data_A1EL7 # _chem_comp.id A1EL7 _chem_comp.name "[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)thieno[3,2-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 2025-02-18 _chem_comp.pdbx_modified_date 2026-02-06 _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 A1EL7 _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 9LSN _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 A1EL7 N1 N1 N 0 1 N N N N N N -20.018 17.606 -3.710 -1.706 0.085 0.192 N A1EL7 1 A1EL7 "C3'" C1 C 0 1 N N S N N N -20.630 15.446 -6.641 1.130 2.289 0.837 C A1EL7 2 A1EL7 "O3'" O1 O 0 1 N N N N N N -20.238 14.123 -6.988 1.484 3.609 0.419 O A1EL7 3 A1EL7 "O2'" O2 O 0 1 N N N N N N -20.670 14.461 -4.363 -1.042 3.293 0.339 O1 A1EL7 4 A1EL7 "C2'" C2 C 0 1 N N R N N N -20.801 15.658 -5.123 -0.402 2.098 0.790 C1 A1EL7 5 A1EL7 C10 C3 C 0 1 Y N N N N N -22.872 19.697 -4.680 -4.398 0.382 -2.266 C10 A1EL7 6 A1EL7 "C1'" C4 C 0 1 N N R N N N -19.700 16.662 -4.777 -0.607 0.956 -0.231 C2 A1EL7 7 A1EL7 "C4'" C5 C 0 1 N N R N N N -19.539 16.442 -7.043 1.670 1.240 -0.161 C3 A1EL7 8 A1EL7 "C5'" C6 C 0 1 N N N N N N -19.829 17.168 -8.330 2.977 0.637 0.356 C4 A1EL7 9 A1EL7 C2 C7 C 0 1 N N N N N N -19.255 17.525 -2.551 -1.591 -0.633 1.321 C5 A1EL7 10 A1EL7 C4 C8 C 0 1 N N N N N N -20.665 19.273 -1.521 -3.718 -1.563 1.046 C6 A1EL7 11 A1EL7 C5 C9 C 0 1 Y N N N N N -21.400 19.301 -2.727 -3.892 -0.816 -0.147 C7 A1EL7 12 A1EL7 C6 C10 C 0 1 Y N N N N N -21.089 18.503 -3.815 -2.873 0.013 -0.581 C8 A1EL7 13 A1EL7 C9 C11 C 0 1 Y N N N N N -21.930 18.723 -4.950 -3.196 0.662 -1.766 C9 A1EL7 14 A1EL7 N3 N2 N 0 1 N N N N N N -19.619 18.370 -1.529 -2.574 -1.444 1.745 N1 A1EL7 15 A1EL7 "O4'" O3 O 0 1 N N N N N N -19.443 17.387 -5.958 0.641 0.229 -0.226 O2 A1EL7 16 A1EL7 "O5'" O4 O 0 1 N N N N N N -18.600 17.763 -8.789 3.519 -0.243 -0.631 O3 A1EL7 17 A1EL7 OP2 O5 O 0 1 N N N N N N -19.674 19.543 -10.178 5.266 -1.838 -1.779 O4 A1EL7 18 A1EL7 OP1 O6 O 0 1 N N N N N N -18.880 17.430 -11.281 5.981 -0.106 -0.089 O5 A1EL7 19 A1EL7 OP3 O7 O 0 1 N Y N N N N -17.181 19.042 -10.330 4.717 -2.112 0.778 O6 A1EL7 20 A1EL7 O2 O8 O 0 1 N N N N N N -18.331 16.735 -2.427 -0.569 -0.547 1.975 O7 A1EL7 21 A1EL7 O4 O9 O 0 1 N N N N N N -20.892 19.964 -0.528 -4.605 -2.298 1.443 O8 A1EL7 22 A1EL7 P P1 P 0 1 N N N N N N -18.591 18.487 -10.239 4.895 -1.054 -0.423 P A1EL7 23 A1EL7 S S1 S 0 1 Y N N N N N -22.737 20.332 -3.079 -5.233 -0.730 -1.282 S A1EL7 24 A1EL7 "H3'" H1 H 0 1 N N N N N N -21.568 15.717 -7.147 1.509 2.092 1.840 H1 A1EL7 25 A1EL7 "HO3'" H2 H 0 1 N Y N N N N -20.921 13.513 -6.735 1.119 4.309 0.979 H2 A1EL7 26 A1EL7 "HO2'" H3 H 0 1 N N N N N N -20.785 14.657 -3.441 -0.895 4.058 0.912 H3 A1EL7 27 A1EL7 "H2'" H4 H 0 1 N N N N N N -21.780 16.124 -4.939 -0.781 1.807 1.770 H4 A1EL7 28 A1EL7 H5 H5 H 0 1 N N N N N N -23.613 20.026 -5.393 -4.793 0.806 -3.178 H5 A1EL7 29 A1EL7 "H1'" H6 H 0 1 N N N N N N -18.802 16.094 -4.492 -0.807 1.364 -1.221 H6 A1EL7 30 A1EL7 "H4'" H7 H 0 1 N N N N N N -18.589 15.898 -7.147 1.821 1.692 -1.141 H7 A1EL7 31 A1EL7 "H5'" H8 H 0 1 N N N N N N -20.581 17.951 -8.156 3.690 1.435 0.562 H8 A1EL7 32 A1EL7 "H5''" H9 H 0 1 N N N N N N -20.205 16.459 -9.082 2.783 0.079 1.272 H9 A1EL7 33 A1EL7 H10 H10 H 0 1 N N N N N N -21.841 18.199 -5.890 -2.517 1.348 -2.251 H10 A1EL7 34 A1EL7 H3 H11 H 0 1 N N N N N N -19.064 18.326 -0.698 -2.459 -1.949 2.565 H11 A1EL7 35 A1EL7 HOP2 H12 H 0 1 N N N N N N -20.348 19.343 -10.817 6.084 -2.350 -1.726 H12 A1EL7 36 A1EL7 HOP3 H13 H 0 1 N Y N N N N -16.718 18.617 -11.043 4.021 -2.765 0.626 H13 A1EL7 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 A1EL7 OP1 P DOUB N N 1 A1EL7 OP3 P SING N N 2 A1EL7 P OP2 SING N N 3 A1EL7 P "O5'" SING N N 4 A1EL7 "O5'" "C5'" SING N N 5 A1EL7 "C5'" "C4'" SING N N 6 A1EL7 "C4'" "C3'" SING N N 7 A1EL7 "C4'" "O4'" SING N N 8 A1EL7 "O3'" "C3'" SING N N 9 A1EL7 "C3'" "C2'" SING N N 10 A1EL7 "O4'" "C1'" SING N N 11 A1EL7 "C2'" "C1'" SING N N 12 A1EL7 "C2'" "O2'" SING N N 13 A1EL7 C9 C10 DOUB Y N 14 A1EL7 C9 C6 SING Y N 15 A1EL7 "C1'" N1 SING N N 16 A1EL7 C10 S SING Y N 17 A1EL7 C6 N1 SING N N 18 A1EL7 C6 C5 DOUB Y N 19 A1EL7 N1 C2 SING N N 20 A1EL7 S C5 SING Y N 21 A1EL7 C5 C4 SING N N 22 A1EL7 C2 O2 DOUB N N 23 A1EL7 C2 N3 SING N N 24 A1EL7 N3 C4 SING N N 25 A1EL7 C4 O4 DOUB N N 26 A1EL7 "C3'" "H3'" SING N N 27 A1EL7 "O3'" "HO3'" SING N N 28 A1EL7 "O2'" "HO2'" SING N N 29 A1EL7 "C2'" "H2'" SING N N 30 A1EL7 C10 H5 SING N N 31 A1EL7 "C1'" "H1'" SING N N 32 A1EL7 "C4'" "H4'" SING N N 33 A1EL7 "C5'" "H5'" SING N N 34 A1EL7 "C5'" "H5''" SING N N 35 A1EL7 C9 H10 SING N N 36 A1EL7 N3 H3 SING N N 37 A1EL7 OP2 HOP2 SING N N 38 A1EL7 OP3 HOP3 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 A1EL7 InChI InChI 1.06 "InChI=1S/C11H13N2O9PS/c14-6-5(3-21-23(18,19)20)22-10(7(6)15)13-4-1-2-24-8(4)9(16)12-11(13)17/h1-2,5-7,10,14-15H,3H2,(H,12,16,17)(H2,18,19,20)/t5-,6-,7-,10-/m1/s1" A1EL7 InChIKey InChI 1.06 XFFDXJGTTZQTKV-DAGMQNCNSA-N A1EL7 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)c3sccc23" A1EL7 SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C(=O)NC(=O)c3sccc23" A1EL7 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1csc2c1N(C(=O)NC2=O)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O" A1EL7 SMILES "OpenEye OEToolkits" 2.0.7 "c1csc2c1N(C(=O)NC2=O)C3C(C(C(O3)COP(=O)(O)O)O)O" # _pdbx_chem_comp_identifier.comp_id A1EL7 _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[3,2-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 A1EL7 "Create component" 2025-02-18 PDBC A1EL7 "Initial release" 2026-02-11 RCSB #