data_PST
# 
_chem_comp.id                                    PST 
_chem_comp.name                                  "THYMIDINE-5'-THIOPHOSPHATE" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H15 N2 O7 P S" 
_chem_comp.mon_nstd_parent_comp_id               DT 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     1999-07-08 
_chem_comp.pdbx_modified_date                    2011-06-04 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         TS 
_chem_comp.formula_weight                        338.274 
_chem_comp.one_letter_code                       T 
_chem_comp.three_letter_code                     PST 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1KSP 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.alt_atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.charge 
_chem_comp_atom.pdbx_align 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_leaving_atom_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.model_Cartn_x 
_chem_comp_atom.model_Cartn_y 
_chem_comp_atom.model_Cartn_z 
_chem_comp_atom.pdbx_model_Cartn_x_ideal 
_chem_comp_atom.pdbx_model_Cartn_y_ideal 
_chem_comp_atom.pdbx_model_Cartn_z_ideal 
_chem_comp_atom.pdbx_component_atom_id 
_chem_comp_atom.pdbx_component_comp_id 
_chem_comp_atom.pdbx_ordinal 
PST P      P    P 0 1 N N N 63.102 30.761 87.771 0.767  -0.337 -3.993 P      PST 1  
PST OP1    O1P  O 0 1 N N N 64.438 30.079 87.987 1.653  -1.476 -4.708 OP1    PST 2  
PST OP2    O2P  O 0 1 N Y N 62.030 29.627 88.088 -0.327 0.221  -5.032 OP2    PST 3  
PST SP     SP   S 0 1 N N N 62.801 31.653 86.143 1.874  1.057  -3.446 SP     PST 4  
PST "O5'"  O5*  O 0 1 N N N 62.936 31.645 89.088 0.020  -0.964 -2.712 "O5'"  PST 5  
PST "C5'"  C5*  C 0 1 N N N 61.657 32.231 89.377 -0.745 0.089  -2.124 "C5'"  PST 6  
PST "C4'"  C4*  C 0 1 N N R 61.563 32.786 90.761 -1.484 -0.442 -0.894 "C4'"  PST 7  
PST "O4'"  O4*  O 0 1 N N N 61.893 31.766 91.685 -0.549 -0.820 0.141  "O4'"  PST 8  
PST "C3'"  C3*  C 0 1 N N S 62.589 33.835 90.981 -2.324 0.681  -0.235 "C3'"  PST 9  
PST "O3'"  O3*  O 0 1 N N N 62.181 35.105 90.456 -3.611 0.782  -0.847 "O3'"  PST 10 
PST "C2'"  C2*  C 0 1 N N N 62.629 33.853 92.478 -2.444 0.181  1.225  "C2'"  PST 11 
PST "C1'"  C1*  C 0 1 N N R 62.595 32.383 92.778 -1.275 -0.811 1.381  "C1'"  PST 12 
PST N1     N1   N 0 1 N N N 63.906 31.678 92.834 -0.396 -0.377 2.470  N1     PST 13 
PST C2     C2   C 0 1 N N N 64.619 31.811 94.020 0.201  0.825  2.405  C2     PST 14 
PST O2     O2   O 0 1 N N N 64.269 32.468 94.992 0.004  1.541  1.442  O2     PST 15 
PST N3     N3   N 0 1 N N N 65.796 31.164 94.099 1.013  1.249  3.392  N3     PST 16 
PST C4     C4   C 0 1 N N N 66.351 30.388 93.106 1.237  0.469  4.469  C4     PST 17 
PST O4     O4   O 0 1 N N N 67.410 29.856 93.347 1.971  0.852  5.362  O4     PST 18 
PST C5     C5   C 0 1 N N N 65.597 30.266 91.872 0.618  -0.801 4.548  C5     PST 19 
PST C5M    C5M  C 0 1 N N N 66.131 29.450 90.686 0.855  -1.693 5.739  C5M    PST 20 
PST C6     C6   C 0 1 N N N 64.410 30.909 91.783 -0.192 -1.200 3.544  C6     PST 21 
PST HOP1   1HOP H 0 0 N N N 65.077 30.755 87.797 2.082  -1.060 -5.468 HOP1   PST 22 
PST HOP2   2HOP H 0 0 N N N 61.192 30.054 87.952 -0.878 -0.530 -5.290 HOP2   PST 23 
PST "H5'"  1H5* H 0 1 N N N 61.395 33.006 88.619 -1.468 0.461  -2.850 "H5'"  PST 24 
PST "H5''" 2H5* H 0 0 N N N 60.834 31.503 89.184 -0.079 0.899  -1.826 "H5''" PST 25 
PST "H4'"  H4*  H 0 1 N N N 60.531 33.188 90.891 -2.117 -1.287 -1.164 "H4'"  PST 26 
PST "H3'"  H3*  H 0 1 N N N 63.566 33.638 90.481 -1.799 1.635  -0.277 "H3'"  PST 27 
PST HO3    HO3  H 0 1 N Y N 62.837 35.776 90.596 -4.114 1.429  -0.334 HO3    PST 28 
PST "H2'"  1H2* H 0 1 N N N 63.479 34.416 92.929 -3.397 -0.324 1.378  "H2'"  PST 29 
PST "H2''" 2H2* H 0 0 N N N 61.837 34.462 92.972 -2.335 1.011  1.922  "H2''" PST 30 
PST "H1'"  H1*  H 0 1 N N N 62.139 32.298 93.792 -1.662 -1.808 1.592  "H1'"  PST 31 
PST HN3    HN3  H 0 1 N N N 66.305 31.269 94.976 1.436  2.119  3.329  HN3    PST 32 
PST H71    1H5M H 0 1 N N N 65.551 29.356 89.737 1.532  -1.198 6.435  H71    PST 33 
PST H72    2H5M H 0 1 N N N 67.145 29.836 90.432 -0.093 -1.894 6.237  H72    PST 34 
PST H73    3H5M H 0 1 N N N 66.360 28.422 91.051 1.298  -2.632 5.407  H73    PST 35 
PST H6     H6   H 0 1 N N N 63.845 30.804 90.841 -0.675 -2.165 3.589  H6     PST 36 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
PST P     OP1    SING N N 1  
PST P     OP2    SING N N 2  
PST P     SP     DOUB N N 3  
PST P     "O5'"  SING N N 4  
PST OP1   HOP1   SING N N 5  
PST OP2   HOP2   SING N N 6  
PST "O5'" "C5'"  SING N N 7  
PST "C5'" "C4'"  SING N N 8  
PST "C5'" "H5'"  SING N N 9  
PST "C5'" "H5''" SING N N 10 
PST "C4'" "O4'"  SING N N 11 
PST "C4'" "C3'"  SING N N 12 
PST "C4'" "H4'"  SING N N 13 
PST "O4'" "C1'"  SING N N 14 
PST "C3'" "O3'"  SING N N 15 
PST "C3'" "C2'"  SING N N 16 
PST "C3'" "H3'"  SING N N 17 
PST "O3'" HO3    SING N N 18 
PST "C2'" "C1'"  SING N N 19 
PST "C2'" "H2'"  SING N N 20 
PST "C2'" "H2''" SING N N 21 
PST "C1'" N1     SING N N 22 
PST "C1'" "H1'"  SING N N 23 
PST N1    C2     SING N N 24 
PST N1    C6     SING N N 25 
PST C2    O2     DOUB N N 26 
PST C2    N3     SING N N 27 
PST N3    C4     SING N N 28 
PST N3    HN3    SING N N 29 
PST C4    O4     DOUB N N 30 
PST C4    C5     SING N N 31 
PST C5    C5M    SING N N 32 
PST C5    C6     DOUB N N 33 
PST C5M   H71    SING N N 34 
PST C5M   H72    SING N N 35 
PST C5M   H73    SING N N 36 
PST C6    H6     SING N N 37 
# 
loop_
_pdbx_chem_comp_descriptor.comp_id 
_pdbx_chem_comp_descriptor.type 
_pdbx_chem_comp_descriptor.program 
_pdbx_chem_comp_descriptor.program_version 
_pdbx_chem_comp_descriptor.descriptor 
PST SMILES           ACDLabs              10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)COP(=S)(O)O"                                                                                                       
PST SMILES_CANONICAL CACTVS               3.341 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=S)O2)C(=O)NC1=O"                                                                                        
PST SMILES           CACTVS               3.341 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=S)O2)C(=O)NC1=O"                                                                                            
PST SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=S)(O)O)O"                                                                                          
PST SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=S)(O)O)O"                                                                                                       
PST InChI            InChI                1.03  "InChI=1S/C10H15N2O7PS/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(19-8)4-18-20(16,17)21/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,21)/t6-,7+,8+/m0/s1" 
PST InChIKey         InChI                1.03  OJRKJKYGUAALCJ-XLPZGREQSA-N                                                                                                                       
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
PST "SYSTEMATIC NAME" ACDLabs              10.04 "5'-O-thiophosphonothymidine"                                                                              
PST "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "1-[(2R,4S,5R)-5-(dihydroxyphosphinothioyloxymethyl)-4-hydroxy-oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
PST "Create component"  1999-07-08 RCSB 
PST "Modify descriptor" 2011-06-04 RCSB 
# 
