data_A1IDZ # _chem_comp.id A1IDZ _chem_comp.name "[[(2~{R},3~{S},5~{R})-5-[2,4-bis(oxidanylidene)-5-selenophen-2-yl-pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H17 N2 O14 P3 Se" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2024-06-07 _chem_comp.pdbx_modified_date 2024-11-08 _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 597.160 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1IDZ _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 9FM3 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE _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 A1IDZ C2 C1 C 0 1 N N N N N N 29.152 7.504 10.116 4.087 0.679 2.189 C2 A1IDZ 1 A1IDZ C4 C2 C 0 1 N N N N N N 30.759 5.900 9.140 2.400 -0.868 1.714 C4 A1IDZ 2 A1IDZ C8 C3 C 0 1 N N N N N N 30.377 4.595 6.193 2.256 -3.407 0.075 C8 A1IDZ 3 A1IDZ C9 C4 C 0 1 N N S N N N 29.644 5.141 4.977 1.010 -4.083 -0.547 C9 A1IDZ 4 A1IDZ O5 O1 O 0 1 N N N N N N 31.552 4.983 9.309 1.430 -1.498 2.088 O5 A1IDZ 5 A1IDZ C12 C5 C 0 1 N N N N N N 29.992 7.287 3.630 -1.266 -3.103 -0.119 C12 A1IDZ 6 A1IDZ C11 C6 C 0 1 N N S N N N 30.612 6.204 4.477 0.060 -2.909 -0.858 C11 A1IDZ 7 A1IDZ O1 O2 O 0 1 N N N N N N 28.618 7.898 11.150 4.642 1.435 2.964 O1 A1IDZ 8 A1IDZ C7 C7 C 0 1 N N S N N N 31.131 5.808 6.727 2.125 -1.950 -0.437 C7 A1IDZ 9 A1IDZ C27 C8 C 0 1 N N N N N N 29.590 7.459 7.739 3.922 -0.351 -0.016 C27 A1IDZ 10 A1IDZ C28 C9 C 0 1 N N N N N N 28.912 8.019 8.782 4.582 0.517 0.812 C28 A1IDZ 11 A1IDZ C29 C10 C 0 1 Y N N N N N 27.983 9.118 8.534 5.753 1.269 0.338 C29 A1IDZ 12 A1IDZ C30 C11 C 0 1 Y N N N N N 27.826 9.877 7.390 6.523 2.161 1.006 C30 A1IDZ 13 A1IDZ C31 C12 C 0 1 Y N N N N N 26.847 10.879 7.469 7.640 2.806 0.381 C31 A1IDZ 14 A1IDZ C32 C13 C 0 1 Y N N N N N 26.212 10.949 8.645 7.983 2.566 -0.891 C32 A1IDZ 15 A1IDZ N3 N1 N 0 1 N N N N N N 30.072 6.472 10.180 3.007 -0.034 2.575 N3 A1IDZ 16 A1IDZ N6 N2 N 0 1 N N N N N N 30.483 6.426 7.893 2.832 -1.025 0.452 N6 A1IDZ 17 A1IDZ O10 O3 O 0 1 N N N N N N 29.458 4.114 4.004 1.361 -4.773 -1.748 O10 A1IDZ 18 A1IDZ O13 O4 O 0 1 N N N N N N 28.921 7.914 4.359 -2.180 -2.075 -0.504 O13 A1IDZ 19 A1IDZ O15 O5 O 0 1 N N N N N N 28.149 8.899 2.188 -3.628 -1.931 1.559 O15 A1IDZ 20 A1IDZ O16 O6 O 0 1 N N N N N N 27.204 9.726 4.400 -4.531 -3.247 -0.397 O16 A1IDZ 21 A1IDZ O17 O7 O 0 1 N N N N N N 26.635 7.427 3.535 -4.372 -0.624 -0.468 O17 A1IDZ 22 A1IDZ O19 O8 O 0 1 N N N N N N 26.780 4.924 3.631 -5.558 0.457 1.481 O19 A1IDZ 23 A1IDZ O20 O9 O 0 1 N N N N N N 27.323 6.152 1.474 -6.996 -0.492 -0.363 O20 A1IDZ 24 A1IDZ O21 O10 O 0 1 N N N N N N 24.960 6.047 2.351 -5.583 1.697 -0.717 O21 A1IDZ 25 A1IDZ O23 O11 O 0 1 N N N N N N 23.613 6.713 0.255 -7.630 2.942 0.077 O23 A1IDZ 26 A1IDZ O24 O12 O 0 1 N N N N N N 23.751 8.305 2.207 -5.380 3.888 0.721 O24 A1IDZ 27 A1IDZ O25 O13 O 0 1 N N N N N N 25.747 7.972 0.712 -6.262 4.016 -1.752 O25 A1IDZ 28 A1IDZ O26 O14 O 0 1 N N N N N N 31.173 6.772 5.678 0.702 -1.707 -0.402 O26 A1IDZ 29 A1IDZ P14 P1 P 0 1 N N N N N N 27.716 8.609 3.571 -3.677 -1.968 0.080 P14 A1IDZ 30 A1IDZ P18 P2 P 0 1 N N N N N N 26.521 6.054 2.718 -5.626 0.264 0.015 P18 A1IDZ 31 A1IDZ P22 P3 P 0 1 N N N N N N 24.501 7.346 1.303 -6.244 3.132 -0.407 P22 A1IDZ 32 A1IDZ SE33 SE1 SE 0 0 Y N N N N N 26.802 9.697 9.848 6.623 1.235 -1.442 SE33 A1IDZ 33 A1IDZ H8A H1 H 0 1 N N N N N N 31.074 3.794 5.905 2.215 -3.442 1.163 H8A A1IDZ 34 A1IDZ H8B H2 H 0 1 N N N N N N 29.667 4.212 6.941 3.173 -3.869 -0.293 H8B A1IDZ 35 A1IDZ H9 H3 H 0 1 N N N N N N 28.690 5.600 5.277 0.551 -4.768 0.166 H9 A1IDZ 36 A1IDZ H12A H4 H 0 0 N N N N N N 30.755 8.039 3.381 -1.685 -4.076 -0.375 H12A A1IDZ 37 A1IDZ H12B H5 H 0 0 N N N N N N 29.596 6.846 2.704 -1.093 -3.053 0.956 H12B A1IDZ 38 A1IDZ H11 H6 H 0 1 N N N N N N 31.405 5.711 3.896 -0.119 -2.852 -1.932 H11 A1IDZ 39 A1IDZ H7 H7 H 0 1 N N N N N N 32.152 5.499 6.997 2.504 -1.866 -1.456 H7 A1IDZ 40 A1IDZ H27 H8 H 0 1 N N N N N N 29.417 7.846 6.746 4.256 -0.495 -1.032 H27 A1IDZ 41 A1IDZ H30 H9 H 0 1 N N N N N N 28.414 9.711 6.500 6.289 2.392 2.035 H30 A1IDZ 42 A1IDZ H31 H10 H 0 1 N N N N N N 26.624 11.541 6.646 8.224 3.511 0.955 H31 A1IDZ 43 A1IDZ H32 H11 H 0 1 N N N N N N 25.435 11.667 8.862 8.795 2.987 -1.466 H32 A1IDZ 44 A1IDZ H3 H12 H 0 1 N N N N N N 30.257 6.100 11.090 2.668 0.056 3.480 H3 A1IDZ 45 A1IDZ H10 H13 H 0 1 N N N N N N 28.568 4.147 3.674 2.003 -5.485 -1.618 H10 A1IDZ 46 A1IDZ H1 H14 H 0 1 N N N N N N 27.225 10.531 3.896 -4.605 -3.335 -1.357 H1 A1IDZ 47 A1IDZ H2 H15 H 0 1 N N N N N N 27.934 5.426 1.433 -7.108 -0.652 -1.311 H2 A1IDZ 48 A1IDZ H4 H16 H 0 1 N N N N N N 22.838 8.337 1.947 -4.459 4.046 0.472 H4 A1IDZ 49 A1IDZ H5 H17 H 0 1 N N N N N N 25.746 7.852 -0.230 -6.648 4.896 -1.640 H5 A1IDZ 50 # 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 A1IDZ O1 C2 DOUB N N 1 A1IDZ C2 N3 SING N N 2 A1IDZ N3 C4 SING N N 3 A1IDZ C4 O5 DOUB N N 4 A1IDZ C4 N6 SING N N 5 A1IDZ N6 C7 SING N N 6 A1IDZ C7 C8 SING N N 7 A1IDZ C8 C9 SING N N 8 A1IDZ C9 O10 SING N N 9 A1IDZ C9 C11 SING N N 10 A1IDZ C11 C12 SING N N 11 A1IDZ C12 O13 SING N N 12 A1IDZ O13 P14 SING N N 13 A1IDZ P14 O15 DOUB N N 14 A1IDZ P14 O16 SING N N 15 A1IDZ P14 O17 SING N N 16 A1IDZ O17 P18 SING N N 17 A1IDZ P18 O19 DOUB N N 18 A1IDZ P18 O20 SING N N 19 A1IDZ P18 O21 SING N N 20 A1IDZ O21 P22 SING N N 21 A1IDZ P22 O23 DOUB N N 22 A1IDZ P22 O24 SING N N 23 A1IDZ P22 O25 SING N N 24 A1IDZ C11 O26 SING N N 25 A1IDZ N6 C27 SING N N 26 A1IDZ C27 C28 DOUB N N 27 A1IDZ C28 C29 SING N N 28 A1IDZ C29 C30 DOUB Y N 29 A1IDZ C30 C31 SING Y N 30 A1IDZ C31 C32 DOUB Y N 31 A1IDZ C32 SE33 SING Y N 32 A1IDZ O26 C7 SING N N 33 A1IDZ C28 C2 SING N N 34 A1IDZ SE33 C29 SING Y N 35 A1IDZ C8 H8A SING N N 36 A1IDZ C8 H8B SING N N 37 A1IDZ C9 H9 SING N N 38 A1IDZ C12 H12A SING N N 39 A1IDZ C12 H12B SING N N 40 A1IDZ C11 H11 SING N N 41 A1IDZ C7 H7 SING N N 42 A1IDZ C27 H27 SING N N 43 A1IDZ C30 H30 SING N N 44 A1IDZ C31 H31 SING N N 45 A1IDZ C32 H32 SING N N 46 A1IDZ N3 H3 SING N N 47 A1IDZ O10 H10 SING N N 48 A1IDZ O16 H1 SING N N 49 A1IDZ O20 H2 SING N N 50 A1IDZ O24 H4 SING N N 51 A1IDZ O25 H5 SING N N 52 # 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 A1IDZ InChI InChI 1.06 "InChI=1S/C13H17N2O14P3Se/c16-8-4-11(15-5-7(10-2-1-3-33-10)12(17)14-13(15)18)27-9(8)6-26-31(22,23)29-32(24,25)28-30(19,20)21/h1-3,5,8-9,11,16H,4,6H2,(H,22,23)(H,24,25)(H,14,17,18)(H2,19,20,21)/t8-,9?,11-/m0/s1" A1IDZ InChIKey InChI 1.06 IFHZFLUXRCNTJE-QCZWPSDZSA-N A1IDZ SMILES_CANONICAL CACTVS 3.385 "O[C@H]1C[C@H](O[C@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=C(C(=O)NC2=O)c3[se]ccc3" A1IDZ SMILES CACTVS 3.385 "O[CH]1C[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=C(C(=O)NC2=O)c3[se]ccc3" A1IDZ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc([se]c1)C2=CN(C(=O)NC2=O)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O" A1IDZ SMILES "OpenEye OEToolkits" 2.0.7 "c1cc([se]c1)C2=CN(C(=O)NC2=O)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O" # _pdbx_chem_comp_identifier.comp_id A1IDZ _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[[(2~{R},3~{S},5~{R})-5-[2,4-bis(oxidanylidene)-5-selenophen-2-yl-pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen 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 A1IDZ "Create component" 2024-06-07 PDBE A1IDZ "Initial release" 2024-11-13 RCSB #