Showing NP-Card for 3-Hydroxyadipic acid (NP0086558)

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Record Information
Version2.0
Created at2022-05-11 16:24:23 UTC
Updated at2022-05-11 16:24:23 UTC
NP-MRD IDNP0086558
Secondary Accession NumbersNone
Natural Product Identification
Common Name3-Hydroxyadipic acid
Description3-Hydroxyadipic acid, also known as 3-hydroxyadipate, belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain. 3-Hydroxyadipic acid was first documented in 1981 (PMID: 7320161). 3-Hydroxyadipic acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral (PMID: 3980660) (PMID: 2739576).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0086558 (3-Hydroxyadipic acid)

  Mrv0541 02231218282D          

 11 10  0  0  0  0            999 V2000
   12.8187  -15.7898    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.9622  -14.5523    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.9608  -14.9648    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.2477  -15.7898    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6753  -13.7272    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.8187  -14.9648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1043  -14.5523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5333  -14.5523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3898  -14.9648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2477  -14.9648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6753  -14.5523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  0  0  0
  2 10  1  0  0  0  0
  3 11  1  0  0  0  0
  4 10  2  0  0  0  0
  5 11  2  0  0  0  0
  6  7  1  0  0  0  0
  6  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
M  END
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3D MOL for NP0086558 (3-Hydroxyadipic acid)

     RDKit          3D

 21 20  0  0  0  0  0  0  0  0999 V2000
    2.4779   -0.0392   -1.4624 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4587    0.3845   -0.2840 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0655    1.6083   -0.0304 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8142   -0.3971    0.7756 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3094   -0.2509    0.7974 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3166   -0.7010   -0.4927 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0147   -2.0442   -0.6696 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8029   -0.5934   -0.5009 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3188    0.7670   -0.3248 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3467    1.2430    0.8285 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7669    1.5229   -1.3820 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5401    2.4150    0.2783 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2305   -0.0978    1.7443 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0352   -1.4733    0.6192 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0749   -0.7901    1.6613 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1150    0.8543    0.8969 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1462   -0.1504   -1.3416 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1886   -2.5189    0.1950 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1843   -1.2817    0.2896 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1476   -0.9380   -1.5178 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0600    2.4811   -1.3250 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  6  1  0
  6  5  1  0
  5  4  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
  6  8  1  0
  8  9  1  0
  9 11  1  0
  9 10  2  0
  7 18  1  0
  6 17  1  6
  5 15  1  0
  5 16  1  0
  4 13  1  0
  4 14  1  0
  3 12  1  0
  8 19  1  0
  8 20  1  0
 11 21  1  0
M  END
Download

3D SDF for NP0086558 (3-Hydroxyadipic acid)

  Mrv0541 02231218282D          

 11 10  0  0  0  0            999 V2000
   12.8187  -15.7898    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.9622  -14.5523    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.9608  -14.9648    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.2477  -15.7898    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6753  -13.7272    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.8187  -14.9648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1043  -14.5523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5333  -14.5523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3898  -14.9648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2477  -14.9648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6753  -14.5523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  0  0  0
  2 10  1  0  0  0  0
  3 11  1  0  0  0  0
  4 10  2  0  0  0  0
  5 11  2  0  0  0  0
  6  7  1  0  0  0  0
  6  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
M  END
> <DATABASE_ID>
NP0086558

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(CCC(O)=O)CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O5/c7-4(3-6(10)11)1-2-5(8)9/h4,7H,1-3H2,(H,8,9)(H,10,11)

> <INCHI_KEY>
YVOMYDHIQVMMTA-UHFFFAOYSA-N

> <FORMULA>
C6H10O5

> <MOLECULAR_WEIGHT>
162.1406

> <EXACT_MASS>
162.05282343

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
14.77758062589532

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-hydroxyhexanedioic acid

> <ALOGPS_LOGP>
-0.89

> <JCHEM_LOGP>
-0.7401567043333332

> <ALOGPS_LOGS>
-0.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.456438347376524

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.6988469573165053

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8079016560382133

> <JCHEM_POLAR_SURFACE_AREA>
94.82999999999998

> <JCHEM_REFRACTIVITY>
34.2545

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.82e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxyadipic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0086558 (3-Hydroxyadipic acid)

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PDB for NP0086558 (3-Hydroxyadipic acid)
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      23.928 -29.474   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      27.929 -27.164   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      18.593 -27.934   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      26.596 -29.474   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      19.927 -25.624   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      23.928 -27.934   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      22.595 -27.164   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      25.262 -27.164   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      21.261 -27.934   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      26.596 -27.934   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      19.927 -27.164   0.000  0.00  0.00           C+0
CONECT    1    6                                                            
CONECT    2   10                                                            
CONECT    3   11                                                            
CONECT    4   10                                                            
CONECT    5   11                                                            
CONECT    6    1    7    8                                                  
CONECT    7    6    9                                                       
CONECT    8    6   10                                                       
CONECT    9    7   11                                                       
CONECT   10    2    4    8                                                  
CONECT   11    3    5    9                                                  
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END

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3D PDB for NP0086558 (3-Hydroxyadipic acid)
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SMILES for NP0086558 (3-Hydroxyadipic acid)
OC(CCC(O)=O)CC(O)=O
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INCHI for NP0086558 (3-Hydroxyadipic acid)
InChI=1S/C6H10O5/c7-4(3-6(10)11)1-2-5(8)9/h4,7H,1-3H2,(H,8,9)(H,10,11)
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View in JSmol
Synonyms
ValueSource
3-HydroxyadipateGenerator
(3S)-3-HydroxyadipateHMDB
(3S)-3-Hydroxyadipic acidHMDB
3-HydroxyhexanedioateHMDB
3-Hydroxyhexanedioic acidHMDB
3-Hydroxy-adipateHMDB
3-Hydroxyadipic acidMeSH
Chemical FormulaC6H10O5
Average Mass162.1406 Da
Monoisotopic Mass162.05282 Da
IUPAC Name3-hydroxyhexanedioic acid
Traditional Name3-hydroxyadipic acid
CAS Registry NumberNot Available
SMILES
OC(CCC(O)=O)CC(O)=O
InChI Identifier
InChI=1S/C6H10O5/c7-4(3-6(10)11)1-2-5(8)9/h4,7H,1-3H2,(H,8,9)(H,10,11)
InChI KeyYVOMYDHIQVMMTA-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Chemical Shift Submissions
Not Available
Species
Species of Origin
Chemical Taxonomy
Description Belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassHydroxy acids and derivatives  
Sub ClassMedium-chain hydroxy acids and derivatives  
Direct ParentMedium-chain hydroxy acids and derivatives  
Alternative Parents
Substituents
  • Medium-chain hydroxy acid
    • 

  • Medium-chain fatty acid
    • 

  • Beta-hydroxy acid
    • 

  • Hydroxy fatty acid
    • 

  • Dicarboxylic acid or derivatives
    • 

  • Fatty acyl
    • 

  • Fatty acid
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Organooxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Alcohol
    • 

  • Carbonyl group
    • 

  • Organic oxygen compound
    • 

  • 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
logP-0.89ALOGPS
logP-0.74ChemAxon
logS-0.26ALOGPS
pKa (Strongest Acidic)3.7ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area94.83 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity34.25 m³·mol⁻¹ChemAxon
Polarizability14.78 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000345  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB021968  
KNApSAcK IDNot Available
Chemspider ID133894  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5334  
PubChem Compound151913  
PDB IDNot Available
ChEBI ID89205  
Good Scents IDNot Available
References
General References
  1. Svendsen JS, Whist JE, Sydnes LK: Absolute configuration of 3-hydroxyadipic acid in human urine. J Chromatogr. 1985 Jan 11;337(1):9-19. [PubMed:3980660  ] 
  2. Grupe A, Spiteller G: New polar acid metabolites in human urine. J Chromatogr. 1981 Dec 11;226(2):301-14. doi: 10.1016/s0378-4347(00)86064-8. [PubMed:7320161  ] 
  3. Tserng KY, Jin SJ, Hoppel CL, Kerr DS, Genuth SM: Urinary 3-hydroxyadipic acid 3,6-lactone: structural identification and effect of fasting in adults and children. Metabolism. 1989 Jul;38(7):655-61. doi: 10.1016/0026-0495(89)90103-0. [PubMed:2739576  ]