data_2YR # _chem_comp.id 2YR _chem_comp.name ;2'-deoxy-N-(2-sulfanylethyl)cytidine 5'-(dihydrogen phosphate) ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C11 H18 N3 O7 P S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-04-28 _chem_comp.pdbx_modified_date 2014-05-16 _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 367.315 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 2YR _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 4MGT _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 2YR P P P 0 1 N N N 39.797 -19.542 12.242 4.782 -1.832 -0.240 P 2YR 1 2YR OP1 OP1 O 0 1 N N N 39.227 -18.478 13.104 3.964 -2.884 0.404 OP1 2YR 2 2YR OP2 OP2 O 0 1 N N N 39.140 -20.869 12.193 5.268 -2.341 -1.687 OP2 2YR 3 2YR "O5'" "O5'" O 0 1 N N N 39.918 -18.945 10.773 3.901 -0.495 -0.409 "O5'" 2YR 4 2YR "C5'" "C5'" C 0 1 N N N 39.659 -17.550 10.536 3.238 0.144 0.684 "C5'" 2YR 5 2YR "C4'" "C4'" C 0 1 N N R 40.942 -16.751 10.518 2.495 1.381 0.176 "C4'" 2YR 6 2YR "O4'" "O4'" O 0 1 N N N 42.088 -17.600 10.279 1.384 0.999 -0.662 "O4'" 2YR 7 2YR "C3'" "C3'" C 0 1 N N S 41.002 -15.709 9.410 1.823 2.135 1.352 "C3'" 2YR 8 2YR "O3'" "O3'" O 0 1 N N N 40.288 -14.530 9.799 2.736 3.052 1.958 "O3'" 2YR 9 2YR "C2'" "C2'" C 0 1 N N N 42.495 -15.506 9.232 0.674 2.888 0.640 "C2'" 2YR 10 2YR "C1'" "C1'" C 0 1 N N R 43.091 -16.873 9.567 0.468 2.107 -0.677 "C1'" 2YR 11 2YR N1 N1 N 0 1 N N N 43.503 -17.676 8.399 -0.909 1.615 -0.754 N1 2YR 12 2YR C2 C2 C 0 1 N N N 44.577 -17.229 7.617 -1.344 0.701 0.133 C2 2YR 13 2YR O2 O2 O 0 1 N N N 45.150 -16.179 7.931 -0.584 0.292 0.995 O2 2YR 14 2YR N3 N3 N 0 1 N N N 44.971 -17.961 6.550 -2.592 0.236 0.086 N3 2YR 15 2YR C4 C4 C 0 1 N N N 44.331 -19.093 6.246 -3.439 0.664 -0.841 C4 2YR 16 2YR N4 N4 N 0 1 N N N 44.757 -19.786 5.188 -4.725 0.178 -0.879 N4 2YR 17 2YR C5 C5 C 0 1 N N N 43.229 -19.567 7.018 -3.014 1.621 -1.785 C5 2YR 18 2YR C6 C6 C 0 1 N N N 42.858 -18.839 8.081 -1.745 2.088 -1.720 C6 2YR 19 2YR S S S 0 1 N N N 45.398 -23.248 3.658 -7.165 -2.416 1.059 S 2YR 20 2YR C8 C8 C 0 1 N N N 46.075 -22.466 5.146 -6.623 -1.186 -0.159 C8 2YR 21 2YR C9 C9 C 0 1 N N N 45.553 -21.041 5.233 -5.162 -0.816 0.104 C9 2YR 22 2YR H2 H2 H 0 1 N N N 38.380 -20.868 12.763 5.805 -3.145 -1.661 H2 2YR 23 2YR H3 H3 H 0 1 N N N 39.008 -17.165 11.335 2.525 -0.550 1.131 H3 2YR 24 2YR H4 H4 H 0 1 N N N 39.153 -17.439 9.565 3.973 0.442 1.431 H4 2YR 25 2YR H5 H5 H 0 1 N N N 41.055 -16.241 11.486 3.175 2.041 -0.364 H5 2YR 26 2YR H6 H6 H 0 1 N N N 40.578 -16.133 8.488 1.432 1.434 2.090 H6 2YR 27 2YR H7 H7 H 0 1 N Y N 39.365 -14.734 9.890 2.362 3.548 2.699 H7 2YR 28 2YR H8 H8 H 0 1 N N N 42.731 -15.219 8.197 -0.232 2.862 1.246 H8 2YR 29 2YR H9 H9 H 0 1 N N N 42.871 -14.735 9.921 0.964 3.918 0.431 H9 2YR 30 2YR H10 H10 H 0 1 N N N 43.964 -16.717 10.218 0.681 2.754 -1.528 H10 2YR 31 2YR H11 H11 H 0 1 N N N 44.520 -19.429 4.284 -5.343 0.493 -1.558 H11 2YR 32 2YR H12 H12 H 0 1 N N N 42.713 -20.479 6.756 -3.692 1.979 -2.546 H12 2YR 33 2YR H13 H13 H 0 1 N N N 42.037 -19.176 8.696 -1.396 2.822 -2.432 H13 2YR 34 2YR H14 H14 H 0 1 N Y N 45.921 -24.437 3.716 -8.444 -2.644 0.711 H14 2YR 35 2YR H15 H15 H 0 1 N N N 45.759 -23.030 6.036 -6.718 -1.602 -1.162 H15 2YR 36 2YR H16 H16 H 0 1 N N N 47.174 -22.454 5.090 -7.245 -0.294 -0.076 H16 2YR 37 2YR H17 H17 H 0 1 N N N 45.781 -20.945 6.305 -4.541 -1.707 0.021 H17 2YR 38 2YR H18 H18 H 0 1 N N N 46.382 -20.623 4.643 -5.068 -0.400 1.107 H18 2YR 39 2YR OP3 OP3 O 0 1 N Y N ? ? ? 6.067 -1.516 0.678 OP3 2YR 40 2YR H20 H20 H 0 1 N Y N ? ? ? 6.650 -0.834 0.316 H20 2YR 41 # 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 2YR S C8 SING N N 1 2YR C8 C9 SING N N 2 2YR N4 C9 SING N N 3 2YR N4 C4 SING N N 4 2YR C4 N3 DOUB N N 5 2YR C4 C5 SING N N 6 2YR N3 C2 SING N N 7 2YR C5 C6 DOUB N N 8 2YR C2 O2 DOUB N N 9 2YR C2 N1 SING N N 10 2YR C6 N1 SING N N 11 2YR N1 "C1'" SING N N 12 2YR "C2'" "C3'" SING N N 13 2YR "C2'" "C1'" SING N N 14 2YR "C3'" "O3'" SING N N 15 2YR "C3'" "C4'" SING N N 16 2YR "C1'" "O4'" SING N N 17 2YR "O4'" "C4'" SING N N 18 2YR "C4'" "C5'" SING N N 19 2YR "C5'" "O5'" SING N N 20 2YR "O5'" P SING N N 21 2YR OP2 P SING N N 22 2YR P OP1 DOUB N N 23 2YR OP2 H2 SING N N 24 2YR "C5'" H3 SING N N 25 2YR "C5'" H4 SING N N 26 2YR "C4'" H5 SING N N 27 2YR "C3'" H6 SING N N 28 2YR "O3'" H7 SING N N 29 2YR "C2'" H8 SING N N 30 2YR "C2'" H9 SING N N 31 2YR "C1'" H10 SING N N 32 2YR N4 H11 SING N N 33 2YR C5 H12 SING N N 34 2YR C6 H13 SING N N 35 2YR S H14 SING N N 36 2YR C8 H15 SING N N 37 2YR C8 H16 SING N N 38 2YR C9 H17 SING N N 39 2YR C9 H18 SING N N 40 2YR P OP3 SING N N 41 2YR OP3 H20 SING N N 42 # 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 2YR SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OC(N1C(=O)N=C(NCCS)C=C1)CC2O" 2YR InChI InChI 1.03 "InChI=1S/C11H18N3O7PS/c15-7-5-10(21-8(7)6-20-22(17,18)19)14-3-1-9(12-2-4-23)13-11(14)16/h1,3,7-8,10,15,23H,2,4-6H2,(H,12,13,16)(H2,17,18,19)/t7-,8+,10+/m0/s1" 2YR InChIKey InChI 1.03 OJZURBTUERORPR-QXFUBDJGSA-N 2YR SMILES_CANONICAL CACTVS 3.385 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=NC2=O)NCCS" 2YR SMILES CACTVS 3.385 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=NC2=O)NCCS" 2YR SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)NCCS)COP(=O)(O)O)O" 2YR SMILES "OpenEye OEToolkits" 1.7.6 "C1C(C(OC1N2C=CC(=NC2=O)NCCS)COP(=O)(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 2YR "SYSTEMATIC NAME" ACDLabs 12.01 ;2'-deoxy-N-(2-sulfanylethyl)cytidine 5'-(dihydrogen phosphate) ; 2YR "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-3-oxidanyl-5-[2-oxidanylidene-4-(2-sulfanylethylamino)pyrimidin-1-yl]oxolan-2-yl]methyl dihydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 2YR "Create component" 2014-04-28 RCSB 2YR "Modify leaving atom flag" 2014-05-14 RCSB 2YR "Initial release" 2014-05-21 RCSB #