data_C7S # _chem_comp.id C7S _chem_comp.name "2'-deoxy-5'-O-thiophosphonocytidine" _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 "2'-deoxy-5'-O-thiophosphonocytidine (thiophospho connection isoform 2)" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2016-04-28 _chem_comp.pdbx_modified_date 2021-03-01 _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 ? _chem_comp.three_letter_code C7S _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 5JLX _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 C7S P P1 P 0 1 N N N 3.050 14.932 -11.305 3.706 1.116 0.093 P C7S 1 C7S "C5'" C1 C 0 1 N N N 3.810 15.138 -13.784 1.761 -0.661 -0.355 "C5'" C7S 2 C7S "O5'" O1 O 0 1 N N N 3.636 14.305 -12.656 2.408 0.265 0.521 "O5'" C7S 3 C7S "C4'" C2 C 0 1 N N R 5.118 14.844 -14.498 0.567 -1.294 0.363 "C4'" C7S 4 C7S "O4'" O2 O 0 1 N N N 6.132 15.765 -14.068 -0.479 -0.317 0.555 "O4'" C7S 5 C7S "C3'" C3 C 0 1 N N S 5.705 13.445 -14.277 -0.072 -2.389 -0.518 "C3'" C7S 6 C7S "O3'" O3 O 0 1 N N N 5.513 12.657 -15.461 0.389 -3.683 -0.123 "O3'" C7S 7 C7S "C2'" C4 C 0 1 N N N 7.203 13.702 -13.992 -1.587 -2.249 -0.251 "C2'" C7S 8 C7S "C1'" C5 C 0 1 N N R 7.376 15.179 -14.336 -1.684 -1.086 0.760 "C1'" C7S 9 C7S N1 N1 N 0 1 N N N 8.435 15.894 -13.527 -2.866 -0.266 0.482 N1 C7S 10 C7S C2 C6 C 0 1 N N N 9.404 16.663 -14.180 -2.978 0.369 -0.699 C2 C7S 11 C7S O2 O4 O 0 1 N N N 9.384 16.736 -15.413 -2.090 0.255 -1.528 O2 C7S 12 C7S N3 N2 N 0 1 N N N 10.340 17.307 -13.442 -4.041 1.120 -0.978 N3 C7S 13 C7S C4 C7 C 0 1 N N N 10.334 17.208 -12.115 -5.021 1.262 -0.095 C4 C7S 14 C7S N4 N3 N 0 1 N N N 11.280 17.864 -11.434 -6.115 2.040 -0.394 N4 C7S 15 C7S C5 C8 C 0 1 N N N 9.355 16.434 -11.426 -4.935 0.610 1.153 C5 C7S 16 C7S C6 C9 C 0 1 N N N 8.431 15.802 -12.164 -3.849 -0.154 1.419 C6 C7S 17 C7S SP1 S1 S 0 1 N N N 1.101 14.689 -11.338 5.333 -0.200 -0.245 SP1 C7S 18 C7S OP2 O5 O 0 1 N N N 3.938 14.445 -10.197 3.415 1.870 -1.147 OP2 C7S 19 C7S OP3 O6 O 0 1 N Y N 3.307 16.504 -11.464 4.084 2.146 1.271 OP3 C7S 20 C7S H1 H1 H 0 1 N N N 3.810 16.188 -13.456 1.413 -0.138 -1.245 H1 C7S 21 C7S H2 H2 H 0 1 N N N 2.977 14.972 -14.483 2.466 -1.441 -0.644 H2 C7S 22 C7S H3 H3 H 0 1 N N N 4.951 14.972 -15.578 0.877 -1.711 1.321 H3 C7S 23 C7S H4 H4 H 0 1 N N N 5.235 12.974 -13.401 0.148 -2.210 -1.571 H4 C7S 24 C7S H5 H5 H 0 1 N Y N 5.876 11.789 -15.327 0.019 -4.409 -0.644 H5 C7S 25 C7S H6 H6 H 0 1 N N N 7.840 13.071 -14.630 -2.116 -2.001 -1.171 H6 C7S 26 C7S H7 H7 H 0 1 N N N 7.441 13.513 -12.935 -1.986 -3.168 0.180 H7 C7S 27 C7S H8 H8 H 0 1 N N N 7.622 15.267 -15.404 -1.720 -1.471 1.779 H8 C7S 28 C7S H9 H9 H 0 1 N N N 11.962 18.407 -11.923 -6.172 2.487 -1.253 H9 C7S 29 C7S H10 H10 H 0 1 N N N 11.305 17.811 -10.436 -6.830 2.142 0.254 H10 C7S 30 C7S H11 H11 H 0 1 N N N 9.357 16.359 -10.349 -5.724 0.716 1.882 H11 C7S 31 C7S H12 H12 H 0 1 N N N 7.672 15.211 -11.673 -3.762 -0.668 2.366 H12 C7S 32 C7S HSP1 H13 H 0 0 N N N 0.742 15.227 -10.210 5.483 -0.809 0.945 HSP1 C7S 33 C7S HOP3 H14 H 0 0 N Y N 3.957 16.785 -10.831 4.859 2.693 1.082 HOP3 C7S 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 C7S "O3'" "C3'" SING N N 1 C7S O2 C2 DOUB N N 2 C7S "C4'" "C3'" SING N N 3 C7S "C4'" "O4'" SING N N 4 C7S "C4'" "C5'" SING N N 5 C7S "C1'" "O4'" SING N N 6 C7S "C1'" "C2'" SING N N 7 C7S "C1'" N1 SING N N 8 C7S "C3'" "C2'" SING N N 9 C7S C2 N1 SING N N 10 C7S C2 N3 SING N N 11 C7S "C5'" "O5'" SING N N 12 C7S N1 C6 SING N N 13 C7S N3 C4 DOUB N N 14 C7S "O5'" P SING N N 15 C7S C6 C5 DOUB N N 16 C7S C4 N4 SING N N 17 C7S C4 C5 SING N N 18 C7S SP1 P SING N N 19 C7S P OP2 DOUB N N 20 C7S P OP3 SING N N 21 C7S "C5'" H1 SING N N 22 C7S "C5'" H2 SING N N 23 C7S "C4'" H3 SING N N 24 C7S "C3'" H4 SING N N 25 C7S "O3'" H5 SING N N 26 C7S "C2'" H6 SING N N 27 C7S "C2'" H7 SING N N 28 C7S "C1'" H8 SING N N 29 C7S N4 H9 SING N N 30 C7S N4 H10 SING N N 31 C7S C5 H11 SING N N 32 C7S C6 H12 SING N N 33 C7S SP1 HSP1 SING N N 34 C7S OP3 HOP3 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 C7S SMILES ACDLabs 12.01 "P(=O)(O)(OCC1C(CC(O1)N2C=CC(=NC2=O)N)O)S" C7S InChI InChI 1.03 "InChI=1S/C9H14N3O6PS/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(18-8)4-17-19(15,16)20/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,20)/t5-,6+,8+/m0/s1" C7S InChIKey InChI 1.03 FHBXKBNKQMSUIJ-SHYZEUOFSA-N C7S SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(S)=O)O2" C7S SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(S)=O)O2" C7S SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)S)O" C7S SMILES "OpenEye OEToolkits" 2.0.4 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)S)O" # # 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 C7S "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-5'-O-thiophosphonocytidine" C7S "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.4 "[(2~{R},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphinic 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 C7S "Create component" 2016-04-28 RCSB C7S "Initial release" 2016-06-22 RCSB C7S "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id C7S _pdbx_chem_comp_synonyms.name "2'-deoxy-5'-O-thiophosphonocytidine (thiophospho connection isoform 2)" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##