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Showing NP-Card for (3e,20s)-20-[(2r,4r)-2,4-dihydroxypentyl]-1-oxacycloicos-3-en-2-one (NP0315633)

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Record Information
Version2.0
Created at2022-09-11 14:21:41 UTC
Updated at2022-09-11 14:21:42 UTC
NP-MRD IDNP0315633
Secondary Accession NumbersNone
Natural Product Identification
Common Name(3e,20s)-20-[(2r,4r)-2,4-dihydroxypentyl]-1-oxacycloicos-3-en-2-one
DescriptionRickiol E belongs to the class of organic compounds known as macrolides and analogues. These are organic compounds containing a lactone ring of at least twelve members. (3e,20s)-20-[(2r,4r)-2,4-dihydroxypentyl]-1-oxacycloicos-3-en-2-one is found in Hypoxylon rickii. (3e,20s)-20-[(2r,4r)-2,4-dihydroxypentyl]-1-oxacycloicos-3-en-2-one was first documented in 2018 (PMID: 29168908). Based on a literature review very few articles have been published on Rickiol E.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0315633 ((3e,20s)-20-[(2r,4r)-2,4-dihydroxypentyl]-1-oxacycloicos-3-en-2-one)


  Mrv1652309112216212D          

 28 28  0  0  1  0            999 V2000
   -2.1434   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4289   -3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0000   -3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  6  0  0  0
  2  4  1  0  0  0  0
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  9 10  1  0  0  0  0
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 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
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 17 18  1  0  0  0  0
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 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 26 28  1  0  0  0  0
  8 28  1  0  0  0  0
M  END
Download

3D MOL for NP0315633 ((3e,20s)-20-[(2r,4r)-2,4-dihydroxypentyl]-1-oxacycloicos-3-en-2-one)

Download
3D SDF for NP0315633 ((3e,20s)-20-[(2r,4r)-2,4-dihydroxypentyl]-1-oxacycloicos-3-en-2-one)

  Mrv1652309112216212D          

 28 28  0  0  1  0            999 V2000
   -2.1434   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4289   -3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0000   -3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  6  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  8  7  1  1  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
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 13 14  1  0  0  0  0
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 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
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 26 27  2  0  0  0  0
 26 28  1  0  0  0  0
  8 28  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0315633

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H](O)C[C@@H](O)C[C@@H]1CCCCCCCCCCCCCCC\C=C\C(=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C24H44O4/c1-21(25)19-22(26)20-23-17-15-13-11-9-7-5-3-2-4-6-8-10-12-14-16-18-24(27)28-23/h16,18,21-23,25-26H,2-15,17,19-20H2,1H3/b18-16+/t21-,22-,23+/m1/s1

> <INCHI_KEY>
SQCWVFMWNBADBV-KGMVHGDISA-N

> <FORMULA>
C24H44O4

> <MOLECULAR_WEIGHT>
396.612

> <EXACT_MASS>
396.323959897

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_POLARIZABILITY>
48.51935353933087

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3E,20S)-20-[(2R,4R)-2,4-dihydroxypentyl]-1-oxacycloicos-3-en-2-one

> <JCHEM_LOGP>
6.325062722333334

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.803526666074106

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.970723727023923

> <JCHEM_PKA_STRONGEST_BASIC>
-2.544972931956586

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
116.49099999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(3E,20S)-20-[(2R,4R)-2,4-dihydroxypentyl]-1-oxacycloicos-3-en-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0315633 ((3e,20s)-20-[(2r,4r)-2,4-dihydroxypentyl]-1-oxacycloicos-3-en-2-one)
Download
PDB for NP0315633 ((3e,20s)-20-[(2r,4r)-2,4-dihydroxypentyl]-1-oxacycloicos-3-en-2-one)
HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0      -4.001  -3.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -2.667  -6.160   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -1.334  -3.850   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.000  -4.620   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -0.000  -6.160   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       1.334  -3.850   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.002  -9.240   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.336 -10.010   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       9.336 -11.550   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.002 -12.320   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.668 -11.550   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.335 -12.320   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.001 -11.550   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -0.000  -7.700   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       1.334  -5.390   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    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   28                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26    8                                                       
MASTER        0    0    0    0    0    0    0    0   28    0   56    0
END

Download
3D PDB for NP0315633 ((3e,20s)-20-[(2r,4r)-2,4-dihydroxypentyl]-1-oxacycloicos-3-en-2-one)
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SMILES for NP0315633 ((3e,20s)-20-[(2r,4r)-2,4-dihydroxypentyl]-1-oxacycloicos-3-en-2-one)
C[C@@H](O)C[C@@H](O)C[C@@H]1CCCCCCCCCCCCCCC\C=C\C(=O)O1
Download
INCHI for NP0315633 ((3e,20s)-20-[(2r,4r)-2,4-dihydroxypentyl]-1-oxacycloicos-3-en-2-one)
InChI=1S/C24H44O4/c1-21(25)19-22(26)20-23-17-15-13-11-9-7-5-3-2-4-6-8-10-12-14-16-18-24(27)28-23/h16,18,21-23,25-26H,2-15,17,19-20H2,1H3/b18-16+/t21-,22-,23+/m1/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC24H44O4
Average Mass396.6120 Da
Monoisotopic Mass396.32396 Da
IUPAC Name(3E,20S)-20-[(2R,4R)-2,4-dihydroxypentyl]-1-oxacycloicos-3-en-2-one
Traditional Name(3E,20S)-20-[(2R,4R)-2,4-dihydroxypentyl]-1-oxacycloicos-3-en-2-one
CAS Registry NumberNot Available
SMILES
C[C@@H](O)C[C@@H](O)C[C@@H]1CCCCCCCCCCCCCCC\C=C\C(=O)O1
InChI Identifier
InChI=1S/C24H44O4/c1-21(25)19-22(26)20-23-17-15-13-11-9-7-5-3-2-4-6-8-10-12-14-16-18-24(27)28-23/h16,18,21-23,25-26H,2-15,17,19-20H2,1H3/b18-16+/t21-,22-,23+/m1/s1
InChI KeySQCWVFMWNBADBV-KGMVHGDISA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Hypoxylon rickiiLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as macrolides and analogues. These are organic compounds containing a lactone ring of at least twelve members.
KingdomOrganic compounds  
Super ClassPhenylpropanoids and polyketides  
ClassMacrolides and analogues  
Sub ClassNot Available
Direct ParentMacrolides and analogues  
Alternative Parents
Substituents
  • Macrolide
    • 

  • Alpha,beta-unsaturated carboxylic ester
    • 

  • Enoate ester
    • 

  • Secondary alcohol
    • 

  • Lactone
    • 

  • Carboxylic acid ester
    • 

  • Oxacycle
    • 

  • Organoheterocyclic compound
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid derivative
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Carbonyl group
    • 

  • Alcohol
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP6.33ChemAxon
pKa (Strongest Acidic)14.97ChemAxon
pKa (Strongest Basic)-2.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area66.76 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity116.49 m³·mol⁻¹ChemAxon
Polarizability48.52 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound146683942  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Surup F, Kuhnert E, Bohm A, Pendzialek T, Solga D, Wiebach V, Engler H, Berkessel A, Stadler M, Kalesse M: The Rickiols: 20-, 22-, and 24-membered Macrolides from the Ascomycete Hypoxylon rickii. Chemistry. 2018 Feb 9;24(9):2200-2213. doi: 10.1002/chem.201704928. Epub 2018 Jan 19. [PubMed:29168908  ] 
  2. LOTUS database [Link]