data_YTI # _chem_comp.id YTI _chem_comp.name "(3R,5R)-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)oxolan-3-yl dihydrogen phosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H13 N2 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-06-20 _chem_comp.pdbx_modified_date 2024-08-23 _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 292.182 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YTI _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 8T3X _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 YTI P P1 P 0 1 N N N N N N 12.109 11.249 4.358 4.108 0.125 -0.375 P YTI 1 YTI O1P O1 O 0 1 N N N N N N 12.906 11.964 3.328 4.735 -0.382 0.866 O1P YTI 2 YTI O2P O2 O 0 1 N N N N N N 11.739 12.185 5.437 4.246 -0.981 -1.537 O2P YTI 3 YTI "C4'" C1 C 0 1 N N N N N N 11.035 8.223 3.764 1.003 -0.065 1.740 "C4'" YTI 4 YTI "O4'" O3 O 0 1 N N N N N N 10.260 7.216 4.710 -0.248 -0.765 1.826 "O4'" YTI 5 YTI "C3'" C2 C 0 1 N N R N N N 10.059 9.469 3.717 1.647 -0.549 0.416 "C3'" YTI 6 YTI "O3'" O4 O 0 1 N N N N N N 10.743 10.748 3.637 2.550 0.428 -0.105 "O3'" YTI 7 YTI "C2'" C3 C 0 1 N N N N N N 9.234 9.395 4.819 0.392 -0.690 -0.488 "C2'" YTI 8 YTI "C1'" C4 C 0 1 N N R N N N 9.021 7.991 5.033 -0.687 -1.147 0.517 "C1'" YTI 9 YTI N1 N1 N 0 1 N N N N N N 8.676 7.733 6.416 -1.962 -0.495 0.209 N1 YTI 10 YTI C2 C5 C 0 1 N N N N N N 8.102 6.424 6.747 -2.071 0.842 0.323 C2 YTI 11 YTI O2 O5 O 0 1 N N N N N N 7.931 5.619 5.883 -1.108 1.493 0.680 O2 YTI 12 YTI N3 N2 N 0 1 N N N N N N 7.758 6.129 8.104 -3.230 1.467 0.047 N3 YTI 13 YTI C4 C6 C 0 1 N N N N N N 7.980 7.101 9.118 -4.306 0.759 -0.350 C4 YTI 14 YTI O4 O6 O 0 1 N N N N N N 7.710 6.889 10.271 -5.356 1.324 -0.601 O4 YTI 15 YTI C5 C7 C 0 1 N N N N N N 8.581 8.458 8.769 -4.205 -0.647 -0.474 C5 YTI 16 YTI C6 C8 C 0 1 N N N N N N 8.912 8.747 7.476 -3.029 -1.249 -0.196 C6 YTI 17 YTI C5M C9 C 0 1 N N N N N N 8.770 9.475 9.936 -5.393 -1.462 -0.917 C5M YTI 18 YTI H2 H2 H 0 1 N N N N N N 12.089 13.047 5.243 3.856 -0.716 -2.381 H2 YTI 19 YTI H3 H3 H 0 1 N N N N N N 11.181 7.794 2.762 0.833 1.011 1.706 H3 YTI 20 YTI H4 H4 H 0 1 N N N N N N 12.011 8.498 4.191 1.639 -0.321 2.587 H4 YTI 21 YTI H5 H5 H 0 1 N N N N N N 9.451 9.353 2.808 2.144 -1.510 0.550 H5 YTI 22 YTI H6 H6 H 0 1 N N N N N N 9.718 9.850 5.695 0.126 0.269 -0.933 H6 YTI 23 YTI H7 H7 H 0 1 N N N N N N 8.279 9.905 4.622 0.551 -1.445 -1.258 H7 YTI 24 YTI H8 H8 H 0 1 N N N N N N 8.206 7.640 4.383 -0.803 -2.230 0.467 H8 YTI 25 YTI H9 H9 H 0 1 N N N N N N 7.362 5.241 8.339 -3.291 2.431 0.135 H9 YTI 26 YTI H10 H10 H 0 1 N N N N N N 9.342 9.706 7.226 -2.931 -2.320 -0.290 H10 YTI 27 YTI H11 H11 H 0 1 N N N N N N 8.435 9.018 10.879 -6.241 -0.801 -1.097 H11 YTI 28 YTI H12 H12 H 0 1 N N N N N N 9.833 9.746 10.018 -5.147 -1.995 -1.836 H12 YTI 29 YTI H13 H13 H 0 1 N N N N N N 8.176 10.378 9.735 -5.651 -2.181 -0.139 H13 YTI 30 YTI O3P O3P O 0 1 N Y N N N N 13.093 10.146 4.977 4.846 1.480 -0.835 O3P YTI 31 YTI H3P H3P H 0 1 N Y N N N N 13.941 10.203 4.552 5.790 1.373 -1.015 H3P YTI 32 # 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 YTI O1P P DOUB N N 1 YTI "O3'" "C3'" SING N N 2 YTI "O3'" P SING N N 3 YTI "C3'" "C4'" SING N N 4 YTI "C3'" "C2'" SING N N 5 YTI "C4'" "O4'" SING N N 6 YTI P O2P SING N N 7 YTI "O4'" "C1'" SING N N 8 YTI "C2'" "C1'" SING N N 9 YTI "C1'" N1 SING N N 10 YTI O2 C2 DOUB N N 11 YTI N1 C2 SING N N 12 YTI N1 C6 SING N N 13 YTI C2 N3 SING N N 14 YTI C6 C5 DOUB N N 15 YTI N3 C4 SING N N 16 YTI C5 C4 SING N N 17 YTI C5 C5M SING N N 18 YTI C4 O4 DOUB N N 19 YTI O2P H2 SING N N 20 YTI "C4'" H3 SING N N 21 YTI "C4'" H4 SING N N 22 YTI "C3'" H5 SING N N 23 YTI "C2'" H6 SING N N 24 YTI "C2'" H7 SING N N 25 YTI "C1'" H8 SING N N 26 YTI N3 H9 SING N N 27 YTI C6 H10 SING N N 28 YTI C5M H11 SING N N 29 YTI C5M H12 SING N N 30 YTI C5M H13 SING N N 31 YTI P O3P SING N N 32 YTI O3P H3P SING N N 33 # 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 YTI SMILES ACDLabs 12.01 "O=P(O)(O)OC1COC(C1)N1C=C(C)C(=O)NC1=O" YTI InChI InChI 1.06 "InChI=1S/C9H13N2O7P/c1-5-3-11(9(13)10-8(5)12)7-2-6(4-17-7)18-19(14,15)16/h3,6-7H,2,4H2,1H3,(H,10,12,13)(H2,14,15,16)/t6-,7-/m1/s1" YTI InChIKey InChI 1.06 KKIOPTSGYFLUCQ-RNFRBKRXSA-N YTI SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@H]2C[C@H](CO2)O[P](O)(O)=O)C(=O)NC1=O" YTI SMILES CACTVS 3.385 "CC1=CN([CH]2C[CH](CO2)O[P](O)(O)=O)C(=O)NC1=O" YTI SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@H](CO2)OP(=O)(O)O" YTI SMILES "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)C2CC(CO2)OP(=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 YTI "SYSTEMATIC NAME" ACDLabs 12.01 "(3R,5R)-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)oxolan-3-yl dihydrogen phosphate" YTI "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(3~{R},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]oxolan-3-yl] 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 YTI "Create component" 2023-06-21 RCSB YTI "Initial release" 2024-08-28 RCSB #