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Showing NP-Card for 3-[(2r)-2-methyl-3-oxobutyl]oxolan-2-one (NP0290927)

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Record Information
Version1.0
Created at2022-09-09 21:49:48 UTC
Updated at2022-09-09 21:49:48 UTC
NP-MRD IDNP0290927
Secondary Accession NumbersNone
Natural Product Identification
Common Name3-[(2r)-2-methyl-3-oxobutyl]oxolan-2-one
DescriptionDiffusible extracellular factor belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom. It was first documented in 2011 (PMID: 21821958). Based on a literature review very few articles have been published on Diffusible extracellular factor.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0290927 (3-[(2r)-2-methyl-3-oxobutyl]oxolan-2-one)


  Mrv1652309092223492D          

 12 12  0  0  1  0            999 V2000
   -0.8612    3.5893    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    3.1768    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    3.5893    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    2.3518    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8612    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  1  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  7 11  1  0  0  0  0
 11 12  2  0  0  0  0
M  END
Download

3D MOL for NP0290927 (3-[(2r)-2-methyl-3-oxobutyl]oxolan-2-one)

     RDKit          3D

 26 26  0  0  0  0  0  0  0  0999 V2000
   -2.5756    1.7001   -0.7184 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5414    0.3857   -0.0402 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4902    0.0424    0.6263 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3473   -0.4744   -0.1949 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5563   -1.7457    0.5846 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1444    0.2951    0.2369 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1440   -0.4407    0.1051 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2532    0.4981    0.5906 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4580    0.0140   -0.1761 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9620   -0.7727   -1.2447 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5585   -0.6737   -1.2923 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8930   -0.7754   -2.3452 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6088    1.9767   -1.0214 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2734    2.4679    0.0409 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9266    1.7240   -1.6167 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2338   -0.6763   -1.2945 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9127   -1.8274    1.4640 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6124   -1.8055    0.9628 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4178   -2.6300   -0.0567 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1000    1.2255   -0.3540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2773    0.5627    1.3070 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2054   -1.3331    0.7360 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9807    1.5175    0.2183 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3626    0.4610    1.6711 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1370   -0.5799    0.4882 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0636    0.8640   -0.5924 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  4  1  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
  4  2  1  0
  2  1  1  0
  2  3  2  0
 11  7  1  0
  5 17  1  0
  5 18  1  0
  5 19  1  0
  4 16  1  6
  6 20  1  0
  6 21  1  0
  7 22  1  1
  8 23  1  0
  8 24  1  0
  9 25  1  0
  9 26  1  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
M  END
Download

3D SDF for NP0290927 (3-[(2r)-2-methyl-3-oxobutyl]oxolan-2-one)


  Mrv1652309092223492D          

 12 12  0  0  1  0            999 V2000
   -0.8612    3.5893    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    3.1768    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    3.5893    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    2.3518    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8612    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  1  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  7 11  1  0  0  0  0
 11 12  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0290927

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H](CC1CCOC1=O)C(C)=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H14O3/c1-6(7(2)10)5-8-3-4-12-9(8)11/h6,8H,3-5H2,1-2H3/t6-,8?/m1/s1

> <INCHI_KEY>
IBSYDXNDQOJSLK-XPJFZRNWSA-N

> <FORMULA>
C9H14O3

> <MOLECULAR_WEIGHT>
170.208

> <EXACT_MASS>
170.094294311

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
17.822866893222894

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-[(2R)-2-methyl-3-oxobutyl]oxolan-2-one

> <JCHEM_LOGP>
1.1340449499999998

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
19.41740791850044

> <JCHEM_PKA_STRONGEST_BASIC>
-6.885636147347326

> <JCHEM_POLAR_SURFACE_AREA>
43.370000000000005

> <JCHEM_REFRACTIVITY>
43.875600000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
3-[(2R)-2-methyl-3-oxobutyl]oxolan-2-one

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0290927 (3-[(2r)-2-methyl-3-oxobutyl]oxolan-2-one)

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PDB for NP0290927 (3-[(2r)-2-methyl-3-oxobutyl]oxolan-2-one)
HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0      -1.608   6.700   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.274   5.930   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       1.060   6.700   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -0.274   4.390   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.608   3.620   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       0.290  -0.290   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8   11                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10    7   12                                                  
CONECT   12   11                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

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3D PDB for NP0290927 (3-[(2r)-2-methyl-3-oxobutyl]oxolan-2-one)
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SMILES for NP0290927 (3-[(2r)-2-methyl-3-oxobutyl]oxolan-2-one)
C[C@H](CC1CCOC1=O)C(C)=O
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INCHI for NP0290927 (3-[(2r)-2-methyl-3-oxobutyl]oxolan-2-one)
InChI=1S/C9H14O3/c1-6(7(2)10)5-8-3-4-12-9(8)11/h6,8H,3-5H2,1-2H3/t6-,8?/m1/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC9H14O3
Average Mass170.2080 Da
Monoisotopic Mass170.09429 Da
IUPAC Name3-[(2R)-2-methyl-3-oxobutyl]oxolan-2-one
Traditional Name3-[(2R)-2-methyl-3-oxobutyl]oxolan-2-one
CAS Registry NumberNot Available
SMILES
C[C@H](CC1CCOC1=O)C(C)=O
InChI Identifier
InChI=1S/C9H14O3/c1-6(7(2)10)5-8-3-4-12-9(8)11/h6,8H,3-5H2,1-2H3/t6-,8?/m1/s1
InChI KeyIBSYDXNDQOJSLK-XPJFZRNWSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassLactones  
Sub ClassGamma butyrolactones  
Direct ParentGamma butyrolactones  
Alternative Parents
Substituents
  • Gamma butyrolactone
    • 

  • Oxolane
    • 

  • Ketone
    • 

  • Carboxylic acid ester
    • 

  • Oxacycle
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid derivative
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Carbonyl group
    • 

  • 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
logP1.13ChemAxon
pKa (Strongest Acidic)19.42ChemAxon
pKa (Strongest Basic)-6.9ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area43.37 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity43.88 m³·mol⁻¹ChemAxon
Polarizability17.82 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID61677384  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound46201938  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Yajima A: Synthesis of microbial signaling molecules and their stereochemistry-activity relationships. Biosci Biotechnol Biochem. 2011;75(8):1418-29. doi: 10.1271/bbb.110283. Epub 2011  Aug 7. [PubMed:21821958  ] 
  2. LOTUS database [Link]