data_38S # _chem_comp.id 38S _chem_comp.name "1-[(2R,5S)-5-(hydroxymethyl)tetrahydrofuran-2-yl]-5-methylpyrimidine-2,4(1H,3H)-dione" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H14 N2 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "3'-deoxy thymidine" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-07-08 _chem_comp.pdbx_modified_date 2020-06-17 _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 226.229 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 38S _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 4QSX _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 38S OAC OAC O 0 1 N N N 28.418 44.278 -12.359 1.530 2.528 0.520 OAC 38S 1 38S CAM CAM C 0 1 N N N 27.317 44.444 -11.839 1.596 1.331 0.317 CAM 38S 2 38S NAI NAI N 0 1 N N N 26.326 43.547 -12.169 2.801 0.743 0.203 NAI 38S 3 38S CAL CAL C 0 1 N N N 25.040 43.654 -11.627 2.892 -0.583 -0.023 CAL 38S 4 38S OAB OAB O 0 1 N N N 24.258 42.790 -11.984 3.982 -1.116 -0.126 OAB 38S 5 38S CAK CAK C 0 1 N N N 24.745 44.654 -10.710 1.708 -1.351 -0.137 CAK 38S 6 38S CAA CAA C 0 1 N N N 23.474 44.801 -10.119 1.781 -2.835 -0.388 CAA 38S 7 38S CAE CAE C 0 1 N N N 25.766 45.551 -10.380 0.512 -0.735 -0.017 CAE 38S 8 38S NAP NAP N 0 1 N N N 27.056 45.428 -10.961 0.463 0.612 0.216 NAP 38S 9 38S CAO CAO C 0 1 N N R 28.112 46.396 -10.595 -0.834 1.279 0.351 CAO 38S 10 38S OAJ OAJ O 0 1 N N N 28.100 46.576 -9.175 -1.817 0.341 0.805 OAJ 38S 11 38S CAH CAH C 0 1 N N N 27.750 47.700 -11.186 -1.295 1.811 -1.023 CAH 38S 12 38S CAG CAG C 0 1 N N N 28.576 48.590 -10.348 -2.271 0.699 -1.496 CAG 38S 13 38S CAN CAN C 0 1 N N S 28.465 47.944 -8.945 -2.891 0.258 -0.146 CAN 38S 14 38S CAF CAF C 0 1 N N N 27.449 48.646 -8.034 -3.404 -1.181 -0.243 CAF 38S 15 38S OAD OAD O 0 1 N N N 26.235 48.774 -8.813 -4.016 -1.552 0.994 OAD 38S 16 38S H1 H1 H 0 1 N N N 26.529 42.805 -12.808 3.608 1.276 0.282 H1 38S 17 38S H2 H2 H 0 1 N N N 23.486 45.659 -9.431 2.825 -3.141 -0.453 H2 38S 18 38S H3 H3 H 0 1 N N N 22.722 44.971 -10.904 1.297 -3.366 0.431 H3 38S 19 38S H4 H4 H 0 1 N N N 23.221 43.887 -9.561 1.274 -3.070 -1.324 H4 38S 20 38S H5 H5 H 0 1 N N N 25.571 46.346 -9.675 -0.402 -1.305 -0.102 H5 38S 21 38S H6 H6 H 0 1 N N N 29.096 46.060 -10.954 -0.754 2.103 1.060 H6 38S 22 38S H7 H7 H 0 1 N N N 28.031 47.760 -12.248 -1.815 2.763 -0.916 H7 38S 23 38S H8 H8 H 0 1 N N N 26.677 47.915 -11.078 -0.451 1.903 -1.707 H8 38S 24 38S H9 H9 H 0 1 N N N 29.620 48.605 -10.696 -3.032 1.102 -2.164 H9 38S 25 38S H10 H10 H 0 1 N N N 28.176 49.615 -10.345 -1.732 -0.122 -1.968 H10 38S 26 38S H11 H11 H 0 1 N N N 29.454 47.990 -8.465 -3.700 0.931 0.137 H11 38S 27 38S H12 H12 H 0 1 N N N 27.263 48.043 -7.133 -4.137 -1.252 -1.047 H12 38S 28 38S H13 H13 H 0 1 N N N 27.821 49.639 -7.740 -2.570 -1.851 -0.451 H13 38S 29 38S H14 H14 H 0 1 N N N 25.568 49.206 -8.292 -4.365 -2.453 1.005 H14 38S 30 # # 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 38S OAC CAM DOUB N N 1 38S NAI CAM SING N N 2 38S NAI CAL SING N N 3 38S OAB CAL DOUB N N 4 38S CAM NAP SING N N 5 38S CAL CAK SING N N 6 38S CAH CAO SING N N 7 38S CAH CAG SING N N 8 38S NAP CAO SING N N 9 38S NAP CAE SING N N 10 38S CAK CAE DOUB N N 11 38S CAK CAA SING N N 12 38S CAO OAJ SING N N 13 38S CAG CAN SING N N 14 38S OAJ CAN SING N N 15 38S CAN CAF SING N N 16 38S OAD CAF SING N N 17 38S NAI H1 SING N N 18 38S CAA H2 SING N N 19 38S CAA H3 SING N N 20 38S CAA H4 SING N N 21 38S CAE H5 SING N N 22 38S CAO H6 SING N N 23 38S CAH H7 SING N N 24 38S CAH H8 SING N N 25 38S CAG H9 SING N N 26 38S CAG H10 SING N N 27 38S CAN H11 SING N N 28 38S CAF H12 SING N N 29 38S CAF H13 SING N N 30 38S OAD H14 SING N N 31 # # 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 38S SMILES ACDLabs 12.01 "O=C1NC(=O)N(C=C1C)C2OC(CC2)CO" 38S InChI InChI 1.03 "InChI=1S/C10H14N2O4/c1-6-4-12(10(15)11-9(6)14)8-3-2-7(5-13)16-8/h4,7-8,13H,2-3,5H2,1H3,(H,11,14,15)/t7-,8+/m0/s1" 38S InChIKey InChI 1.03 XKKCQTLDIPIRQD-JGVFFNPUSA-N 38S SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@H]2CC[C@@H](CO)O2)C(=O)NC1=O" 38S SMILES CACTVS 3.385 "CC1=CN([CH]2CC[CH](CO)O2)C(=O)NC1=O" 38S SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)NC1=O)[C@H]2CC[C@H](O2)CO" 38S SMILES "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)NC1=O)C2CCC(O2)CO" # # 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 38S "SYSTEMATIC NAME" ACDLabs 12.01 "1-[(2R,5S)-5-(hydroxymethyl)tetrahydrofuran-2-yl]-5-methylpyrimidine-2,4(1H,3H)-dione" 38S "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "1-[(2R,5S)-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 38S "Create component" 2014-07-08 RCSB 38S "Initial release" 2014-07-23 RCSB 38S "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 38S _pdbx_chem_comp_synonyms.name "3'-deoxy thymidine" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##