data_A1EY1 # _chem_comp.id A1EY1 _chem_comp.name "[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)thieno[2,3-d]pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H13 N2 O9 P S" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-10-13 _chem_comp.pdbx_modified_date 2026-01-23 _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 380.268 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1EY1 _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 9LMZ _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBC _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 A1EY1 "C1'" C1 C 0 1 N N R N N N 19.538 10.058 -14.485 -0.732 -0.951 0.079 C2 A1EY1 1 A1EY1 C2 C2 C 0 1 Y N N N N N 23.193 10.855 -14.020 -3.883 1.032 0.240 C7 A1EY1 2 A1EY1 C4 C3 C 0 1 Y N N N N N 21.957 10.684 -14.591 -2.945 0.049 0.493 C8 A1EY1 3 A1EY1 C10 C4 C 0 1 Y N N N N N 24.131 11.358 -14.970 -5.094 0.848 1.020 C10 A1EY1 4 A1EY1 C9 C5 C 0 1 Y N N N N N 23.572 11.543 -16.205 -5.058 -0.209 1.812 C9 A1EY1 5 A1EY1 "C5'" C6 C 0 1 N N N N N N 18.918 9.215 -17.933 2.824 -0.697 -0.397 C4 A1EY1 6 A1EY1 C1 C7 C 0 1 N N N N N N 20.966 9.948 -12.524 -1.460 1.054 -1.070 C5 A1EY1 7 A1EY1 C3 C8 C 0 1 N N N N N N 23.359 10.554 -12.625 -3.539 2.076 -0.744 C6 A1EY1 8 A1EY1 N3 N1 N 0 1 N N N N N N 22.214 10.130 -11.979 -2.338 2.031 -1.351 N1 A1EY1 9 A1EY1 N1 N2 N 0 1 N N N N N N 20.854 10.236 -13.877 -1.732 0.086 -0.183 N A1EY1 10 A1EY1 "C3'" C9 C 0 1 N N S N N N 18.178 10.998 -16.261 0.974 -2.315 -0.939 C A1EY1 11 A1EY1 "O3'" O1 O 0 1 N N N N N N 16.759 11.117 -16.205 0.919 -3.650 -0.433 O A1EY1 12 A1EY1 "C2'" C10 C 0 1 N N R N N N 18.826 11.352 -14.909 -0.453 -1.776 -1.204 C1 A1EY1 13 A1EY1 "C4'" C11 C 0 1 N N R N N N 18.561 9.537 -16.503 1.548 -1.358 0.129 C3 A1EY1 14 A1EY1 "O2'" O2 O 0 1 N N N N N N 17.835 11.724 -13.958 -1.387 -2.850 -1.332 O1 A1EY1 15 A1EY1 "O4'" O3 O 0 1 N N N N N N 19.686 9.272 -15.647 0.548 -0.357 0.386 O2 A1EY1 16 A1EY1 "O5'" O4 O 0 1 N N N N N N 18.956 7.777 -18.096 3.410 0.096 0.637 O3 A1EY1 17 A1EY1 OP3 O5 O 0 1 N N N N N N 20.409 7.688 -20.162 5.993 -0.077 0.178 O4 A1EY1 18 A1EY1 OP1 O6 O 0 1 N N N N N N 17.898 7.606 -20.347 4.621 1.838 -0.730 O5 A1EY1 19 A1EY1 OP2 O7 O 0 1 N N N N N N 19.146 5.644 -19.395 5.062 1.809 1.755 O6 A1EY1 20 A1EY1 O2 O8 O 0 1 N N N N N N 20.025 9.547 -11.855 -0.385 1.046 -1.639 O7 A1EY1 21 A1EY1 O4 O9 O 0 1 N N N N N N 24.428 10.614 -12.020 -4.329 2.965 -1.004 O8 A1EY1 22 A1EY1 P P1 P 0 1 N N N N N N 19.121 7.147 -19.579 4.768 0.937 0.434 P A1EY1 23 A1EY1 S S1 S 0 1 Y N N N N N 21.917 11.114 -16.258 -3.533 -1.057 1.653 S A1EY1 24 A1EY1 "H1'" H1 H 0 1 N N N N N N 18.886 9.535 -13.770 -1.058 -1.602 0.890 H1 A1EY1 25 A1EY1 H2 H2 H 0 1 N N N N N N 25.165 11.569 -14.740 -5.944 1.512 0.959 H2 A1EY1 26 A1EY1 H1 H3 H 0 1 N N N N N N 24.118 11.920 -17.057 -5.862 -0.511 2.467 H3 A1EY1 27 A1EY1 "H5'" H4 H 0 1 N N N N N N 19.904 9.640 -18.172 3.530 -1.467 -0.709 H4 A1EY1 28 A1EY1 "H5''" H5 H 0 1 N N N N N N 18.162 9.643 -18.607 2.579 -0.061 -1.248 H5 A1EY1 29 A1EY1 H3 H6 H 0 1 N N N N N N 22.304 9.933 -11.003 -2.103 2.714 -1.999 H6 A1EY1 30 A1EY1 "H3'" H7 H 0 1 N N N N N N 18.603 11.632 -17.053 1.571 -2.278 -1.850 H7 A1EY1 31 A1EY1 "HO3'" H8 H 0 1 N N N N N N 16.523 12.025 -16.055 0.512 -4.284 -1.039 H8 A1EY1 32 A1EY1 "H2'" H9 H 0 1 N N N N N N 19.566 12.153 -15.051 -0.470 -1.139 -2.088 H9 A1EY1 33 A1EY1 "H4'" H10 H 0 1 N N N N N N 17.713 8.903 -16.202 1.766 -1.910 1.043 H10 A1EY1 34 A1EY1 "HO2'" H11 H 0 1 N N N N N N 18.253 11.938 -13.132 -1.201 -3.447 -2.069 H11 A1EY1 35 A1EY1 HOP3 H12 H 0 1 N N N N N N 20.212 8.228 -20.919 6.147 -0.698 0.902 H12 A1EY1 36 A1EY1 HOP2 H13 H 0 1 N N N N N N 18.377 5.262 -19.802 5.867 2.342 1.704 H13 A1EY1 37 # 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 A1EY1 OP1 P DOUB N N 1 A1EY1 OP3 P SING N N 2 A1EY1 P OP2 SING N N 3 A1EY1 P "O5'" SING N N 4 A1EY1 "O5'" "C5'" SING N N 5 A1EY1 "C5'" "C4'" SING N N 6 A1EY1 "C4'" "C3'" SING N N 7 A1EY1 "C4'" "O4'" SING N N 8 A1EY1 "C3'" "O3'" SING N N 9 A1EY1 "C3'" "C2'" SING N N 10 A1EY1 S C9 SING Y N 11 A1EY1 S C4 SING Y N 12 A1EY1 C9 C10 DOUB Y N 13 A1EY1 "O4'" "C1'" SING N N 14 A1EY1 C10 C2 SING Y N 15 A1EY1 "C2'" "C1'" SING N N 16 A1EY1 "C2'" "O2'" SING N N 17 A1EY1 C4 C2 DOUB Y N 18 A1EY1 C4 N1 SING N N 19 A1EY1 "C1'" N1 SING N N 20 A1EY1 C2 C3 SING N N 21 A1EY1 N1 C1 SING N N 22 A1EY1 C3 O4 DOUB N N 23 A1EY1 C3 N3 SING N N 24 A1EY1 C1 N3 SING N N 25 A1EY1 C1 O2 DOUB N N 26 A1EY1 "C1'" "H1'" SING N N 27 A1EY1 C10 H2 SING N N 28 A1EY1 C9 H1 SING N N 29 A1EY1 "C5'" "H5'" SING N N 30 A1EY1 "C5'" "H5''" SING N N 31 A1EY1 N3 H3 SING N N 32 A1EY1 "C3'" "H3'" SING N N 33 A1EY1 "O3'" "HO3'" SING N N 34 A1EY1 "C2'" "H2'" SING N N 35 A1EY1 "C4'" "H4'" SING N N 36 A1EY1 "O2'" "HO2'" SING N N 37 A1EY1 OP3 HOP3 SING N N 38 A1EY1 OP2 HOP2 SING N N 39 # 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 A1EY1 InChI InChI 1.06 "InChI=1S/C11H13N2O9PS/c14-6-5(3-21-23(18,19)20)22-9(7(6)15)13-10-4(1-2-24-10)8(16)12-11(13)17/h1-2,5-7,9,14-15H,3H2,(H,12,16,17)(H2,18,19,20)/t5-,6-,7-,9-/m1/s1" A1EY1 InChIKey InChI 1.06 WTJWLDXEEZVLGX-JXOAFFINSA-N A1EY1 SMILES_CANONICAL CACTVS 3.385 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C(=O)NC(=O)c3ccsc23" A1EY1 SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C(=O)NC(=O)c3ccsc23" A1EY1 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1csc2c1C(=O)NC(=O)N2[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O" A1EY1 SMILES "OpenEye OEToolkits" 2.0.7 "c1csc2c1C(=O)NC(=O)N2C3C(C(C(O3)COP(=O)(O)O)O)O" # _pdbx_chem_comp_identifier.comp_id A1EY1 _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~{R})-5-[2,4-bis(oxidanylidene)thieno[2,3-d]pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl 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 A1EY1 "Create component" 2025-10-13 PDBC A1EY1 "Initial release" 2026-01-28 RCSB #