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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (5)transporters (2) Show 7 proteins XML

enzymes (5)transporters (2) Show 7 proteins

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-06 15:16:49 UTC

Update Date

2022-03-07 02:51:40 UTC

HMDB ID

HMDB0014584

Secondary Accession Numbers

HMDB14584

Metabolite Identification

Common Name

Gemcitabine

Description

Gemcitabine is a nucleoside analog used as chemotherapy. It is marketed as Gemzar by Eli Lilly and Company. As with fluorouracil and other analogues of pyrimidines, the drug replaces one of the building blocks of nucleic acids, in this case cytidine, during DNA replication. The process arrests tumor growth, as new nucleosides cannot be attached to the 'faulty' nucleoside, resulting in apoptosis (cellular 'suicide').

Structure

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

HMDB0014584
     RDKit          3D
Gemcitabine
 29 30  0  0  0  0  0  0  0  0999 V2000
    4.8055   -1.4458   -0.4353 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5433   -0.7719   -0.2645 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3758   -1.4755   -0.0472 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1741   -0.7857    0.1133 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1386    0.5635    0.0586 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1090    1.1948    0.2287 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7358    0.5135    1.2799 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0788    0.4719    1.0149 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7893   -0.6055    1.7705 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3089   -1.8597    1.4815 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0966    0.2373   -0.4850 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.3549    0.5812   -0.9619 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0776    1.3446   -0.8156 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8308    2.4980   -0.6085 F   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7429    1.3804   -2.1116 F   0  0  0  0  0  0  0  0  0  0  0  0
    2.2856    1.2175   -0.1532 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1593    2.4671   -0.1890 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4541    0.5720   -0.3104 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.8040   -2.4349   -0.7869 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6990   -0.9659   -0.2161 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4419   -2.5498   -0.0097 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2938   -1.3965    0.2809 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1141    2.2144    0.6758 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4958    1.4798    1.1925 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8735   -0.5671    1.4659 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7782   -0.3483    2.8489 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8229   -2.2974    0.7823 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7537   -0.7451   -0.7850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4404    1.5133   -1.2273 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  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
  8 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 13 15  1  0
  5 16  1  0
 16 17  2  0
 16 18  1  0
 18  2  2  0
 13  6  1  0
  1 19  1  0
  1 20  1  0
  3 21  1  0
  4 22  1  0
  6 23  1  1
  8 24  1  6
  9 25  1  0
  9 26  1  0
 10 27  1  0
 11 28  1  1
 12 29  1  0
M  END

441
  Mrv0541 02231214412D          

 18 19  0  0  1  0            999 V2000
    5.1206   -1.3156    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    4.8209   -0.3932    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    3.0011   -1.0607    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5660   -2.5127    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9506   -2.4265    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2396    0.2492    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6685    0.2492    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9541    1.4867    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6685    2.7242    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0810   -1.8453    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.3361   -1.0607    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2560   -1.8453    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6685   -0.5758    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.7711   -2.5127    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3831    0.6617    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9541    0.6617    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3831    1.4867    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6685    1.8992    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 11  1  0  0  0  0
  2 11  1  0  0  0  0
  3 12  1  0  0  0  0
  3 13  1  0  0  0  0
 10  4  1  6  0  0  0
  5 14  1  0  0  0  0
  6 16  2  0  0  0  0
 13  7  1  1  0  0  0
  7 15  1  0  0  0  0
  7 16  1  0  0  0  0
  8 16  1  0  0  0  0
  8 18  2  0  0  0  0
  9 18  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 11 13  1  0  0  0  0
 12 14  1  1  0  0  0
 15 17  2  0  0  0  0
 17 18  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0014584

> <DATABASE_NAME>
hmdb

> <SMILES>
NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](CO)[C@@H](O)C1(F)F

> <INCHI_IDENTIFIER>
InChI=1S/C9H11F2N3O4/c10-9(11)6(16)4(3-15)18-7(9)14-2-1-5(12)13-8(14)17/h1-2,4,6-7,15-16H,3H2,(H2,12,13,17)/t4-,6-,7-/m1/s1

> <INCHI_KEY>
SDUQYLNIPVEERB-QPPQHZFASA-N

> <FORMULA>
C9H11F2N3O4

> <MOLECULAR_WEIGHT>
263.1981

> <EXACT_MASS>
263.071762265

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
21.453914981710017

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-amino-1-[(2R,4R,5R)-3,3-difluoro-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one

> <ALOGPS_LOGP>
0.14

> <JCHEM_LOGP>
-1.466539628

> <ALOGPS_LOGS>
-1.07

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.678672317989776

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.51706980194467

> <JCHEM_PKA_STRONGEST_BASIC>
-1.2568558951684876

> <JCHEM_POLAR_SURFACE_AREA>
108.37999999999998

> <JCHEM_REFRACTIVITY>
53.2503

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.23e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
gemcitabine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0014584
     RDKit          3D
Gemcitabine
 29 30  0  0  0  0  0  0  0  0999 V2000
    4.8055   -1.4458   -0.4353 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5433   -0.7719   -0.2645 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3758   -1.4755   -0.0472 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1741   -0.7857    0.1133 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1386    0.5635    0.0586 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1090    1.1948    0.2287 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7358    0.5135    1.2799 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0788    0.4719    1.0149 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7893   -0.6055    1.7705 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3089   -1.8597    1.4815 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0966    0.2373   -0.4850 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.3549    0.5812   -0.9619 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0776    1.3446   -0.8156 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8308    2.4980   -0.6085 F   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7429    1.3804   -2.1116 F   0  0  0  0  0  0  0  0  0  0  0  0
    2.2856    1.2175   -0.1532 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1593    2.4671   -0.1890 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4541    0.5720   -0.3104 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.8040   -2.4349   -0.7869 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6990   -0.9659   -0.2161 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4419   -2.5498   -0.0097 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2938   -1.3965    0.2809 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1141    2.2144    0.6758 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4958    1.4798    1.1925 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8735   -0.5671    1.4659 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7782   -0.3483    2.8489 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8229   -2.2974    0.7823 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7537   -0.7451   -0.7850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4404    1.5133   -1.2273 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  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
  8 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 13 15  1  0
  5 16  1  0
 16 17  2  0
 16 18  1  0
 18  2  2  0
 13  6  1  0
  1 19  1  0
  1 20  1  0
  3 21  1  0
  4 22  1  0
  6 23  1  1
  8 24  1  6
  9 25  1  0
  9 26  1  0
 10 27  1  0
 11 28  1  1
 12 29  1  0
M  END

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 441                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  F   UNK     0       9.558  -2.456   0.000  0.00  0.00           F+0
HETATM    2  F   UNK     0       8.999  -0.734   0.000  0.00  0.00           F+0
HETATM    3  O   UNK     0       5.602  -1.980   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       8.523  -4.690   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       3.641  -4.529   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       4.181   0.465   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0       6.848   0.465   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0       5.514   2.775   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0       6.848   5.085   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       7.618  -3.445   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.094  -1.980   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.078  -3.445   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.848  -1.075   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.173  -4.690   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.182   1.235   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.514   1.235   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.182   2.775   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.848   3.545   0.000  0.00  0.00           C+0
CONECT    1   11                                                            
CONECT    2   11                                                            
CONECT    3   12   13                                                       
CONECT    4   10                                                            
CONECT    5   14                                                            
CONECT    6   16                                                            
CONECT    7   13   15   16                                                  
CONECT    8   16   18                                                       
CONECT    9   18                                                            
CONECT   10    4   11   12                                                  
CONECT   11    1    2   10   13                                             
CONECT   12    3   10   14                                                  
CONECT   13    3    7   11                                                  
CONECT   14    5   12                                                       
CONECT   15    7   17                                                       
CONECT   16    6    7    8                                                  
CONECT   17   15   18                                                       
CONECT   18    8    9   17                                                  
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

COMPND    HMDB0014584
HETATM    1  N1  UNL     1       4.805  -1.446  -0.435  1.00  0.00           N  
HETATM    2  C1  UNL     1       3.543  -0.772  -0.265  1.00  0.00           C  
HETATM    3  C2  UNL     1       2.376  -1.476  -0.047  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.174  -0.786   0.113  1.00  0.00           C  
HETATM    5  N2  UNL     1       1.139   0.564   0.059  1.00  0.00           N  
HETATM    6  C4  UNL     1      -0.109   1.195   0.229  1.00  0.00           C  
HETATM    7  O1  UNL     1      -0.736   0.513   1.280  1.00  0.00           O  
HETATM    8  C5  UNL     1      -2.079   0.472   1.015  1.00  0.00           C  
HETATM    9  C6  UNL     1      -2.789  -0.606   1.770  1.00  0.00           C  
HETATM   10  O2  UNL     1      -2.309  -1.860   1.482  1.00  0.00           O  
HETATM   11  C7  UNL     1      -2.097   0.237  -0.485  1.00  0.00           C  
HETATM   12  O3  UNL     1      -3.355   0.581  -0.962  1.00  0.00           O  
HETATM   13  C8  UNL     1      -1.078   1.345  -0.816  1.00  0.00           C  
HETATM   14  F1  UNL     1      -1.831   2.498  -0.608  1.00  0.00           F  
HETATM   15  F2  UNL     1      -0.743   1.380  -2.112  1.00  0.00           F  
HETATM   16  C9  UNL     1       2.286   1.217  -0.153  1.00  0.00           C  
HETATM   17  O4  UNL     1       2.159   2.467  -0.189  1.00  0.00           O  
HETATM   18  N3  UNL     1       3.454   0.572  -0.310  1.00  0.00           N  
HETATM   19  H1  UNL     1       4.804  -2.435  -0.787  1.00  0.00           H  
HETATM   20  H2  UNL     1       5.699  -0.966  -0.216  1.00  0.00           H  
HETATM   21  H3  UNL     1       2.442  -2.550  -0.010  1.00  0.00           H  
HETATM   22  H4  UNL     1       0.294  -1.397   0.281  1.00  0.00           H  
HETATM   23  H5  UNL     1       0.114   2.214   0.676  1.00  0.00           H  
HETATM   24  H6  UNL     1      -2.496   1.480   1.193  1.00  0.00           H  
HETATM   25  H7  UNL     1      -3.873  -0.567   1.466  1.00  0.00           H  
HETATM   26  H8  UNL     1      -2.778  -0.348   2.849  1.00  0.00           H  
HETATM   27  H9  UNL     1      -2.823  -2.297   0.782  1.00  0.00           H  
HETATM   28  H10 UNL     1      -1.754  -0.745  -0.785  1.00  0.00           H  
HETATM   29  H11 UNL     1      -3.440   1.513  -1.227  1.00  0.00           H  
CONECT    1    2   19   20
CONECT    2    3   18   18
CONECT    3    4    4   21
CONECT    4    5   22
CONECT    5    6   16
CONECT    6    7   13   23
CONECT    7    8
CONECT    8    9   11   24
CONECT    9   10   25   26
CONECT   10   27
CONECT   11   12   13   28
CONECT   12   29
CONECT   13   14   15
CONECT   16   17   17   18
END

HMDB0014584
     RDKit          3D
Gemcitabine
 29 30  0  0  0  0  0  0  0  0999 V2000
    4.8055   -1.4458   -0.4353 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5433   -0.7719   -0.2645 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3758   -1.4755   -0.0472 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1741   -0.7857    0.1133 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1386    0.5635    0.0586 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1090    1.1948    0.2287 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7358    0.5135    1.2799 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0788    0.4719    1.0149 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7893   -0.6055    1.7705 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3089   -1.8597    1.4815 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0966    0.2373   -0.4850 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.3549    0.5812   -0.9619 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0776    1.3446   -0.8156 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8308    2.4980   -0.6085 F   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7429    1.3804   -2.1116 F   0  0  0  0  0  0  0  0  0  0  0  0
    2.2856    1.2175   -0.1532 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1593    2.4671   -0.1890 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4541    0.5720   -0.3104 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.8040   -2.4349   -0.7869 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6990   -0.9659   -0.2161 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4419   -2.5498   -0.0097 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2938   -1.3965    0.2809 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1141    2.2144    0.6758 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4958    1.4798    1.1925 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8735   -0.5671    1.4659 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7782   -0.3483    2.8489 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8229   -2.2974    0.7823 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7537   -0.7451   -0.7850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4404    1.5133   -1.2273 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  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
  8 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 13 15  1  0
  5 16  1  0
 16 17  2  0
 16 18  1  0
 18  2  2  0
 13  6  1  0
  1 19  1  0
  1 20  1  0
  3 21  1  0
  4 22  1  0
  6 23  1  1
  8 24  1  6
  9 25  1  0
  9 26  1  0
 10 27  1  0
 11 28  1  1
 12 29  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
2',2'-Difluorodeoxycytidine	ChEBI
2'-Deoxy-2',2'-difluorocytidine	ChEBI
4-Amino-1-((2R,4R,5R)-3,3-difluoro-4-hydroxy-5-(hydroxymethyl)-tetrahydrofuran-2-yl)pyrimidin-2(1H)-one	ChEBI
Gemcitabina	ChEBI
Gemcitabinum	ChEBI
DFdCyd	HMDB
2',2'-Difluoro-2'-deoxycytidine	HMDB
2'-Deoxy-2'-difluorocytidine	HMDB
Gemcitabine, (D-threo-pentafuranosyl)-isomer	HMDB
Gemcitabine, (alpha-D-threo-pentofuranosyl)-isomer	HMDB
2'-Deoxy-2',2''-difluorocytidine-5'-O-monophosphate	HMDB
Gemcitabine hydrochloride	HMDB
2',2'-DFDC	HMDB
Gemzar	HMDB
Gemcitabine, (beta-D-threo-pentafuranosyl)-isomer	HMDB

Chemical Formula

C₉H₁₁F₂N₃O₄

Average Molecular Weight

263.1981

Monoisotopic Molecular Weight

263.071762265

IUPAC Name

4-amino-1-[(2R,4R,5R)-3,3-difluoro-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one

Traditional Name

gemcitabine

CAS Registry Number

95058-81-4

SMILES

NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](CO)[C@@H](O)C1(F)F

InChI Identifier

InChI=1S/C9H11F2N3O4/c10-9(11)6(16)4(3-15)18-7(9)14-2-1-5(12)13-8(14)17/h1-2,4,6-7,15-16H,3H2,(H2,12,13,17)/t4-,6-,7-/m1/s1

InChI Key

SDUQYLNIPVEERB-QPPQHZFASA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Pyrimidine 2'-deoxyribonucleosides

Direct Parent

Pyrimidine 2'-deoxyribonucleosides

Alternative Parents

Substituents

Pyrimidine 2'-deoxyribonucleoside
Aminopyrimidine
Pyrimidone
Hydropyrimidine
Pyrimidine
Imidolactam
Heteroaromatic compound
Tetrahydrofuran
Fluorohydrin
Halohydrin
Secondary alcohol
Organoheterocyclic compound
Azacycle
Oxacycle
Alkyl halide
Organopnictogen compound
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organofluoride
Organohalogen compound
Organic oxygen compound
Alkyl fluoride
Alcohol
Organic nitrogen compound
Amine
Organic oxide
Hydrocarbon derivative
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

organofluorine compound (CHEBI:175901 )
pyrimidine 2'-deoxyribonucleoside (CHEBI:175901 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 21059682)

Excreta

Biofluid or Excreta

Urine (PMID: 21059682)

Cellular substructure

Cytoplasm (HMDB: HMDB0014584)
Membrane (HMDB: HMDB0014584)

Source

Exogenous

Exogenous (HMDB: HMDB0014584)

Process

Naturally occurring process

Biological process

Biochemical pathway

Drug action pathway

Gemcitabine Action Pathway (PathBank: SMP0000446)

Metabolic pathway

Gemcitabine Metabolism Pathway (PathBank: SMP0000603)

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	168.64 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	22.3 g/L	Not Available
LogP	-1.4	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	22.3 g/L	ALOGPS
logP	0.14	ALOGPS
logP	-1.5	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	11.52	ChemAxon
pKa (Strongest Basic)	-1.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	108.38 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	53.25 m³·mol⁻¹	ChemAxon
Polarizability	21.45 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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]+	160.223	30932474
DeepCCS	[M-H]-	157.828	30932474
DeepCCS	[M-2H]-	192.124	30932474
DeepCCS	[M+Na]+	167.132	30932474
AllCCS	[M+H]+	158.3	32859911
AllCCS	[M+H-H2O]+	154.6	32859911
AllCCS	[M+NH4]+	161.7	32859911
AllCCS	[M+Na]+	162.6	32859911
AllCCS	[M-H]-	153.7	32859911
AllCCS	[M+Na-2H]-	153.6	32859911
AllCCS	[M+HCOO]-	153.5	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.	1.89 minutes	32390414
Predicted by Siyang on May 30, 2022	9.3531 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	3.95 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	81.2 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	539.8 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	243.9 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	72.7 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	162.6 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	56.0 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	295.8 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	265.2 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	575.7 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	603.0 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	56.0 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	761.1 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	169.4 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	182.8 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	523.0 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	361.8 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	163.9 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Gemcitabine	NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](CO)[C@@H](O)C1(F)F	2778.2	Standard polar	33892256
Gemcitabine	NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](CO)[C@@H](O)C1(F)F	1978.8	Standard non polar	33892256
Gemcitabine	NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](CO)[C@@H](O)C1(F)F	2375.9	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Gemcitabine,1TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)C(F)(F)[C@@H]1O	2133.3	Semi standard non polar	33892256
Gemcitabine,1TMS,isomer #2	C[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C=CC(N)=NC2=O)C1(F)F	2157.9	Semi standard non polar	33892256
Gemcitabine,1TMS,isomer #3	C[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO)[C@@H](O)C2(F)F)C=C1	2231.3	Semi standard non polar	33892256
Gemcitabine,2TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)C(F)(F)[C@@H]1O[Si](C)(C)C	2132.7	Semi standard non polar	33892256
Gemcitabine,2TMS,isomer #2	C[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O)C2(F)F)C=C1	2200.7	Semi standard non polar	33892256
Gemcitabine,2TMS,isomer #3	C[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C)C2(F)F)C=C1	2211.2	Semi standard non polar	33892256
Gemcitabine,2TMS,isomer #4	C[Si](C)(C)N(C1=NC(=O)N([C@@H]2O[C@H](CO)[C@@H](O)C2(F)F)C=C1)[Si](C)(C)C	2178.7	Semi standard non polar	33892256
Gemcitabine,3TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)C2(F)F)C=C1	2229.2	Semi standard non polar	33892256
Gemcitabine,3TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)C2(F)F)C=C1	2261.3	Standard non polar	33892256
Gemcitabine,3TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)C2(F)F)C=C1	2509.1	Standard polar	33892256
Gemcitabine,3TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C(F)(F)[C@@H]1O	2195.7	Semi standard non polar	33892256
Gemcitabine,3TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C(F)(F)[C@@H]1O	2314.7	Standard non polar	33892256
Gemcitabine,3TMS,isomer #2	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C(F)(F)[C@@H]1O	2486.2	Standard polar	33892256
Gemcitabine,3TMS,isomer #3	C[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C1(F)F	2181.0	Semi standard non polar	33892256
Gemcitabine,3TMS,isomer #3	C[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C1(F)F	2300.3	Standard non polar	33892256
Gemcitabine,3TMS,isomer #3	C[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C1(F)F	2373.9	Standard polar	33892256
Gemcitabine,4TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C(F)(F)[C@@H]1O[Si](C)(C)C	2239.1	Semi standard non polar	33892256
Gemcitabine,4TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C(F)(F)[C@@H]1O[Si](C)(C)C	2323.3	Standard non polar	33892256
Gemcitabine,4TMS,isomer #1	C[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)C(F)(F)[C@@H]1O[Si](C)(C)C	2267.0	Standard polar	33892256
Gemcitabine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)C(F)(F)[C@@H]1O	2349.0	Semi standard non polar	33892256
Gemcitabine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C=CC(N)=NC2=O)C1(F)F	2362.9	Semi standard non polar	33892256
Gemcitabine,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO)[C@@H](O)C2(F)F)C=C1	2471.3	Semi standard non polar	33892256
Gemcitabine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)C(F)(F)[C@@H]1O[Si](C)(C)C(C)(C)C	2577.4	Semi standard non polar	33892256
Gemcitabine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O)C2(F)F)C=C1	2650.7	Semi standard non polar	33892256
Gemcitabine,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO)[C@@H](O[Si](C)(C)C(C)(C)C)C2(F)F)C=C1	2635.5	Semi standard non polar	33892256
Gemcitabine,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)N(C1=NC(=O)N([C@@H]2O[C@H](CO)[C@@H](O)C2(F)F)C=C1)[Si](C)(C)C(C)(C)C	2620.5	Semi standard non polar	33892256
Gemcitabine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)C2(F)F)C=C1	2845.2	Semi standard non polar	33892256
Gemcitabine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)C2(F)F)C=C1	2838.0	Standard non polar	33892256
Gemcitabine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N([C@@H]2O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)C2(F)F)C=C1	2813.9	Standard polar	33892256
Gemcitabine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C(F)(F)[C@@H]1O	2795.3	Semi standard non polar	33892256
Gemcitabine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C(F)(F)[C@@H]1O	2885.4	Standard non polar	33892256
Gemcitabine,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C(F)(F)[C@@H]1O	2765.9	Standard polar	33892256
Gemcitabine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C1(F)F	2791.9	Semi standard non polar	33892256
Gemcitabine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C1(F)F	2872.1	Standard non polar	33892256
Gemcitabine,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@@H]1[C@@H](CO)O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C1(F)F	2671.6	Standard polar	33892256
Gemcitabine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C(F)(F)[C@@H]1O[Si](C)(C)C(C)(C)C	3016.7	Semi standard non polar	33892256
Gemcitabine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C(F)(F)[C@@H]1O[Si](C)(C)C(C)(C)C	3067.1	Standard non polar	33892256
Gemcitabine,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)C(F)(F)[C@@H]1O[Si](C)(C)C(C)(C)C	2679.9	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Gemcitabine GC-MS (Non-derivatized) - 70eV, Positive	splash10-00c3-9210000000-49e8caef8629bb5b3f0b	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Gemcitabine GC-MS (2 TMS) - 70eV, Positive	splash10-00or-7902000000-4e3542be1d6d35b1b0c4	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Gemcitabine 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
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gemcitabine LC-ESI-ITFT , negative-QTOF	splash10-03di-0930000000-e2122f1423d3060097b9	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gemcitabine LC-ESI-ITFT , negative-QTOF	splash10-03di-0790000000-e66897c78fa010a45ab8	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gemcitabine LC-ESI-ITFT , negative-QTOF	splash10-0cfs-0910000000-e4e73c07b687772a1108	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gemcitabine LC-ESI-ITFT , negative-QTOF	splash10-0a4i-0900000000-99f619802e3ba7bd8b2e	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gemcitabine LC-ESI-ITFT , negative-QTOF	splash10-0a4i-0900000000-18dd55d7372a11b9dfb7	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gemcitabine LC-ESI-ITFT , negative-QTOF	splash10-0a4i-1900000000-fdc016f6d17808e4cf1b	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gemcitabine LC-ESI-ITFT , negative-QTOF	splash10-0a4i-5900000000-ec478d4dfe03f80b91ad	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gemcitabine LC-ESI-ITFT , negative-QTOF	splash10-03di-0790000000-0d953fc9632751f00f72	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gemcitabine LC-ESI-ITFT , negative-QTOF	splash10-07xs-0920000000-0e8154089a57b6bef7c4	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gemcitabine LC-ESI-ITFT , negative-QTOF	splash10-0a4i-0900000000-c54a530153a028d6ffcc	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gemcitabine LC-ESI-ITFT , negative-QTOF	splash10-0a4i-0900000000-1f4cd6bc7d377fe7731e	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gemcitabine LC-ESI-ITFT , negative-QTOF	splash10-0a4i-0900000000-c3cdcfa5d386ac7222fa	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gemcitabine LC-ESI-ITFT , negative-QTOF	splash10-0aor-4900000000-337f45a27b7b12b1b2f0	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gemcitabine LC-ESI-ITFT , negative-QTOF	splash10-03di-0920000000-52d24e07b71b7d08dcdb	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gemcitabine LC-ESI-QTOF , positive-QTOF	splash10-03di-0190000000-6d052797bc5b8b31bf7b	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gemcitabine LC-ESI-QTOF , positive-QTOF	splash10-03dl-0900000000-01d92fca070f980c2668	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gemcitabine LC-ESI-ITFT , positive-QTOF	splash10-03di-0900000000-95712722811cd50ab160	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gemcitabine LC-ESI-ITFT , positive-QTOF	splash10-03di-0190000000-b97d64dba479bbac0253	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Gemcitabine LC-ESI-ITFT , positive-QTOF	splash10-03di-0930000000-fce77aa139fbedd4910b	2017-09-14	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gemcitabine 10V, Positive-QTOF	splash10-03di-0900000000-83efc18ba2f8876de391	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gemcitabine 20V, Positive-QTOF	splash10-03di-6900000000-10cb8c7171afb23abcc4	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gemcitabine 40V, Positive-QTOF	splash10-0292-9200000000-6bc1af7531a9c978723c	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gemcitabine 10V, Negative-QTOF	splash10-03di-2970000000-6f2d6b7661e187a5d944	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gemcitabine 20V, Negative-QTOF	splash10-02vi-7950000000-cec9468697b640599e3f	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gemcitabine 40V, Negative-QTOF	splash10-0006-9100000000-91bfffe7dcfe08cb1aba	2016-08-03	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Membrane

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Name	SMPDB/PathBank	KEGG
Gemcitabine Action Pathway		Not Available
Gemcitabine 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 DB00441	21059682	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB00441	21059682	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB00441

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

54753

KEGG Compound ID

C07650

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Gemcitabine

METLIN ID

Not Available

PubChem Compound

60750

PDB ID

Not Available

ChEBI ID

175901

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

(). FDA label . .
BC Cancer Agency [Link]

Enzymes

Enzyme Details

1. UMP-CMP kinase

General function:: Involved in ATP binding
Specific function:: Catalyzes specific phosphoryl transfer from ATP to UMP and CMP.
Gene Name:: CMPK1
Uniprot ID:: P30085
Molecular weight:: 20180.12

References

Vernejoul F, Ghenassia L, Souque A, Lulka H, Drocourt D, Cordelier P, Pradayrol L, Pyronnet S, Buscail L, Tiraby G: Gene therapy based on gemcitabine chemosensitization suppresses pancreatic tumor growth. Mol Ther. 2006 Dec;14(6):758-67. Epub 2006 Sep 25. [PubMed:17000136 ]
Hsu CH, Liou JY, Dutschman GE, Cheng YC: Phosphorylation of Cytidine, Deoxycytidine, and Their Analog Monophosphates by Human UMP/CMP Kinase Is Differentially Regulated by ATP and Magnesium. Mol Pharmacol. 2005 Mar;67(3):806-14. Epub 2004 Nov 18. [PubMed:15550676 ]
Maring JG, Groen HJ, Wachters FM, Uges DR, de Vries EG: Genetic factors influencing pyrimidine-antagonist chemotherapy. Pharmacogenomics J. 2005;5(4):226-43. [PubMed:16041392 ]
Lam W, Leung CH, Bussom S, Cheng YC: The impact of hypoxic treatment on the expression of phosphoglycerate kinase and the cytotoxicity of troxacitabine and gemcitabine. Mol Pharmacol. 2007 Sep;72(3):536-44. Epub 2007 Jun 12. [PubMed:17565005 ]

Enzyme Details

2. Deoxycytidine kinase

General function:: Involved in ATP binding
Specific function:: Required for the phosphorylation of the deoxyribonucleosides deoxycytidine (dC), deoxyguanosine (dG) and deoxyadenosine (dA). Has broad substrate specificity, and does not display selectivity based on the chirality of the substrate. It is also an essential enzyme for the phosphorylation of numerous nucleoside analogs widely employed as antiviral and chemotherapeutic agents.
Gene Name:: DCK
Uniprot ID:: P27707
Molecular weight:: 30518.315

References

Wong A, Soo RA, Yong WP, Innocenti F: Clinical pharmacology and pharmacogenetics of gemcitabine. Drug Metab Rev. 2009;41(2):77-88. doi: 10.1080/03602530902741828. [PubMed:19514966 ]
Marechal R, Mackey JR, Lai R, Demetter P, Peeters M, Polus M, Cass CE, Salmon I, Deviere J, Van Laethem JL: Deoxycitidine kinase is associated with prolonged survival after adjuvant gemcitabine for resected pancreatic adenocarcinoma. Cancer. 2010 Nov 15;116(22):5200-6. doi: 10.1002/cncr.25303. [PubMed:20669326 ]

Enzyme Details

3. Ribonucleoside-diphosphate reductase large subunit

General function:: Involved in oxidation reduction
Specific function:: Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.
Gene Name:: RRM1
Uniprot ID:: P23921
Molecular weight:: 90069.375

References

Kwon WS, Rha SY, Choi YH, Lee JO, Park KH, Jung JJ, Kim TS, Jeung HC, Chung HC: Ribonucleotide reductase M1 (RRM1) 2464G>A polymorphism shows an association with gemcitabine chemosensitivity in cancer cell lines. Pharmacogenet Genomics. 2006 Jun;16(6):429-38. [PubMed:16708051 ]
Rosell R, Cobo M, Isla D, Camps C, Massuti B: Pharmacogenomics and gemcitabine. Ann Oncol. 2006 May;17 Suppl 5:v13-16. [PubMed:16807441 ]
Bepler G, Kusmartseva I, Sharma S, Gautam A, Cantor A, Sharma A, Simon G: RRM1 modulated in vitro and in vivo efficacy of gemcitabine and platinum in non-small-cell lung cancer. J Clin Oncol. 2006 Oct 10;24(29):4731-7. Epub 2006 Sep 11. [PubMed:16966686 ]
Smid K, Bergman AM, Eijk PP, Veerman G, van Haperen VW, van den Ijssel P, Ylstra B, Peters GJ: Micro-array analysis of resistance for gemcitabine results in increased expression of ribonucleotide reductase subunits. Nucleosides Nucleotides Nucleic Acids. 2006;25(9-11):1001-7. [PubMed:17065054 ]
Nakahira S, Nakamori S, Tsujie M, Takahashi Y, Okami J, Yoshioka S, Yamasaki M, Marubashi S, Takemasa I, Miyamoto A, Takeda Y, Nagano H, Dono K, Umeshita K, Sakon M, Monden M: Involvement of ribonucleotide reductase M1 subunit overexpression in gemcitabine resistance of human pancreatic cancer. Int J Cancer. 2007 Mar 15;120(6):1355-63. [PubMed:17131328 ]
Cerqueira NM, Fernandes PA, Ramos MJ: Understanding ribonucleotide reductase inactivation by gemcitabine. Chemistry. 2007;13(30):8507-15. [PubMed:17636467 ]

Enzyme Details

4. 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

Rosell R, Taron M, Sanchez JM, Moran T, Reguart N, Besse B, Isla D, Massuti B, Alberola V, Sanchez JJ: The promise of pharmacogenomics: gemcitabine and pemetrexed. Oncology (Williston Park). 2004 Nov;18(13 Suppl 8):70-6. [PubMed:15655942 ]
Huang CL, Yokomise H, Fukushima M, Kinoshita M: Tailor-made chemotherapy for non-small cell lung cancer patients. Future Oncol. 2006 Apr;2(2):289-99. [PubMed:16563096 ]
Giovannetti E, Mey V, Nannizzi S, Pasqualetti G, Marini L, Del Tacca M, Danesi R: Cellular and pharmacogenetics foundation of synergistic interaction of pemetrexed and gemcitabine in human non-small-cell lung cancer cells. Mol Pharmacol. 2005 Jul;68(1):110-8. Epub 2005 Mar 28. [PubMed:15795320 ]
Zhao XD, Zhang Y: [Routine chemotherapeutic drug treatment effectiveness predictive molecules and chemotherapeutic drug selection]. Ai Zheng. 2006 Dec;25(12):1577-80. [PubMed:17166391 ]
Giovannetti E, Mey V, Nannizzi S, Pasqualetti G, Del Tacca M, Danesi R: Pharmacogenetics of anticancer drug sensitivity in pancreatic cancer. Mol Cancer Ther. 2006 Jun;5(6):1387-95. [PubMed:16818496 ]
Chen X, Ji ZL, Chen YZ: TTD: Therapeutic Target Database. Nucleic Acids Res. 2002 Jan 1;30(1):412-5. [PubMed:11752352 ]

Enzyme Details

5. 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

Giovannetti E, Laan AC, Vasile E, Tibaldi C, Nannizzi S, Ricciardi S, Falcone A, Danesi R, Peters GJ: Correlation between cytidine deaminase genotype and gemcitabine deamination in blood samples. Nucleosides Nucleotides Nucleic Acids. 2008 Jun;27(6):720-5. doi: 10.1080/15257770802145447. [PubMed:18600531 ]
Gusella M, Pasini F, Bolzonella C, Meneghetti S, Barile C, Bononi A, Toso S, Menon D, Crepaldi G, Modena Y, Stievano L, Padrini R: Equilibrative nucleoside transporter 1 genotype, cytidine deaminase activity and age predict gemcitabine plasma clearance in patients with solid tumours. Br J Clin Pharmacol. 2011 Mar;71(3):437-44. doi: 10.1111/j.1365-2125.2010.03838.x. [PubMed:21284703 ]
Wong A, Soo RA, Yong WP, Innocenti F: Clinical pharmacology and pharmacogenetics of gemcitabine. Drug Metab Rev. 2009;41(2):77-88. doi: 10.1080/03602530902741828. [PubMed:19514966 ]

Transporters

Enzyme Details

1. Multidrug resistance protein 1

General function:: Involved in ATP binding
Specific function:: Energy-dependent efflux pump responsible for decreased drug accumulation in multidrug-resistant cells
Gene Name:: ABCB1
Uniprot ID:: P08183
Molecular weight:: 141477.3

References

Bergman AM, Pinedo HM, Talianidis I, Veerman G, Loves WJ, van der Wilt CL, Peters GJ: Increased sensitivity to gemcitabine of P-glycoprotein and multidrug resistance-associated protein-overexpressing human cancer cell lines. Br J Cancer. 2003 Jun 16;88(12):1963-70. [PubMed:12799644 ]

Enzyme Details

2. Equilibrative nucleoside transporter 1

General function:: Involved in nucleoside transmembrane transporter activity
Specific function:: Mediates both influx and efflux of nucleosides across the membrane (equilibrative transporter). It is sensitive (ES) to low concentrations of the inhibitor nitrobenzylmercaptopurine riboside (NBMPR) and is sodium-independent. It has a higher affinity for adenosine. Inhibited by dipyridamole and dilazep (anticancer chemotherapeutics drugs)
Gene Name:: SLC29A1
Uniprot ID:: Q99808
Molecular weight:: 50218.8

References

Santini D, Vincenzi B, Fratto ME, Perrone G, Lai R, Catalano V, Cass C, Ruffini PA, Spoto C, Muretto P, Rizzo S, Muda AO, Mackey JR, Russo A, Tonini G, Graziano F: Prognostic role of human equilibrative transporter 1 (hENT1) in patients with resected gastric cancer. J Cell Physiol. 2010 May;223(2):384-8. doi: 10.1002/jcp.22045. [PubMed:20082300 ]

Showing metabocard for Gemcitabine (HMDB0014584)

MOL for HMDB0014584 (Gemcitabine)

3D MOL for HMDB0014584 (Gemcitabine)

3D SDF for HMDB0014584 (Gemcitabine)

3D-SDF for HMDB0014584 (Gemcitabine)

PDB for HMDB0014584 (Gemcitabine)

3D PDB for HMDB0014584 (Gemcitabine)

SMILES for HMDB0014584 (Gemcitabine)

INCHI for HMDB0014584 (Gemcitabine)

Structure for HMDB0014584 (Gemcitabine)

3D Structure for HMDB0014584 (Gemcitabine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes

References

References

References

References

References

Transporters

References

References