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Showing NP-Card for 3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid (NP0335569)

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Record Information
Version2.0
Created at2024-09-11 02:12:37 UTC
Updated at2024-09-11 02:12:38 UTC
NP-MRD IDNP0335569
Secondary Accession NumbersNone
Natural Product Identification
Common Name3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid
Description3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms. 3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, 3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid has been detected, but not quantified in, a few different foods, such as fats and oils, fruits, and herbs and spices. This could make 3-(1-hydroxymethyl-1-propenyl)pentanedioic acid a potential biomarker for the consumption of these foods.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0335569 (3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid)


  Mrv0541 02241209312D          

 14 13  0  0  0  0            999 V2000
   -1.4430   -0.7146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6184   -0.7146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2062   -1.4292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8553   -1.4292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2062    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6184   -2.1439    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6184    0.7146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6184    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2062    1.4292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0306   -0.7146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6184    2.1439    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6184    1.4292    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8553   -0.7146    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6184   -1.4292    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  4  1  0  0  0  0
  2  3  1  0  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  5  7  1  0  0  0  0
  5  8  1  0  0  0  0
  7  9  1  0  0  0  0
  8 10  1  0  0  0  0
  9 11  1  0  0  0  0
  9 12  2  0  0  0  0
 10 13  1  0  0  0  0
 10 14  2  0  0  0  0
M  END
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3D MOL for NP0335569 (3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid)

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3D SDF for NP0335569 (3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid)

  Mrv0541 02241209312D          

 14 13  0  0  0  0            999 V2000
   -1.4430   -0.7146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6184   -0.7146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2062   -1.4292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8553   -1.4292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2062    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6184   -2.1439    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6184    0.7146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6184    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2062    1.4292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0306   -0.7146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6184    2.1439    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6184    1.4292    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8553   -0.7146    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6184   -1.4292    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  4  1  0  0  0  0
  2  3  1  0  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  5  7  1  0  0  0  0
  5  8  1  0  0  0  0
  7  9  1  0  0  0  0
  8 10  1  0  0  0  0
  9 11  1  0  0  0  0
  9 12  2  0  0  0  0
 10 13  1  0  0  0  0
 10 14  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0335569

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C=C(/CO)C(CC(O)=O)CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H14O5/c1-2-6(5-10)7(3-8(11)12)4-9(13)14/h2,7,10H,3-5H2,1H3,(H,11,12)(H,13,14)/b6-2+

> <INCHI_KEY>
FUMUSIMACHNZQF-QHHAFSJGSA-N

> <FORMULA>
C9H14O5

> <MOLECULAR_WEIGHT>
202.2045

> <EXACT_MASS>
202.084123558

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
19.46576894043794

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-[(2Z)-1-hydroxybut-2-en-2-yl]pentanedioic acid

> <ALOGPS_LOGP>
0.07

> <JCHEM_LOGP>
-0.17708941766666672

> <ALOGPS_LOGS>
-1.42

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.7155394020362404

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.987878471650757

> <JCHEM_PKA_STRONGEST_BASIC>
-1.778809481325288

> <JCHEM_POLAR_SURFACE_AREA>
94.83000000000001

> <JCHEM_REFRACTIVITY>
49.06190000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.62e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-[(2Z)-1-hydroxybut-2-en-2-yl]pentanedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0335569 (3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid)
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PDB for NP0335569 (3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid)
HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -2.694  -1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.154  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.385  -2.668   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.463  -2.668   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.385   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.154  -4.002   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -1.154   1.334   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.154   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.385   2.668   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.924  -1.334   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.154   4.002   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       1.154   2.668   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       3.463  -1.334   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       1.154  -2.668   0.000  0.00  0.00           O+0
CONECT    1    2    4                                                       
CONECT    2    1    3    5                                                  
CONECT    3    2    6                                                       
CONECT    4    1                                                            
CONECT    5    2    7    8                                                  
CONECT    6    3                                                            
CONECT    7    5    9                                                       
CONECT    8    5   10                                                       
CONECT    9    7   11   12                                                  
CONECT   10    8   13   14                                                  
CONECT   11    9                                                            
CONECT   12    9                                                            
CONECT   13   10                                                            
CONECT   14   10                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

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3D PDB for NP0335569 (3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid)
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SMILES for NP0335569 (3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid)
C\C=C(/CO)C(CC(O)=O)CC(O)=O
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INCHI for NP0335569 (3-(1-Hydroxymethyl-1-propenyl)pentanedioic acid)
InChI=1S/C9H14O5/c1-2-6(5-10)7(3-8(11)12)4-9(13)14/h2,7,10H,3-5H2,1H3,(H,11,12)(H,13,14)/b6-2+
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Synonyms
ValueSource
3-(1-Hydroxymethyl-1-propenyl)pentanedioateGenerator
3-(1-Hydroxymethyl-1-propenyl)glutaric acidHMDB
3-[(2Z)-1-Hydroxybut-2-en-2-yl]pentanedioateGenerator
Chemical FormulaC9H14O5
Average Mass202.2045 Da
Monoisotopic Mass202.08412 Da
IUPAC Name3-[(2Z)-1-hydroxybut-2-en-2-yl]pentanedioic acid
Traditional Name3-[(2Z)-1-hydroxybut-2-en-2-yl]pentanedioic acid
CAS Registry NumberNot Available
SMILES
C\C=C(/CO)C(CC(O)=O)CC(O)=O
InChI Identifier
InChI=1S/C9H14O5/c1-2-6(5-10)7(3-8(11)12)4-9(13)14/h2,7,10H,3-5H2,1H3,(H,11,12)(H,13,14)/b6-2+
InChI KeyFUMUSIMACHNZQF-QHHAFSJGSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassFatty Acyls  
Sub ClassFatty acids and conjugates  
Direct ParentMedium-chain fatty acids  
Alternative Parents
Substituents
  • Medium-chain fatty acid
    • 

  • Hydroxy fatty acid
    • 

  • Branched fatty acid
    • 

  • Unsaturated fatty acid
    • 

  • Dicarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Carbonyl group
    • 

  • Alcohol
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic 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
logP0.07ALOGPS
logP-0.18ChemAxon
logS-1.4ALOGPS
pKa (Strongest Acidic)3.99ChemAxon
pKa (Strongest Basic)-1.8ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area94.83 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity49.06 m³·mol⁻¹ChemAxon
Polarizability19.47 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0033092  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB011087  
KNApSAcK IDNot Available
Chemspider ID25936984  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound101414422  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References