data_TSP
#

_chem_comp.id                                   TSP
_chem_comp.name                                 "3'-THIO-THYMIDINE-5'-PHOSPHATE"
_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                   2019-09-04
_chem_comp.pdbx_ambiguous_flag                  N
_chem_comp.pdbx_release_status                  REL
_chem_comp.pdbx_replaced_by                     ?
_chem_comp.pdbx_replaces                        ?
_chem_comp.formula_weight                       338.274
_chem_comp.one_letter_code                      T
_chem_comp.three_letter_code                    TSP
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       1EO3
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 EBI
#   #
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
TSP  P       P       P  0  1  N  N  N  -3.306  -10.652   6.869  -4.126  -1.354   0.076  P       TSP   1  
TSP  OP1     O1P     O  0  1  N  N  N  -4.628  -10.072   6.664  -5.204  -0.448  -0.379  OP1     TSP   2  
TSP  OP2     O2P     O  0  1  N  N  N  -2.781  -10.820   8.233  -4.658  -2.247   1.306  OP2     TSP   3  
TSP  OP3     O3P     O  0  1  N  Y  N  -3.218  -12.036   6.093  -3.688  -2.319  -1.137  OP3     TSP   4  
TSP  "O5'"   "O5'"   O  0  1  N  N  N  -2.229   -9.768   6.088  -2.859  -0.483   0.553  "O5'"   TSP   5  
TSP  "C5'"   "C5'"   C  0  1  N  N  N  -0.850  -10.207   5.963  -2.224   0.489  -0.280  "C5'"   TSP   6  
TSP  "C4'"   "C4'"   C  0  1  N  N  R   0.017   -9.103   5.391  -1.060   1.129   0.479  "C4'"   TSP   7  
TSP  "O4'"   "O4'"   O  0  1  N  N  N  -0.024   -9.173   3.943  -0.018   0.159   0.724  "O4'"   TSP   8  
TSP  "C3'"   "C3'"   C  0  1  N  N  S  -0.520   -7.725   5.715  -0.359   2.198  -0.397  "C3'"   TSP   9  
TSP  "S3'"   "S3'"   S  0  1  N  N  N   0.067   -6.871   7.085  -1.183   3.807  -0.237  "S3'"   TSP  10  
TSP  "C2'"   "C2'"   C  0  1  N  N  N  -0.364   -6.899   4.456   1.061   2.242   0.218  "C2'"   TSP  11  
TSP  "C1'"   "C1'"   C  0  1  N  N  R  -0.117   -7.881   3.347   1.194   0.896   0.956  "C1'"   TSP  12  
TSP  N1      N1      N  0  1  N  N  N  -1.350   -7.822   2.522   2.339   0.149   0.427  N1      TSP  13  
TSP  C2      C2      C  0  1  N  N  N  -1.267   -7.230   1.283   2.330  -0.266  -0.852  C2      TSP  14  
TSP  O2      O2      O  0  1  N  N  N  -0.206   -6.906   0.766   1.371  -0.017  -1.557  O2      TSP  15  
TSP  N3      N3      N  0  1  N  N  N  -2.467   -7.046   0.654   3.368  -0.953  -1.364  N3      TSP  16  
TSP  C4      C4      C  0  1  N  N  N  -3.707   -7.440   1.102   4.440  -1.237  -0.596  C4      TSP  17  
TSP  O4      O4      O  0  1  N  N  N  -4.690   -7.214   0.425   5.379  -1.859  -1.058  O4      TSP  18  
TSP  C5      C5      C  0  1  N  N  N  -3.720   -8.126   2.378   4.462  -0.806   0.752  C5      TSP  19  
TSP  C5M     C5M     C  0  1  N  N  N  -5.025   -8.622   2.913   5.647  -1.110   1.632  C5M     TSP  20  
TSP  C6      C6      C  0  1  N  N  N  -2.554   -8.281   3.014   3.409  -0.113   1.238  C6      TSP  21  
TSP  HOP2    HOP2    H  0  0  N  N  N  -3.421  -10.504   8.860  -5.422  -2.799   1.090  HOP2    TSP  22  
TSP  HOP3    HOP3    H  0  0  N  N  N  -4.043  -12.206   5.653  -2.983  -2.941  -0.910  HOP3    TSP  23  
TSP  "H5'"   "H5'1"  H  0  1  N  N  N  -0.469  -10.486   6.956  -1.847   0.004  -1.181  "H5'"   TSP  24  
TSP  "H5''"  "H5'2"  H  0  0  N  N  N  -0.809  -11.080   5.295  -2.945   1.258  -0.555  "H5''"  TSP  25  
TSP  "H4'"   "H4'"   H  0  1  N  N  N   1.048   -9.203   5.761  -1.407   1.564   1.416  "H4'"   TSP  26  
TSP  "H3'"   "H3'"   H  0  1  N  N  N  -1.600   -7.836   5.893  -0.323   1.884  -1.440  "H3'"   TSP  27  
TSP  "HS3'"  "HS3'"  H  0  0  N  N  N  -0.614   -5.765   7.027  -0.460   4.599  -1.048  "HS3'"  TSP  28  
TSP  "H2'"   "H2'1"  H  0  1  N  N  N  -1.281   -6.323   4.260   1.814   2.324  -0.566  "H2'"   TSP  29  
TSP  "H2''"  "H2'2"  H  0  0  N  N  N   0.488   -6.210   4.554   1.148   3.072   0.919  "H2''"  TSP  30  
TSP  "H1'"   "H1'"   H  0  1  N  N  N   0.778   -7.616   2.764   1.324   1.070   2.024  "H1'"   TSP  31  
TSP  HN3     HN3     H  0  1  N  N  N  -2.441   -6.574  -0.227   3.345  -1.246  -2.288  HN3     TSP  32  
TSP  H71     H5M1    H  0  1  N  N  N  -4.861   -9.115   3.882   6.389  -1.669   1.061  H71     TSP  33  
TSP  H72     H5M2    H  0  1  N  N  N  -5.713   -7.774   3.045   6.087  -0.177   1.985  H72     TSP  34  
TSP  H73     H5M3    H  0  1  N  N  N  -5.462   -9.342   2.205   5.323  -1.705   2.486  H73     TSP  35  
TSP  H6      H6      H  0  1  N  N  N  -2.555   -8.793   3.965   3.411   0.228   2.263  H6      TSP  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
TSP  P      OP1     DOUB  N  N   1  
TSP  P      OP2     SING  N  N   2  
TSP  P      OP3     SING  N  N   3  
TSP  P      "O5'"   SING  N  N   4  
TSP  OP2    HOP2    SING  N  N   5  
TSP  OP3    HOP3    SING  N  N   6  
TSP  "O5'"  "C5'"   SING  N  N   7  
TSP  "C5'"  "C4'"   SING  N  N   8  
TSP  "C5'"  "H5'"   SING  N  N   9  
TSP  "C5'"  "H5''"  SING  N  N  10  
TSP  "C4'"  "O4'"   SING  N  N  11  
TSP  "C4'"  "C3'"   SING  N  N  12  
TSP  "C4'"  "H4'"   SING  N  N  13  
TSP  "O4'"  "C1'"   SING  N  N  14  
TSP  "C3'"  "S3'"   SING  N  N  15  
TSP  "C3'"  "C2'"   SING  N  N  16  
TSP  "C3'"  "H3'"   SING  N  N  17  
TSP  "S3'"  "HS3'"  SING  N  N  18  
TSP  "C2'"  "C1'"   SING  N  N  19  
TSP  "C2'"  "H2'"   SING  N  N  20  
TSP  "C2'"  "H2''"  SING  N  N  21  
TSP  "C1'"  N1      SING  N  N  22  
TSP  "C1'"  "H1'"   SING  N  N  23  
TSP  N1     C2      SING  N  N  24  
TSP  N1     C6      SING  N  N  25  
TSP  C2     O2      DOUB  N  N  26  
TSP  C2     N3      SING  N  N  27  
TSP  N3     C4      SING  N  N  28  
TSP  N3     HN3     SING  N  N  29  
TSP  C4     O4      DOUB  N  N  30  
TSP  C4     C5      SING  N  N  31  
TSP  C5     C5M     SING  N  N  32  
TSP  C5     C6      DOUB  N  N  33  
TSP  C5M    H71     SING  N  N  34  
TSP  C5M    H72     SING  N  N  35  
TSP  C5M    H73     SING  N  N  36  
TSP  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
TSP  SMILES            ACDLabs               12.01  "P(=O)(O)(O)OCC1OC(CC1S)N2C(=O)NC(=O)C(C)=C2"  
TSP  InChI             InChI                 1.03   "InChI=1S/C10H15N2O7PS/c1-5-3-12(10(14)11-9(5)13)8-2-7(21)6(19-8)4-18-20(15,16)17/h3,6-8,21H,2,4H2,1H3,(H,11,13,14)(H2,15,16,17)/t6-,7+,8-/m1/s1"  
TSP  InChIKey          InChI                 1.03   BORVFKJZAOEGOO-GJMOJQLCSA-N  
TSP  SMILES_CANONICAL  CACTVS                3.385  "CC1=CN([C@H]2C[C@H](S)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O"  
TSP  SMILES            CACTVS                3.385  "CC1=CN([CH]2C[CH](S)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O"  
TSP  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)S"  
TSP  SMILES            "OpenEye OEToolkits"  1.7.6  "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)S"  
#   #
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
TSP  "SYSTEMATIC NAME"  ACDLabs               12.01  "3'-thiothymidine 5'-(dihydrogen phosphate)"  
TSP  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-sulfanyl-oxolan-2-yl]methyl dihydrogen phosphate"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
TSP  "Create component"     1999-07-08  EBI   
TSP  "Modify descriptor"    2011-06-04  RCSB  
TSP  "Modify linking type"  2019-07-23  RCSB  
TSP  "Other modification"   2019-09-04  EBI   
##
