyldodeca-2,10-dien-1-yl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one)

3D Structure for NP0149096 (1-[(2r,3s,5r)-5-({[(2e,6s,7r)-6,7-dihydroxy-3,7,11-trimethyldodeca-2,10-dien-1-yl]oxy}methyl)-3,4-dihydroxyoxolan-2-yl]-4-hydroxy-5,6-dihydropyrimidin-2-one)