data_X0O # _chem_comp.id X0O _chem_comp.name "[[(2~{R},3~{S},4~{R},5~{S})-5-(4-azanyl-1-methyl-2-oxidanylidene-pyrimidin-5-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" _chem_comp.type "RNA linking" _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H18 N3 O14 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-05-25 _chem_comp.pdbx_modified_date 2023-12-22 _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 497.183 _chem_comp.one_letter_code ? _chem_comp.three_letter_code X0O _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 8SY7 _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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_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 X0O C14 C1 C 0 1 N N N N N N 132.155 146.073 131.767 -0.822 1.888 0.431 C14 X0O 1 X0O C15 C2 C 0 1 N N R N N N 131.087 145.930 132.645 -1.884 1.677 -0.651 C15 X0O 2 X0O C16 C3 C 0 1 N N S N N N 131.458 146.531 134.071 -3.102 2.603 -0.407 C16 X0O 3 X0O C17 C4 C 0 1 N N R N N N 130.918 145.794 134.904 -4.240 1.839 -1.127 C17 X0O 4 X0O C18 C5 C 0 1 N N S N N N 130.457 144.388 134.133 -3.724 0.389 -1.215 C18 X0O 5 X0O C19 C6 C 0 1 N N N N N N 131.156 143.216 134.780 -4.685 -0.540 -0.521 C19 X0O 6 X0O C20 C7 C 0 1 N N N N N N 130.828 142.802 136.304 -4.894 -0.445 0.870 C20 X0O 7 X0O C22 C8 C 0 1 N N N N N N 132.383 141.035 136.181 -6.404 -2.191 0.759 C22 X0O 8 X0O C24 C9 C 0 1 N N N N N N 133.700 140.700 133.855 -6.972 -3.320 -1.319 C24 X0O 9 X0O C25 C10 C 0 1 N N N N N N 132.167 142.429 134.011 -5.366 -1.476 -1.224 C25 X0O 10 X0O N21 N1 N 0 1 N N N N N N 131.525 141.665 136.904 -5.745 -1.272 1.464 N21 X0O 11 X0O N23 N2 N 0 1 N N N N N N 132.728 141.433 134.640 -6.229 -2.303 -0.571 N23 X0O 12 X0O N27 N3 N 0 1 N N N N N N 129.854 143.549 137.076 -4.220 0.500 1.608 N27 X0O 13 X0O O02 O1 O 0 1 N N N N N N 132.451 143.906 128.573 2.159 2.356 1.244 O02 X0O 14 X0O O03 O2 O 0 1 N N N N N N 131.592 146.208 128.706 1.194 0.440 2.574 O03 X0O 15 X0O O04 O3 O 0 1 N N N N N N 134.103 145.793 129.155 2.703 0.018 0.462 O04 X0O 16 X0O O06 O4 O 0 1 N N N N N N 134.913 147.556 130.856 4.480 -1.158 2.002 O06 X0O 17 X0O O07 O5 O 0 1 N N N N N N 133.421 148.288 129.041 4.939 1.086 0.940 O07 X0O 18 X0O O08 O6 O 0 1 N N N N N N 135.868 147.711 128.470 4.923 -0.930 -0.579 O08 X0O 19 X0O O10 O7 O 0 1 N N N N N N 134.446 147.975 126.328 7.010 0.228 -1.680 O10 X0O 20 X0O O11 O8 O 0 1 N N N N N N 136.377 146.439 126.278 7.276 -1.604 0.035 O11 X0O 21 X0O O12 O9 O 0 1 N N N N N N 136.740 148.872 126.346 6.443 -2.275 -2.251 O12 X0O 22 X0O O13 O10 O 0 1 N N N N N N 132.202 144.977 130.899 0.294 1.033 0.176 O13 X0O 23 X0O O26 O11 O 0 1 N N N N N N 132.906 140.127 136.729 -7.181 -2.940 1.328 O26 X0O 24 X0O O28 O12 O 0 1 N N N N N N 130.814 144.465 132.910 -2.445 0.350 -0.559 O28 X0O 25 X0O O29 O13 O 0 1 N N N N N N 129.732 146.465 135.483 -4.453 2.374 -2.435 O29 X0O 26 X0O O30 O14 O 0 1 N N N N N N 130.919 147.938 134.197 -2.895 3.886 -1.002 O30 X0O 27 X0O P01 P1 P 0 1 N N N N N N 132.563 145.221 129.307 1.600 0.991 1.117 P01 X0O 28 X0O P05 P2 P 0 1 N N N N N N 134.554 147.360 129.403 4.276 -0.217 0.711 P05 X0O 29 X0O P09 P3 P 0 1 N N N N N N 135.855 147.747 126.822 6.431 -1.155 -1.094 P09 X0O 30 X0O H1 H1 H 0 1 N N N N N N 133.093 146.127 132.338 -0.493 2.928 0.419 H1 X0O 31 X0O H2 H2 H 0 1 N N N N N N 132.027 146.997 131.183 -1.245 1.653 1.407 H2 X0O 32 X0O H3 H3 H 0 1 N N N N N N 130.177 146.423 132.272 -1.461 1.847 -1.641 H3 X0O 33 X0O H4 H4 H 0 1 N N N N N N 132.554 146.558 134.155 -3.311 2.699 0.658 H4 X0O 34 X0O H5 H5 H 0 1 N N N N N N 131.596 145.501 135.719 -5.159 1.883 -0.543 H5 X0O 35 X0O H6 H6 H 0 1 N N N N N N 129.370 144.281 134.261 -3.615 0.097 -2.260 H6 X0O 36 X0O H7 H7 H 0 1 N N N N N N 134.120 139.883 134.460 -6.395 -4.244 -1.349 H7 X0O 37 X0O H8 H8 H 0 1 N N N N N N 133.210 140.281 132.963 -7.929 -3.505 -0.830 H8 X0O 38 X0O H9 H9 H 0 1 N N N N N N 134.508 141.379 133.545 -7.146 -2.968 -2.336 H9 X0O 39 X0O H10 H10 H 0 1 N N N N N N 132.420 142.672 132.989 -5.226 -1.566 -2.291 H10 X0O 40 X0O H11 H11 H 0 1 N N N N N N 129.658 143.287 138.021 -3.598 1.103 1.172 H11 X0O 41 X0O H12 H12 H 0 1 N N N N N N 129.379 144.326 136.664 -4.366 0.563 2.565 H12 X0O 42 X0O H13 H13 H 0 1 N N N N N N 131.118 145.793 127.995 0.820 -0.452 2.567 H13 X0O 43 X0O H14 H14 H 0 1 N N N N N N 134.350 148.221 131.235 4.070 -2.030 1.923 H14 X0O 44 X0O H15 H15 H 0 1 N N N N N N 134.181 147.247 125.777 6.504 0.582 -2.425 H15 X0O 45 X0O H16 H16 H 0 1 N Y N N N N 137.437 148.520 125.806 7.321 -2.462 -2.609 H16 X0O 46 X0O H17 H17 H 0 1 N N N N N N 129.324 145.892 136.121 -4.723 3.303 -2.440 H17 X0O 47 X0O H18 H18 H 0 1 N N N N N N 131.145 148.289 135.050 -3.630 4.501 -0.876 H18 X0O 48 # 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 X0O O11 P09 DOUB N N 1 X0O O10 P09 SING N N 2 X0O O12 P09 SING N N 3 X0O P09 O08 SING N N 4 X0O O08 P05 SING N N 5 X0O O02 P01 DOUB N N 6 X0O O03 P01 SING N N 7 X0O O07 P05 DOUB N N 8 X0O O04 P01 SING N N 9 X0O O04 P05 SING N N 10 X0O P01 O13 SING N N 11 X0O P05 O06 SING N N 12 X0O O13 C14 SING N N 13 X0O C14 C15 SING N N 14 X0O C15 O28 SING N N 15 X0O C15 C16 SING N N 16 X0O O28 C18 SING N N 17 X0O C24 N23 SING N N 18 X0O C25 N23 SING N N 19 X0O C25 C19 DOUB N N 20 X0O C16 O30 SING N N 21 X0O C16 C17 SING N N 22 X0O C18 C19 SING N N 23 X0O C18 C17 SING N N 24 X0O N23 C22 SING N N 25 X0O C19 C20 SING N N 26 X0O C17 O29 SING N N 27 X0O C22 O26 DOUB N N 28 X0O C22 N21 SING N N 29 X0O C20 N21 DOUB N N 30 X0O C20 N27 SING N N 31 X0O C14 H1 SING N N 32 X0O C14 H2 SING N N 33 X0O C15 H3 SING N N 34 X0O C16 H4 SING N N 35 X0O C17 H5 SING N N 36 X0O C18 H6 SING N N 37 X0O C24 H7 SING N N 38 X0O C24 H8 SING N N 39 X0O C24 H9 SING N N 40 X0O C25 H10 SING N N 41 X0O N27 H11 SING N N 42 X0O N27 H12 SING N N 43 X0O O03 H13 SING N N 44 X0O O06 H14 SING N N 45 X0O O10 H15 SING N N 46 X0O O12 H16 SING N N 47 X0O O29 H17 SING N N 48 X0O O30 H18 SING N N 49 # 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 X0O InChI InChI 1.06 "InChI=1S/C10H18N3O14P3/c1-13-2-4(9(11)12-10(13)16)8-7(15)6(14)5(25-8)3-24-29(20,21)27-30(22,23)26-28(17,18)19/h2,5-8,14-15H,3H2,1H3,(H,20,21)(H,22,23)(H2,11,12,16)(H2,17,18,19)/t5-,6-,7-,8+/m1/s1" X0O InChIKey InChI 1.06 JCPRKVWIOJLDIF-XUTVFYLZSA-N X0O SMILES_CANONICAL CACTVS 3.385 "CN1C=C([C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O)C(=NC1=O)N" X0O SMILES CACTVS 3.385 "CN1C=C([CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O)C(=NC1=O)N" X0O SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN1C=C(C(=NC1=O)N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O" X0O SMILES "OpenEye OEToolkits" 2.0.7 "CN1C=C(C(=NC1=O)N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O" # _pdbx_chem_comp_identifier.comp_id X0O _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},4~{R},5~{S})-5-(4-azanyl-1-methyl-2-oxidanylidene-pyrimidin-5-yl)-3,4-bis(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 X0O "Create component" 2023-05-25 RCSB X0O "Initial release" 2023-12-27 RCSB #