data_A1CY1 # _chem_comp.id A1CY1 _chem_comp.name "1-(5-deoxy-3-O-phosphono-beta-D-xylofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-10-20 _chem_comp.pdbx_modified_date 2026-10-16 _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 322.208 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1CY1 _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 9YRE _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm ? _chem_comp.pdbx_comp_type ? # 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 A1CY1 O2 O1 O 0 1 N N N N N N 36.401 9.756 13.807 0.403 0.905 -0.817 O2 A1CY1 1 A1CY1 C4 C1 C 0 1 N N N N N N 36.840 8.681 17.150 3.756 1.306 -0.164 C4 A1CY1 2 A1CY1 C5 C2 C 0 1 N N N N N N 36.040 9.610 17.816 4.075 0.001 0.280 C5 A1CY1 3 A1CY1 C6 C3 C 0 1 N N N N N N 35.370 10.584 17.083 3.103 -0.935 0.323 C6 A1CY1 4 A1CY1 "C1'" C4 C 0 1 N N R N N N 34.843 11.666 14.864 0.775 -1.623 -0.014 "C1'" A1CY1 5 A1CY1 C2 C5 C 0 1 N N N N N N 36.302 9.725 15.032 1.540 0.637 -0.481 C2 A1CY1 6 A1CY1 "C2'" C6 C 0 1 N N R N N N 33.310 11.789 15.154 -0.288 -1.226 1.028 "C2'" A1CY1 7 A1CY1 "C3'" C7 C 0 1 N N R N N N 33.247 13.199 15.703 -1.604 -1.145 0.216 "C3'" A1CY1 8 A1CY1 "C4'" C8 C 0 1 N N R N N N 34.297 13.847 14.879 -1.271 -2.008 -1.028 "C4'" A1CY1 9 A1CY1 "C5'" C9 C 0 1 N N N N N N 34.594 15.254 15.336 -2.145 -1.600 -2.216 "C5'" A1CY1 10 A1CY1 C7 C10 C 0 1 N N N N N N 35.931 9.527 19.335 5.482 -0.341 0.698 C7 A1CY1 11 A1CY1 N1 N1 N 0 1 N N N N N N 35.543 10.638 15.678 1.831 -0.608 -0.061 N1 A1CY1 12 A1CY1 N3 N2 N 0 1 N N N N N N 36.950 8.762 15.769 2.490 1.588 -0.534 N3 A1CY1 13 A1CY1 "O2'" O2 O 0 1 N N N N N N 32.619 11.784 13.883 -0.389 -2.224 2.045 "O2'" A1CY1 14 A1CY1 "O3'" O3 O 0 1 N N N N N N 33.560 13.243 17.106 -1.888 0.204 -0.161 "O3'" A1CY1 15 A1CY1 O4 O4 O 0 1 N N N N N N 37.436 7.796 17.779 4.615 2.168 -0.207 O4 A1CY1 16 A1CY1 "O4'" O5 O 0 1 N N N N N N 35.410 12.935 15.210 0.116 -1.702 -1.289 "O4'" A1CY1 17 A1CY1 OP1 O6 O 0 1 N N N N N N 32.430 15.175 18.083 -4.412 0.186 -0.119 OP1 A1CY1 18 A1CY1 OP2 O7 O 0 1 N N N N N N 32.519 13.033 19.443 -3.231 1.161 1.888 OP2 A1CY1 19 A1CY1 P P1 P 0 1 N N N N N N 32.378 13.727 18.146 -3.228 0.975 0.288 P A1CY1 20 A1CY1 H6 H1 H 0 1 N N N N N N 34.724 11.292 17.580 3.328 -1.937 0.658 H6 A1CY1 21 A1CY1 "H1'" H2 H 0 1 N N N N N N 34.986 11.456 13.794 1.204 -2.592 0.244 "H1'" A1CY1 22 A1CY1 "H2'" H3 H 0 1 N N N N N N 32.955 11.030 15.867 -0.048 -0.257 1.467 "H2'" A1CY1 23 A1CY1 "H3'" H4 H 0 1 N N N N N N 32.262 13.644 15.498 -2.434 -1.574 0.777 "H3'" A1CY1 24 A1CY1 "H4'" H5 H 0 1 N N N N N N 34.049 13.818 13.808 -1.395 -3.068 -0.807 "H4'" A1CY1 25 A1CY1 "H5'" H6 H 0 1 N N N N N N 33.750 15.910 15.077 -1.842 -2.162 -3.099 "H5'" A1CY1 26 A1CY1 H74 H7 H 0 1 N N N N N N 34.743 15.262 16.426 -3.190 -1.815 -1.989 H74 A1CY1 27 A1CY1 H75 H8 H 0 1 N N N N N N 35.506 15.616 14.839 -2.027 -0.534 -2.405 H75 A1CY1 28 A1CY1 H71 H9 H 0 1 N N N N N N 35.268 10.325 19.700 6.116 0.539 0.592 H71 A1CY1 29 A1CY1 H72 H10 H 0 1 N N N N N N 35.518 8.548 19.620 5.483 -0.667 1.738 H72 A1CY1 30 A1CY1 H73 H11 H 0 1 N N N N N N 36.929 9.648 19.781 5.865 -1.142 0.066 H73 A1CY1 31 A1CY1 H3 H12 H 0 1 N N N N N N 37.522 8.095 15.292 2.263 2.482 -0.836 H3 A1CY1 32 A1CY1 H76 H13 H 0 1 N N N N N N 31.683 11.858 14.030 0.426 -2.358 2.547 H76 A1CY1 33 A1CY1 H1 H14 H 0 1 N N N N N N 32.636 13.674 20.134 -2.481 1.670 2.226 H1 A1CY1 34 A1CY1 OP3 OP3 O 0 1 N Y N N N N 31.345 12.609 18.176 -3.278 2.421 -0.420 OP3 A1CY1 35 A1CY1 H2 H2 H 0 1 N Y N N N N 30.472 12.983 18.143 -4.061 2.942 -0.194 H2 A1CY1 36 # 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 A1CY1 C2 O2 DOUB N N 1 A1CY1 C2 N3 SING N N 2 A1CY1 C2 N1 SING N N 3 A1CY1 C4 N3 SING N N 4 A1CY1 C4 O4 DOUB N N 5 A1CY1 C4 C5 SING N N 6 A1CY1 C5 C7 SING N N 7 A1CY1 C5 C6 DOUB N N 8 A1CY1 N1 C6 SING N N 9 A1CY1 "C1'" N1 SING N N 10 A1CY1 "C1'" "C2'" SING N N 11 A1CY1 "C1'" "O4'" SING N N 12 A1CY1 "C2'" "O2'" SING N N 13 A1CY1 "C2'" "C3'" SING N N 14 A1CY1 "C4'" "O4'" SING N N 15 A1CY1 "C4'" "C5'" SING N N 16 A1CY1 "C4'" "C3'" SING N N 17 A1CY1 "C3'" "O3'" SING N N 18 A1CY1 P "O3'" SING N N 19 A1CY1 P OP1 DOUB N N 20 A1CY1 P OP2 SING N N 21 A1CY1 C6 H6 SING N N 22 A1CY1 "C1'" "H1'" SING N N 23 A1CY1 "C2'" "H2'" SING N N 24 A1CY1 "C3'" "H3'" SING N N 25 A1CY1 "C4'" "H4'" SING N N 26 A1CY1 "C5'" "H5'" SING N N 27 A1CY1 "C5'" H74 SING N N 28 A1CY1 "C5'" H75 SING N N 29 A1CY1 C7 H71 SING N N 30 A1CY1 C7 H72 SING N N 31 A1CY1 C7 H73 SING N N 32 A1CY1 N3 H3 SING N N 33 A1CY1 "O2'" H76 SING N N 34 A1CY1 OP2 H1 SING N N 35 A1CY1 P OP3 SING N N 36 A1CY1 OP3 H2 SING N N 37 # 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 A1CY1 SMILES ACDLabs 14.52 "O=P(O)(O)OC1C(C)OC(N2C=C(C)C(=O)NC2=O)C1O" A1CY1 InChI InChI 1.06 "InChI=1S/C10H15N2O8P/c1-4-3-12(10(15)11-8(4)14)9-6(13)7(5(2)19-9)20-21(16,17)18/h3,5-7,9,13H,1-2H3,(H,11,14,15)(H2,16,17,18)/t5-,6-,7+,9-/m1/s1" A1CY1 InChIKey InChI 1.06 HRWNUYQJWGICCU-JAGXHNFQSA-N A1CY1 SMILES_CANONICAL CACTVS 3.385 "C[C@H]1O[C@H]([C@H](O)[C@H]1O[P](O)(O)=O)N2C=C(C)C(=O)NC2=O" A1CY1 SMILES CACTVS 3.385 "C[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)N2C=C(C)C(=O)NC2=O" A1CY1 SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "C[C@@H]1[C@@H]([C@H]([C@@H](O1)N2C=C(C(=O)NC2=O)C)O)OP(=O)(O)O" A1CY1 SMILES "OpenEye OEToolkits" 3.1.0.0 "CC1C(C(C(O1)N2C=C(C(=O)NC2=O)C)O)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 A1CY1 "SYSTEMATIC NAME" ACDLabs 14.52 "1-(5-deoxy-3-O-phosphono-beta-D-xylofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione" A1CY1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "[(2~{R},3~{R},4~{R},5~{R})-2-methyl-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-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 A1CY1 "Create component" 2025-10-20 RCSB A1CY1 "Initial release" 2026-10-21 RCSB #