data_A1L9Q # _chem_comp.id A1L9Q _chem_comp.name "4-azanyl-1-[(2~{R},3~{R},4~{R},5~{R})-3-methoxy-4-oxidanyl-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]pyrimidine-2-thione" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H16 N3 O7 P S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-05-20 _chem_comp.pdbx_modified_date 2025-11-07 _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 353.289 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1L9Q _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 9UYT _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ _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 A1L9Q "C1'" C1 C 0 1 N N R N N N 0.732 9.935 3.190 1.269 0.819 0.876 "C1'" A1L9Q 1 A1L9Q C2 C2 C 0 1 N N N N N N 3.177 9.762 3.772 2.126 -1.072 -0.393 C2 A1L9Q 2 A1L9Q "C2'" C3 C 0 1 N N R N N N 0.014 9.387 4.420 1.224 1.826 -0.302 "C2'" A1L9Q 3 A1L9Q "C3'" C4 C 0 1 N N R N N N -0.819 10.594 4.804 -0.217 2.383 -0.196 "C3'" A1L9Q 4 A1L9Q C4 C5 C 0 1 N N N N N N 4.499 11.680 4.270 4.105 -2.143 0.127 C4 A1L9Q 5 A1L9Q "C4'" C6 C 0 1 N N R N N N -1.298 11.071 3.448 -0.978 1.314 0.611 "C4'" A1L9Q 6 A1L9Q C5 C7 C 0 1 N N N N N N 3.342 12.534 4.059 4.296 -1.260 1.211 C5 A1L9Q 7 A1L9Q "C5'" C8 C 0 1 N N N N N N -1.776 12.492 3.374 -2.162 0.791 -0.204 "C5'" A1L9Q 8 A1L9Q C6 C9 C 0 1 N N N N N N 2.150 11.940 3.715 3.370 -0.301 1.446 C6 A1L9Q 9 A1L9Q CM2 C10 C 0 1 N N N N N N -0.244 7.056 4.131 2.696 3.405 -1.343 CM2 A1L9Q 10 A1L9Q N1 N1 N 0 1 N N N N N N 2.022 10.571 3.556 2.279 -0.214 0.632 N1 A1L9Q 11 A1L9Q N3 N2 N 0 1 N N N N N N 4.420 10.342 4.130 3.029 -2.020 -0.637 N3 A1L9Q 12 A1L9Q N4 N3 N 0 1 N N N N N N 5.733 12.232 4.621 5.031 -3.127 -0.135 N4 A1L9Q 13 A1L9Q "O2'" O1 O 0 1 N N N N N N -0.822 8.323 3.992 2.187 2.865 -0.122 "O2'" A1L9Q 14 A1L9Q "O3'" O2 O 0 1 N N N N N N -1.862 10.309 5.714 -0.220 3.632 0.499 "O3'" A1L9Q 15 A1L9Q "O4'" O3 O 0 1 N N N N N N -0.124 10.904 2.610 -0.055 0.244 0.879 "O4'" A1L9Q 16 A1L9Q "O5'" O4 O 0 1 N N N N N N -0.714 13.392 3.608 -2.928 -0.113 0.595 "O5'" A1L9Q 17 A1L9Q OP1 O5 O 0 1 N N N N N N -2.402 15.138 3.821 -5.212 0.154 -0.446 OP1 A1L9Q 18 A1L9Q OP2 O6 O 0 1 N N N N N N 0.093 15.731 4.217 -3.855 -1.858 -1.140 OP2 A1L9Q 19 A1L9Q P P1 P 0 1 N N N N N N -0.952 14.951 3.460 -4.251 -0.854 0.055 P A1L9Q 20 A1L9Q S2 S1 S 0 1 N N N N N N 3.083 8.166 3.606 0.745 -0.946 -1.396 S2 A1L9Q 21 A1L9Q H1 H1 H 0 1 N N N N N N 0.915 9.111 2.485 1.468 1.335 1.815 H1 A1L9Q 22 A1L9Q H2 H2 H 0 1 N N N N N N 0.720 9.102 5.214 1.375 1.318 -1.254 H2 A1L9Q 23 A1L9Q H3 H3 H 0 1 N N N N N N -0.151 11.359 5.227 -0.655 2.499 -1.188 H3 A1L9Q 24 A1L9Q H4 H4 H 0 1 N N N N N N -2.100 10.404 3.100 -1.333 1.740 1.549 H4 A1L9Q 25 A1L9Q H5 H5 H 0 1 N N N N N N 3.416 13.606 4.169 5.168 -1.347 1.842 H5 A1L9Q 26 A1L9Q H6 H6 H 0 1 N N N N N N -2.194 12.680 2.374 -2.790 1.628 -0.509 H6 A1L9Q 27 A1L9Q H7 H7 H 0 1 N N N N N N -2.556 12.650 4.133 -1.794 0.272 -1.089 H7 A1L9Q 28 A1L9Q H8 H8 H 0 1 N N N N N N 1.282 12.565 3.563 3.493 0.388 2.268 H8 A1L9Q 29 A1L9Q H9 H9 H 0 1 N N N N N N -0.951 6.290 3.780 3.180 2.614 -1.916 H9 A1L9Q 30 A1L9Q H10 H10 H 0 1 N N N N N N 0.678 7.006 3.533 1.875 3.825 -1.925 H10 A1L9Q 31 A1L9Q H11 H11 H 0 1 N N N N N N -0.005 6.876 5.190 3.421 4.188 -1.121 H11 A1L9Q 32 A1L9Q H12 H12 H 0 1 N N N N N N 6.525 11.638 4.761 5.818 -3.214 0.426 H12 A1L9Q 33 A1L9Q H13 H13 H 0 1 N N N N N N 5.825 13.222 4.733 4.897 -3.733 -0.880 H13 A1L9Q 34 A1L9Q H14 H14 H 0 1 N N N N N N -1.492 10.017 6.539 -1.098 4.026 0.595 H14 A1L9Q 35 A1L9Q H16 H16 H 0 1 N N N N N N -0.330 16.277 4.869 -3.226 -2.546 -0.883 H16 A1L9Q 36 A1L9Q OP3 OP3 O 0 1 N N N N N N -0.823 15.198 1.886 -4.926 -1.689 1.255 OP3 A1L9Q 37 A1L9Q H18 H18 H 0 1 N N N N N N -1.677 15.406 1.527 -5.730 -2.163 1.001 H18 A1L9Q 38 # 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 A1L9Q "O4'" "C1'" SING N N 1 A1L9Q "O4'" "C4'" SING N N 2 A1L9Q "C1'" N1 SING N N 3 A1L9Q "C1'" "C2'" SING N N 4 A1L9Q "C5'" "C4'" SING N N 5 A1L9Q "C5'" "O5'" SING N N 6 A1L9Q "C4'" "C3'" SING N N 7 A1L9Q P "O5'" SING N N 8 A1L9Q P OP1 DOUB N N 9 A1L9Q P OP2 SING N N 10 A1L9Q N1 C6 SING N N 11 A1L9Q N1 C2 SING N N 12 A1L9Q S2 C2 DOUB N N 13 A1L9Q C6 C5 DOUB N N 14 A1L9Q C2 N3 SING N N 15 A1L9Q "O2'" CM2 SING N N 16 A1L9Q "O2'" "C2'" SING N N 17 A1L9Q C5 C4 SING N N 18 A1L9Q N3 C4 DOUB N N 19 A1L9Q C4 N4 SING N N 20 A1L9Q "C2'" "C3'" SING N N 21 A1L9Q "C3'" "O3'" SING N N 22 A1L9Q "C1'" H1 SING N N 23 A1L9Q "C2'" H2 SING N N 24 A1L9Q "C3'" H3 SING N N 25 A1L9Q "C4'" H4 SING N N 26 A1L9Q C5 H5 SING N N 27 A1L9Q "C5'" H6 SING N N 28 A1L9Q "C5'" H7 SING N N 29 A1L9Q C6 H8 SING N N 30 A1L9Q CM2 H9 SING N N 31 A1L9Q CM2 H10 SING N N 32 A1L9Q CM2 H11 SING N N 33 A1L9Q N4 H12 SING N N 34 A1L9Q N4 H13 SING N N 35 A1L9Q "O3'" H14 SING N N 36 A1L9Q OP2 H16 SING N N 37 A1L9Q P OP3 SING N N 38 A1L9Q OP3 H18 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 A1L9Q InChI InChI 1.06 "InChI=1S/C10H16N3O7PS/c1-18-8-7(14)5(4-19-21(15,16)17)20-9(8)13-3-2-6(11)12-10(13)22/h2-3,5,7-9,14H,4H2,1H3,(H2,11,12,22)(H2,15,16,17)/t5-,7-,8-,9-/m1/s1" A1L9Q InChIKey InChI 1.06 GWFOPAUVJXMOAL-ZOQUXTDFSA-N A1L9Q SMILES_CANONICAL CACTVS 3.385 "CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=NC2=S)N" A1L9Q SMILES CACTVS 3.385 "CO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=NC2=S)N" A1L9Q SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=S)N)COP(=O)(O)O)O" A1L9Q SMILES "OpenEye OEToolkits" 2.0.7 "COC1C(C(OC1N2C=CC(=NC2=S)N)COP(=O)(O)O)O" # _pdbx_chem_comp_identifier.comp_id A1L9Q _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~{R},4~{R},5~{R})-5-(4-azanyl-2-sulfanylidene-pyrimidin-1-yl)-4-methoxy-3-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 A1L9Q "Create component" 2025-05-20 PDBJ A1L9Q "Initial release" 2025-11-12 RCSB #