data_A1EL8 # _chem_comp.id A1EL8 _chem_comp.name "[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)thieno[3,4-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 A1EL8 _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 9LSO _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 A1EL8 N3 N1 N 0 1 N N N N N N 20.477 10.599 -14.543 -1.722 0.027 0.245 N A1EL8 1 A1EL8 "C2'" C1 C 0 1 N N R N N N 18.548 11.675 -15.782 -0.437 2.020 0.944 C1 A1EL8 2 A1EL8 "C1'" C2 C 0 1 N N R N N N 19.170 10.428 -15.166 -0.640 0.937 -0.139 C2 A1EL8 3 A1EL8 "O3'" O1 O 0 1 N N N N N N 16.234 11.011 -16.243 1.423 3.575 0.637 O A1EL8 4 A1EL8 "C3'" C3 C 0 1 N N S N N N 17.552 11.067 -16.783 1.093 2.229 0.984 C A1EL8 5 A1EL8 "O2'" O2 O 0 1 N N N N N N 17.908 12.461 -14.786 -1.099 3.230 0.571 O1 A1EL8 6 A1EL8 C4 C4 C 0 1 Y N N N N N 21.583 11.038 -15.278 -2.901 -0.024 -0.531 C10 A1EL8 7 A1EL8 "C4'" C5 C 0 1 N N R N N N 18.128 9.667 -17.068 1.634 1.248 -0.080 C3 A1EL8 8 A1EL8 "C5'" C6 C 0 1 N N N N N N 18.499 9.385 -18.502 2.956 0.633 0.386 C4 A1EL8 9 A1EL8 C2 C7 C 0 1 N N N N N N 20.574 10.303 -13.186 -1.580 -0.751 1.327 C5 A1EL8 10 A1EL8 C1 C8 C 0 1 N N N N N N 22.999 10.815 -13.230 -3.688 -1.764 1.098 C6 A1EL8 11 A1EL8 C5 C9 C 0 1 Y N N N N N 22.872 11.136 -14.633 -3.949 -0.950 -0.112 C7 A1EL8 12 A1EL8 C8 C10 C 0 1 Y N N N N N 23.838 11.564 -15.509 -5.040 -0.915 -0.933 C8 A1EL8 13 A1EL8 C9 C11 C 0 1 Y N N N N N 21.633 11.395 -16.586 -3.235 0.661 -1.632 C9 A1EL8 14 A1EL8 N2 N2 N 0 1 N N N N N N 21.824 10.424 -12.619 -2.520 -1.609 1.746 N1 A1EL8 15 A1EL8 "O4'" O3 O 0 1 N N N N N N 19.298 9.518 -16.234 0.618 0.228 -0.192 O2 A1EL8 16 A1EL8 "O5'" O4 O 0 1 N N N N N N 18.561 7.949 -18.650 3.497 -0.179 -0.657 O3 A1EL8 17 A1EL8 OP3 O5 O 0 1 N Y N N N N 19.899 7.845 -20.765 4.738 -2.110 0.626 O4 A1EL8 18 A1EL8 OP2 O6 O 0 1 N N N N N N 18.647 5.808 -19.960 5.250 -1.680 -1.917 O5 A1EL8 19 A1EL8 OP1 O7 O 0 1 N N N N N N 17.374 7.800 -20.835 5.963 -0.039 -0.137 O6 A1EL8 20 A1EL8 O2 O8 O 0 1 N N N N N N 19.605 9.959 -12.519 -0.545 -0.675 1.960 O7 A1EL8 21 A1EL8 O4 O9 O 0 1 N N N N N N 24.042 10.880 -12.574 -4.521 -2.552 1.505 O8 A1EL8 22 A1EL8 P P1 P 0 1 N N N N N N 18.630 7.311 -20.141 4.886 -0.982 -0.513 P A1EL8 23 A1EL8 S S1 S 0 1 Y N N N N N 23.201 11.847 -17.068 -4.830 0.206 -2.196 S A1EL8 24 A1EL8 "H2'" H1 H 0 1 N N N N N N 19.314 12.251 -16.321 -0.802 1.668 1.909 H1 A1EL8 25 A1EL8 "H1'" H2 H 0 1 N N N N N N 18.468 10.027 -14.420 -0.857 1.399 -1.102 H2 A1EL8 26 A1EL8 "HO3'" H3 H 0 1 N Y N N N N 15.919 11.893 -16.083 1.057 4.238 1.238 H3 A1EL8 27 A1EL8 "H3'" H4 H 0 1 N N N N N N 17.567 11.658 -17.711 1.487 1.982 1.970 H4 A1EL8 28 A1EL8 "HO2'" H5 H 0 1 N N N N N N 18.561 12.814 -14.193 -1.004 3.945 1.216 H5 A1EL8 29 A1EL8 "H4'" H6 H 0 1 N N N N N N 17.375 8.927 -16.759 1.767 1.758 -1.034 H6 A1EL8 30 A1EL8 "H5'" H7 H 0 1 N N N N N N 19.478 9.831 -18.733 3.660 1.429 0.630 H7 A1EL8 31 A1EL8 "H5''" H8 H 0 1 N N N N N N 17.737 9.801 -19.178 2.780 0.021 1.270 H8 A1EL8 32 A1EL8 H9 H9 H 0 1 N N N N N N 24.876 11.705 -15.244 -5.923 -1.523 -0.798 H9 A1EL8 33 A1EL8 H10 H10 H 0 1 N N N N N N 20.777 11.393 -17.245 -2.605 1.397 -2.108 H10 A1EL8 34 A1EL8 H3 H11 H 0 1 N N N N N N 21.888 10.201 -11.646 -2.348 -2.142 2.538 H11 A1EL8 35 A1EL8 HOP3 H12 H 0 1 N Y N N N N 19.679 8.406 -21.499 4.048 -2.763 0.445 H12 A1EL8 36 A1EL8 HOP2 H13 H 0 1 N N N N N N 17.851 5.436 -20.322 6.076 -2.182 -1.904 H13 A1EL8 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 A1EL8 OP1 P DOUB N N 1 A1EL8 OP3 P SING N N 2 A1EL8 P OP2 SING N N 3 A1EL8 P "O5'" SING N N 4 A1EL8 "O5'" "C5'" SING N N 5 A1EL8 "C5'" "C4'" SING N N 6 A1EL8 S C9 SING Y N 7 A1EL8 S C8 SING Y N 8 A1EL8 "C4'" "C3'" SING N N 9 A1EL8 "C4'" "O4'" SING N N 10 A1EL8 "C3'" "O3'" SING N N 11 A1EL8 "C3'" "C2'" SING N N 12 A1EL8 C9 C4 DOUB Y N 13 A1EL8 "O4'" "C1'" SING N N 14 A1EL8 "C2'" "C1'" SING N N 15 A1EL8 "C2'" "O2'" SING N N 16 A1EL8 C8 C5 DOUB Y N 17 A1EL8 C4 C5 SING Y N 18 A1EL8 C4 N3 SING N N 19 A1EL8 "C1'" N3 SING N N 20 A1EL8 C5 C1 SING N N 21 A1EL8 N3 C2 SING N N 22 A1EL8 C1 N2 SING N N 23 A1EL8 C1 O4 DOUB N N 24 A1EL8 C2 N2 SING N N 25 A1EL8 C2 O2 DOUB N N 26 A1EL8 "C2'" "H2'" SING N N 27 A1EL8 "C1'" "H1'" SING N N 28 A1EL8 "O3'" "HO3'" SING N N 29 A1EL8 "C3'" "H3'" SING N N 30 A1EL8 "O2'" "HO2'" SING N N 31 A1EL8 "C4'" "H4'" SING N N 32 A1EL8 "C5'" "H5'" SING N N 33 A1EL8 "C5'" "H5''" SING N N 34 A1EL8 C8 H9 SING N N 35 A1EL8 C9 H10 SING N N 36 A1EL8 N2 H3 SING N N 37 A1EL8 OP3 HOP3 SING N N 38 A1EL8 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 A1EL8 InChI InChI 1.06 "InChI=1S/C11H13N2O9PS/c14-7-6(1-21-23(18,19)20)22-10(8(7)15)13-5-3-24-2-4(5)9(16)12-11(13)17/h2-3,6-8,10,14-15H,1H2,(H,12,16,17)(H2,18,19,20)/t6-,7-,8-,10-/m1/s1" A1EL8 InChIKey InChI 1.06 TXOBYKIAUSPDRX-FDDDBJFASA-N A1EL8 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)c3cscc23" A1EL8 SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C(=O)NC(=O)c3cscc23" A1EL8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1c2c(cs1)N(C(=O)NC2=O)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O" A1EL8 SMILES "OpenEye OEToolkits" 2.0.7 "c1c2c(cs1)N(C(=O)NC2=O)C3C(C(C(O3)COP(=O)(O)O)O)O" # _pdbx_chem_comp_identifier.comp_id A1EL8 _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[3,4-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 A1EL8 "Create component" 2025-02-18 PDBC A1EL8 "Initial release" 2026-02-11 RCSB #