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Showing NP-Card for 1,3-Propanediol (NP0002689)

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Record Information
Version2.0
Created at2020-11-23 19:38:00 UTC
Updated at2024-09-17 15:45:31 UTC
NP-MRD IDNP0002689
Secondary Accession NumbersNone
Natural Product Identification
Common Name1,3-Propanediol
Provided ByBMRBBMRB logo
Description1,3-Propanediol, also known as (HOCH2)2ch2 or 2-deoxyglycerol, belongs to the class of organic compounds known as primary alcohols. Primary alcohols are compounds comprising the primary alcohol functional group, with the general structure RCOH (R=alkyl, aryl). In humans, 1,3-propanediol is involved in the felbamate metabolism pathway. 1,3-Propanediol is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. 1,3-Propanediol was first documented in 1999 (PMID: 10531640). Based on a literature review a small amount of articles have been published on 1,3-propanediol (PMID: 16020043) (PMID: 34542700).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0002689 (1,3-Propanediol)


  Mrv0541 02231216272D          

  5  4  0  0  0  0            999 V2000
    2.4750   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    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
    0.0000    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  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
M  END
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3D MOL for NP0002689 (1,3-Propanediol)

NP0002689
     RDKit          3D

 13 12  0  0  0  0  0  0  0  0999 V2000
    2.2173    0.6328   -0.2346 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0614    0.3380    0.4897 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0500   -0.1967   -0.5200 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2546   -0.5528    0.1597 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8063    0.5870    0.7812 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3120   -0.0288   -0.9466 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3417   -0.4643    1.2144 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7007    1.2500    0.9925 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1058    0.5381   -1.3073 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4801   -1.1139   -0.9404 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9464   -0.8856   -0.6433 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1232   -1.3637    0.8873 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9269    1.2598    0.0674 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  1  6  1  0
  2  7  1  0
  2  8  1  0
  3  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
M  END
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3D SDF for NP0002689 (1,3-Propanediol)


  Mrv0541 02231216272D          

  5  4  0  0  0  0            999 V2000
    2.4750   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    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
    0.0000    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  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0002689

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCCCO

> <INCHI_IDENTIFIER>
InChI=1S/C3H8O2/c4-2-1-3-5/h4-5H,1-3H2

> <INCHI_KEY>
YPFDHNVEDLHUCE-UHFFFAOYSA-N

> <FORMULA>
C3H8O2

> <MOLECULAR_WEIGHT>
76.0944

> <EXACT_MASS>
76.0524295

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
8.154905089871434

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
propane-1,3-diol

> <ALOGPS_LOGP>
-1.18

> <JCHEM_LOGP>
-1.1487193416666668

> <ALOGPS_LOGS>
1.05

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
16.301568215730207

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.599171219017617

> <JCHEM_PKA_STRONGEST_BASIC>
-2.4050519886982684

> <JCHEM_POLAR_SURFACE_AREA>
40.46

> <JCHEM_REFRACTIVITY>
19.418999999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.59e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
propanediol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0002689 (1,3-Propanediol)

NP0002689
     RDKit          3D

 13 12  0  0  0  0  0  0  0  0999 V2000
    2.2173    0.6328   -0.2346 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0614    0.3380    0.4897 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0500   -0.1967   -0.5200 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2546   -0.5528    0.1597 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8063    0.5870    0.7812 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3120   -0.0288   -0.9466 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3417   -0.4643    1.2144 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7007    1.2500    0.9925 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1058    0.5381   -1.3073 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4801   -1.1139   -0.9404 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9464   -0.8856   -0.6433 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1232   -1.3637    0.8873 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9269    1.2598    0.0674 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  1  6  1  0
  2  7  1  0
  2  8  1  0
  3  9  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
M  END
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PDB for NP0002689 (1,3-Propanediol)

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  O   UNK     0       4.620  -2.667   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       3.850  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4                                                            
MASTER        0    0    0    0    0    0    0    0    5    0    8    0
END
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3D PDB for NP0002689 (1,3-Propanediol)

COMPND    NP0002689
HETATM    1  O1  UNL     1       2.217   0.633  -0.235  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.061   0.338   0.490  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.050  -0.197  -0.520  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.255  -0.553   0.160  1.00  0.00           C  
HETATM    5  O2  UNL     1      -1.806   0.587   0.781  1.00  0.00           O  
HETATM    6  H1  UNL     1       2.312  -0.029  -0.947  1.00  0.00           H  
HETATM    7  H2  UNL     1       1.342  -0.464   1.214  1.00  0.00           H  
HETATM    8  H3  UNL     1       0.701   1.250   0.993  1.00  0.00           H  
HETATM    9  H4  UNL     1      -0.106   0.538  -1.307  1.00  0.00           H  
HETATM   10  H5  UNL     1       0.480  -1.114  -0.940  1.00  0.00           H  
HETATM   11  H6  UNL     1      -1.946  -0.886  -0.643  1.00  0.00           H  
HETATM   12  H7  UNL     1      -1.123  -1.364   0.887  1.00  0.00           H  
HETATM   13  H8  UNL     1      -1.927   1.260   0.067  1.00  0.00           H  
CONECT    1    2    6
CONECT    2    3    7    8
CONECT    3    4    9   10
CONECT    4    5   11   12
CONECT    5   13
END
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SMILES for NP0002689 (1,3-Propanediol)

OCCCO
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INCHI for NP0002689 (1,3-Propanediol)

InChI=1S/C3H8O2/c4-2-1-3-5/h4-5H,1-3H2
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View in JSmolView NMR Assignments
Synonyms
ValueSource
(HOCH2)2ch2ChEBI
1,3-DihydroxypropaneChEBI
1,3-PROPANDIOLChEBI
1,3-Propylene glycolChEBI
1,3-PropylenediolChEBI
2-(Hydroxymethyl)ethanolChEBI
2-DeoxyglycerolChEBI
beta-Propylene glycolChEBI
CH2(CH2OH)2ChEBI
HO(CH2)3ohChEBI
HOCH2CH2CH2OHChEBI
Omega-propanediolChEBI
Trimethylene glycolChEBI
b-Propylene glycolGenerator
Β-propylene glycolGenerator
1,3-PropanediolChEBI
Chemical FormulaC3H8O2
Average Mass76.0944 Da
Monoisotopic Mass76.05243 Da
IUPAC Namepropane-1,3-diol
Traditional Namepropanediol
CAS Registry NumberNot Available
SMILES
OCCCO
InChI Identifier
InChI=1S/C3H8O2/c4-2-1-3-5/h4-5H,1-3H2
InChI KeyYPFDHNVEDLHUCE-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Perityle emoryiKNApSAcK Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as primary alcohols. Primary alcohols are compounds comprising the primary alcohol functional group, with the general structure RCOH (R=alkyl, aryl).
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassAlcohols and polyols
Direct ParentPrimary alcohols
Alternative Parents
Substituents
  • Hydrocarbon derivative
  • Primary alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point214.00 to 215.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility1000000 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP-1.040 (est)The Good Scents Company Information System
Predicted Properties
PropertyValueSource
logP-1.2ALOGPS
logP-1.1ChemAxon
logS1.05ALOGPS
pKa (Strongest Acidic)15.6ChemAxon
pKa (Strongest Basic)-2.4ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area40.46 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity19.42 m³·mol⁻¹ChemAxon
Polarizability8.15 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0062150
DrugBank IDDB02774
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00010857
Chemspider ID13839553
KEGG Compound IDC02457
BioCyc IDCPD-347
BiGG IDNot Available
Wikipedia Link1,3-Propanediol
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID16109
Good Scents IDrw1147941
References
General References
  1. Biebl H, Menzel K, Zeng AP, Deckwer WD: Microbial production of 1,3-propanediol. Appl Microbiol Biotechnol. 1999 Sep;52(3):289-97. doi: 10.1007/s002530051523. [PubMed:10531640 ]
  2. Scott RS, Frame SR, Ross PE, Loveless SE, Kennedy GL: Inhalation toxicity of 1,3-propanediol in the rat. Inhal Toxicol. 2005 Aug;17(9):487-93. doi: 10.1080/08958370590964485. [PubMed:16020043 ]
  3. de Fouchecour F, Lemarchand A, Spinnler HE, Saulou-Berion C: Efficient 3-hydroxypropionic acid production by Acetobacter sp. CIP 58.66 through a feeding strategy based on pH control. AMB Express. 2021 Sep 20;11(1):130. doi: 10.1186/s13568-021-01291-9. [PubMed:34542700 ]