data_SC # _chem_comp.id SC _chem_comp.name "2'-deoxycytidine-5'-thio-monophosphate" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type HETAIN _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 1999-07-08 _chem_comp.pdbx_modified_date 2026-08-06 _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 SC _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 8PSH _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm ? # 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.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 SC N1 N1 N 0 1 N N N N N N 2.165 -3.490 -3.913 2.823 -0.222 -0.580 N1 SC 1 SC C2 C2 C 0 1 N N N N N N 2.507 -3.067 -2.627 2.828 0.318 0.652 C2 SC 2 SC N3 N3 N 0 1 N N N N N N 1.521 -2.597 -1.811 3.844 1.072 1.068 N3 SC 3 SC C4 C4 C 0 1 N N N N N N 0.239 -2.594 -2.207 4.880 1.310 0.275 C4 SC 4 SC C5 C5 C 0 1 N N N N N N -0.150 -3.143 -3.474 4.906 0.758 -1.022 C5 SC 5 SC C6 C6 C 0 1 N N N N N N 0.844 -3.584 -4.280 3.866 -0.006 -1.431 C6 SC 6 SC O2 O2 O 0 1 N N N N N N 3.667 -3.130 -2.226 1.886 0.115 1.400 O2 SC 7 SC N4 N4 N 0 1 N N N N N N -0.695 -2.131 -1.371 5.924 2.091 0.716 N4 SC 8 SC "C1'" C1* C 0 1 N N R N N N 3.259 -3.905 -4.835 1.694 -1.052 -1.008 "C1'" SC 9 SC "C2'" C2* C 0 1 N N N N N N 3.544 -5.396 -4.669 1.630 -2.331 -0.151 "C2'" SC 10 SC "C3'" C3* C 0 1 N N S N N N 2.901 -6.025 -5.895 0.226 -2.283 0.498 "C3'" SC 11 SC "C4'" C4* C 0 1 N N R N N N 3.143 -4.907 -6.911 -0.537 -1.320 -0.448 "C4'" SC 12 SC "O4'" O4* O 0 1 N N N N N N 2.901 -3.707 -6.196 0.461 -0.341 -0.807 "O4'" SC 13 SC "O3'" O3* O 0 1 N N N N N N 3.541 -7.242 -6.240 -0.379 -3.578 0.503 "O3'" SC 14 SC "C5'" C5* C 0 1 N N N N N N 2.257 -4.986 -8.161 -1.704 -0.657 0.285 "C5'" SC 15 SC "O5'" O5* O 0 1 N N N N N N 0.889 -4.977 -7.790 -2.458 0.133 -0.636 "O5'" SC 16 SC P P P 0 1 N N N N N N -0.310 -5.030 -8.875 -3.761 0.976 -0.208 P SC 17 SC OP1 O1P O 0 1 N N N N N N 0.152 -5.830 -10.032 -4.574 1.415 -1.526 OP1 SC 18 SC S2P S2P S 0 1 N N N N N N -2.064 -5.600 -7.808 -4.854 -0.078 0.874 S2P SC 19 SC OP3 O3P O 0 1 N Y N N N N -0.515 -3.503 -9.382 -3.308 2.289 0.605 OP3 SC 20 SC H5 H5 H 0 1 N N N N N N -1.187 -3.202 -3.771 5.743 0.942 -1.679 H5 SC 21 SC H6 H6 H 0 1 N N N N N N 0.593 -4.021 -5.235 3.863 -0.440 -2.420 H6 SC 22 SC HN41 1HN4 H 0 0 N N N N N N -0.434 -1.794 -0.466 5.903 2.470 1.609 HN41 SC 23 SC HN42 2HN4 H 0 0 N N N N N N -1.655 -2.121 -1.650 6.680 2.263 0.134 HN42 SC 24 SC "H1'" H1* H 0 1 N N N N N N 4.172 -3.340 -4.594 1.806 -1.315 -2.060 "H1'" SC 25 SC "H2'" 1H2* H 0 1 N N N N N N 4.627 -5.589 -4.652 1.730 -3.216 -0.779 "H2'" SC 26 SC "H2''" 2H2* H 0 0 N N N N N N 3.088 -5.782 -3.745 2.405 -2.317 0.615 "H2''" SC 27 SC "H3'" H3* H 0 1 N N N N N N 1.822 -6.162 -5.732 0.278 -1.876 1.508 "H3'" SC 28 SC "H4'" H4* H 0 1 N N N N N N 4.195 -4.948 -7.229 -0.889 -1.851 -1.332 "H4'" SC 29 SC "HO3'" *HO3 H 0 0 N Y N N N N 3.122 -7.614 -7.007 0.113 -4.239 1.009 "HO3'" SC 30 SC "H5'" 1H5* H 0 1 N N N N N N 2.464 -4.121 -8.809 -2.346 -1.425 0.716 "H5'" SC 31 SC "H5''" 2H5* H 0 0 N N N N N N 2.480 -5.915 -8.707 -1.318 -0.018 1.080 "H5''" SC 32 SC HOP1 1HOP H 0 0 N N N N N N -0.538 -5.874 -10.683 -5.374 1.927 -1.343 HOP1 SC 33 SC HOP3 3HOP H 0 0 N N N N N N -1.213 -3.474 -10.026 -2.736 2.885 0.102 HOP3 SC 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 SC N1 C2 SING N N 1 SC N1 C6 SING N N 2 SC N1 "C1'" SING N N 3 SC C2 N3 SING N N 4 SC C2 O2 DOUB N N 5 SC N3 C4 DOUB N N 6 SC C4 C5 SING N N 7 SC C4 N4 SING N N 8 SC C5 C6 DOUB N N 9 SC C5 H5 SING N N 10 SC C6 H6 SING N N 11 SC N4 HN41 SING N N 12 SC N4 HN42 SING N N 13 SC "C1'" "C2'" SING N N 14 SC "C1'" "O4'" SING N N 15 SC "C1'" "H1'" SING N N 16 SC "C2'" "C3'" SING N N 17 SC "C2'" "H2'" SING N N 18 SC "C2'" "H2''" SING N N 19 SC "C3'" "C4'" SING N N 20 SC "C3'" "O3'" SING N N 21 SC "C3'" "H3'" SING N N 22 SC "C4'" "O4'" SING N N 23 SC "C4'" "C5'" SING N N 24 SC "C4'" "H4'" SING N N 25 SC "O3'" "HO3'" SING N N 26 SC "C5'" "O5'" SING N N 27 SC "C5'" "H5'" SING N N 28 SC "C5'" "H5''" SING N N 29 SC "O5'" P SING N N 30 SC P OP1 SING N N 31 SC P S2P DOUB N N 32 SC P OP3 SING N N 33 SC OP1 HOP1 SING N N 34 SC 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 SC SMILES ACDLabs 14.52 "OP(O)(=S)OCC1OC(CC1O)N1C=CC(N)=NC1=O" SC InChI InChI 1.06 "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" SC InChIKey InChI 1.06 FHBXKBNKQMSUIJ-SHYZEUOFSA-N SC SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=S)O2" SC SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(O)=S)O2" SC SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=S)(O)O)O" SC SMILES "OpenEye OEToolkits" 3.1.0.0 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=S)(O)O)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 SC "SYSTEMATIC NAME" ACDLabs 14.52 "2'-deoxy-5'-O-thiophosphonocytidine" SC "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "4-azanyl-1-[(2~{R},4~{S},5~{R})-5-[bis(oxidanyl)phosphinothioyloxymethyl]-4-oxidanyl-oxolan-2-yl]pyrimidin-2-one" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site SC "Create component" 1999-07-08 RCSB SC "Modify descriptor" 2011-06-04 RCSB SC "Modify name" 2026-08-06 RCSB #