Np mrd loader

Showing NP-Card for 3-Hydroxysuberic acid (NP0000506)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2020-11-24 22:16:02 UTC
NP-MRD IDNP0000506
Secondary Accession NumbersNone
Natural Product Identification
Common Name3-Hydroxysuberic acid
Description3-Hydroxysuberic acid is a metabolite derived from the w-oxidation of 3-hydroxy fatty acids and the subsequent beta-oxidation of longer-chain 3-hydroxy dicarboxylic acids (PMID 2001377 ). It has been found increased in ketoaciduria (PMID 1591279 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000506 (3-Hydroxysuberic acid)

3-Hydroxysuberic acid.mol
  Mrv1652305261923572D          

 13 12  0  0  0  0            999 V2000
   -2.5006   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7862    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0717    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7862   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5006    0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5006   -1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2151    0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5006    1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2151   -0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717   -1.0313    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
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  1  9  2  0  0  0  0
  1 10  1  0  0  0  0
  8 11  2  0  0  0  0
  8 12  1  0  0  0  0
  3 13  1  0  0  0  0
M  END
Download

3D MOL for NP0000506 (3-Hydroxysuberic acid)

HMDB0000325
     RDKit          3D
3-Hydroxysuberic acid
 27 26  0  0  0  0  0  0  0  0999 V2000
   -5.0530   -0.8530   -0.1593 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0708   -0.0913    0.1349 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4048    1.0700    0.8168 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6722   -0.4414   -0.2362 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7865    0.6590    0.2570 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3244    0.4346   -0.0532 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2155   -0.8123    0.5530 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6687   -0.9638    0.1847 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8420   -1.0323   -1.2005 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4628    0.1397    0.7888 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9288    0.0149    0.4445 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3449   -0.9262   -0.2647 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7515    1.0101    0.9703 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1869    2.0005    0.4913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6406   -0.4071   -1.3575 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3877   -1.4401    0.1290 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8793    0.7146    1.3540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0862    1.5998   -0.2265 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0765    0.4856   -1.1124 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1952    1.3095    0.4389 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1423   -0.8052    1.6738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3712   -1.7194    0.2493 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0906   -1.9294    0.5668 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9871   -1.2248   -1.6778 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1855    1.1340    0.3601 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4101    0.1034    1.8887 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7149    1.9707    0.6055 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  6 19  1  0
  6 20  1  0
  7 21  1  0
  7 22  1  0
  8 23  1  0
  9 24  1  0
 10 25  1  0
 10 26  1  0
 13 27  1  0
M  END
Download

3D SDF for NP0000506 (3-Hydroxysuberic acid)

3-Hydroxysuberic acid.mol
  Mrv1652305261923572D          

 13 12  0  0  0  0            999 V2000
   -2.5006   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7862    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0717    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7862   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5006    0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5006   -1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2151    0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5006    1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2151   -0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717   -1.0313    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
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  1  9  2  0  0  0  0
  1 10  1  0  0  0  0
  8 11  2  0  0  0  0
  8 12  1  0  0  0  0
  3 13  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000506

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C8H14O5/c9-6(5-8(12)13)3-1-2-4-7(10)11/h6,9H,1-5H2,(H,10,11)(H,12,13)

> <INCHI_KEY>
ARJZZFJXSNJKGR-UHFFFAOYSA-N

> <FORMULA>
C8H14O5

> <MOLECULAR_WEIGHT>
190.1938

> <EXACT_MASS>
190.084123558

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
19.135545855339032

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-hydroxyoctanedioic acid

> <ALOGPS_LOGP>
-0.17

> <JCHEM_LOGP>
0.14898062566666642

> <ALOGPS_LOGS>
-0.99

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.678024185855329

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.941893251590358

> <JCHEM_PKA_STRONGEST_BASIC>
-2.798595834991789

> <JCHEM_POLAR_SURFACE_AREA>
94.83

> <JCHEM_REFRACTIVITY>
43.4565

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.95e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxysuberic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000506 (3-Hydroxysuberic acid)

HMDB0000325
     RDKit          3D
3-Hydroxysuberic acid
 27 26  0  0  0  0  0  0  0  0999 V2000
   -5.0530   -0.8530   -0.1593 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0708   -0.0913    0.1349 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4048    1.0700    0.8168 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6722   -0.4414   -0.2362 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7865    0.6590    0.2570 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3244    0.4346   -0.0532 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2155   -0.8123    0.5530 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6687   -0.9638    0.1847 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8420   -1.0323   -1.2005 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4628    0.1397    0.7888 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9288    0.0149    0.4445 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3449   -0.9262   -0.2647 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7515    1.0101    0.9703 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1869    2.0005    0.4913 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6406   -0.4071   -1.3575 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3877   -1.4401    0.1290 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8793    0.7146    1.3540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0862    1.5998   -0.2265 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0765    0.4856   -1.1124 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1952    1.3095    0.4389 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1423   -0.8052    1.6738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3712   -1.7194    0.2493 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0906   -1.9294    0.5668 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9871   -1.2248   -1.6778 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1855    1.1340    0.3601 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4101    0.1034    1.8887 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7149    1.9707    0.6055 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  6 19  1  0
  6 20  1  0
  7 21  1  0
  7 22  1  0
  8 23  1  0
  9 24  1  0
 10 25  1  0
 10 26  1  0
 13 27  1  0
M  END
Download

PDB for NP0000506 (3-Hydroxysuberic acid)

HEADER    PROTEIN                                 26-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 3-Hydroxysuberic acid.mol                         
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-19         0                                  
HETATM    1  C   UNK     0      -4.668  -0.385   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.334   0.385   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.001  -0.385   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.667   0.385   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.667  -0.385   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.001   0.385   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.334  -0.385   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.668   0.385   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -4.668  -1.925   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -6.002   0.385   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       4.668   1.925   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       6.002  -0.385   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -2.001  -1.925   0.000  0.00  0.00           O+0
CONECT    1    2    9   10                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4   13                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7   11   12                                                  
CONECT    9    1                                                            
CONECT   10    1                                                            
CONECT   11    8                                                            
CONECT   12    8                                                            
CONECT   13    3                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END
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3D PDB for NP0000506 (3-Hydroxysuberic acid)

COMPND    HMDB0000325
HETATM    1  O1  UNL     1      -5.053  -0.853  -0.159  1.00  0.00           O  
HETATM    2  C1  UNL     1      -4.071  -0.091   0.135  1.00  0.00           C  
HETATM    3  O2  UNL     1      -4.405   1.070   0.817  1.00  0.00           O  
HETATM    4  C2  UNL     1      -2.672  -0.441  -0.236  1.00  0.00           C  
HETATM    5  C3  UNL     1      -1.786   0.659   0.257  1.00  0.00           C  
HETATM    6  C4  UNL     1      -0.324   0.435  -0.053  1.00  0.00           C  
HETATM    7  C5  UNL     1       0.215  -0.812   0.553  1.00  0.00           C  
HETATM    8  C6  UNL     1       1.669  -0.964   0.185  1.00  0.00           C  
HETATM    9  O3  UNL     1       1.842  -1.032  -1.200  1.00  0.00           O  
HETATM   10  C7  UNL     1       2.463   0.140   0.789  1.00  0.00           C  
HETATM   11  C8  UNL     1       3.929   0.015   0.444  1.00  0.00           C  
HETATM   12  O4  UNL     1       4.345  -0.926  -0.265  1.00  0.00           O  
HETATM   13  O5  UNL     1       4.752   1.010   0.970  1.00  0.00           O  
HETATM   14  H1  UNL     1      -4.187   2.000   0.491  1.00  0.00           H  
HETATM   15  H2  UNL     1      -2.641  -0.407  -1.358  1.00  0.00           H  
HETATM   16  H3  UNL     1      -2.388  -1.440   0.129  1.00  0.00           H  
HETATM   17  H4  UNL     1      -1.879   0.715   1.354  1.00  0.00           H  
HETATM   18  H5  UNL     1      -2.086   1.600  -0.226  1.00  0.00           H  
HETATM   19  H6  UNL     1      -0.076   0.486  -1.112  1.00  0.00           H  
HETATM   20  H7  UNL     1       0.195   1.310   0.439  1.00  0.00           H  
HETATM   21  H8  UNL     1       0.142  -0.805   1.674  1.00  0.00           H  
HETATM   22  H9  UNL     1      -0.371  -1.719   0.249  1.00  0.00           H  
HETATM   23  H10 UNL     1       2.091  -1.929   0.567  1.00  0.00           H  
HETATM   24  H11 UNL     1       0.987  -1.225  -1.678  1.00  0.00           H  
HETATM   25  H12 UNL     1       2.185   1.134   0.360  1.00  0.00           H  
HETATM   26  H13 UNL     1       2.410   0.103   1.889  1.00  0.00           H  
HETATM   27  H14 UNL     1       4.715   1.971   0.605  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   14
CONECT    4    5   15   16
CONECT    5    6   17   18
CONECT    6    7   19   20
CONECT    7    8   21   22
CONECT    8    9   10   23
CONECT    9   24
CONECT   10   11   25   26
CONECT   11   12   12   13
CONECT   13   27
END
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SMILES for NP0000506 (3-Hydroxysuberic acid)

OC(CCCCC(O)=O)CC(O)=O
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INCHI for NP0000506 (3-Hydroxysuberic acid)

InChI=1S/C8H14O5/c9-6(5-8(12)13)3-1-2-4-7(10)11/h6,9H,1-5H2,(H,10,11)(H,12,13)
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View in JSmol
Synonyms
ValueSource
3-HydroxysuberateGenerator
3-HydroxyoctanedioateHMDB
3-Hydroxyoctanedioic acidHMDB
3-Hydroxy-suberateHMDB
Chemical FormulaC8H14O5
Average Mass190.1938 Da
Monoisotopic Mass190.08412 Da
IUPAC Name3-hydroxyoctanedioic acid
Traditional Name3-hydroxysuberic acid
CAS Registry Number73141-47-6
SMILES
OC(CCCCC(O)=O)CC(O)=O
InChI Identifier
InChI=1S/C8H14O5/c9-6(5-8(12)13)3-1-2-4-7(10)11/h6,9H,1-5H2,(H,10,11)(H,12,13)
InChI KeyARJZZFJXSNJKGR-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
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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
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility19.5 g/LALOGPS
logP-0.17ALOGPS
logP0.15ChemAxon
logS-0.99ALOGPS
pKa (Strongest Acidic)3.94ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area94.83 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity43.46 m³·mol⁻¹ChemAxon
Polarizability19.14 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000325
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB021951
KNApSAcK IDNot Available
Chemspider ID13498677
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5314
PubChem Compound22328017
PDB IDNot Available
ChEBI ID70766
Good Scents IDNot Available
References
General References