NP-MRD: Showing NP-Card for 3-Hydroxydodecanedioic acid (NP0000193)

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Record Information

Version

1.0

Created at

2005-11-16 15:48:42 UTC

Updated at

2020-11-24 22:13:34 UTC

NP-MRD ID

NP0000193

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3-Hydroxydodecanedioic acid

Description

3-Hydroxydecanedioic acid appears in the urine of children affected with peroxisomal disorders. Peroxisomal biogenesis disorders (PBDs) are characterized by generalized peroxisomal dysfunction due to defective assembly of the organelle and include the Zellweger, neonatal adrenoleukodystrophy and infantile Refsum phenotypes (PMID 10896310 ).

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0000413
     RDKit          3D
3-Hydroxydodecanedioic acid
 39 38  0  0  0  0  0  0  0  0999 V2000
    5.4071   -2.1119   -0.8516 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6775   -0.8959   -0.7467 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4151   -0.3136   -1.7863 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2361   -0.1100    0.4254 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8715    0.4784    0.1521 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9071   -0.6346   -0.0976 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4984   -0.1590   -0.3869 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9881    0.6073    0.7839 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4104    1.0880    0.5056 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3184   -0.0658    0.2665 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7439    0.4733    0.0049 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5888   -0.7594   -0.2250 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5172   -1.5422    0.9333 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9878   -0.4594   -0.6305 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7504    0.3216    0.3432 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2386    0.6787    1.4253 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0626    0.6724    0.0631 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8525    0.5915   -1.5944 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1959   -0.7354    1.3457 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9848    0.6996    0.6490 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9417    1.0877   -0.7735 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5841    1.1570    0.9854 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2729   -1.2672   -0.9398 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8337   -1.2366    0.8531 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5387    0.4340   -1.3207 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8948   -1.0685   -0.6072 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9804   -0.0429    1.7005 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6333    1.4702    1.0602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8299    1.6795    1.3455 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4450    1.7320   -0.4116 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0402   -0.6827   -0.6291 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4090   -0.7032    1.1594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7368    1.1413   -0.8764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9992    1.0084    0.9413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0830   -1.3277   -1.0341 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4754   -0.9497    1.7319 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4856   -1.4228   -0.8710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9282    0.0844   -1.6174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6631    1.0829    0.7842 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
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
  3 18  1  0
  4 19  1  0
  4 20  1  0
  5 21  1  0
  5 22  1  0
  6 23  1  0
  6 24  1  0
  7 25  1  0
  7 26  1  0
  8 27  1  0
  8 28  1  0
  9 29  1  0
  9 30  1  0
 10 31  1  0
 10 32  1  0
 11 33  1  0
 11 34  1  0
 12 35  1  0
 13 36  1  0
 14 37  1  0
 14 38  1  0
 17 39  1  0
M  END

3-Hydroxydodecanedioic acid.mol
  Mrv1652305261923572D          

 17 16  0  0  0  0            999 V2000
    3.2151    1.0312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2151    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 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7862   -1.4438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0717   -1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -1.4438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572   -1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717   -1.4438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7862   -1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5006   -1.4438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2151   -1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5006    1.4438    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9296    1.4438    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2151   -0.2063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9296   -1.4438    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7862    0.2062    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
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
  1 13  2  0  0  0  0
  1 14  1  0  0  0  0
 12 15  2  0  0  0  0
 12 16  1  0  0  0  0
  3 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000193

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C12H22O5/c13-10(9-12(16)17)7-5-3-1-2-4-6-8-11(14)15/h10,13H,1-9H2,(H,14,15)(H,16,17)

> <INCHI_KEY>
FYVQCLGZFXHEGL-UHFFFAOYSA-N

> <FORMULA>
C12H22O5

> <MOLECULAR_WEIGHT>
246.3001

> <EXACT_MASS>
246.146723814

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
27.581064277535233

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-hydroxydodecanedioic acid

> <ALOGPS_LOGP>
1.49

> <JCHEM_LOGP>
1.9272552856666674

> <ALOGPS_LOGS>
-2.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.135176336436662

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.488693485812775

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7985874263187887

> <JCHEM_POLAR_SURFACE_AREA>
94.83

> <JCHEM_REFRACTIVITY>
61.8605

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.30e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxydodecanedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0000413
     RDKit          3D
3-Hydroxydodecanedioic acid
 39 38  0  0  0  0  0  0  0  0999 V2000
    5.4071   -2.1119   -0.8516 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6775   -0.8959   -0.7467 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4151   -0.3136   -1.7863 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2361   -0.1100    0.4254 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8715    0.4784    0.1521 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9071   -0.6346   -0.0976 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4984   -0.1590   -0.3869 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9881    0.6073    0.7839 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4104    1.0880    0.5056 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3184   -0.0658    0.2665 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7439    0.4733    0.0049 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5888   -0.7594   -0.2250 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5172   -1.5422    0.9333 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9878   -0.4594   -0.6305 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7504    0.3216    0.3432 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2386    0.6787    1.4253 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0626    0.6724    0.0631 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8525    0.5915   -1.5944 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1959   -0.7354    1.3457 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9848    0.6996    0.6490 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9417    1.0877   -0.7735 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5841    1.1570    0.9854 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2729   -1.2672   -0.9398 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8337   -1.2366    0.8531 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5387    0.4340   -1.3207 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8948   -1.0685   -0.6072 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9804   -0.0429    1.7005 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6333    1.4702    1.0602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8299    1.6795    1.3455 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4450    1.7320   -0.4116 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0402   -0.6827   -0.6291 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4090   -0.7032    1.1594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7368    1.1413   -0.8764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9992    1.0084    0.9413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0830   -1.3277   -1.0341 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4754   -0.9497    1.7319 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4856   -1.4228   -0.8710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9282    0.0844   -1.6174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6631    1.0829    0.7842 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
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
  3 18  1  0
  4 19  1  0
  4 20  1  0
  5 21  1  0
  5 22  1  0
  6 23  1  0
  6 24  1  0
  7 25  1  0
  7 26  1  0
  8 27  1  0
  8 28  1  0
  9 29  1  0
  9 30  1  0
 10 31  1  0
 10 32  1  0
 11 33  1  0
 11 34  1  0
 12 35  1  0
 13 36  1  0
 14 37  1  0
 14 38  1  0
 17 39  1  0
M  END

HEADER    PROTEIN                                 26-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 3-Hydroxydodecanedioic acid.mol                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-19         0                                  
HETATM    1  C   UNK     0       6.002   1.925   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.002   0.385   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.668  -0.385   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.668  -1.925   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.334  -2.695   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.001  -1.925   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.667  -2.695   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.667  -1.925   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.001  -2.695   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -3.334  -1.925   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -4.668  -2.695   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -6.002  -1.925   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       4.668   2.695   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       7.335   2.695   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -6.002  -0.385   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -7.335  -2.695   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       3.334   0.385   0.000  0.00  0.00           O+0
CONECT    1    2   13   14                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4   17                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   15   16                                                  
CONECT   13    1                                                            
CONECT   14    1                                                            
CONECT   15   12                                                            
CONECT   16   12                                                            
CONECT   17    3                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   32    0
END

COMPND    HMDB0000413
HETATM    1  O1  UNL     1       5.407  -2.112  -0.852  1.00  0.00           O  
HETATM    2  C1  UNL     1       5.678  -0.896  -0.747  1.00  0.00           C  
HETATM    3  O2  UNL     1       6.415  -0.314  -1.786  1.00  0.00           O  
HETATM    4  C2  UNL     1       5.236  -0.110   0.425  1.00  0.00           C  
HETATM    5  C3  UNL     1       3.871   0.478   0.152  1.00  0.00           C  
HETATM    6  C4  UNL     1       2.907  -0.635  -0.098  1.00  0.00           C  
HETATM    7  C5  UNL     1       1.498  -0.159  -0.387  1.00  0.00           C  
HETATM    8  C6  UNL     1       0.988   0.607   0.784  1.00  0.00           C  
HETATM    9  C7  UNL     1      -0.410   1.088   0.506  1.00  0.00           C  
HETATM   10  C8  UNL     1      -1.318  -0.066   0.267  1.00  0.00           C  
HETATM   11  C9  UNL     1      -2.744   0.473   0.005  1.00  0.00           C  
HETATM   12  C10 UNL     1      -3.589  -0.759  -0.225  1.00  0.00           C  
HETATM   13  O3  UNL     1      -3.517  -1.542   0.933  1.00  0.00           O  
HETATM   14  C11 UNL     1      -4.988  -0.459  -0.630  1.00  0.00           C  
HETATM   15  C12 UNL     1      -5.750   0.322   0.343  1.00  0.00           C  
HETATM   16  O4  UNL     1      -5.239   0.679   1.425  1.00  0.00           O  
HETATM   17  O5  UNL     1      -7.063   0.672   0.063  1.00  0.00           O  
HETATM   18  H1  UNL     1       6.853   0.592  -1.594  1.00  0.00           H  
HETATM   19  H2  UNL     1       5.196  -0.735   1.346  1.00  0.00           H  
HETATM   20  H3  UNL     1       5.985   0.700   0.649  1.00  0.00           H  
HETATM   21  H4  UNL     1       3.942   1.088  -0.773  1.00  0.00           H  
HETATM   22  H5  UNL     1       3.584   1.157   0.985  1.00  0.00           H  
HETATM   23  H6  UNL     1       3.273  -1.267  -0.940  1.00  0.00           H  
HETATM   24  H7  UNL     1       2.834  -1.237   0.853  1.00  0.00           H  
HETATM   25  H8  UNL     1       1.539   0.434  -1.321  1.00  0.00           H  
HETATM   26  H9  UNL     1       0.895  -1.068  -0.607  1.00  0.00           H  
HETATM   27  H10 UNL     1       0.980  -0.043   1.701  1.00  0.00           H  
HETATM   28  H11 UNL     1       1.633   1.470   1.060  1.00  0.00           H  
HETATM   29  H12 UNL     1      -0.830   1.680   1.346  1.00  0.00           H  
HETATM   30  H13 UNL     1      -0.445   1.732  -0.412  1.00  0.00           H  
HETATM   31  H14 UNL     1      -1.040  -0.683  -0.629  1.00  0.00           H  
HETATM   32  H15 UNL     1      -1.409  -0.703   1.159  1.00  0.00           H  
HETATM   33  H16 UNL     1      -2.737   1.141  -0.876  1.00  0.00           H  
HETATM   34  H17 UNL     1      -2.999   1.008   0.941  1.00  0.00           H  
HETATM   35  H18 UNL     1      -3.083  -1.328  -1.034  1.00  0.00           H  
HETATM   36  H19 UNL     1      -3.475  -0.950   1.732  1.00  0.00           H  
HETATM   37  H20 UNL     1      -5.486  -1.423  -0.871  1.00  0.00           H  
HETATM   38  H21 UNL     1      -4.928   0.084  -1.617  1.00  0.00           H  
HETATM   39  H22 UNL     1      -7.663   1.083   0.784  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   18
CONECT    4    5   19   20
CONECT    5    6   21   22
CONECT    6    7   23   24
CONECT    7    8   25   26
CONECT    8    9   27   28
CONECT    9   10   29   30
CONECT   10   11   31   32
CONECT   11   12   33   34
CONECT   12   13   14   35
CONECT   13   36
CONECT   14   15   37   38
CONECT   15   16   16   17
CONECT   17   39
END

HMDB0000413
     RDKit          3D
3-Hydroxydodecanedioic acid
 39 38  0  0  0  0  0  0  0  0999 V2000
    5.4071   -2.1119   -0.8516 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6775   -0.8959   -0.7467 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4151   -0.3136   -1.7863 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2361   -0.1100    0.4254 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8715    0.4784    0.1521 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9071   -0.6346   -0.0976 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4984   -0.1590   -0.3869 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9881    0.6073    0.7839 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4104    1.0880    0.5056 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3184   -0.0658    0.2665 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7439    0.4733    0.0049 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5888   -0.7594   -0.2250 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5172   -1.5422    0.9333 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9878   -0.4594   -0.6305 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7504    0.3216    0.3432 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2386    0.6787    1.4253 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0626    0.6724    0.0631 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8525    0.5915   -1.5944 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1959   -0.7354    1.3457 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9848    0.6996    0.6490 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9417    1.0877   -0.7735 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5841    1.1570    0.9854 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2729   -1.2672   -0.9398 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8337   -1.2366    0.8531 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5387    0.4340   -1.3207 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8948   -1.0685   -0.6072 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9804   -0.0429    1.7005 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6333    1.4702    1.0602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8299    1.6795    1.3455 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4450    1.7320   -0.4116 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0402   -0.6827   -0.6291 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4090   -0.7032    1.1594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7368    1.1413   -0.8764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9992    1.0084    0.9413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0830   -1.3277   -1.0341 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4754   -0.9497    1.7319 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4856   -1.4228   -0.8710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9282    0.0844   -1.6174 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6631    1.0829    0.7842 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
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
  3 18  1  0
  4 19  1  0
  4 20  1  0
  5 21  1  0
  5 22  1  0
  6 23  1  0
  6 24  1  0
  7 25  1  0
  7 26  1  0
  8 27  1  0
  8 28  1  0
  9 29  1  0
  9 30  1  0
 10 31  1  0
 10 32  1  0
 11 33  1  0
 11 34  1  0
 12 35  1  0
 13 36  1  0
 14 37  1  0
 14 38  1  0
 17 39  1  0
M  END

View in JSmol

Synonyms

Value	Source
3-Hydroxydodecanedioate	Generator
3-Hydroxy-dodecanedioate	HMDB

Chemical Formula

C₁₂H₂₂O₅

Average Mass

246.3001 Da

Monoisotopic Mass

246.14672 Da

IUPAC Name

3-hydroxydodecanedioic acid

Traditional Name

3-hydroxydodecanedioic acid

CAS Registry Number

34574-69-1

SMILES

OC(CCCCCCCCC(O)=O)CC(O)=O

InChI Identifier

InChI=1S/C12H22O5/c13-10(9-12(16)17)7-5-3-1-2-4-6-8-11(14)15/h10,13H,1-9H2,(H,14,15)(H,16,17)

InChI Key

FYVQCLGZFXHEGL-UHFFFAOYSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, CD₃OD, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phaseolus vulgaris	LOTUS Database	35616633
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

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.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Hydroxy acids and derivatives

Sub Class

Medium-chain hydroxy acids and derivatives

Direct Parent

Medium-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 Framework

Aliphatic acyclic compounds

External Descriptors

Dicarboxylic acids (LMFA01170089 )

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	0.83 g/L	ALOGPS
logP	1.49	ALOGPS
logP	1.93	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	4.49	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	94.83 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	61.86 m³·mol⁻¹	ChemAxon
Polarizability	27.58 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0000413

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB022029

KNApSAcK ID

Not Available

Chemspider ID

13628081

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

5402

PubChem Compound

16663321

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Boulat O, Gradwohl M, Matos V, Guignard JP, Bachmann C: Organic acids in the second morning urine in a healthy Swiss paediatric population. Clin Chem Lab Med. 2003 Dec;41(12):1642-58. [PubMed:14708889 ]
Chickos JS, Way BA, Wilson J, Shaharuzzaman M, Laird J, Landt M: Analysis of 3-hydroxydodecanedioic acid for studies of fatty acid metabolic disorders: preparation of stable isotope standards. J Clin Lab Anal. 2002;16(2):115-20. [PubMed:11948802 ]
Korman SH, Mandel H, Gutman A: Characteristic urine organic acid profile in peroxisomal biogenesis disorders. J Inherit Metab Dis. 2000 Jun;23(4):425-8. [PubMed:10896310 ]
Shi D, Tan Q, Ruan J, Tian Z, Wang X, Liu J, Liu X, Liu Z, Zhang Y, Sun C, Niu Y: Aging-related markers in rat urine revealed by dynamic metabolic profiling using machine learning. Aging (Albany NY). 2021 May 19;13(10):14322-14341. doi: 10.18632/aging.203046. Epub 2021 May 19. [PubMed:34016789 ]

Showing NP-Card for 3-Hydroxydodecanedioic acid (NP0000193)

MOL for NP0000193 (3-Hydroxydodecanedioic acid)

3D MOL for NP0000193 (3-Hydroxydodecanedioic acid)

3D SDF for NP0000193 (3-Hydroxydodecanedioic acid)

3D-SDF for NP0000193 (3-Hydroxydodecanedioic acid)

PDB for NP0000193 (3-Hydroxydodecanedioic acid)

3D PDB for NP0000193 (3-Hydroxydodecanedioic acid)

SMILES for NP0000193 (3-Hydroxydodecanedioic acid)

INCHI for NP0000193 (3-Hydroxydodecanedioic acid)

Structure for NP0000193 (3-Hydroxydodecanedioic acid)

3D Structure for NP0000193 (3-Hydroxydodecanedioic acid)