data_SC # _chem_comp.id SC _chem_comp.name "2-DEOXY-CYTIDINE-5'-THIOPHOSPHORATE" _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 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 SC _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 8PSH _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 SC N1 N1 N 0 1 N N N 2.165 -3.490 -3.913 -0.332 -0.565 2.711 N1 SC 1 SC C2 C2 C 0 1 N N N 2.507 -3.067 -2.627 0.333 0.603 2.693 C2 SC 2 SC N3 N3 N 0 1 N N N 1.521 -2.597 -1.811 1.178 0.928 3.669 N3 SC 3 SC C4 C4 C 0 1 N N N 0.239 -2.594 -2.207 1.386 0.104 4.687 C4 SC 4 SC C5 C5 C 0 1 N N N -0.150 -3.143 -3.474 0.708 -1.131 4.734 C5 SC 5 SC C6 C6 C 0 1 N N N 0.844 -3.584 -4.280 -0.152 -1.444 3.737 C6 SC 6 SC O2 O2 O 0 1 N N N 3.667 -3.130 -2.226 0.159 1.378 1.766 O2 SC 7 SC N4 N4 N 0 1 N N N -0.695 -2.131 -1.371 2.262 0.450 5.690 N4 SC 8 SC "C1'" C1* C 0 1 N N R 3.259 -3.905 -4.835 -1.256 -0.895 1.623 "C1'" SC 9 SC "C2'" C2* C 0 1 N N N 3.544 -5.396 -4.669 -2.369 0.166 1.540 "C2'" SC 10 SC "C3'" C3* C 0 1 N N S 2.901 -6.025 -5.895 -2.250 0.730 0.103 "C3'" SC 11 SC "C4'" C4* C 0 1 N N R 3.143 -4.907 -6.911 -1.488 -0.404 -0.628 "C4'" SC 12 SC "O4'" O4* O 0 1 N N N 2.901 -3.707 -6.196 -0.556 -0.884 0.367 "O4'" SC 13 SC "O3'" O3* O 0 1 N N N 3.541 -7.242 -6.240 -3.541 0.932 -0.473 "O3'" SC 14 SC "C5'" C5* C 0 1 N N N 2.257 -4.986 -8.161 -0.744 0.144 -1.847 "C5'" SC 15 SC "O5'" O5* O 0 1 N N N 0.889 -4.977 -7.790 -0.052 -0.919 -2.502 "O5'" SC 16 SC P P P 0 1 N N N -0.310 -5.030 -8.875 0.703 -0.273 -3.768 P SC 17 SC OP1 O1P O 0 1 N N N 0.152 -5.830 -10.032 1.509 -1.423 -4.556 OP1 SC 18 SC S2P S2P S 0 1 N N N -2.064 -5.600 -7.808 1.898 1.029 -3.180 S2P SC 19 SC OP3 O3P O 0 1 N Y N -0.515 -3.503 -9.382 -0.378 0.396 -4.754 OP3 SC 20 SC H5 H5 H 0 1 N N N -1.177 -3.226 -3.799 0.866 -1.812 5.556 H5 SC 21 SC H6 H6 H 0 1 N N N 0.579 -4.037 -5.222 -0.686 -2.383 3.752 H6 SC 22 SC HN41 1HN4 H 0 0 N N N -1.665 -2.124 -1.648 2.730 1.299 5.653 HN41 SC 23 SC HN42 2HN4 H 0 0 N N N -0.426 -1.759 -0.471 2.409 -0.152 6.435 HN42 SC 24 SC "H1'" H1* H 0 1 N N N 4.171 -3.339 -4.642 -1.694 -1.879 1.794 "H1'" SC 25 SC "H2'" 1H2* H 0 1 N N N 3.123 -5.791 -3.751 -3.346 -0.292 1.690 "H2'" SC 26 SC "H2''" 2H2* H 0 0 N N N 4.622 -5.555 -4.691 -2.200 0.954 2.274 "H2''" SC 27 SC "H3'" H3* H 0 1 N N N 1.831 -6.155 -5.732 -1.673 1.654 0.094 "H3'" SC 28 SC "H4'" H4* H 0 1 N N N 4.193 -4.923 -7.210 -2.173 -1.198 -0.923 "H4'" SC 29 SC "HO3'" *HO3 H 0 0 N Y N 3.139 -7.635 -7.006 -3.997 1.580 0.080 "HO3'" SC 30 SC "H5'" 1H5* H 0 1 N N N 2.473 -4.134 -8.808 -1.460 0.591 -2.537 "H5'" SC 31 SC "H5''" 2H5* H 0 0 N N N 2.488 -5.906 -8.698 -0.028 0.900 -1.525 "H5''" SC 32 SC HOP1 1HOP H 0 0 N N N -0.552 -5.861 -10.669 1.946 -0.995 -5.305 HOP1 SC 33 SC HOP3 3HOP H 0 0 N N N -1.219 -3.534 -10.019 -0.975 -0.310 -5.035 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 10.04 "O=C1N=C(N)C=CN1C2OC(C(O)C2)COP(=S)(O)O" SC SMILES_CANONICAL CACTVS 3.341 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=S)O2" SC SMILES CACTVS 3.341 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(O)=S)O2" SC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=S)(O)O)O" SC SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=S)(O)O)O" SC 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" SC InChIKey InChI 1.03 FHBXKBNKQMSUIJ-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 SC "SYSTEMATIC NAME" ACDLabs 10.04 "2'-deoxy-5'-O-thiophosphonocytidine" SC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "4-amino-1-[(2R,4S,5R)-5-(dihydroxyphosphinothioyloxymethyl)-4-hydroxy-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 #