data_A1LX0 # _chem_comp.id A1LX0 _chem_comp.name "2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-2-[(~{R})-cyclobutyl(oxidanyl)methyl]-4-methyl-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H27 N4 O8 P2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2024-02-07 _chem_comp.pdbx_modified_date 2024-12-27 _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 509.431 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1LX0 _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 8XOD _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 A1LX0 C5 C1 C 0 1 Y N N N N N 20.193 -18.872 -2.309 -0.474 -0.305 -0.261 C5 A1LX0 1 A1LX0 CM4 C2 C 0 1 N N N N N N 22.396 -17.768 -2.713 -0.962 1.911 0.783 CM4 A1LX0 2 A1LX0 C8 C3 C 0 1 N N R N N N 18.563 -18.609 -6.068 -3.773 -2.178 0.858 C8 A1LX0 3 A1LX0 C7 C4 C 0 1 N N N N N N 19.412 -18.980 0.226 1.964 -0.195 0.179 C7 A1LX0 4 A1LX0 "C2'" C5 C 0 1 Y N N N N N 21.690 -13.346 -4.769 -5.076 3.658 -0.691 "C2'" A1LX0 5 A1LX0 "C4'" C6 C 0 1 Y N N N N N 20.413 -15.129 -5.226 -5.127 1.465 0.002 "C4'" A1LX0 6 A1LX0 "C5'" C7 C 0 1 Y N N N N N 21.494 -15.943 -5.240 -4.010 1.708 0.806 "C5'" A1LX0 7 A1LX0 "C6'" C8 C 0 1 Y N N N N N 22.739 -15.360 -5.020 -3.476 2.981 0.817 "C6'" A1LX0 8 A1LX0 CM2 C9 C 0 1 N N N N N N 21.756 -11.834 -4.509 -5.670 4.759 -1.531 CM2 A1LX0 9 A1LX0 "C7'" C10 C 0 1 N N N N N N 21.375 -17.449 -5.505 -3.404 0.608 1.639 "C7'" A1LX0 10 A1LX0 C2 C11 C 0 1 Y N N N N N 19.373 -18.595 -4.716 -2.571 -1.341 0.503 C2 A1LX0 11 A1LX0 C4 C12 C 0 1 Y N N N N N 21.035 -18.249 -3.221 -1.289 0.477 0.453 C4 A1LX0 12 A1LX0 C6 C13 C 0 1 N N N N N N 20.533 -19.144 -0.814 0.859 0.097 -0.838 C6 A1LX0 13 A1LX0 C9 C14 C 0 1 N N N N N N 18.837 -19.823 -6.841 -4.696 -2.285 -0.357 C9 A1LX0 14 A1LX0 C10 C15 C 0 1 N N N N N N 18.396 -21.029 -6.088 -6.015 -3.020 -0.066 C10 A1LX0 15 A1LX0 C12 C16 C 0 1 N N N N N N 19.793 -21.587 -6.132 -5.858 -3.684 -1.444 C12 A1LX0 16 A1LX0 C11 C17 C 0 1 N N N N N N 20.257 -20.339 -6.816 -4.345 -3.451 -1.297 C11 A1LX0 17 A1LX0 "N1'" N1 N 0 1 Y N N N N N 22.791 -14.091 -4.785 -4.026 3.920 0.060 "N1'" A1LX0 18 A1LX0 "N3'" N2 N 0 1 Y N N N N N 20.538 -13.847 -4.989 -5.625 2.460 -0.725 "N3'" A1LX0 19 A1LX0 "N4'" N3 N 0 1 N N N N N N 19.270 -15.568 -5.411 -5.699 0.204 -0.045 "N4'" A1LX0 20 A1LX0 N3 N4 N 1 1 Y N N N N N 20.581 -18.113 -4.468 -2.402 -0.109 0.847 N3 A1LX0 21 A1LX0 O8 O1 O 0 1 N N N N N N 17.177 -18.700 -5.882 -3.346 -3.484 1.248 O8 A1LX0 22 A1LX0 "O7'" O2 O 0 1 N N N N N N 19.975 -18.912 1.490 3.228 0.186 -0.368 "O7'" A1LX0 23 A1LX0 O1A O3 O 0 1 N N N N N N 18.804 -17.022 2.583 4.771 -1.388 0.863 O1A A1LX0 24 A1LX0 O2A O4 O 0 1 N N N N N N 19.442 -18.873 3.887 4.608 0.979 1.725 O2A A1LX0 25 A1LX0 O2B O5 O 0 1 N N N N N N 16.262 -21.194 2.759 8.048 0.474 -1.958 O2B A1LX0 26 A1LX0 O1B O6 O 0 1 N N N N N N 18.216 -21.102 3.695 7.640 -1.320 -0.230 O1B A1LX0 27 A1LX0 O3B O7 O 0 1 N N N N N N 18.081 -21.763 1.319 8.135 1.006 0.615 O3B A1LX0 28 A1LX0 O3A O8 O 0 1 N N N N N N 17.678 -19.211 2.257 5.841 0.425 -0.530 O3A A1LX0 29 A1LX0 PA P1 P 0 1 N N N N N N 18.995 -18.419 2.622 4.615 0.020 0.432 PA A1LX0 30 A1LX0 PB P2 P 0 1 N N N N N N 17.611 -20.803 2.503 7.421 0.115 -0.519 PB A1LX0 31 A1LX0 S1 S1 S 0 1 Y N N N N N 18.882 -19.210 -3.233 -1.230 -1.890 -0.404 S1 A1LX0 32 A1LX0 H152 H1 H 0 0 N N N N N N 23.139 -18.570 -2.838 -1.348 2.561 -0.002 H152 A1LX0 33 A1LX0 H151 H2 H 0 0 N N N N N N 22.710 -16.884 -3.287 -1.420 2.179 1.735 H151 A1LX0 34 A1LX0 H153 H3 H 0 0 N N N N N N 22.317 -17.504 -1.648 0.119 2.030 0.854 H153 A1LX0 35 A1LX0 H171 H4 H 0 0 N N N N N N 18.830 -17.716 -6.652 -4.311 -1.710 1.683 H171 A1LX0 36 A1LX0 H202 H5 H 0 0 N N N N N N 18.852 -18.056 0.022 1.777 0.372 1.091 H202 A1LX0 37 A1LX0 H201 H6 H 0 0 N N N N N N 18.730 -19.841 0.172 1.974 -1.260 0.410 H201 A1LX0 38 A1LX0 H061 H7 H 0 0 N N N N N N 23.640 -15.955 -5.045 -2.614 3.207 1.427 H061 A1LX0 39 A1LX0 H073 H8 H 0 0 N N N N N N 22.803 -11.533 -4.355 -6.431 5.286 -0.954 H073 A1LX0 40 A1LX0 H072 H9 H 0 0 N N N N N N 21.343 -11.295 -5.374 -4.886 5.458 -1.821 H072 A1LX0 41 A1LX0 H071 H10 H 0 0 N N N N N N 21.169 -11.590 -3.611 -6.124 4.331 -2.425 H071 A1LX0 42 A1LX0 H092 H11 H 0 0 N N N N N N 20.891 -17.604 -6.480 -2.930 1.040 2.520 H092 A1LX0 43 A1LX0 H091 H12 H 0 0 N N N N N N 22.383 -17.890 -5.522 -4.185 -0.085 1.950 H091 A1LX0 44 A1LX0 H161 H13 H 0 0 N N N N N N 20.894 -20.181 -0.745 1.046 -0.470 -1.750 H161 A1LX0 45 A1LX0 H162 H14 H 0 0 N N N N N N 21.343 -18.455 -0.533 0.850 1.162 -1.068 H162 A1LX0 46 A1LX0 H191 H15 H 0 0 N N N N N N 18.425 -19.786 -7.860 -4.831 -1.334 -0.872 H191 A1LX0 47 A1LX0 H302 H16 H 0 0 N N N N N N 18.033 -20.813 -5.072 -5.950 -3.721 0.766 H302 A1LX0 48 A1LX0 H301 H17 H 0 0 N N N N N N 17.653 -21.641 -6.621 -6.878 -2.358 0.003 H301 A1LX0 49 A1LX0 H312 H18 H 0 0 N N N N N N 20.244 -21.753 -5.142 -6.138 -4.738 -1.456 H312 A1LX0 50 A1LX0 H311 H19 H 0 0 N N N N N N 19.895 -22.499 -6.739 -6.310 -3.116 -2.257 H311 A1LX0 51 A1LX0 H322 H20 H 0 0 N N N N N N 20.946 -19.728 -6.215 -3.860 -3.136 -2.221 H322 A1LX0 52 A1LX0 H321 H21 H 0 0 N N N N N N 20.691 -20.508 -7.813 -3.823 -4.269 -0.801 H321 A1LX0 53 A1LX0 H081 H23 H 0 0 N N N N N N 18.610 -14.820 -5.342 -5.508 -0.441 0.654 H081 A1LX0 54 A1LX0 H181 H24 H 0 0 N N N N N N 16.743 -18.704 -6.727 -2.859 -3.960 0.561 H181 A1LX0 55 A1LX0 H1 H25 H 0 1 N N N N N N 19.529 -18.133 4.477 4.510 1.918 1.518 H1 A1LX0 56 A1LX0 H281 H22 H 0 0 N N N N N N 18.713 -22.390 1.651 8.032 1.959 0.489 H281 A1LX0 57 A1LX0 H2 H26 H 0 1 N N N N N N 16.192 -21.531 3.645 8.999 0.312 -2.024 H2 A1LX0 58 A1LX0 H5 H27 H 0 1 N N N N N N 19.214 -15.979 -6.321 -6.290 -0.034 -0.776 H5 A1LX0 59 # 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 A1LX0 "N1'" "C2'" DOUB Y N 1 A1LX0 "C2'" "N3'" SING Y N 2 A1LX0 "N3'" "C4'" DOUB Y N 3 A1LX0 "C4'" "C5'" SING Y N 4 A1LX0 "C5'" "C6'" DOUB Y N 5 A1LX0 "C6'" "N1'" SING Y N 6 A1LX0 "C2'" CM2 SING N N 7 A1LX0 "C4'" "N4'" SING N N 8 A1LX0 "C5'" "C7'" SING N N 9 A1LX0 "C7'" N3 SING N N 10 A1LX0 N3 C2 DOUB Y N 11 A1LX0 C2 S1 SING Y N 12 A1LX0 S1 C5 SING Y N 13 A1LX0 C5 C4 DOUB Y N 14 A1LX0 C4 N3 SING Y N 15 A1LX0 C4 CM4 SING N N 16 A1LX0 C5 C6 SING N N 17 A1LX0 C2 C8 SING N N 18 A1LX0 C8 O8 SING N N 19 A1LX0 C8 C9 SING N N 20 A1LX0 C6 C7 SING N N 21 A1LX0 C7 "O7'" SING N N 22 A1LX0 "O7'" PA SING N N 23 A1LX0 PA O1A DOUB N N 24 A1LX0 PA O2A SING N N 25 A1LX0 PB O2B SING N N 26 A1LX0 PB O1B DOUB N N 27 A1LX0 PB O3B SING N N 28 A1LX0 PA O3A SING N N 29 A1LX0 PB O3A SING N N 30 A1LX0 C9 C10 SING N N 31 A1LX0 C10 C12 SING N N 32 A1LX0 C12 C11 SING N N 33 A1LX0 C11 C9 SING N N 34 A1LX0 CM4 H152 SING N N 35 A1LX0 CM4 H151 SING N N 36 A1LX0 CM4 H153 SING N N 37 A1LX0 C8 H171 SING N N 38 A1LX0 C7 H202 SING N N 39 A1LX0 C7 H201 SING N N 40 A1LX0 "C6'" H061 SING N N 41 A1LX0 CM2 H073 SING N N 42 A1LX0 CM2 H072 SING N N 43 A1LX0 CM2 H071 SING N N 44 A1LX0 "C7'" H092 SING N N 45 A1LX0 "C7'" H091 SING N N 46 A1LX0 C6 H161 SING N N 47 A1LX0 C6 H162 SING N N 48 A1LX0 C9 H191 SING N N 49 A1LX0 C10 H302 SING N N 50 A1LX0 C10 H301 SING N N 51 A1LX0 C12 H312 SING N N 52 A1LX0 C12 H311 SING N N 53 A1LX0 C11 H322 SING N N 54 A1LX0 C11 H321 SING N N 55 A1LX0 "N4'" H081 SING N N 56 A1LX0 O8 H181 SING N N 57 A1LX0 O2A H1 SING N N 58 A1LX0 O3B H281 SING N N 59 A1LX0 O2B H2 SING N N 60 A1LX0 "N4'" H5 SING N N 61 # 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 A1LX0 InChI InChI 1.06 "InChI=1S/C17H26N4O8P2S/c1-10-14(6-7-28-31(26,27)29-30(23,24)25)32-17(15(22)12-4-3-5-12)21(10)9-13-8-19-11(2)20-16(13)18/h8,12,15,22H,3-7,9H2,1-2H3,(H4-,18,19,20,23,24,25,26,27)/p+1/t15-/m1/s1" A1LX0 InChIKey InChI 1.06 FVAVQECWBZFMTG-OAHLLOKOSA-O A1LX0 SMILES_CANONICAL CACTVS 3.385 "Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C@H](O)C3CCC3)c(N)n1" A1LX0 SMILES CACTVS 3.385 "Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[CH](O)C3CCC3)c(N)n1" A1LX0 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@H](C3CCC3)O)CCOP(=O)(O)OP(=O)(O)O" A1LX0 SMILES "OpenEye OEToolkits" 2.0.7 "Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(C3CCC3)O)CCOP(=O)(O)OP(=O)(O)O" # _pdbx_chem_comp_identifier.comp_id A1LX0 _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-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-2-[(~{R})-cyclobutyl(oxidanyl)methyl]-4-methyl-1,3-thiazol-3-ium-5-yl]ethyl phosphono hydrogen 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 A1LX0 "Create component" 2024-02-07 PDBJ A1LX0 "Initial release" 2025-01-01 RCSB #