Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-06-12 17:33:17 UTC

Update Date

2019-07-23 07:14:34 UTC

HMDB ID

HMDB0060545

Secondary Accession Numbers

HMDB60545

Metabolite Identification

Common Name

O-Desmethylindomethacin

Description

O-Desmethylindomethacin is a metaboite of Indomethacin. Indomethacin is metabolized in humans by O-demethylation, and by acyl glucuronidation to the 1-O-glucuronide. Indomethacin and O-desmethylindomethacin may be glucuronidated in the kidney. Probenecid is a known substrate for renal glucuronidation. If indomethacin is glucuronidated in the human kidney like probenecid, then this glucuronidation might be reduced or inhibited under probenecid co-medication. (PMID: 8156046 )

Structure

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

HMDB0060545
     RDKit          3D
O-Desmethylindomethacin
 38 40  0  0  0  0  0  0  0  0999 V2000
   -1.6364   -2.7257   -0.2385 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3343   -1.2639   -0.2364 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2318   -0.2367   -0.3482 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7063   -0.3045   -0.4955 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3741   -0.6329    0.7879 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6871   -0.8119    1.8227 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7444   -0.7451    0.8615 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4706    0.9205   -0.2939 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8279    2.2589   -0.3547 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8928    3.2614   -0.2772 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3334    4.5699   -0.3459 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4299    2.9083   -0.1356 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8368    1.5931   -0.0701 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1149    0.6005   -0.1497 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0688   -0.7598   -0.1180 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1130   -1.5179    0.0104 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9810   -2.7986    0.0440 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4710   -1.0558    0.1103 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2694   -0.8222   -1.0043 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5610   -0.4033   -0.8907 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1499   -0.1870    0.3476 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8110    0.3519    0.5226 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    4.3754   -0.4133    1.4576 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0712   -0.8359    1.3515 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2341   -3.1623    0.6728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1098   -3.2334   -1.0988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7038   -2.8996   -0.4112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1353    0.6548   -0.8474 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9537   -1.0714   -1.2410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1867   -1.6518    0.9926 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8920    2.4602   -0.4663 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7319    5.3742   -0.2979 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1990    3.6985   -0.0699 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8826    1.3697    0.0441 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8321   -0.9836   -1.9840 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1958   -0.2164   -1.7565 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7545   -0.2689    2.4642 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4365   -1.0201    2.2330 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  3  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 10 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  2  0
 21 22  1  0
 21 23  1  0
 23 24  2  0
 15  2  1  0
 24 18  1  0
 14  8  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  4 28  1  0
  4 29  1  0
  7 30  1  0
  9 31  1  0
 11 32  1  0
 12 33  1  0
 13 34  1  0
 19 35  1  0
 20 36  1  0
 23 37  1  0
 24 38  1  0
M  END

328
  Mrv0541 02271201052D          

 24 26  0  0  0  0            999 V2000
    8.7741    2.4559    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -0.4977    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9939    2.3894    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2503   -2.5191    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1866   -1.5648    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2886    0.9912    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.2886   -0.3367    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5080   -0.0852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5080    0.7398    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7701    0.3273    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5449   -1.1209    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935   -0.4977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935    1.1523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5951    0.3273    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5449    1.7754    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791   -0.0852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    0.7398    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3522    1.9455    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9939   -1.7349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6086    2.7297    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9032    1.3314    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4158    2.8999    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7105    1.5016    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9668    2.2858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 24  1  0  0  0  0
  2 16  1  0  0  0  0
  3 15  2  0  0  0  0
  4 19  1  0  0  0  0
  5 19  2  0  0  0  0
  6  9  1  0  0  0  0
  6 10  1  0  0  0  0
  6 15  1  0  0  0  0
  7  8  1  0  0  0  0
  7 10  2  0  0  0  0
  7 11  1  0  0  0  0
  8  9  2  0  0  0  0
  8 12  1  0  0  0  0
  9 13  1  0  0  0  0
 10 14  1  0  0  0  0
 11 19  1  0  0  0  0
 12 16  2  0  0  0  0
 13 17  2  0  0  0  0
 15 18  1  0  0  0  0
 16 17  1  0  0  0  0
 18 20  2  0  0  0  0
 18 21  1  0  0  0  0
 20 22  1  0  0  0  0
 21 23  2  0  0  0  0
 22 24  2  0  0  0  0
 23 24  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060545

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=C(CC(O)=O)C2=C(C=CC(O)=C2)N1C(=O)C1=CC=C(Cl)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C18H14ClNO4/c1-10-14(9-17(22)23)15-8-13(21)6-7-16(15)20(10)18(24)11-2-4-12(19)5-3-11/h2-8,21H,9H2,1H3,(H,22,23)

> <INCHI_KEY>
KMLNWQPYFBIALN-UHFFFAOYSA-N

> <FORMULA>
C18H14ClNO4

> <MOLECULAR_WEIGHT>
343.761

> <EXACT_MASS>
343.061135648

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
34.44040379956778

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-[1-(4-chlorobenzoyl)-5-hydroxy-2-methyl-1H-indol-3-yl]acetic acid

> <ALOGPS_LOGP>
3.59

> <JCHEM_LOGP>
3.383780323666666

> <ALOGPS_LOGS>
-4.37

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.541041769849194

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.7346263441462626

> <JCHEM_PKA_STRONGEST_BASIC>
-2.2663561251577935

> <JCHEM_POLAR_SURFACE_AREA>
79.53

> <JCHEM_REFRACTIVITY>
90.32830000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.46e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[1-(4-chlorobenzoyl)-5-hydroxy-2-methylindol-3-yl]acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0060545
     RDKit          3D
O-Desmethylindomethacin
 38 40  0  0  0  0  0  0  0  0999 V2000
   -1.6364   -2.7257   -0.2385 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3343   -1.2639   -0.2364 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2318   -0.2367   -0.3482 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7063   -0.3045   -0.4955 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3741   -0.6329    0.7879 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6871   -0.8119    1.8227 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7444   -0.7451    0.8615 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4706    0.9205   -0.2939 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8279    2.2589   -0.3547 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8928    3.2614   -0.2772 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3334    4.5699   -0.3459 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4299    2.9083   -0.1356 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8368    1.5931   -0.0701 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1149    0.6005   -0.1497 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0688   -0.7598   -0.1180 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1130   -1.5179    0.0104 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9810   -2.7986    0.0440 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4710   -1.0558    0.1103 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2694   -0.8222   -1.0043 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5610   -0.4033   -0.8907 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1499   -0.1870    0.3476 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8110    0.3519    0.5226 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    4.3754   -0.4133    1.4576 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0712   -0.8359    1.3515 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2341   -3.1623    0.6728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1098   -3.2334   -1.0988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7038   -2.8996   -0.4112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1353    0.6548   -0.8474 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9537   -1.0714   -1.2410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1867   -1.6518    0.9926 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8920    2.4602   -0.4663 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7319    5.3742   -0.2979 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1990    3.6985   -0.0699 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8826    1.3697    0.0441 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8321   -0.9836   -1.9840 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1958   -0.2164   -1.7565 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7545   -0.2689    2.4642 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4365   -1.0201    2.2330 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  3  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 10 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  2  0
 21 22  1  0
 21 23  1  0
 23 24  2  0
 15  2  1  0
 24 18  1  0
 14  8  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  4 28  1  0
  4 29  1  0
  7 30  1  0
  9 31  1  0
 11 32  1  0
 12 33  1  0
 13 34  1  0
 19 35  1  0
 20 36  1  0
 23 37  1  0
 24 38  1  0
M  END

HEADER    PROTEIN                                 27-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 328                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-FEB-12         0                                  
HETATM    1 Cl   UNK     0      16.378   4.584   0.000  0.00  0.00          Cl+0
HETATM    2  O   UNK     0       4.414  -0.929   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       9.322   4.460   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       9.801  -4.702   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       7.815  -2.921   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0       9.872   1.850   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       9.872  -0.629   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.415  -0.159   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.415   1.381   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      10.771   0.611   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.350  -2.092   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.081  -0.929   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.081   2.151   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      12.311   0.611   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      10.350   3.314   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.748  -0.159   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.748   1.381   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      11.857   3.632   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       9.322  -3.238   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      12.336   5.095   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      12.886   2.485   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      13.843   5.413   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      14.393   2.803   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      14.871   4.267   0.000  0.00  0.00           C+0
CONECT    1   24                                                            
CONECT    2   16                                                            
CONECT    3   15                                                            
CONECT    4   19                                                            
CONECT    5   19                                                            
CONECT    6    9   10   15                                                  
CONECT    7    8   10   11                                                  
CONECT    8    7    9   12                                                  
CONECT    9    6    8   13                                                  
CONECT   10    6    7   14                                                  
CONECT   11    7   19                                                       
CONECT   12    8   16                                                       
CONECT   13    9   17                                                       
CONECT   14   10                                                            
CONECT   15    3    6   18                                                  
CONECT   16    2   12   17                                                  
CONECT   17   13   16                                                       
CONECT   18   15   20   21                                                  
CONECT   19    4    5   11                                                  
CONECT   20   18   22                                                       
CONECT   21   18   23                                                       
CONECT   22   20   24                                                       
CONECT   23   21   24                                                       
CONECT   24    1   22   23                                                  
MASTER        0    0    0    0    0    0    0    0   24    0   52    0
END

COMPND    HMDB0060545
HETATM    1  C1  UNL     1      -1.636  -2.726  -0.238  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.334  -1.264  -0.236  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.232  -0.237  -0.348  1.00  0.00           C  
HETATM    4  C4  UNL     1      -3.706  -0.305  -0.496  1.00  0.00           C  
HETATM    5  C5  UNL     1      -4.374  -0.633   0.788  1.00  0.00           C  
HETATM    6  O1  UNL     1      -3.687  -0.812   1.823  1.00  0.00           O  
HETATM    7  O2  UNL     1      -5.744  -0.745   0.862  1.00  0.00           O  
HETATM    8  C6  UNL     1      -1.471   0.921  -0.294  1.00  0.00           C  
HETATM    9  C7  UNL     1      -1.828   2.259  -0.355  1.00  0.00           C  
HETATM   10  C8  UNL     1      -0.893   3.261  -0.277  1.00  0.00           C  
HETATM   11  O3  UNL     1      -1.333   4.570  -0.346  1.00  0.00           O  
HETATM   12  C9  UNL     1       0.430   2.908  -0.136  1.00  0.00           C  
HETATM   13  C10 UNL     1       0.837   1.593  -0.070  1.00  0.00           C  
HETATM   14  C11 UNL     1      -0.115   0.601  -0.150  1.00  0.00           C  
HETATM   15  N1  UNL     1      -0.069  -0.760  -0.118  1.00  0.00           N  
HETATM   16  C12 UNL     1       1.113  -1.518   0.010  1.00  0.00           C  
HETATM   17  O4  UNL     1       0.981  -2.799   0.044  1.00  0.00           O  
HETATM   18  C13 UNL     1       2.471  -1.056   0.110  1.00  0.00           C  
HETATM   19  C14 UNL     1       3.269  -0.822  -1.004  1.00  0.00           C  
HETATM   20  C15 UNL     1       4.561  -0.403  -0.891  1.00  0.00           C  
HETATM   21  C16 UNL     1       5.150  -0.187   0.348  1.00  0.00           C  
HETATM   22 CL1  UNL     1       6.811   0.352   0.523  1.00  0.00          CL  
HETATM   23  C17 UNL     1       4.375  -0.413   1.458  1.00  0.00           C  
HETATM   24  C18 UNL     1       3.071  -0.836   1.352  1.00  0.00           C  
HETATM   25  H1  UNL     1      -1.234  -3.162   0.673  1.00  0.00           H  
HETATM   26  H2  UNL     1      -1.110  -3.233  -1.099  1.00  0.00           H  
HETATM   27  H3  UNL     1      -2.704  -2.900  -0.411  1.00  0.00           H  
HETATM   28  H4  UNL     1      -4.135   0.655  -0.847  1.00  0.00           H  
HETATM   29  H5  UNL     1      -3.954  -1.071  -1.241  1.00  0.00           H  
HETATM   30  H6  UNL     1      -6.187  -1.652   0.993  1.00  0.00           H  
HETATM   31  H7  UNL     1      -2.892   2.460  -0.466  1.00  0.00           H  
HETATM   32  H8  UNL     1      -0.732   5.374  -0.298  1.00  0.00           H  
HETATM   33  H9  UNL     1       1.199   3.699  -0.070  1.00  0.00           H  
HETATM   34  H10 UNL     1       1.883   1.370   0.044  1.00  0.00           H  
HETATM   35  H11 UNL     1       2.832  -0.984  -1.984  1.00  0.00           H  
HETATM   36  H12 UNL     1       5.196  -0.216  -1.756  1.00  0.00           H  
HETATM   37  H13 UNL     1       4.755  -0.269   2.464  1.00  0.00           H  
HETATM   38  H14 UNL     1       2.437  -1.020   2.233  1.00  0.00           H  
CONECT    1    2   25   26   27
CONECT    2    3    3   15
CONECT    3    4    8
CONECT    4    5   28   29
CONECT    5    6    6    7
CONECT    7   30
CONECT    8    9    9   14
CONECT    9   10   31
CONECT   10   11   12   12
CONECT   11   32
CONECT   12   13   33
CONECT   13   14   14   34
CONECT   14   15
CONECT   15   16
CONECT   16   17   17   18
CONECT   18   19   19   24
CONECT   19   20   35
CONECT   20   21   21   36
CONECT   21   22   23
CONECT   23   24   24   37
CONECT   24   38
END

HMDB0060545
     RDKit          3D
O-Desmethylindomethacin
 38 40  0  0  0  0  0  0  0  0999 V2000
   -1.6364   -2.7257   -0.2385 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3343   -1.2639   -0.2364 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2318   -0.2367   -0.3482 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7063   -0.3045   -0.4955 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3741   -0.6329    0.7879 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6871   -0.8119    1.8227 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7444   -0.7451    0.8615 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4706    0.9205   -0.2939 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8279    2.2589   -0.3547 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8928    3.2614   -0.2772 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3334    4.5699   -0.3459 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4299    2.9083   -0.1356 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8368    1.5931   -0.0701 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1149    0.6005   -0.1497 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0688   -0.7598   -0.1180 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1130   -1.5179    0.0104 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9810   -2.7986    0.0440 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4710   -1.0558    0.1103 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2694   -0.8222   -1.0043 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5610   -0.4033   -0.8907 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1499   -0.1870    0.3476 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8110    0.3519    0.5226 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    4.3754   -0.4133    1.4576 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0712   -0.8359    1.3515 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2341   -3.1623    0.6728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1098   -3.2334   -1.0988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7038   -2.8996   -0.4112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1353    0.6548   -0.8474 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9537   -1.0714   -1.2410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1867   -1.6518    0.9926 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8920    2.4602   -0.4663 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7319    5.3742   -0.2979 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1990    3.6985   -0.0699 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8826    1.3697    0.0441 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8321   -0.9836   -1.9840 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1958   -0.2164   -1.7565 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7545   -0.2689    2.4642 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4365   -1.0201    2.2330 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  3  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 10 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  2  0
 21 22  1  0
 21 23  1  0
 23 24  2  0
 15  2  1  0
 24 18  1  0
 14  8  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  4 28  1  0
  4 29  1  0
  7 30  1  0
  9 31  1  0
 11 32  1  0
 12 33  1  0
 13 34  1  0
 19 35  1  0
 20 36  1  0
 23 37  1  0
 24 38  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Desmethyl-indomethacin	HMDB
5-Hydroxyindomethacin sulfate(1:1)	HMDB
5-Hydroxyindomethacin	HMDB

Chemical Formula

C₁₈H₁₄ClNO₄

Average Molecular Weight

343.761

Monoisotopic Molecular Weight

343.061135648

IUPAC Name

2-[1-(4-chlorobenzoyl)-5-hydroxy-2-methyl-1H-indol-3-yl]acetic acid

Traditional Name

[1-(4-chlorobenzoyl)-5-hydroxy-2-methylindol-3-yl]acetic acid

CAS Registry Number

Not Available

SMILES

CC1=C(CC(O)=O)C2=C(C=CC(O)=C2)N1C(=O)C1=CC=C(Cl)C=C1

InChI Identifier

InChI=1S/C18H14ClNO4/c1-10-14(9-17(22)23)15-8-13(21)6-7-16(15)20(10)18(24)11-2-4-12(19)5-3-11/h2-8,21H,9H2,1H3,(H,22,23)

InChI Key

KMLNWQPYFBIALN-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as benzoylindoles. These are organic compounds containing an indole attached to a benzoyl moiety through the acyl group.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Benzoylindoles

Direct Parent

Benzoylindoles

Alternative Parents

Substituents

Benzoylindole
Indole-3-acetic acid derivative
Indolyl carboxylic acid derivative
Indolecarboxylic acid derivative
4-halobenzoic acid or derivatives
Halobenzoic acid or derivatives
3-alkylindole
Hydroxyindole
Indole
Benzoic acid or derivatives
Benzoyl
1-hydroxy-2-unsubstituted benzenoid
Chlorobenzene
Halobenzene
Monocyclic benzene moiety
Benzenoid
Aryl chloride
Substituted pyrrole
Aryl halide
Pyrrole
Heteroaromatic compound
Azacycle
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Organooxygen compound
Organic oxygen compound
Organic nitrogen compound
Carbonyl group
Hydrocarbon derivative
Organic oxide
Organonitrogen compound
Organochloride
Organohalogen compound
Organopnictogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (HMDB: HMDB0060545)

Organ

Kidney (HMDB: HMDB0060545)
Liver (HMDB: HMDB0060545)

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0060545)

Cellular substructure

Cytoplasm (HMDB: HMDB0060545)
Membrane (HMDB: HMDB0060545)

Source

Endogenous

Endogenous (HMDB: HMDB0060545)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular 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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.015 g/L	ALOGPS
logP	3.59	ALOGPS
logP	3.38	ChemAxon
logS	-4.4	ALOGPS
pKa (Strongest Acidic)	3.73	ChemAxon
pKa (Strongest Basic)	-2.3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	79.53 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	90.33 m³·mol⁻¹	ChemAxon
Polarizability	34.44 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	181.327	30932474
DeepCCS	[M-H]-	178.969	30932474
DeepCCS	[M-2H]-	213.246	30932474
DeepCCS	[M+Na]+	188.474	30932474
AllCCS	[M+H]+	176.6	32859911
AllCCS	[M+H-H2O]+	173.5	32859911
AllCCS	[M+NH4]+	179.5	32859911
AllCCS	[M+Na]+	180.3	32859911
AllCCS	[M-H]-	176.0	32859911
AllCCS	[M+Na-2H]-	175.2	32859911
AllCCS	[M+HCOO]-	174.3	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	7.27 minutes	32390414
Predicted by Siyang on May 30, 2022	13.5097 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.3 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2289.5 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	338.5 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	172.4 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	195.2 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	303.3 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	716.7 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	489.5 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	75.2 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1134.8 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	469.8 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1504.5 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	401.7 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	413.4 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	283.5 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	126.6 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	76.6 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
O-Desmethylindomethacin	CC1=C(CC(O)=O)C2=C(C=CC(O)=C2)N1C(=O)C1=CC=C(Cl)C=C1	4484.4	Standard polar	33892256
O-Desmethylindomethacin	CC1=C(CC(O)=O)C2=C(C=CC(O)=C2)N1C(=O)C1=CC=C(Cl)C=C1	2550.7	Standard non polar	33892256
O-Desmethylindomethacin	CC1=C(CC(O)=O)C2=C(C=CC(O)=C2)N1C(=O)C1=CC=C(Cl)C=C1	3185.9	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
O-Desmethylindomethacin,1TMS,isomer #1	CC1=C(CC(=O)O[Si](C)(C)C)C2=CC(O)=CC=C2N1C(=O)C1=CC=C(Cl)C=C1	2957.7	Semi standard non polar	33892256
O-Desmethylindomethacin,1TMS,isomer #2	CC1=C(CC(=O)O)C2=CC(O[Si](C)(C)C)=CC=C2N1C(=O)C1=CC=C(Cl)C=C1	3023.4	Semi standard non polar	33892256
O-Desmethylindomethacin,2TMS,isomer #1	CC1=C(CC(=O)O[Si](C)(C)C)C2=CC(O[Si](C)(C)C)=CC=C2N1C(=O)C1=CC=C(Cl)C=C1	2976.1	Semi standard non polar	33892256
O-Desmethylindomethacin,1TBDMS,isomer #1	CC1=C(CC(=O)O[Si](C)(C)C(C)(C)C)C2=CC(O)=CC=C2N1C(=O)C1=CC=C(Cl)C=C1	3209.9	Semi standard non polar	33892256
O-Desmethylindomethacin,1TBDMS,isomer #2	CC1=C(CC(=O)O)C2=CC(O[Si](C)(C)C(C)(C)C)=CC=C2N1C(=O)C1=CC=C(Cl)C=C1	3270.1	Semi standard non polar	33892256
O-Desmethylindomethacin,2TBDMS,isomer #1	CC1=C(CC(=O)O[Si](C)(C)C(C)(C)C)C2=CC(O[Si](C)(C)C(C)(C)C)=CC=C2N1C(=O)C1=CC=C(Cl)C=C1	3410.1	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - O-Desmethylindomethacin GC-MS (Non-derivatized) - 70eV, Positive	splash10-01p9-0931000000-08ae12731d1009bab9ae	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - O-Desmethylindomethacin GC-MS (2 TMS) - 70eV, Positive	splash10-000i-4904200000-d43c7bc4448e17e0ca47	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - O-Desmethylindomethacin GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - O-Desmethylindomethacin 10V, Positive-QTOF	splash10-004i-0019000000-abf0492a0a23ca9511fc	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - O-Desmethylindomethacin 20V, Positive-QTOF	splash10-000j-0975000000-7947cf8b43da961e7f14	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - O-Desmethylindomethacin 40V, Positive-QTOF	splash10-000i-3900000000-fba681a2d0d88f7f3dc3	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - O-Desmethylindomethacin 10V, Negative-QTOF	splash10-0007-0049000000-57ec60062d75239701c5	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - O-Desmethylindomethacin 20V, Negative-QTOF	splash10-006y-0259000000-8a8c589ccae2bd36ca5a	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - O-Desmethylindomethacin 40V, Negative-QTOF	splash10-03dr-0930000000-2a8b45256d5adfe18cea	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - O-Desmethylindomethacin 10V, Positive-QTOF	splash10-0006-0109000000-c78beb1d062424159de8	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - O-Desmethylindomethacin 20V, Positive-QTOF	splash10-000i-0966000000-95e708ac9d20e69a0e9f	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - O-Desmethylindomethacin 40V, Positive-QTOF	splash10-000i-0900000000-e31bba49f73999be4ea9	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - O-Desmethylindomethacin 10V, Negative-QTOF	splash10-0005-0095000000-7c37ad6d5b3366099ab6	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - O-Desmethylindomethacin 20V, Negative-QTOF	splash10-0002-1191000000-8d8abc587d2acc238db2	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - O-Desmethylindomethacin 40V, Negative-QTOF	splash10-001i-7950000000-13ee36355249a28d2125	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Membrane (predicted from logP)

Biospecimen Locations

Blood
Urine

Tissue Locations

Kidney
Liver

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

159665

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for O-Desmethylindomethacin (HMDB0060545)

MOL for HMDB0060545 (O-Desmethylindomethacin)

3D MOL for HMDB0060545 (O-Desmethylindomethacin)

3D SDF for HMDB0060545 (O-Desmethylindomethacin)

3D-SDF for HMDB0060545 (O-Desmethylindomethacin)

PDB for HMDB0060545 (O-Desmethylindomethacin)

3D PDB for HMDB0060545 (O-Desmethylindomethacin)

SMILES for HMDB0060545 (O-Desmethylindomethacin)

INCHI for HMDB0060545 (O-Desmethylindomethacin)

Structure for HMDB0060545 (O-Desmethylindomethacin)

3D Structure for HMDB0060545 (O-Desmethylindomethacin)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra