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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2013-06-15 18:25:14 UTC

Update Date

2021-09-14 15:48:16 UTC

HMDB ID

HMDB0060641

Secondary Accession Numbers

HMDB60641

Metabolite Identification

Common Name

Lamivudine-monophosphate

Description

Lamivudine-monophosphate belongs to the class of organic compounds known as nucleoside and nucleotide analogues. These are analogues of nucleosides and nucleotides. These include phosphonated nucleosides, C-glycosylated nucleoside bases, analogues where the sugar unit is a pyranose, and carbocyclic nucleosides, among others. Lamivudine-monophosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). Within humans, lamivudine-monophosphate participates in a number of enzymatic reactions. In particular, lamivudine-monophosphate and uridine 5'-diphosphate can be converted into lamivudine and uridine triphosphate through the action of the enzyme 5'(3')-deoxyribonucleotidase, cytosolic type. In addition, lamivudine-monophosphate can be converted into lamivudine-diphosphate; which is mediated by the enzyme UMP-CMP kinase. Lamivudine-monophosphate is a metabolite of lamivudine. In humans, lamivudine-monophosphate is involved in lamivudine metabolism pathway. Lamivudine has been used for treatment of chronic hepatitis B at a lower dose than for treatment of HIV. It improves the seroconversion of e-antigen positive hepatitis B and also improves histology staging of the liver. It is marketed by GlaxoSmithKline with the brand names Zeffix, Heptovir, Epivir, and Epivir-HBV. Lamivudine (2',3'-dideoxy-3'-thiacytidine, commonly called 3TC) is a potent nucleoside analog reverse transcriptase inhibitor (nRTI).

Structure

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

HMDB0060641
     RDKit          3D
Lamivudine-monophosphate
 31 32  0  0  0  0  0  0  0  0999 V2000
   -5.6395    1.4717   -0.2601 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3078    0.9893   -0.3549 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2200    1.7258   -0.0030 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9442    1.1875   -0.1226 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7809   -0.0619   -0.5861 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5022   -0.7166   -0.7502 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4764   -2.0522   -0.0775 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7255   -1.7034    1.2693 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.0420    0.0309    0.7509 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5585    0.2698    0.7065 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1388   -0.7874   -0.0301 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8046   -0.5375   -0.0867 P   0  0  0  0  0  5  0  0  0  0  0  0
    5.4769   -1.7577    0.4714 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2649   -0.2654   -1.7046 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2377    0.8524    0.7786 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5872    0.0177   -0.5149 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8778   -0.7607   -0.9245 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8181   -1.9564   -1.3751 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1243   -0.2598   -0.8171 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8890    2.1403    0.4974 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3678    1.1789   -0.9206 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3662    2.7338    0.3701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0723    1.7706    0.1547 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4748   -0.9657   -1.8627 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1431   -2.8816   -0.7054 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4298   -2.2968    0.4603 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6373    0.7415    1.4609 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9705    0.2372    1.7322 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8006    1.1892    0.1712 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2627   -0.3552   -1.7977 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9271    0.8219    1.6970 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
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 12 15  1  0
  9 16  1  0
  5 17  1  0
 17 18  2  0
 17 19  1  0
 19  2  2  0
 16  6  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  0
  4 23  1  0
  6 24  1  0
  7 25  1  0
  7 26  1  0
  9 27  1  0
 10 28  1  0
 10 29  1  0
 14 30  1  0
 15 31  1  0
M  END


  Mrv0541 06151311252D          

 19 20  0  0  0  0            999 V2000
    0.7145    6.7661    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    5.9411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    5.5286    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    4.7036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    4.2911    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    4.2911    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    4.7036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    5.5286    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    3.4661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3819    2.9812    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270    2.1965    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020    2.1965    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1830    1.5291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0034    1.6153    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4884    0.9479    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9733    0.2804    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1558    1.4328    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8209    0.4630    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470    2.9812    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  2  8  1  0  0  0  0
  6  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 15 18  2  0  0  0  0
 12 19  1  0  0  0  0
  9 19  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060641

> <DATABASE_NAME>
hmdb

> <SMILES>
NC1=NC(=O)N(C=C1)C1CSC(COP(O)(O)=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C8H12N3O6PS/c9-5-1-2-11(8(12)10-5)6-4-19-7(17-6)3-16-18(13,14)15/h1-2,6-7H,3-4H2,(H2,9,10,12)(H2,13,14,15)

> <INCHI_KEY>
WUMZLKDCOINBEA-UHFFFAOYSA-N

> <FORMULA>
C8H12N3O6PS

> <MOLECULAR_WEIGHT>
309.236

> <EXACT_MASS>
309.018442333

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
26.44128249590426

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy}phosphonic acid

> <ALOGPS_LOGP>
-1.48

> <JCHEM_LOGP>
-1.5543763222381044

> <ALOGPS_LOGS>
-1.25

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.059169632686921

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.0930607165142332

> <JCHEM_PKA_STRONGEST_BASIC>
0.06997933385651534

> <JCHEM_POLAR_SURFACE_AREA>
134.68

> <JCHEM_REFRACTIVITY>
66.0374

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.74e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[5-(4-amino-2-oxopyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0060641
     RDKit          3D
Lamivudine-monophosphate
 31 32  0  0  0  0  0  0  0  0999 V2000
   -5.6395    1.4717   -0.2601 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3078    0.9893   -0.3549 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2200    1.7258   -0.0030 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9442    1.1875   -0.1226 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7809   -0.0619   -0.5861 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5022   -0.7166   -0.7502 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4764   -2.0522   -0.0775 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7255   -1.7034    1.2693 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.0420    0.0309    0.7509 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5585    0.2698    0.7065 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1388   -0.7874   -0.0301 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8046   -0.5375   -0.0867 P   0  0  0  0  0  5  0  0  0  0  0  0
    5.4769   -1.7577    0.4714 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2649   -0.2654   -1.7046 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2377    0.8524    0.7786 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5872    0.0177   -0.5149 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8778   -0.7607   -0.9245 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8181   -1.9564   -1.3751 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1243   -0.2598   -0.8171 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8890    2.1403    0.4974 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3678    1.1789   -0.9206 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3662    2.7338    0.3701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0723    1.7706    0.1547 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4748   -0.9657   -1.8627 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1431   -2.8816   -0.7054 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4298   -2.2968    0.4603 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6373    0.7415    1.4609 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9705    0.2372    1.7322 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8006    1.1892    0.1712 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2627   -0.3552   -1.7977 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9271    0.8219    1.6970 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
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 12 15  1  0
  9 16  1  0
  5 17  1  0
 17 18  2  0
 17 19  1  0
 19  2  2  0
 16  6  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  0
  4 23  1  0
  6 24  1  0
  7 25  1  0
  7 26  1  0
  9 27  1  0
 10 28  1  0
 10 29  1  0
 14 30  1  0
 15 31  1  0
M  END

HEADER    PROTEIN                                 15-JUN-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-JUN-13         0                                  
HETATM    1  N   UNK     0       1.334  12.630   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       1.334  11.090   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       2.667  10.320   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       2.667   8.780   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       4.001   8.010   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0       1.334   8.010   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       0.000   8.780   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000  10.320   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334   6.470   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.580   5.565   0.000  0.00  0.00           C+0
HETATM   11  S   UNK     0       2.104   4.100   0.000  0.00  0.00           S+0
HETATM   12  C   UNK     0       0.564   4.100   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.342   2.854   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -1.873   3.015   0.000  0.00  0.00           O+0
HETATM   15  P   UNK     0      -2.778   1.769   0.000  0.00  0.00           P+0
HETATM   16  O   UNK     0      -3.683   0.523   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -4.024   2.675   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -1.532   0.864   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.088   5.565   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    9                                                  
CONECT    7    6    8                                                       
CONECT    8    7    2                                                       
CONECT    9    6   10   19                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   19                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17   18                                             
CONECT   16   15                                                            
CONECT   17   15                                                            
CONECT   18   15                                                            
CONECT   19   12    9                                                       
MASTER        0    0    0    0    0    0    0    0   19    0   40    0
END

COMPND    HMDB0060641
HETATM    1  N1  UNL     1      -5.640   1.472  -0.260  1.00  0.00           N  
HETATM    2  C1  UNL     1      -4.308   0.989  -0.355  1.00  0.00           C  
HETATM    3  C2  UNL     1      -3.220   1.726  -0.003  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.944   1.188  -0.123  1.00  0.00           C  
HETATM    5  N2  UNL     1      -1.781  -0.062  -0.586  1.00  0.00           N  
HETATM    6  C4  UNL     1      -0.502  -0.717  -0.750  1.00  0.00           C  
HETATM    7  C5  UNL     1      -0.476  -2.052  -0.078  1.00  0.00           C  
HETATM    8  S1  UNL     1       0.726  -1.703   1.269  1.00  0.00           S  
HETATM    9  C6  UNL     1       1.042   0.031   0.751  1.00  0.00           C  
HETATM   10  C7  UNL     1       2.558   0.270   0.706  1.00  0.00           C  
HETATM   11  O1  UNL     1       3.139  -0.787  -0.030  1.00  0.00           O  
HETATM   12  P1  UNL     1       4.805  -0.537  -0.087  1.00  0.00           P  
HETATM   13  O2  UNL     1       5.477  -1.758   0.471  1.00  0.00           O  
HETATM   14  O3  UNL     1       5.265  -0.265  -1.705  1.00  0.00           O  
HETATM   15  O4  UNL     1       5.238   0.852   0.779  1.00  0.00           O  
HETATM   16  O5  UNL     1       0.587   0.018  -0.515  1.00  0.00           O  
HETATM   17  C8  UNL     1      -2.878  -0.761  -0.924  1.00  0.00           C  
HETATM   18  O6  UNL     1      -2.818  -1.956  -1.375  1.00  0.00           O  
HETATM   19  N3  UNL     1      -4.124  -0.260  -0.817  1.00  0.00           N  
HETATM   20  H1  UNL     1      -5.889   2.140   0.497  1.00  0.00           H  
HETATM   21  H2  UNL     1      -6.368   1.179  -0.921  1.00  0.00           H  
HETATM   22  H3  UNL     1      -3.366   2.734   0.370  1.00  0.00           H  
HETATM   23  H4  UNL     1      -1.072   1.771   0.155  1.00  0.00           H  
HETATM   24  H5  UNL     1      -0.475  -0.966  -1.863  1.00  0.00           H  
HETATM   25  H6  UNL     1      -0.143  -2.882  -0.705  1.00  0.00           H  
HETATM   26  H7  UNL     1      -1.430  -2.297   0.460  1.00  0.00           H  
HETATM   27  H8  UNL     1       0.637   0.742   1.461  1.00  0.00           H  
HETATM   28  H9  UNL     1       2.970   0.237   1.732  1.00  0.00           H  
HETATM   29  H10 UNL     1       2.801   1.189   0.171  1.00  0.00           H  
HETATM   30  H11 UNL     1       6.263  -0.355  -1.798  1.00  0.00           H  
HETATM   31  H12 UNL     1       4.927   0.822   1.697  1.00  0.00           H  
CONECT    1    2   20   21
CONECT    2    3   19   19
CONECT    3    4    4   22
CONECT    4    5   23
CONECT    5    6   17
CONECT    6    7   16   24
CONECT    7    8   25   26
CONECT    8    9
CONECT    9   10   16   27
CONECT   10   11   28   29
CONECT   11   12
CONECT   12   13   13   14   15
CONECT   14   30
CONECT   15   31
CONECT   17   18   18   19
END

HMDB0060641
     RDKit          3D
Lamivudine-monophosphate
 31 32  0  0  0  0  0  0  0  0999 V2000
   -5.6395    1.4717   -0.2601 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3078    0.9893   -0.3549 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2200    1.7258   -0.0030 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9442    1.1875   -0.1226 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7809   -0.0619   -0.5861 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5022   -0.7166   -0.7502 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4764   -2.0522   -0.0775 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7255   -1.7034    1.2693 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.0420    0.0309    0.7509 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5585    0.2698    0.7065 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1388   -0.7874   -0.0301 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8046   -0.5375   -0.0867 P   0  0  0  0  0  5  0  0  0  0  0  0
    5.4769   -1.7577    0.4714 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2649   -0.2654   -1.7046 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2377    0.8524    0.7786 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5872    0.0177   -0.5149 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8778   -0.7607   -0.9245 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8181   -1.9564   -1.3751 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1243   -0.2598   -0.8171 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8890    2.1403    0.4974 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3678    1.1789   -0.9206 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3662    2.7338    0.3701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0723    1.7706    0.1547 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4748   -0.9657   -1.8627 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1431   -2.8816   -0.7054 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4298   -2.2968    0.4603 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6373    0.7415    1.4609 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9705    0.2372    1.7322 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8006    1.1892    0.1712 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2627   -0.3552   -1.7977 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9271    0.8219    1.6970 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
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 12 15  1  0
  9 16  1  0
  5 17  1  0
 17 18  2  0
 17 19  1  0
 19  2  2  0
 16  6  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  0
  4 23  1  0
  6 24  1  0
  7 25  1  0
  7 26  1  0
  9 27  1  0
 10 28  1  0
 10 29  1  0
 14 30  1  0
 15 31  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
Lamivudine-monophosphoric acid	Generator

Chemical Formula

C₈H₁₂N₃O₆PS

Average Molecular Weight

309.236

Monoisotopic Molecular Weight

309.018442333

IUPAC Name

{[5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy}phosphonic acid

Traditional Name

[5-(4-amino-2-oxopyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxyphosphonic acid

CAS Registry Number

Not Available

SMILES

NC1=NC(=O)N(C=C1)C1CSC(COP(O)(O)=O)O1

InChI Identifier

InChI=1S/C8H12N3O6PS/c9-5-1-2-11(8(12)10-5)6-4-19-7(17-6)3-16-18(13,14)15/h1-2,6-7H,3-4H2,(H2,9,10,12)(H2,13,14,15)

InChI Key

WUMZLKDCOINBEA-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as nucleoside and nucleotide analogues. These are analogues of nucleosides and nucleotides. These include phosphonated nucleosides, C-glycosylated nucleoside bases, analogues where the sugar unit is a pyranose, and carbocyclic nucleosides, among others.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Nucleoside and nucleotide analogues

Sub Class

Not Available

Direct Parent

Nucleoside and nucleotide analogues

Alternative Parents

Substituents

Hydroxypyrimidine
Monoalkyl phosphate
Hydropyrimidine
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Pyrimidine
Monothioacetal
Oxathiolane
Heteroaromatic compound
Oxacycle
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Organic oxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (HMDB: HMDB0060641)

Excreta

Biofluid or Excreta

Urine (HMDB: HMDB0060641)

Organ

Kidney (HMDB: HMDB0060641)
Liver (HMDB: HMDB0060641)

Cellular substructure

Cytoplasm (HMDB: HMDB0060641)

Source

Endogenous

Endogenous (HMDB: HMDB0060641)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Lamivudine Metabolism Pathway (PathBank: SMP0000649)

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	17.4 g/L	ALOGPS
logP	-1.5	ALOGPS
logP	-1.6	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	1.09	ChemAxon
pKa (Strongest Basic)	0.07	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	134.68 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	66.04 m³·mol⁻¹	ChemAxon
Polarizability	26.44 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
DarkChem	[M+H]+	165.981	31661259
DarkChem	[M-H]-	162.636	31661259
DeepCCS	[M+H]+	159.686	30932474
DeepCCS	[M-H]-	157.328	30932474
DeepCCS	[M-2H]-	190.529	30932474
DeepCCS	[M+Na]+	166.19	30932474
AllCCS	[M+H]+	164.4	32859911
AllCCS	[M+H-H2O]+	161.2	32859911
AllCCS	[M+NH4]+	167.3	32859911
AllCCS	[M+Na]+	168.2	32859911
AllCCS	[M-H]-	159.6	32859911
AllCCS	[M+Na-2H]-	159.7	32859911
AllCCS	[M+HCOO]-	159.8	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.	2.41 minutes	32390414
Predicted by Siyang on May 30, 2022	9.2335 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	8.42 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	417.2 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	234.1 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	56.5 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	151.8 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	46.1 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	297.4 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	267.6 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	743.9 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	590.7 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	52.8 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	571.3 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	152.9 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	175.4 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	642.3 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	361.0 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	307.4 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Lamivudine-monophosphate	NC1=NC(=O)N(C=C1)C1CSC(COP(O)(O)=O)O1	4006.7	Standard polar	33892256
Lamivudine-monophosphate	NC1=NC(=O)N(C=C1)C1CSC(COP(O)(O)=O)O1	2375.6	Standard non polar	33892256
Lamivudine-monophosphate	NC1=NC(=O)N(C=C1)C1CSC(COP(O)(O)=O)O1	3084.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Lamivudine-monophosphate,1TMS,isomer #1	C[Si](C)(C)OP(=O)(O)OCC1OC(N2C=CC(N)=NC2=O)CS1	2907.7	Semi standard non polar	33892256
Lamivudine-monophosphate,1TMS,isomer #1	C[Si](C)(C)OP(=O)(O)OCC1OC(N2C=CC(N)=NC2=O)CS1	2750.6	Standard non polar	33892256
Lamivudine-monophosphate,1TMS,isomer #1	C[Si](C)(C)OP(=O)(O)OCC1OC(N2C=CC(N)=NC2=O)CS1	4601.4	Standard polar	33892256
Lamivudine-monophosphate,1TMS,isomer #2	C[Si](C)(C)NC1=NC(=O)N(C2CSC(COP(=O)(O)O)O2)C=C1	2940.0	Semi standard non polar	33892256
Lamivudine-monophosphate,1TMS,isomer #2	C[Si](C)(C)NC1=NC(=O)N(C2CSC(COP(=O)(O)O)O2)C=C1	2807.8	Standard non polar	33892256
Lamivudine-monophosphate,1TMS,isomer #2	C[Si](C)(C)NC1=NC(=O)N(C2CSC(COP(=O)(O)O)O2)C=C1	4866.7	Standard polar	33892256
Lamivudine-monophosphate,2TMS,isomer #1	C[Si](C)(C)OP(=O)(OCC1OC(N2C=CC(N)=NC2=O)CS1)O[Si](C)(C)C	2887.9	Semi standard non polar	33892256
Lamivudine-monophosphate,2TMS,isomer #1	C[Si](C)(C)OP(=O)(OCC1OC(N2C=CC(N)=NC2=O)CS1)O[Si](C)(C)C	2799.2	Standard non polar	33892256
Lamivudine-monophosphate,2TMS,isomer #1	C[Si](C)(C)OP(=O)(OCC1OC(N2C=CC(N)=NC2=O)CS1)O[Si](C)(C)C	4082.1	Standard polar	33892256
Lamivudine-monophosphate,2TMS,isomer #2	C[Si](C)(C)NC1=NC(=O)N(C2CSC(COP(=O)(O)O[Si](C)(C)C)O2)C=C1	2957.9	Semi standard non polar	33892256
Lamivudine-monophosphate,2TMS,isomer #2	C[Si](C)(C)NC1=NC(=O)N(C2CSC(COP(=O)(O)O[Si](C)(C)C)O2)C=C1	2874.2	Standard non polar	33892256
Lamivudine-monophosphate,2TMS,isomer #2	C[Si](C)(C)NC1=NC(=O)N(C2CSC(COP(=O)(O)O[Si](C)(C)C)O2)C=C1	4088.9	Standard polar	33892256
Lamivudine-monophosphate,2TMS,isomer #3	C[Si](C)(C)N(C1=NC(=O)N(C2CSC(COP(=O)(O)O)O2)C=C1)[Si](C)(C)C	2916.1	Semi standard non polar	33892256
Lamivudine-monophosphate,2TMS,isomer #3	C[Si](C)(C)N(C1=NC(=O)N(C2CSC(COP(=O)(O)O)O2)C=C1)[Si](C)(C)C	2941.4	Standard non polar	33892256
Lamivudine-monophosphate,2TMS,isomer #3	C[Si](C)(C)N(C1=NC(=O)N(C2CSC(COP(=O)(O)O)O2)C=C1)[Si](C)(C)C	4412.8	Standard polar	33892256
Lamivudine-monophosphate,3TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N(C2CSC(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O2)C=C1	2948.9	Semi standard non polar	33892256
Lamivudine-monophosphate,3TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N(C2CSC(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O2)C=C1	2926.5	Standard non polar	33892256
Lamivudine-monophosphate,3TMS,isomer #1	C[Si](C)(C)NC1=NC(=O)N(C2CSC(COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O2)C=C1	3595.6	Standard polar	33892256
Lamivudine-monophosphate,3TMS,isomer #2	C[Si](C)(C)OP(=O)(O)OCC1OC(N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)CS1	2927.6	Semi standard non polar	33892256
Lamivudine-monophosphate,3TMS,isomer #2	C[Si](C)(C)OP(=O)(O)OCC1OC(N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)CS1	2968.2	Standard non polar	33892256
Lamivudine-monophosphate,3TMS,isomer #2	C[Si](C)(C)OP(=O)(O)OCC1OC(N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)CS1	3734.4	Standard polar	33892256
Lamivudine-monophosphate,4TMS,isomer #1	C[Si](C)(C)OP(=O)(OCC1OC(N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)CS1)O[Si](C)(C)C	2925.4	Semi standard non polar	33892256
Lamivudine-monophosphate,4TMS,isomer #1	C[Si](C)(C)OP(=O)(OCC1OC(N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)CS1)O[Si](C)(C)C	3011.6	Standard non polar	33892256
Lamivudine-monophosphate,4TMS,isomer #1	C[Si](C)(C)OP(=O)(OCC1OC(N2C=CC(N([Si](C)(C)C)[Si](C)(C)C)=NC2=O)CS1)O[Si](C)(C)C	3297.8	Standard polar	33892256
Lamivudine-monophosphate,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OP(=O)(O)OCC1OC(N2C=CC(N)=NC2=O)CS1	3140.3	Semi standard non polar	33892256
Lamivudine-monophosphate,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OP(=O)(O)OCC1OC(N2C=CC(N)=NC2=O)CS1	2979.1	Standard non polar	33892256
Lamivudine-monophosphate,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OP(=O)(O)OCC1OC(N2C=CC(N)=NC2=O)CS1	4634.6	Standard polar	33892256
Lamivudine-monophosphate,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NC1=NC(=O)N(C2CSC(COP(=O)(O)O)O2)C=C1	3187.6	Semi standard non polar	33892256
Lamivudine-monophosphate,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NC1=NC(=O)N(C2CSC(COP(=O)(O)O)O2)C=C1	3025.1	Standard non polar	33892256
Lamivudine-monophosphate,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NC1=NC(=O)N(C2CSC(COP(=O)(O)O)O2)C=C1	4784.5	Standard polar	33892256
Lamivudine-monophosphate,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OP(=O)(OCC1OC(N2C=CC(N)=NC2=O)CS1)O[Si](C)(C)C(C)(C)C	3334.6	Semi standard non polar	33892256
Lamivudine-monophosphate,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OP(=O)(OCC1OC(N2C=CC(N)=NC2=O)CS1)O[Si](C)(C)C(C)(C)C	3207.5	Standard non polar	33892256
Lamivudine-monophosphate,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OP(=O)(OCC1OC(N2C=CC(N)=NC2=O)CS1)O[Si](C)(C)C(C)(C)C	4152.7	Standard polar	33892256
Lamivudine-monophosphate,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NC1=NC(=O)N(C2CSC(COP(=O)(O)O[Si](C)(C)C(C)(C)C)O2)C=C1	3398.0	Semi standard non polar	33892256
Lamivudine-monophosphate,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NC1=NC(=O)N(C2CSC(COP(=O)(O)O[Si](C)(C)C(C)(C)C)O2)C=C1	3294.7	Standard non polar	33892256
Lamivudine-monophosphate,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)NC1=NC(=O)N(C2CSC(COP(=O)(O)O[Si](C)(C)C(C)(C)C)O2)C=C1	4151.0	Standard polar	33892256
Lamivudine-monophosphate,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N(C1=NC(=O)N(C2CSC(COP(=O)(O)O)O2)C=C1)[Si](C)(C)C(C)(C)C	3344.4	Semi standard non polar	33892256
Lamivudine-monophosphate,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N(C1=NC(=O)N(C2CSC(COP(=O)(O)O)O2)C=C1)[Si](C)(C)C(C)(C)C	3364.6	Standard non polar	33892256
Lamivudine-monophosphate,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)N(C1=NC(=O)N(C2CSC(COP(=O)(O)O)O2)C=C1)[Si](C)(C)C(C)(C)C	4333.1	Standard polar	33892256
Lamivudine-monophosphate,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N(C2CSC(COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)O2)C=C1	3571.8	Semi standard non polar	33892256
Lamivudine-monophosphate,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N(C2CSC(COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)O2)C=C1	3503.2	Standard non polar	33892256
Lamivudine-monophosphate,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)NC1=NC(=O)N(C2CSC(COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)O2)C=C1	3811.0	Standard polar	33892256
Lamivudine-monophosphate,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OP(=O)(O)OCC1OC(N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)CS1	3534.2	Semi standard non polar	33892256
Lamivudine-monophosphate,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OP(=O)(O)OCC1OC(N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)CS1	3566.6	Standard non polar	33892256
Lamivudine-monophosphate,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OP(=O)(O)OCC1OC(N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)CS1	3847.0	Standard polar	33892256
Lamivudine-monophosphate,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OP(=O)(OCC1OC(N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)CS1)O[Si](C)(C)C(C)(C)C	3696.0	Semi standard non polar	33892256
Lamivudine-monophosphate,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OP(=O)(OCC1OC(N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)CS1)O[Si](C)(C)C(C)(C)C	3715.6	Standard non polar	33892256
Lamivudine-monophosphate,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OP(=O)(OCC1OC(N2C=CC(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=NC2=O)CS1)O[Si](C)(C)C(C)(C)C	3571.9	Standard polar	33892256

Spectra

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Blood
Urine

Tissue Locations

Kidney
Liver

Pathways

Name	SMPDB/PathBank	KEGG
Lamivudine 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	Normal	Not Available	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

75607387

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for Lamivudine-monophosphate (HMDB0060641)

MOL for HMDB0060641 (Lamivudine-monophosphate)

3D MOL for HMDB0060641 (Lamivudine-monophosphate)

3D SDF for HMDB0060641 (Lamivudine-monophosphate)

3D-SDF for HMDB0060641 (Lamivudine-monophosphate)

PDB for HMDB0060641 (Lamivudine-monophosphate)

3D PDB for HMDB0060641 (Lamivudine-monophosphate)

SMILES for HMDB0060641 (Lamivudine-monophosphate)

INCHI for HMDB0060641 (Lamivudine-monophosphate)

Structure for HMDB0060641 (Lamivudine-monophosphate)

3D Structure for HMDB0060641 (Lamivudine-monophosphate)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized