data_TPC
# 
_chem_comp.id                                    TPC 
_chem_comp.name                                  
;5'-THIO-2'-DEOXY-CYTOSINE PHOSPHONIC ACID
;
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C9 H14 N3 O6 P S" 
_chem_comp.mon_nstd_parent_comp_id               DC 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2004-10-06 
_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                         ? 
_chem_comp.formula_weight                        323.263 
_chem_comp.one_letter_code                       C 
_chem_comp.three_letter_code                     TPC 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1TL8 
_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 
TPC "S5'"  "S5'"  S 0 1 N N N 24.990 1.619  34.789 -2.684 -1.263 3.575  "S5'"  TPC 1  
TPC N1     N1     N 0 1 N N N 22.423 -1.528 31.452 1.164  -2.047 0.989  N1     TPC 2  
TPC C6     C6     C 0 1 N N N 23.714 -1.971 31.578 -0.008 -2.785 0.956  C6     TPC 3  
TPC C2     C2     C 0 1 N N N 21.388 -2.443 31.228 2.328  -2.561 0.367  C2     TPC 4  
TPC O2     O2     O 0 1 N N N 20.217 -2.048 31.256 3.386  -1.929 0.379  O2     TPC 5  
TPC N3     N3     N 0 1 N N N 21.693 -3.742 31.001 2.260  -3.794 -0.259 N3     TPC 6  
TPC C4     C4     C 0 1 N N N 22.962 -4.153 31.082 1.147  -4.479 -0.282 C4     TPC 7  
TPC N4     N4     N 0 1 N N N 23.229 -5.440 30.843 1.101  -5.702 -0.910 N4     TPC 8  
TPC C5     C5     C 0 1 N N N 24.023 -3.260 31.409 -0.094 -3.972 0.359  C5     TPC 9  
TPC "C2'"  "C2'"  C 0 1 N N N 21.616 0.378  32.894 0.710  0.360  0.754  "C2'"  TPC 10 
TPC "C5'"  "C5'"  C 0 1 N N N 24.883 1.011  33.065 -2.005 -0.136 2.327  "C5'"  TPC 11 
TPC "C4'"  "C4'"  C 0 1 N N S 23.642 1.524  32.353 -0.611 0.328  2.728  "C4'"  TPC 12 
TPC "O4'"  "O4'"  O 0 1 N N N 23.334 0.607  31.279 0.247  -0.829 2.764  "O4'"  TPC 13 
TPC "C1'"  "C1'"  C 0 1 N N R 22.115 -0.088 31.529 1.157  -0.778 1.657  "C1'"  TPC 14 
TPC "C3'"  "C3'"  C 0 1 N N S 22.314 1.717  33.099 0.008  1.286  1.720  "C3'"  TPC 15 
TPC "O3'"  "O3'"  O 0 1 N N N 21.583 2.778  32.428 0.965  2.121  2.368  "O3'"  TPC 16 
TPC P      P      P 0 1 N N N ?      ?      ?      -4.581 -1.788 2.860  P      TPC 17 
TPC OP1    O1P    O 0 1 N N N ?      ?      ?      -5.461 -0.578 2.699  OP1    TPC 18 
TPC OP2    O2P    O 0 1 N N N ?      ?      ?      -5.230 -2.909 3.837  OP2    TPC 19 
TPC OP3    O3P    O 0 1 N Y N ?      ?      ?      -4.407 -2.624 1.480  OP3    TPC 20 
TPC H6     H6     H 0 1 N N N 24.496 -1.265 31.818 -0.867 -2.341 1.449  H6     TPC 21 
TPC HN41   1HN4   H 0 0 N N N 24.210 -5.612 30.937 0.349  -6.310 -0.691 HN41   TPC 22 
TPC HN42   2HN4   H 0 0 N N N 22.547 -6.131 30.605 1.822  -5.923 -1.553 HN42   TPC 23 
TPC H5     H5     H 0 1 N N N 25.039 -3.612 31.516 -1.005 -4.554 0.330  H5     TPC 24 
TPC "H2'1" "1H2'" H 0 0 N N N 20.522 0.490  32.905 -0.003 -0.001 0.003  "H2'1" TPC 25 
TPC "H2'2" "2H2'" H 0 0 N N N 21.840 -0.342 33.695 1.556  0.818  0.232  "H2'2" TPC 26 
TPC "H5'1" "1H5'" H 0 0 N N N 25.771 1.357  32.515 -1.969 -0.654 1.365  "H5'1" TPC 27 
TPC "H5'2" "2H5'" H 0 0 N N N 24.828 -0.087 33.095 -2.674 0.724  2.226  "H5'2" TPC 28 
TPC "H4'"  "H4'"  H 0 1 N N N 23.958 2.546  32.098 -0.644 0.753  3.736  "H4'"  TPC 29 
TPC "H1'"  "H1'"  H 0 1 N N N 21.313 0.112  30.803 2.163  -0.604 2.054  "H1'"  TPC 30 
TPC H1     H1     H 0 1 N N N 22.409 1.986  34.161 -0.722 1.941  1.236  H1     TPC 31 
TPC "H3'"  "H3'"  H 0 1 N N N 21.423 3.488  33.038 0.743  3.042  2.146  "H3'"  TPC 32 
TPC HO2P   HO2P   H 0 0 N N N ?      ?      ?      -6.164 -3.174 3.696  HO2P   TPC 33 
TPC HO3P   HO3P   H 0 0 N N N ?      ?      ?      -5.208 -2.843 0.957  HO3P   TPC 34 
# 
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 
TPC "S5'" "C5'"  SING N N 1  
TPC "S5'" P      SING N N 2  
TPC N1    C6     SING N N 3  
TPC N1    C2     SING N N 4  
TPC N1    "C1'"  SING N N 5  
TPC C6    C5     DOUB N N 6  
TPC C6    H6     SING N N 7  
TPC C2    O2     DOUB N N 8  
TPC C2    N3     SING N N 9  
TPC N3    C4     DOUB N N 10 
TPC C4    N4     SING N N 11 
TPC C4    C5     SING N N 12 
TPC N4    HN41   SING N N 13 
TPC N4    HN42   SING N N 14 
TPC C5    H5     SING N N 15 
TPC "C2'" "C1'"  SING N N 16 
TPC "C2'" "C3'"  SING N N 17 
TPC "C2'" "H2'1" SING N N 18 
TPC "C2'" "H2'2" SING N N 19 
TPC "C5'" "C4'"  SING N N 20 
TPC "C5'" "H5'1" SING N N 21 
TPC "C5'" "H5'2" SING N N 22 
TPC "C4'" "O4'"  SING N N 23 
TPC "C4'" "C3'"  SING N N 24 
TPC "C4'" "H4'"  SING N N 25 
TPC "O4'" "C1'"  SING N N 26 
TPC "C1'" "H1'"  SING N N 27 
TPC "C3'" "O3'"  SING N N 28 
TPC "C3'" H1     SING N N 29 
TPC "O3'" "H3'"  SING N N 30 
TPC P     OP1    DOUB N N 31 
TPC P     OP2    SING N N 32 
TPC P     OP3    SING N N 33 
TPC OP2   HO2P   SING N N 34 
TPC OP3   HO3P   SING N N 35 
# 
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 
TPC SMILES           ACDLabs              10.04 "O=P(O)(O)SCC2OC(N1C(=O)N=C(N)C=C1)CC2O"                                                                                                       
TPC SMILES_CANONICAL CACTVS               3.341 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CS[P](O)(O)=O)O2"                                                                                      
TPC SMILES           CACTVS               3.341 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CS[P](O)(O)=O)O2"                                                                                          
TPC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CSP(=O)(O)O)O"                                                                                          
TPC SMILES           "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=CC(=NC2=O)N)CSP(=O)(O)O)O"                                                                                                       
TPC InChI            InChI                1.03  "InChI=1S/C9H14N3O6PS/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(18-8)4-20-19(15,16)17/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1" 
TPC InChIKey         InChI                1.03  MECRPJIAIGIPSF-SHYZEUOFSA-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 
TPC "SYSTEMATIC NAME" ACDLabs              10.04 "2'-deoxy-5'-S-phosphono-5'-thiocytidine"                                                          
TPC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2S,3S,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methylsulfanylphosphonic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
TPC "Create component"  2004-10-06 EBI  
TPC "Modify descriptor" 2011-06-04 RCSB 
# 
