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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-06 15:16:51 UTC

Update Date

2022-03-07 02:51:54 UTC

HMDB ID

HMDB0015233

Secondary Accession Numbers

HMDB15233

Metabolite Identification

Common Name

Capecitabine

Description

Capecitabine, also known as xeloda or R340, belongs to the class of organic compounds known as 5'-deoxyribonucleosides. These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom. The nucleobases here are limited to purine, pyrimidine, and pyridine derivatives. Capecitabine is a drug which is used for the treatment of patients with metastatic breast cancer resistant to both paclitaxel and an anthracycline-containing chemotherapy regimen. may also be used in combination with docetaxel for the treatment of metastatic breast cancer in patients who have failed to respond to, or recurred or relasped during or following anthracycline-containing chemotherapy. capecitabine is used alone as an adjuvant therapy following the complete resection of primary tumor in patients with stage iii colon cancer when monotherapy with fluroprymidine is preferred. the use or capecitabine in combination regimens for advanced gastric cancer is currently being investigated. Capecitabine is an extremely weak basic (essentially neutral) compound (based on its pKa). capecitabine can be converted into 5'-deoxy-5-fluorouridine and meprobamate through its interaction with the enzymes liver carboxylesterase 1 and cytidine deaminase. In humans, capecitabine is involved in capecitabine metabolism pathway. Capecitabine is a potentially toxic compound.

Structure

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

HMDB0015233
     RDKit          3D
Capecitabine
 47 48  0  0  0  0  0  0  0  0999 V2000
    8.0891    0.3207   -1.2687 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1020   -0.3877    0.0704 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8604    0.0484    0.8228 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6659   -0.3554   -0.0048 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3638    0.0323    0.6529 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3221   -0.4031   -0.2258 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0044   -0.1888    0.1044 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7238    0.3850    1.1697 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9880   -0.6187   -0.7623 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3690   -0.3932   -0.4134 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6928    0.2291    0.7408 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9465    0.4726    1.1294 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2199    1.0586    2.2179 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9353    0.0719    0.3192 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3166    0.3031    0.6774 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.0133   -0.8870    0.4968 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3486   -0.5059    0.2890 C   0  0  2  0  0  0  0  0  0  0  0  0
   -7.0750   -1.7007   -0.2662 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2231    0.6225   -0.6941 C   0  0  1  0  0  0  0  0  0  0  0  0
   -7.2126    1.5670   -0.5737 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9002    1.2641   -0.3361 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.0538    2.4970    0.2687 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6857   -0.5541   -0.8460 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4021   -0.7992   -1.2360 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1100   -1.4350   -2.4174 F   0  0  0  0  0  0  0  0  0  0  0  0
    7.5935   -0.2791   -2.0577 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.1394    0.4781   -1.5899 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5920    1.3112   -1.2080 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.0040   -0.1339    0.6654 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0323   -1.4949   -0.0505 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8237   -0.4293    1.8359 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8533    1.1656    0.9365 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7281    0.1871   -0.9622 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7350   -1.4325   -0.2074 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3208    1.1427    0.6886 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2348   -0.3956    1.6489 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1929   -1.1051   -1.6674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4286    0.6573    1.7105 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7978   -0.1928    1.2493 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6782   -2.6178    0.2480 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1452   -1.6182    0.0004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9083   -1.8189   -1.3402 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1324    0.2206   -1.7243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8490    2.4567   -0.4263 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2506    1.3739   -1.2252 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1751    2.7595    0.6272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4995   -0.8783   -1.5023 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
 19 21  1  0
 21 22  1  0
 14 23  1  0
 23 24  2  0
 24 25  1  0
 24 10  1  0
 21 15  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  2 29  1  0
  2 30  1  0
  3 31  1  0
  3 32  1  0
  4 33  1  0
  4 34  1  0
  5 35  1  0
  5 36  1  0
  9 37  1  0
 15 38  1  1
 17 39  1  1
 18 40  1  0
 18 41  1  0
 18 42  1  0
 19 43  1  6
 20 44  1  0
 21 45  1  6
 22 46  1  0
 23 47  1  0
M  END

1101
  Mrv0541 02231215142D          

 25 26  0  0  1  0            999 V2000
    5.9370   -0.0354    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    5.1754   -2.9954    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0559   -2.7404    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6105   -4.4474    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791   -1.6854    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935    2.0272    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    0.7896    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5080   -1.6854    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935   -0.4479    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5080    0.7896    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8405   -2.9954    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0955   -3.7800    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.5080   -2.5104    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.9205   -3.7800    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.4054   -4.4474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2224   -1.2729    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935   -1.2729    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2224   -0.4479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5080   -0.0354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    3.6772    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    3.2647    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    4.5022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    2.4397    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935    1.2021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    4.9147    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 18  1  0  0  0  0
  2 13  1  0  0  0  0
  2 14  1  0  0  0  0
 11  3  1  1  0  0  0
 12  4  1  1  0  0  0
  5 17  2  0  0  0  0
  6 23  1  0  0  0  0
  6 24  1  0  0  0  0
  7 24  2  0  0  0  0
 13  8  1  6  0  0  0
  8 16  1  0  0  0  0
  8 17  1  0  0  0  0
  9 17  1  0  0  0  0
  9 19  2  0  0  0  0
 10 19  1  0  0  0  0
 10 24  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  6  0  0  0
 16 18  2  0  0  0  0
 18 19  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 21 23  1  0  0  0  0
 22 25  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0015233

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCOC(=O)NC1=NC(=O)N(C=C1F)[C@@H]1O[C@H](C)[C@@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C15H22FN3O6/c1-3-4-5-6-24-15(23)18-12-9(16)7-19(14(22)17-12)13-11(21)10(20)8(2)25-13/h7-8,10-11,13,20-21H,3-6H2,1-2H3,(H,17,18,22,23)/t8-,10-,11-,13-/m1/s1

> <INCHI_KEY>
GAGWJHPBXLXJQN-UORFTKCHSA-N

> <FORMULA>
C15H22FN3O6

> <MOLECULAR_WEIGHT>
359.3501

> <EXACT_MASS>
359.149263656

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
35.80629651170085

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
pentyl N-{1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-methyloxolan-2-yl]-5-fluoro-2-oxo-1,2-dihydropyrimidin-4-yl}carbamate

> <ALOGPS_LOGP>
1.17

> <JCHEM_LOGP>
0.7680360469999987

> <ALOGPS_LOGS>
-3.16

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.588438615389556

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.226097931361227

> <JCHEM_PKA_STRONGEST_BASIC>
-3.627374620495517

> <JCHEM_POLAR_SURFACE_AREA>
120.69

> <JCHEM_REFRACTIVITY>
82.746

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.48e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
capecitabine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0015233
     RDKit          3D
Capecitabine
 47 48  0  0  0  0  0  0  0  0999 V2000
    8.0891    0.3207   -1.2687 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1020   -0.3877    0.0704 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8604    0.0484    0.8228 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6659   -0.3554   -0.0048 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3638    0.0323    0.6529 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3221   -0.4031   -0.2258 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0044   -0.1888    0.1044 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7238    0.3850    1.1697 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9880   -0.6187   -0.7623 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3690   -0.3932   -0.4134 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6928    0.2291    0.7408 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9465    0.4726    1.1294 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2199    1.0586    2.2179 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9353    0.0719    0.3192 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3166    0.3031    0.6774 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.0133   -0.8870    0.4968 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3486   -0.5059    0.2890 C   0  0  2  0  0  0  0  0  0  0  0  0
   -7.0750   -1.7007   -0.2662 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2231    0.6225   -0.6941 C   0  0  1  0  0  0  0  0  0  0  0  0
   -7.2126    1.5670   -0.5737 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9002    1.2641   -0.3361 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.0538    2.4970    0.2687 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6857   -0.5541   -0.8460 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4021   -0.7992   -1.2360 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1100   -1.4350   -2.4174 F   0  0  0  0  0  0  0  0  0  0  0  0
    7.5935   -0.2791   -2.0577 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.1394    0.4781   -1.5899 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5920    1.3112   -1.2080 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.0040   -0.1339    0.6654 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0323   -1.4949   -0.0505 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8237   -0.4293    1.8359 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8533    1.1656    0.9365 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7281    0.1871   -0.9622 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7350   -1.4325   -0.2074 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3208    1.1427    0.6886 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2348   -0.3956    1.6489 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1929   -1.1051   -1.6674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4286    0.6573    1.7105 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7978   -0.1928    1.2493 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6782   -2.6178    0.2480 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1452   -1.6182    0.0004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9083   -1.8189   -1.3402 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1324    0.2206   -1.7243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8490    2.4567   -0.4263 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2506    1.3739   -1.2252 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1751    2.7595    0.6272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4995   -0.8783   -1.5023 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
 19 21  1  0
 21 22  1  0
 14 23  1  0
 23 24  2  0
 24 25  1  0
 24 10  1  0
 21 15  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  2 29  1  0
  2 30  1  0
  3 31  1  0
  3 32  1  0
  4 33  1  0
  4 34  1  0
  5 35  1  0
  5 36  1  0
  9 37  1  0
 15 38  1  1
 17 39  1  1
 18 40  1  0
 18 41  1  0
 18 42  1  0
 19 43  1  6
 20 44  1  0
 21 45  1  6
 22 46  1  0
 23 47  1  0
M  END

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 1101                                              
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  F   UNK     0      11.082  -0.066   0.000  0.00  0.00           F+0
HETATM    2  O   UNK     0       9.661  -5.591   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       5.704  -5.115   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       6.740  -8.302   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       5.748  -3.146   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       7.081   3.784   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       5.748   1.474   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0       8.415  -3.146   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0       7.081  -0.836   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0       8.415   1.474   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       7.169  -5.591   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.645  -7.056   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.415  -4.686   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.185  -7.056   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      10.090  -8.302   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.748  -2.376   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.081  -2.376   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       9.748  -0.836   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.415  -0.066   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.414   6.864   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.748   6.094   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.414   8.404   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.748   4.554   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       7.081   2.244   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       3.080   9.174   0.000  0.00  0.00           C+0
CONECT    1   18                                                            
CONECT    2   13   14                                                       
CONECT    3   11                                                            
CONECT    4   12                                                            
CONECT    5   17                                                            
CONECT    6   23   24                                                       
CONECT    7   24                                                            
CONECT    8   13   16   17                                                  
CONECT    9   17   19                                                       
CONECT   10   19   24                                                       
CONECT   11    3   12   13                                                  
CONECT   12    4   11   14                                                  
CONECT   13    2    8   11                                                  
CONECT   14    2   12   15                                                  
CONECT   15   14                                                            
CONECT   16    8   18                                                       
CONECT   17    5    8    9                                                  
CONECT   18    1   16   19                                                  
CONECT   19    9   10   18                                                  
CONECT   20   21   22                                                       
CONECT   21   20   23                                                       
CONECT   22   20   25                                                       
CONECT   23    6   21                                                       
CONECT   24    6    7   10                                                  
CONECT   25   22                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   52    0
END

COMPND    HMDB0015233
HETATM    1  C1  UNL     1       8.089   0.321  -1.269  1.00  0.00           C  
HETATM    2  C2  UNL     1       8.102  -0.388   0.070  1.00  0.00           C  
HETATM    3  C3  UNL     1       6.860   0.048   0.823  1.00  0.00           C  
HETATM    4  C4  UNL     1       5.666  -0.355  -0.005  1.00  0.00           C  
HETATM    5  C5  UNL     1       4.364   0.032   0.653  1.00  0.00           C  
HETATM    6  O1  UNL     1       3.322  -0.403  -0.226  1.00  0.00           O  
HETATM    7  C6  UNL     1       2.004  -0.189   0.104  1.00  0.00           C  
HETATM    8  O2  UNL     1       1.724   0.385   1.170  1.00  0.00           O  
HETATM    9  N1  UNL     1       0.988  -0.619  -0.762  1.00  0.00           N  
HETATM   10  C7  UNL     1      -0.369  -0.393  -0.413  1.00  0.00           C  
HETATM   11  N2  UNL     1      -0.693   0.229   0.741  1.00  0.00           N  
HETATM   12  C8  UNL     1      -1.946   0.473   1.129  1.00  0.00           C  
HETATM   13  O3  UNL     1      -2.220   1.059   2.218  1.00  0.00           O  
HETATM   14  N3  UNL     1      -2.935   0.072   0.319  1.00  0.00           N  
HETATM   15  C9  UNL     1      -4.317   0.303   0.677  1.00  0.00           C  
HETATM   16  O4  UNL     1      -5.013  -0.887   0.497  1.00  0.00           O  
HETATM   17  C10 UNL     1      -6.349  -0.506   0.289  1.00  0.00           C  
HETATM   18  C11 UNL     1      -7.075  -1.701  -0.266  1.00  0.00           C  
HETATM   19  C12 UNL     1      -6.223   0.622  -0.694  1.00  0.00           C  
HETATM   20  O5  UNL     1      -7.213   1.567  -0.574  1.00  0.00           O  
HETATM   21  C13 UNL     1      -4.900   1.264  -0.336  1.00  0.00           C  
HETATM   22  O6  UNL     1      -5.054   2.497   0.269  1.00  0.00           O  
HETATM   23  C14 UNL     1      -2.686  -0.554  -0.846  1.00  0.00           C  
HETATM   24  C15 UNL     1      -1.402  -0.799  -1.236  1.00  0.00           C  
HETATM   25  F1  UNL     1      -1.110  -1.435  -2.417  1.00  0.00           F  
HETATM   26  H1  UNL     1       7.594  -0.279  -2.058  1.00  0.00           H  
HETATM   27  H2  UNL     1       9.139   0.478  -1.590  1.00  0.00           H  
HETATM   28  H3  UNL     1       7.592   1.311  -1.208  1.00  0.00           H  
HETATM   29  H4  UNL     1       9.004  -0.134   0.665  1.00  0.00           H  
HETATM   30  H5  UNL     1       8.032  -1.495  -0.050  1.00  0.00           H  
HETATM   31  H6  UNL     1       6.824  -0.429   1.836  1.00  0.00           H  
HETATM   32  H7  UNL     1       6.853   1.166   0.937  1.00  0.00           H  
HETATM   33  H8  UNL     1       5.728   0.187  -0.962  1.00  0.00           H  
HETATM   34  H9  UNL     1       5.735  -1.433  -0.207  1.00  0.00           H  
HETATM   35  H10 UNL     1       4.321   1.143   0.689  1.00  0.00           H  
HETATM   36  H11 UNL     1       4.235  -0.396   1.649  1.00  0.00           H  
HETATM   37  H12 UNL     1       1.193  -1.105  -1.667  1.00  0.00           H  
HETATM   38  H13 UNL     1      -4.429   0.657   1.711  1.00  0.00           H  
HETATM   39  H14 UNL     1      -6.798  -0.193   1.249  1.00  0.00           H  
HETATM   40  H15 UNL     1      -6.678  -2.618   0.248  1.00  0.00           H  
HETATM   41  H16 UNL     1      -8.145  -1.618   0.000  1.00  0.00           H  
HETATM   42  H17 UNL     1      -6.908  -1.819  -1.340  1.00  0.00           H  
HETATM   43  H18 UNL     1      -6.132   0.221  -1.724  1.00  0.00           H  
HETATM   44  H19 UNL     1      -6.849   2.457  -0.426  1.00  0.00           H  
HETATM   45  H20 UNL     1      -4.251   1.374  -1.225  1.00  0.00           H  
HETATM   46  H21 UNL     1      -4.175   2.760   0.627  1.00  0.00           H  
HETATM   47  H22 UNL     1      -3.500  -0.878  -1.502  1.00  0.00           H  
CONECT    1    2   26   27   28
CONECT    2    3   29   30
CONECT    3    4   31   32
CONECT    4    5   33   34
CONECT    5    6   35   36
CONECT    6    7
CONECT    7    8    8    9
CONECT    9   10   37
CONECT   10   11   11   24
CONECT   11   12
CONECT   12   13   13   14
CONECT   14   15   23
CONECT   15   16   21   38
CONECT   16   17
CONECT   17   18   19   39
CONECT   18   40   41   42
CONECT   19   20   21   43
CONECT   20   44
CONECT   21   22   45
CONECT   22   46
CONECT   23   24   24   47
CONECT   24   25
END

HMDB0015233
     RDKit          3D
Capecitabine
 47 48  0  0  0  0  0  0  0  0999 V2000
    8.0891    0.3207   -1.2687 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1020   -0.3877    0.0704 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8604    0.0484    0.8228 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6659   -0.3554   -0.0048 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3638    0.0323    0.6529 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3221   -0.4031   -0.2258 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0044   -0.1888    0.1044 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7238    0.3850    1.1697 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9880   -0.6187   -0.7623 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3690   -0.3932   -0.4134 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6928    0.2291    0.7408 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9465    0.4726    1.1294 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2199    1.0586    2.2179 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9353    0.0719    0.3192 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3166    0.3031    0.6774 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.0133   -0.8870    0.4968 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3486   -0.5059    0.2890 C   0  0  2  0  0  0  0  0  0  0  0  0
   -7.0750   -1.7007   -0.2662 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2231    0.6225   -0.6941 C   0  0  1  0  0  0  0  0  0  0  0  0
   -7.2126    1.5670   -0.5737 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9002    1.2641   -0.3361 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.0538    2.4970    0.2687 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6857   -0.5541   -0.8460 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4021   -0.7992   -1.2360 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1100   -1.4350   -2.4174 F   0  0  0  0  0  0  0  0  0  0  0  0
    7.5935   -0.2791   -2.0577 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.1394    0.4781   -1.5899 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5920    1.3112   -1.2080 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.0040   -0.1339    0.6654 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0323   -1.4949   -0.0505 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8237   -0.4293    1.8359 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8533    1.1656    0.9365 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7281    0.1871   -0.9622 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7350   -1.4325   -0.2074 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3208    1.1427    0.6886 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2348   -0.3956    1.6489 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1929   -1.1051   -1.6674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4286    0.6573    1.7105 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7978   -0.1928    1.2493 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6782   -2.6178    0.2480 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1452   -1.6182    0.0004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9083   -1.8189   -1.3402 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1324    0.2206   -1.7243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8490    2.4567   -0.4263 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2506    1.3739   -1.2252 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1751    2.7595    0.6272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4995   -0.8783   -1.5023 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
 19 21  1  0
 21 22  1  0
 14 23  1  0
 23 24  2  0
 24 25  1  0
 24 10  1  0
 21 15  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  2 29  1  0
  2 30  1  0
  3 31  1  0
  3 32  1  0
  4 33  1  0
  4 34  1  0
  5 35  1  0
  5 36  1  0
  9 37  1  0
 15 38  1  1
 17 39  1  1
 18 40  1  0
 18 41  1  0
 18 42  1  0
 19 43  1  6
 20 44  1  0
 21 45  1  6
 22 46  1  0
 23 47  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(1-(5-Deoxy-beta-D-ribofuranosyl)-5-fluoro-1,2-dihydro-2-oxo-4-pyrimidinyl)-carbamic acid pentyl ester	ChEBI
Capecitabin	ChEBI
Capecitabina	ChEBI
Capecitabinum	ChEBI
Pentyl 1-(5-deoxy-beta-D-ribofuranosyl)-5-fluoro-1,2-dihydro-2-oxo-4-pyrimidinecarbamate	ChEBI
Pentyl [1-(5-deoxy-beta-D-ribofuranosyl)-5-fluoro-2-oxo-1,2-dihydropyrimidin-4-yl]carbamate	ChEBI
Xeloda	ChEBI
(1-(5-Deoxy-b-D-ribofuranosyl)-5-fluoro-1,2-dihydro-2-oxo-4-pyrimidinyl)-carbamate pentyl ester	Generator
(1-(5-Deoxy-b-D-ribofuranosyl)-5-fluoro-1,2-dihydro-2-oxo-4-pyrimidinyl)-carbamic acid pentyl ester	Generator
(1-(5-Deoxy-beta-D-ribofuranosyl)-5-fluoro-1,2-dihydro-2-oxo-4-pyrimidinyl)-carbamate pentyl ester	Generator
(1-(5-Deoxy-β-D-ribofuranosyl)-5-fluoro-1,2-dihydro-2-oxo-4-pyrimidinyl)-carbamate pentyl ester	Generator
(1-(5-Deoxy-β-D-ribofuranosyl)-5-fluoro-1,2-dihydro-2-oxo-4-pyrimidinyl)-carbamic acid pentyl ester	Generator
Pentyl 1-(5-deoxy-b-D-ribofuranosyl)-5-fluoro-1,2-dihydro-2-oxo-4-pyrimidinecarbamate	Generator
Pentyl 1-(5-deoxy-b-D-ribofuranosyl)-5-fluoro-1,2-dihydro-2-oxo-4-pyrimidinecarbamic acid	Generator
Pentyl 1-(5-deoxy-beta-D-ribofuranosyl)-5-fluoro-1,2-dihydro-2-oxo-4-pyrimidinecarbamic acid	Generator
Pentyl 1-(5-deoxy-β-D-ribofuranosyl)-5-fluoro-1,2-dihydro-2-oxo-4-pyrimidinecarbamate	Generator
Pentyl 1-(5-deoxy-β-D-ribofuranosyl)-5-fluoro-1,2-dihydro-2-oxo-4-pyrimidinecarbamic acid	Generator
Pentyl [1-(5-deoxy-b-D-ribofuranosyl)-5-fluoro-2-oxo-1,2-dihydropyrimidin-4-yl]carbamate	Generator
Pentyl [1-(5-deoxy-b-D-ribofuranosyl)-5-fluoro-2-oxo-1,2-dihydropyrimidin-4-yl]carbamic acid	Generator
Pentyl [1-(5-deoxy-beta-D-ribofuranosyl)-5-fluoro-2-oxo-1,2-dihydropyrimidin-4-yl]carbamic acid	Generator
Pentyl [1-(5-deoxy-β-D-ribofuranosyl)-5-fluoro-2-oxo-1,2-dihydropyrimidin-4-yl]carbamate	Generator
Pentyl [1-(5-deoxy-β-D-ribofuranosyl)-5-fluoro-2-oxo-1,2-dihydropyrimidin-4-yl]carbamic acid	Generator
R340	HMDB
N(4)-Pentyloxycarbonyl-5'-deoxy-5-fluorocytidine	HMDB

Chemical Formula

C₁₅H₂₂FN₃O₆

Average Molecular Weight

359.3501

Monoisotopic Molecular Weight

359.149263656

IUPAC Name

pentyl N-{1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-methyloxolan-2-yl]-5-fluoro-2-oxo-1,2-dihydropyrimidin-4-yl}carbamate

Traditional Name

capecitabine

CAS Registry Number

154361-50-9

SMILES

CCCCCOC(=O)NC1=NC(=O)N(C=C1F)[C@@H]1O[C@H](C)[C@@H](O)[C@H]1O

InChI Identifier

InChI=1S/C15H22FN3O6/c1-3-4-5-6-24-15(23)18-12-9(16)7-19(14(22)17-12)13-11(21)10(20)8(2)25-13/h7-8,10-11,13,20-21H,3-6H2,1-2H3,(H,17,18,22,23)/t8-,10-,11-,13-/m1/s1

InChI Key

GAGWJHPBXLXJQN-UORFTKCHSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 5'-deoxyribonucleosides. These are nucleosides in which the oxygen atom at the 5'position of the ribose moiety has been replaced by another atom. The nucleobases here are limited to purine, pyrimidine, and pyridine derivatives.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

5'-deoxyribonucleosides

Sub Class

Not Available

Direct Parent

5'-deoxyribonucleosides

Alternative Parents

Substituents

5'-deoxyribonucleoside
Glycosyl compound
N-glycosyl compound
Halopyrimidine
Pyrimidone
Aryl fluoride
Aryl halide
Pyrimidine
Hydropyrimidine
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
1,2-diol
Oxacycle
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboximidic acid derivative
Organopnictogen compound
Organohalogen compound
Organofluoride
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Organooxygen compound
Alcohol
Hydrocarbon derivative
Organic oxide
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

organofluorine compound (CHEBI:31348 )
carbamate ester (CHEBI:31348 )
cytidines (CHEBI:31348 )

Ontology

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	110 - 121 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	0.25 g/L	Not Available
LogP	0.4	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.25 g/L	ALOGPS
logP	1.17	ALOGPS
logP	0.77	ChemAxon
logS	-3.2	ALOGPS
pKa (Strongest Acidic)	8.23	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	120.69 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	82.75 m³·mol⁻¹	ChemAxon
Polarizability	35.81 Å³	ChemAxon
Number of Rings	2	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]+	187.662	30932474
DeepCCS	[M-H]-	185.267	30932474
DeepCCS	[M-2H]-	218.147	30932474
DeepCCS	[M+Na]+	194.504	30932474
AllCCS	[M+H]+	182.0	32859911
AllCCS	[M+H-H2O]+	179.4	32859911
AllCCS	[M+NH4]+	184.4	32859911
AllCCS	[M+Na]+	185.1	32859911
AllCCS	[M-H]-	181.3	32859911
AllCCS	[M+Na-2H]-	181.5	32859911
AllCCS	[M+HCOO]-	182.0	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.	4.16 minutes	32390414
Predicted by Siyang on May 30, 2022	11.241 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.03 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1898.1 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	198.4 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	143.0 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	153.6 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	109.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	448.3 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	473.9 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	75.4 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	930.7 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	430.8 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	1249.6 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	295.6 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	327.6 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	260.0 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	171.2 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	15.9 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Capecitabine	CCCCCOC(=O)NC1=NC(=O)N(C=C1F)[C@@H]1O[C@H](C)[C@@H](O)[C@H]1O	4203.5	Standard polar	33892256
Capecitabine	CCCCCOC(=O)NC1=NC(=O)N(C=C1F)[C@@H]1O[C@H](C)[C@@H](O)[C@H]1O	2480.9	Standard non polar	33892256
Capecitabine	CCCCCOC(=O)NC1=NC(=O)N(C=C1F)[C@@H]1O[C@H](C)[C@@H](O)[C@H]1O	2988.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Capecitabine,1TMS,isomer #1	CCCCCOC(=O)NC1=NC(=O)N([C@@H]2O[C@H](C)[C@@H](O[Si](C)(C)C)[C@H]2O)C=C1F	2724.3	Semi standard non polar	33892256
Capecitabine,1TMS,isomer #2	CCCCCOC(=O)NC1=NC(=O)N([C@@H]2O[C@H](C)[C@@H](O)[C@H]2O[Si](C)(C)C)C=C1F	2710.2	Semi standard non polar	33892256
Capecitabine,1TMS,isomer #3	CCCCCOC(=O)N(C1=NC(=O)N([C@@H]2O[C@H](C)[C@@H](O)[C@H]2O)C=C1F)[Si](C)(C)C	2623.5	Semi standard non polar	33892256
Capecitabine,2TMS,isomer #1	CCCCCOC(=O)NC1=NC(=O)N([C@@H]2O[C@H](C)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C=C1F	2712.3	Semi standard non polar	33892256
Capecitabine,2TMS,isomer #2	CCCCCOC(=O)N(C1=NC(=O)N([C@@H]2O[C@H](C)[C@@H](O[Si](C)(C)C)[C@H]2O)C=C1F)[Si](C)(C)C	2643.9	Semi standard non polar	33892256
Capecitabine,2TMS,isomer #3	CCCCCOC(=O)N(C1=NC(=O)N([C@@H]2O[C@H](C)[C@@H](O)[C@H]2O[Si](C)(C)C)C=C1F)[Si](C)(C)C	2630.3	Semi standard non polar	33892256
Capecitabine,3TMS,isomer #1	CCCCCOC(=O)N(C1=NC(=O)N([C@@H]2O[C@H](C)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C=C1F)[Si](C)(C)C	2685.4	Semi standard non polar	33892256
Capecitabine,3TMS,isomer #1	CCCCCOC(=O)N(C1=NC(=O)N([C@@H]2O[C@H](C)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C=C1F)[Si](C)(C)C	2612.3	Standard non polar	33892256
Capecitabine,3TMS,isomer #1	CCCCCOC(=O)N(C1=NC(=O)N([C@@H]2O[C@H](C)[C@@H](O[Si](C)(C)C)[C@H]2O[Si](C)(C)C)C=C1F)[Si](C)(C)C	3040.8	Standard polar	33892256
Capecitabine,1TBDMS,isomer #1	CCCCCOC(=O)NC1=NC(=O)N([C@@H]2O[C@H](C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O)C=C1F	2941.3	Semi standard non polar	33892256
Capecitabine,1TBDMS,isomer #2	CCCCCOC(=O)NC1=NC(=O)N([C@@H]2O[C@H](C)[C@@H](O)[C@H]2O[Si](C)(C)C(C)(C)C)C=C1F	2919.4	Semi standard non polar	33892256
Capecitabine,1TBDMS,isomer #3	CCCCCOC(=O)N(C1=NC(=O)N([C@@H]2O[C@H](C)[C@@H](O)[C@H]2O)C=C1F)[Si](C)(C)C(C)(C)C	2863.7	Semi standard non polar	33892256
Capecitabine,2TBDMS,isomer #1	CCCCCOC(=O)NC1=NC(=O)N([C@@H]2O[C@H](C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O[Si](C)(C)C(C)(C)C)C=C1F	3127.2	Semi standard non polar	33892256
Capecitabine,2TBDMS,isomer #2	CCCCCOC(=O)N(C1=NC(=O)N([C@@H]2O[C@H](C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O)C=C1F)[Si](C)(C)C(C)(C)C	3127.0	Semi standard non polar	33892256
Capecitabine,2TBDMS,isomer #3	CCCCCOC(=O)N(C1=NC(=O)N([C@@H]2O[C@H](C)[C@@H](O)[C@H]2O[Si](C)(C)C(C)(C)C)C=C1F)[Si](C)(C)C(C)(C)C	3097.9	Semi standard non polar	33892256
Capecitabine,3TBDMS,isomer #1	CCCCCOC(=O)N(C1=NC(=O)N([C@@H]2O[C@H](C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O[Si](C)(C)C(C)(C)C)C=C1F)[Si](C)(C)C(C)(C)C	3327.5	Semi standard non polar	33892256
Capecitabine,3TBDMS,isomer #1	CCCCCOC(=O)N(C1=NC(=O)N([C@@H]2O[C@H](C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O[Si](C)(C)C(C)(C)C)C=C1F)[Si](C)(C)C(C)(C)C	3229.1	Standard non polar	33892256
Capecitabine,3TBDMS,isomer #1	CCCCCOC(=O)N(C1=NC(=O)N([C@@H]2O[C@H](C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H]2O[Si](C)(C)C(C)(C)C)C=C1F)[Si](C)(C)C(C)(C)C	3346.6	Standard polar	33892256

Spectra

Biological Properties

Cellular Locations

Cytoplasm
Membrane

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Name	SMPDB/PathBank	KEGG
Capecitabine Action Pathway		Not Available
Capecitabine Metabolism Pathway		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB01101	21059682	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB01101	21059682	details

Abnormal Concentrations

Not Available

Predicted Concentrations

Biospecimen	Value	Original age	Original sex	Original condition	Comments
Blood	0.000 uM	Adult (>18 years old)	Both	Normal	Predicted based on drug qualities
Blood	0.000 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	Predicted based on drug qualities

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB01101

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

54916

KEGG Compound ID

C12650

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Capecitabine

METLIN ID

Not Available

PubChem Compound

60953

PDB ID

Not Available

ChEBI ID

31348

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

de Bono JS, Twelves CJ: The oral fluorinated pyrimidines. Invest New Drugs. 2001;19(1):41-59. [PubMed:11291832 ]
Walko CM, Lindley C: Capecitabine: a review. Clin Ther. 2005 Jan;27(1):23-44. [PubMed:15763604 ]
Twelves C: Vision of the future: capecitabine. Oncologist. 2001;6 Suppl 4:35-9. [PubMed:11585973 ]
Wagstaff AJ, Ibbotson T, Goa KL: Capecitabine: a review of its pharmacology and therapeutic efficacy in the management of advanced breast cancer. Drugs. 2003;63(2):217-36. [PubMed:12515569 ]
Milano G, Ferrero JM, Francois E: Comparative pharmacology of oral fluoropyrimidines: a focus on pharmacokinetics, pharmacodynamics and pharmacomodulation. Br J Cancer. 2004 Aug 16;91(4):613-7. [PubMed:15280932 ]
Koukourakis GV, Kouloulias V, Koukourakis MJ, Zacharias GA, Zabatis H, Kouvaris J: Efficacy of the oral fluorouracil pro-drug capecitabine in cancer treatment: a review. Molecules. 2008 Aug 27;13(8):1897-922. [PubMed:18794792 ]

Enzymes

Enzyme Details

1. Liver carboxylesterase 1

General function:: Lipid transport and metabolism
Specific function:: Involved in the detoxification of xenobiotics and in the activation of ester and amide prodrugs. Hydrolyzes aromatic and aliphatic esters, but has no catalytic activity toward amides or a fatty acyl-CoA ester. Hydrolyzes the methyl ester group of cocaine to form benzoylecgonine. Catalyzes the transesterification of cocaine to form cocaethylene. Displays fatty acid ethyl ester synthase activity, catalyzing the ethyl esterification of oleic acid to ethyloleate.
Gene Name:: CES1
Uniprot ID:: P23141
Molecular weight:: 62520.62

Reactions

Capecitabine + Water → 5'-Deoxy-5-fluorocytidine + 1-Pentanol + Carbon dioxide	details

References

de Bono JS, Twelves CJ: The oral fluorinated pyrimidines. Invest New Drugs. 2001;19(1):41-59. [PubMed:11291832 ]
Tsukamoto Y, Kato Y, Ura M, Horii I, Ishitsuka H, Kusuhara H, Sugiyama Y: A physiologically based pharmacokinetic analysis of capecitabine, a triple prodrug of 5-FU, in humans: the mechanism for tumor-selective accumulation of 5-FU. Pharm Res. 2001 Aug;18(8):1190-202. [PubMed:11587492 ]
Ishitsuka H, Shimma N, Horii I: [Discovery and development of novel anticancer drug capecitabine]. Yakugaku Zasshi. 1999 Dec;119(12):881-97. [PubMed:10630095 ]
Ishitsuka H: Capecitabine: preclinical pharmacology studies. Invest New Drugs. 2000 Nov;18(4):343-54. [PubMed:11081570 ]
Endo M, Miwa M, Eda H, Ura M, Tanimura H, Ishikawa T, Miyazaki-Nose T, Hattori K, Shimma N, Yamada-Okabe H, Ishitsuka H: Augmentation of the antitumor activity of capecitabine by a tumor selective dihydropyrimidine dehydrogenase inhibitor, RO0094889. Int J Cancer. 2003 Sep 20;106(5):799-805. [PubMed:12866042 ]

Enzyme Details

2. Cocaine esterase

General function:: Lipid transport and metabolism
Specific function:: Involved in the detoxification of xenobiotics and in the activation of ester and amide prodrugs. Shows high catalytic efficiency for hydrolysis of cocaine, 4-methylumbelliferyl acetate, heroin and 6-monoacetylmorphine.
Gene Name:: CES2
Uniprot ID:: O00748
Molecular weight:: 68898.39

Reactions

Capecitabine + Water → 5'-Deoxy-5-fluorocytidine + 1-Pentanol + Carbon dioxide	details

Enzyme Details

3. Dihydropyrimidine dehydrogenase [NADP(+)]

General function:: Involved in electron carrier activity
Specific function:: Involved in pyrimidine base degradation. Catalyzes the reduction of uracil and thymine. Also involved the degradation of the chemotherapeutic drug 5-fluorouracil.
Gene Name:: DPYD
Uniprot ID:: Q12882
Molecular weight:: 111400.32

References

Tsukamoto Y, Kato Y, Ura M, Horii I, Ishitsuka H, Kusuhara H, Sugiyama Y: A physiologically based pharmacokinetic analysis of capecitabine, a triple prodrug of 5-FU, in humans: the mechanism for tumor-selective accumulation of 5-FU. Pharm Res. 2001 Aug;18(8):1190-202. [PubMed:11587492 ]
Blanquicett C, Gillespie GY, Nabors LB, Miller CR, Bharara S, Buchsbaum DJ, Diasio RB, Johnson MR: Induction of thymidine phosphorylase in both irradiated and shielded, contralateral human U87MG glioma xenografts: implications for a dual modality treatment using capecitabine and irradiation. Mol Cancer Ther. 2002 Oct;1(12):1139-45. [PubMed:12481438 ]
de Bono JS, Twelves CJ: The oral fluorinated pyrimidines. Invest New Drugs. 2001;19(1):41-59. [PubMed:11291832 ]
Gross E, Seck K, Neubauer S, Mayr J, Hellebrand H, Ratanaphan A, Lutz V, Stockinger H, Kiechle M: High-throughput genotyping by DHPLC of the dihydropyrimidine dehydrogenase gene implicated in (fluoro)pyrimidine catabolism. Int J Oncol. 2003 Feb;22(2):325-32. [PubMed:12527930 ]
Ishitsuka H: Capecitabine: preclinical pharmacology studies. Invest New Drugs. 2000 Nov;18(4):343-54. [PubMed:11081570 ]
Endo M, Miwa M, Eda H, Ura M, Tanimura H, Ishikawa T, Miyazaki-Nose T, Hattori K, Shimma N, Yamada-Okabe H, Ishitsuka H: Augmentation of the antitumor activity of capecitabine by a tumor selective dihydropyrimidine dehydrogenase inhibitor, RO0094889. Int J Cancer. 2003 Sep 20;106(5):799-805. [PubMed:12866042 ]
Patel A, Pluim T, Helms A, Bauer A, Tuttle RM, Francis GL: Enzyme expression profiles suggest the novel tumor-activated fluoropyrimidine carbamate capecitabine (Xeloda) might be effective against papillary thyroid cancers of children and young adults. Cancer Chemother Pharmacol. 2004 May;53(5):409-14. [PubMed:15132128 ]
Eliason JF, Megyeri A: Potential for predicting toxicity and response of fluoropyrimidines in patients. Curr Drug Targets. 2004 May;5(4):383-8. [PubMed:15134221 ]
Walko CM, Lindley C: Capecitabine: a review. Clin Ther. 2005 Jan;27(1):23-44. [PubMed:15763604 ]

Enzyme Details

4. Cytochrome P450 2C9

General function:: Involved in monooxygenase activity
Specific function:: Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. This enzyme contributes to the wide pharmacokinetics variability of the metabolism of drugs such as S-warfarin, diclofenac, phenytoin, tolbutamide and losartan.
Gene Name:: CYP2C9
Uniprot ID:: P11712
Molecular weight:: 55627.365

References

Preissner S, Kroll K, Dunkel M, Senger C, Goldsobel G, Kuzman D, Guenther S, Winnenburg R, Schroeder M, Preissner R: SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions. Nucleic Acids Res. 2010 Jan;38(Database issue):D237-43. doi: 10.1093/nar/gkp970. Epub 2009 Nov 24. [PubMed:19934256 ]

Enzyme Details

5. Thymidine phosphorylase

General function:: Involved in transferase activity, transferring glycosyl groups
Specific function:: May have a role in maintaining the integrity of the blood vessels. Has growth promoting activity on endothelial cells, angiogenic activity in vivo and chemotactic activity on endothelial cells in vitro. Catalyzes the reversible phosphorolysis of thymidine. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.
Gene Name:: TYMP
Uniprot ID:: P19971
Molecular weight:: 49954.965

References

de Bono JS, Twelves CJ: The oral fluorinated pyrimidines. Invest New Drugs. 2001;19(1):41-59. [PubMed:11291832 ]
Tsukamoto Y, Kato Y, Ura M, Horii I, Ishitsuka H, Kusuhara H, Sugiyama Y: A physiologically based pharmacokinetic analysis of capecitabine, a triple prodrug of 5-FU, in humans: the mechanism for tumor-selective accumulation of 5-FU. Pharm Res. 2001 Aug;18(8):1190-202. [PubMed:11587492 ]
Blanquicett C, Gillespie GY, Nabors LB, Miller CR, Bharara S, Buchsbaum DJ, Diasio RB, Johnson MR: Induction of thymidine phosphorylase in both irradiated and shielded, contralateral human U87MG glioma xenografts: implications for a dual modality treatment using capecitabine and irradiation. Mol Cancer Ther. 2002 Oct;1(12):1139-45. [PubMed:12481438 ]
Ishitsuka H, Shimma N, Horii I: [Discovery and development of novel anticancer drug capecitabine]. Yakugaku Zasshi. 1999 Dec;119(12):881-97. [PubMed:10630095 ]
Ishitsuka H: Capecitabine: preclinical pharmacology studies. Invest New Drugs. 2000 Nov;18(4):343-54. [PubMed:11081570 ]
Endo M, Miwa M, Eda H, Ura M, Tanimura H, Ishikawa T, Miyazaki-Nose T, Hattori K, Shimma N, Yamada-Okabe H, Ishitsuka H: Augmentation of the antitumor activity of capecitabine by a tumor selective dihydropyrimidine dehydrogenase inhibitor, RO0094889. Int J Cancer. 2003 Sep 20;106(5):799-805. [PubMed:12866042 ]
Schuller J, Cassidy J, Dumont E, Roos B, Durston S, Banken L, Utoh M, Mori K, Weidekamm E, Reigner B: Preferential activation of capecitabine in tumor following oral administration to colorectal cancer patients. Cancer Chemother Pharmacol. 2000;45(4):291-7. [PubMed:10755317 ]
Patel A, Pluim T, Helms A, Bauer A, Tuttle RM, Francis GL: Enzyme expression profiles suggest the novel tumor-activated fluoropyrimidine carbamate capecitabine (Xeloda) might be effective against papillary thyroid cancers of children and young adults. Cancer Chemother Pharmacol. 2004 May;53(5):409-14. [PubMed:15132128 ]
Eliason JF, Megyeri A: Potential for predicting toxicity and response of fluoropyrimidines in patients. Curr Drug Targets. 2004 May;5(4):383-8. [PubMed:15134221 ]
Fischel JL, Ciccolini J, Formento P, Ferrero JM, Milano G: Synergistic cytotoxic interaction in hormone-refractory prostate cancer with the triple combination docetaxel-erlotinib and 5-fluoro-5'-deoxyuridine. Anticancer Drugs. 2006 Aug;17(7):807-13. [PubMed:16926630 ]
Walko CM, Lindley C: Capecitabine: a review. Clin Ther. 2005 Jan;27(1):23-44. [PubMed:15763604 ]

Enzyme Details

6. Thymidylate synthase

General function:: Involved in thymidylate synthase activity
Specific function:: Contributes to the de novo mitochondrial thymidylate biosynthesis pathway.
Gene Name:: TYMS
Uniprot ID:: P04818
Molecular weight:: 35715.65

References

Patel A, Pluim T, Helms A, Bauer A, Tuttle RM, Francis GL: Enzyme expression profiles suggest the novel tumor-activated fluoropyrimidine carbamate capecitabine (Xeloda) might be effective against papillary thyroid cancers of children and young adults. Cancer Chemother Pharmacol. 2004 May;53(5):409-14. [PubMed:15132128 ]
Eliason JF, Megyeri A: Potential for predicting toxicity and response of fluoropyrimidines in patients. Curr Drug Targets. 2004 May;5(4):383-8. [PubMed:15134221 ]
Carlini LE, Meropol NJ, Bever J, Andria ML, Hill T, Gold P, Rogatko A, Wang H, Blanchard RL: UGT1A7 and UGT1A9 polymorphisms predict response and toxicity in colorectal cancer patients treated with capecitabine/irinotecan. Clin Cancer Res. 2005 Feb 1;11(3):1226-36. [PubMed:15709193 ]
Li KM, Rivory LP, Clarke SJ: Rapid quantitation of plasma 2'-deoxyuridine by high-performance liquid chromatography/atmospheric pressure chemical ionization mass spectrometry and its application to pharmacodynamic studies in cancer patients. J Chromatogr B Analyt Technol Biomed Life Sci. 2005 Jun 5;820(1):121-30. Epub 2005 Apr 19. [PubMed:15866500 ]
Fischel JL, Ciccolini J, Formento P, Ferrero JM, Milano G: Synergistic cytotoxic interaction in hormone-refractory prostate cancer with the triple combination docetaxel-erlotinib and 5-fluoro-5'-deoxyuridine. Anticancer Drugs. 2006 Aug;17(7):807-13. [PubMed:16926630 ]
Chen X, Ji ZL, Chen YZ: TTD: Therapeutic Target Database. Nucleic Acids Res. 2002 Jan 1;30(1):412-5. [PubMed:11752352 ]

Enzyme Details

7. Cytidine deaminase

General function:: Involved in zinc ion binding
Specific function:: This enzyme scavenge exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis.
Gene Name:: CDA
Uniprot ID:: P32320
Molecular weight:: 16184.545

References

de Bono JS, Twelves CJ: The oral fluorinated pyrimidines. Invest New Drugs. 2001;19(1):41-59. [PubMed:11291832 ]
Tsukamoto Y, Kato Y, Ura M, Horii I, Ishitsuka H, Kusuhara H, Sugiyama Y: A physiologically based pharmacokinetic analysis of capecitabine, a triple prodrug of 5-FU, in humans: the mechanism for tumor-selective accumulation of 5-FU. Pharm Res. 2001 Aug;18(8):1190-202. [PubMed:11587492 ]
Ishitsuka H, Shimma N, Horii I: [Discovery and development of novel anticancer drug capecitabine]. Yakugaku Zasshi. 1999 Dec;119(12):881-97. [PubMed:10630095 ]
Ishitsuka H: Capecitabine: preclinical pharmacology studies. Invest New Drugs. 2000 Nov;18(4):343-54. [PubMed:11081570 ]
Endo M, Miwa M, Eda H, Ura M, Tanimura H, Ishikawa T, Miyazaki-Nose T, Hattori K, Shimma N, Yamada-Okabe H, Ishitsuka H: Augmentation of the antitumor activity of capecitabine by a tumor selective dihydropyrimidine dehydrogenase inhibitor, RO0094889. Int J Cancer. 2003 Sep 20;106(5):799-805. [PubMed:12866042 ]

Showing metabocard for Capecitabine (HMDB0015233)

MOL for HMDB0015233 (Capecitabine)

3D MOL for HMDB0015233 (Capecitabine)

3D SDF for HMDB0015233 (Capecitabine)

3D-SDF for HMDB0015233 (Capecitabine)

PDB for HMDB0015233 (Capecitabine)

3D PDB for HMDB0015233 (Capecitabine)

SMILES for HMDB0015233 (Capecitabine)

INCHI for HMDB0015233 (Capecitabine)

Structure for HMDB0015233 (Capecitabine)

3D Structure for HMDB0015233 (Capecitabine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

Enzymes

Reactions

References

Reactions

References

References

References

References

References