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Showing NP-Card for (4r)-2-methylpentane-2,4-diol (NP0292199)

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Record Information
Version2.0
Created at2022-09-09 23:37:13 UTC
Updated at2022-09-09 23:37:14 UTC
NP-MRD IDNP0292199
Secondary Accession NumbersNone
Natural Product Identification
Common Name(4r)-2-methylpentane-2,4-diol
Description(4R)-2-Methylpentane-2,4-Diol, also known as (4S)-2-methyl-2,4-pentanediol, belongs to the class of organic compounds known as tertiary alcohols. (4r)-2-methylpentane-2,4-diol is found in Ligularia veitchiana and Santolina rosmarinifolia. Tertiary alcohols are compounds in which a hydroxy group, -OH, is attached to a saturated carbon atom R3COH (R not H ) (4r)-2-Methylpentane-2,4-Diol is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0292199 ((4r)-2-methylpentane-2,4-diol)


  Mrv0541 02231217012D          

  8  7  0  0  1  0            999 V2000
    0.1105   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6039   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    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  0  0  0  0
  5  7  1  0  0  0  0
  5  8  1  0  0  0  0
M  END
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3D MOL for NP0292199 ((4r)-2-methylpentane-2,4-diol)

     RDKit          3D

 22 21  0  0  0  0  0  0  0  0999 V2000
    2.0408   -0.6484   -0.3341 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4062    0.6154    0.1452 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3370    1.2682    0.9676 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1048    0.3752    0.8760 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8394   -0.3115   -0.0873 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0642    0.5723   -1.2841 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1968   -0.5553    0.5504 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3291   -1.5625   -0.4254 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1443   -0.4969   -0.4066 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7014   -0.8856   -1.3650 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8868   -1.5201    0.3165 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2594    1.2788   -0.7296 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1641    2.2306    0.9775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3609    1.3389    1.1457 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2694   -0.2168    1.7808 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0977    0.3978   -1.6788 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3358    0.4359   -2.0881 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9668    1.6257   -0.9347 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9293    0.2315    0.2601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1229   -0.5065    1.6648 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6224   -1.5291    0.2645 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4487   -2.1375    0.3846 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  5  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  6
  3 13  1  0
  4 14  1  0
  4 15  1  0
  6 16  1  0
  6 17  1  0
  6 18  1  0
  7 19  1  0
  7 20  1  0
  7 21  1  0
  8 22  1  0
M  END
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3D SDF for NP0292199 ((4r)-2-methylpentane-2,4-diol)


  Mrv0541 02231217012D          

  8  7  0  0  1  0            999 V2000
    0.1105   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6039   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    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  0  0  0  0
  5  7  1  0  0  0  0
  5  8  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0292199

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H](O)CC(C)(C)O

> <INCHI_IDENTIFIER>
InChI=1S/C6H14O2/c1-5(7)4-6(2,3)8/h5,7-8H,4H2,1-3H3/t5-/m0/s1

> <INCHI_KEY>
SVTBMSDMJJWYQN-YFKPBYRVSA-N

> <FORMULA>
C6H14O2

> <MOLECULAR_WEIGHT>
118.1742

> <EXACT_MASS>
118.099379692

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
13.54269292770783

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4S)-2-methylpentane-2,4-diol

> <ALOGPS_LOGP>
0.34

> <JCHEM_LOGP>
-0.03499262399999985

> <ALOGPS_LOGS>
0.14

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.863892389843322

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.122618562424375

> <JCHEM_PKA_STRONGEST_BASIC>
-2.5485532283457237

> <JCHEM_POLAR_SURFACE_AREA>
40.46

> <JCHEM_REFRACTIVITY>
32.894800000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.62e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4r)-2-methylpentane-2,4-diol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0292199 ((4r)-2-methylpentane-2,4-diol)

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PDB for NP0292199 ((4r)-2-methylpentane-2,4-diol)
HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0       0.206  -3.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.206  -2.310   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -1.127  -1.540   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.540  -1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.540   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.080   0.000   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       0.000   0.000   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    8                                             
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    5                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END

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3D PDB for NP0292199 ((4r)-2-methylpentane-2,4-diol)
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SMILES for NP0292199 ((4r)-2-methylpentane-2,4-diol)
C[C@H](O)CC(C)(C)O
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INCHI for NP0292199 ((4r)-2-methylpentane-2,4-diol)
InChI=1S/C6H14O2/c1-5(7)4-6(2,3)8/h5,7-8H,4H2,1-3H3/t5-/m0/s1
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Synonyms
ValueSource
(4S)-2-METHYL-2,4-pentanediolChEBI
Chemical FormulaC6H14O2
Average Mass118.1742 Da
Monoisotopic Mass118.09938 Da
IUPAC Name(4S)-2-methylpentane-2,4-diol
Traditional Name(4r)-2-methylpentane-2,4-diol
CAS Registry NumberNot Available
SMILES
C[C@H](O)CC(C)(C)O
InChI Identifier
InChI=1S/C6H14O2/c1-5(7)4-6(2,3)8/h5,7-8H,4H2,1-3H3/t5-/m0/s1
InChI KeySVTBMSDMJJWYQN-YFKPBYRVSA-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 Origin
Species NameSourceReference
Ligularia veitchianaLOTUS Database
Santolina rosmarinifoliaLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as tertiary alcohols. Tertiary alcohols are compounds in which a hydroxy group, -OH, is attached to a saturated carbon atom R3COH (R not H ).
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassAlcohols and polyols  
Direct ParentTertiary alcohols  
Alternative Parents
Substituents
  • Tertiary alcohol
    • 

  • Secondary alcohol
    • 

  • Hydrocarbon derivative
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
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
logP0.34ALOGPS
logP-0.035ChemAxon
logS0.14ALOGPS
pKa (Strongest Acidic)15.12ChemAxon
pKa (Strongest Basic)-2.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area40.46 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity32.89 m³·mol⁻¹ChemAxon
Polarizability13.54 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDDB03564  
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 Compound5288834  
PDB IDNot Available
ChEBI ID44224  
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]