data_C2S # _chem_comp.id C2S _chem_comp.name "CYTIDINE-5'-DITHIOPHOSPHORATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H14 N3 O5 P S2" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2001-11-02 _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 339.328 _chem_comp.one_letter_code C _chem_comp.three_letter_code C2S _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details "OpenEye/OEToolkits V1.4.2" _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code ? _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 C2S OP3 O3P O 0 1 N Y N ? ? ? -3.988 -2.586 4.525 OP3 C2S 1 C2S P P P 0 1 N N S 10.760 1.198 -11.374 -3.975 -1.694 3.157 P C2S 2 C2S S1P S1P S 0 1 N N N 10.681 2.397 -12.945 -4.140 -2.844 1.583 S1P C2S 3 C2S S2P S2P S 0 1 N N N 12.180 -0.142 -11.691 -5.409 -0.167 3.469 S2P C2S 4 C2S "O5'" O5* O 0 1 N N N 11.062 2.037 -10.032 -2.493 -1.028 3.315 "O5'" C2S 5 C2S "C5'" C5* C 0 1 N N N 10.310 3.199 -9.722 -2.005 -0.136 2.327 "C5'" C2S 6 C2S "C4'" C4* C 0 1 N N R 10.632 3.743 -8.327 -0.611 0.328 2.728 "C4'" C2S 7 C2S "O4'" O4* O 0 1 N N N 10.195 2.834 -7.326 0.247 -0.829 2.764 "O4'" C2S 8 C2S "C3'" C3* C 0 1 N N S 12.125 4.020 -8.078 0.008 1.286 1.720 "C3'" C2S 9 C2S "O3'" O3* O 0 1 N N N 12.273 5.374 -7.671 0.965 2.121 2.368 "O3'" C2S 10 C2S "C2'" C2* C 0 1 N N N 12.446 3.044 -6.948 0.710 0.360 0.754 "C2'" C2S 11 C2S "C1'" C1* C 0 1 N N R 11.094 2.965 -6.247 1.157 -0.778 1.657 "C1'" C2S 12 C2S N1 N1 N 0 1 N N N 10.979 1.825 -5.298 1.164 -2.047 0.989 N1 C2S 13 C2S C2 C2 C 0 1 N N N 10.759 2.094 -3.943 2.328 -2.561 0.367 C2 C2S 14 C2S O2 O2 O 0 1 N N N 10.617 3.240 -3.522 3.386 -1.929 0.379 O2 C2S 15 C2S N3 N3 N 0 1 N N N 10.712 1.076 -3.049 2.260 -3.794 -0.259 N3 C2S 16 C2S C4 C4 C 0 1 N N N 10.850 -0.168 -3.470 1.147 -4.479 -0.282 C4 C2S 17 C2S N4 N4 N 0 1 N N N 10.774 -1.098 -2.553 1.101 -5.702 -0.910 N4 C2S 18 C2S C5 C5 C 0 1 N N N 11.062 -0.501 -4.842 -0.094 -3.972 0.359 C5 C2S 19 C2S C6 C6 C 0 1 N N N 11.118 0.527 -5.728 -0.008 -2.785 0.956 C6 C2S 20 C2S HOP3 3HOP H 0 0 N N N 0.038 -0.576 0.755 -4.102 -2.123 5.382 HOP3 C2S 21 C2S HOP2 2HOP H 0 0 N N N 12.831 -0.069 -12.379 -6.500 -0.946 3.500 HOP2 C2S 22 C2S "H5'" 1H5* H 0 1 N N N 10.527 3.973 -10.460 -1.971 -0.654 1.366 "H5'" C2S 23 C2S "H5''" 2H5* H 0 0 N N N 9.245 2.966 -9.763 -2.683 0.718 2.254 "H5''" C2S 24 C2S "H4'" H4* H 0 1 N N N 10.090 4.681 -8.196 -0.644 0.753 3.736 "H4'" C2S 25 C2S "H3'" H3* H 0 1 N N N 12.730 3.812 -8.963 -0.722 1.941 1.236 "H3'" C2S 26 C2S "HO3'" H3T H 0 0 N Y N 13.195 5.545 -7.517 0.743 3.042 2.146 "HO3'" C2S 27 C2S "H2'1" 1H2* H 0 0 N N N 13.535 2.833 -7.058 -0.003 -0.001 0.003 "H2'1" C2S 28 C2S "H1'" H1* H 0 1 N N N 10.909 3.915 -5.732 2.163 -0.604 2.054 "H1'" C2S 29 C2S H41 1H4 H 0 1 N N N 10.570 -0.771 -1.603 0.349 -6.310 -0.691 H41 C2S 30 C2S H42 2H4 H 0 1 N N N 10.780 -2.070 -2.785 1.822 -5.923 -1.553 H42 C2S 31 C2S H5 H5 H 0 1 N N N 11.170 -1.519 -5.181 -1.005 -4.554 0.330 H5 C2S 32 C2S H6 H6 H 0 1 N N N 11.268 0.346 -6.784 -0.867 -2.341 1.449 H6 C2S 33 C2S "H2'2" 2H2* H 0 0 N N N 12.680 2.266 -6.207 1.556 0.818 0.232 "H2'2" C2S 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 C2S OP3 P SING N N 1 C2S OP3 HOP3 SING N N 2 C2S P S1P DOUB N N 3 C2S P S2P SING N N 4 C2S P "O5'" SING N N 5 C2S S2P HOP2 SING N N 6 C2S "O5'" "C5'" SING N N 7 C2S "C5'" "C4'" SING N N 8 C2S "C5'" "H5'" SING N N 9 C2S "C5'" "H5''" SING N N 10 C2S "C4'" "O4'" SING N N 11 C2S "C4'" "C3'" SING N N 12 C2S "C4'" "H4'" SING N N 13 C2S "O4'" "C1'" SING N N 14 C2S "C3'" "O3'" SING N N 15 C2S "C3'" "C2'" SING N N 16 C2S "C3'" "H3'" SING N N 17 C2S "O3'" "HO3'" SING N N 18 C2S "C2'" "C1'" SING N N 19 C2S "C2'" "H2'1" SING N N 20 C2S "C1'" N1 SING N N 21 C2S "C1'" "H1'" SING N N 22 C2S N1 C2 SING N N 23 C2S N1 C6 SING N N 24 C2S C2 O2 DOUB N N 25 C2S C2 N3 SING N N 26 C2S N3 C4 DOUB N N 27 C2S C4 N4 SING N N 28 C2S C4 C5 SING N N 29 C2S N4 H41 SING N N 30 C2S N4 H42 SING N N 31 C2S C5 C6 DOUB N N 32 C2S C5 H5 SING N N 33 C2S C6 H6 SING N N 34 C2S "C2'" "H2'2" 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 C2S SMILES ACDLabs 10.04 "O=C1N=C(N)C=CN1C2OC(C(O)C2)COP(=S)(O)S" C2S SMILES_CANONICAL CACTVS 3.341 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P@](O)(S)=S)O2" C2S SMILES CACTVS 3.341 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(S)=S)O2" C2S SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=S)(O)S)O" C2S SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=S)(O)S)O" C2S InChI InChI 1.03 "InChI=1S/C9H14N3O5PS2/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(17-8)4-16-18(15,19)20/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,19,20)/t5-,6+,8+/m0/s1" C2S InChIKey InChI 1.03 YPTNEFVBJOMHCI-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 C2S "SYSTEMATIC NAME" ACDLabs 10.04 "2'-deoxy-5'-O-[(dithiophosphono)]cytidine" C2S "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "4-amino-1-[(2R,4S,5R)-4-hydroxy-5-[(hydroxy-sulfanyl-phosphinothioyl)oxymethyl]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 C2S "Create component" 2001-11-02 RCSB C2S "Modify descriptor" 2011-06-04 RCSB #