data_A1ESM # _chem_comp.id A1ESM _chem_comp.name "2-[4-[2-[[1-[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-2,4-bis(oxidanylidene)pyrimidin-5-yl]amino]-2-oxidanylidene-ethyl]phenyl]ethanoic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C19 H22 N3 O12 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-06-27 _chem_comp.pdbx_modified_date 2026-06-26 _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 515.365 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1ESM _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 9VLE _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 A1ESM O35 O1 O 0 1 N N N N N N 24.897 21.390 -26.563 2.592 -0.614 1.511 O35 A1ESM 1 A1ESM C34 C1 C 0 1 N N N N N N 23.947 21.845 -27.174 1.592 -0.666 0.820 C34 A1ESM 2 A1ESM N14 N1 N 0 1 N N N N N N 23.586 21.409 -28.437 1.483 0.144 -0.248 N14 A1ESM 3 A1ESM C5 C2 C 0 1 N N R N N N 24.361 20.323 -29.053 2.565 1.080 -0.563 C5 A1ESM 4 A1ESM C3 C3 C 0 1 N N R N N N 23.554 19.033 -29.263 2.747 2.108 0.582 C3 A1ESM 5 A1ESM O4 O2 O 0 1 N N N N N N 24.355 17.883 -29.028 1.867 3.222 0.412 O4 A1ESM 6 A1ESM O6 O3 O 0 1 N N N N N N 24.785 20.767 -30.330 3.834 0.393 -0.608 O6 A1ESM 7 A1ESM C7 C4 C 0 1 N N R N N N 24.336 19.857 -31.354 4.855 1.385 -0.410 C7 A1ESM 8 A1ESM C8 C5 C 0 1 N N N N N N 24.039 20.617 -32.621 6.024 0.780 0.370 C8 A1ESM 9 A1ESM O9 O4 O 0 1 N N N N N N 25.274 21.199 -33.071 6.675 -0.205 -0.435 O9 A1ESM 10 A1ESM P10 P1 P 0 1 N N N N N N 25.317 21.995 -34.479 7.951 -1.047 0.071 P10 A1ESM 11 A1ESM O13 O5 O 0 1 N N N N N N 26.724 22.530 -34.586 8.338 -2.150 -1.036 O13 A1ESM 12 A1ESM O12 O6 O 0 1 N N N N N N 24.277 23.087 -34.398 9.196 -0.051 0.295 O12 A1ESM 13 A1ESM O11 O7 O 0 1 N N N N N N 24.996 20.963 -35.532 7.623 -1.722 1.347 O11 A1ESM 14 A1ESM C2 C6 C 0 1 N N S N N N 23.151 19.130 -30.738 4.223 2.538 0.401 C2 A1ESM 15 A1ESM O1 O8 O 0 1 N N N N N N 22.976 17.861 -31.356 4.301 3.764 -0.328 O1 A1ESM 16 A1ESM N33 N2 N 0 1 N N N N N N 23.198 22.881 -26.676 0.615 -1.537 1.134 N33 A1ESM 17 A1ESM C31 C7 C 0 1 N N N N N N 22.160 23.519 -27.306 -0.501 -1.609 0.381 C31 A1ESM 18 A1ESM O32 O9 O 0 1 N N N N N N 21.571 24.436 -26.756 -1.385 -2.397 0.666 O32 A1ESM 19 A1ESM C16 C8 C 0 1 N N N N N N 21.856 23.009 -28.630 -0.636 -0.757 -0.748 C16 A1ESM 20 A1ESM C15 C9 C 0 1 N N N N N N 22.556 21.995 -29.127 0.368 0.101 -1.046 C15 A1ESM 21 A1ESM N17 N3 N 0 1 N N N N N N 20.850 23.611 -29.382 -1.789 -0.813 -1.550 N17 A1ESM 22 A1ESM C18 C10 C 0 1 N N N N N N 19.950 24.621 -29.241 -3.000 -0.581 -1.006 C18 A1ESM 23 A1ESM O19 O10 O 0 1 N N N N N N 19.890 25.349 -28.258 -3.088 -0.235 0.154 O19 A1ESM 24 A1ESM C20 C11 C 0 1 N N N N N N 19.017 24.793 -30.424 -4.246 -0.751 -1.838 C20 A1ESM 25 A1ESM C21 C12 C 0 1 Y N N N N N 19.429 24.043 -31.674 -5.457 -0.433 -1.000 C21 A1ESM 26 A1ESM C30 C13 C 0 1 Y N N N N N 19.807 22.709 -31.624 -5.944 0.860 -0.953 C30 A1ESM 27 A1ESM C29 C14 C 0 1 Y N N N N N 20.167 22.027 -32.770 -7.055 1.153 -0.184 C29 A1ESM 28 A1ESM C24 C15 C 0 1 Y N N N N N 20.159 22.654 -34.005 -7.679 0.152 0.538 C24 A1ESM 29 A1ESM C23 C16 C 0 1 Y N N N N N 19.781 23.986 -34.057 -7.192 -1.141 0.490 C23 A1ESM 30 A1ESM C22 C17 C 0 1 Y N N N N N 19.422 24.670 -32.909 -6.084 -1.434 -0.283 C22 A1ESM 31 A1ESM C25 C18 C 0 1 N N N N N N 20.539 21.904 -35.261 -8.889 0.471 1.377 C25 A1ESM 32 A1ESM C26 C19 C 0 1 N N N N N N 21.301 20.605 -35.028 -10.135 0.302 0.546 C26 A1ESM 33 A1ESM O27 O11 O 0 1 N N N N N N 22.410 20.480 -35.597 -10.049 -0.043 -0.609 O27 A1ESM 34 A1ESM O28 O12 O 0 1 N N N N N N 20.774 19.734 -34.303 -11.341 0.533 1.089 O28 A1ESM 35 A1ESM H1 H1 H 0 1 N N N N N N 25.232 20.092 -28.423 2.369 1.588 -1.507 H1 A1ESM 36 A1ESM H2 H2 H 0 1 N N N N N N 22.658 19.042 -28.625 2.594 1.639 1.554 H2 A1ESM 37 A1ESM H3 H3 H 0 1 N N N N N N 24.592 17.844 -28.109 1.944 3.893 1.105 H3 A1ESM 38 A1ESM H4 H4 H 0 1 N N N N N N 25.126 19.121 -31.563 5.203 1.758 -1.373 H4 A1ESM 39 A1ESM H5 H5 H 0 1 N N N N N N 23.301 21.408 -32.421 6.734 1.566 0.628 H5 A1ESM 40 A1ESM H6 H6 H 0 1 N N N N N N 23.645 19.933 -33.387 5.650 0.315 1.282 H6 A1ESM 41 A1ESM H7 H7 H 0 1 N N N N N N 27.168 22.112 -35.315 9.100 -2.695 -0.797 H7 A1ESM 42 A1ESM H8 H8 H 0 1 N N N N N N 23.595 22.923 -35.038 9.466 0.426 -0.501 H8 A1ESM 43 A1ESM H9 H9 H 0 1 N N N N N N 22.245 19.747 -30.833 4.714 2.637 1.369 H9 A1ESM 44 A1ESM H10 H10 H 0 1 N N N N N N 22.234 17.417 -30.963 3.919 4.522 0.134 H10 A1ESM 45 A1ESM H11 H11 H 0 1 N N N N N N 23.433 23.204 -25.759 0.715 -2.115 1.906 H11 A1ESM 46 A1ESM H12 H12 H 0 1 N N N N N N 22.305 21.619 -30.108 0.285 0.757 -1.900 H12 A1ESM 47 A1ESM H13 H13 H 0 1 N N N N N N 20.766 23.178 -30.280 -1.714 -1.019 -2.495 H13 A1ESM 48 A1ESM H14 H14 H 0 1 N N N N N N 18.969 25.864 -30.668 -4.207 -0.075 -2.692 H14 A1ESM 49 A1ESM H15 H15 H 0 1 N N N N N N 18.019 24.439 -30.126 -4.309 -1.780 -2.191 H15 A1ESM 50 A1ESM H16 H16 H 0 1 N N N N N N 19.820 22.196 -30.674 -5.457 1.642 -1.516 H16 A1ESM 51 A1ESM H17 H17 H 0 1 N N N N N N 20.459 20.989 -32.702 -7.435 2.163 -0.146 H17 A1ESM 52 A1ESM H18 H18 H 0 1 N N N N N N 19.766 24.498 -35.008 -7.679 -1.922 1.054 H18 A1ESM 53 A1ESM H19 H19 H 0 1 N N N N N N 19.132 25.708 -32.977 -5.704 -2.444 -0.320 H19 A1ESM 54 A1ESM H20 H20 H 0 1 N N N N N N 21.169 22.564 -35.875 -8.928 -0.205 2.231 H20 A1ESM 55 A1ESM H21 H21 H 0 1 N N N N N N 19.615 21.665 -35.808 -8.825 1.500 1.730 H21 A1ESM 56 A1ESM H22 H22 H 0 1 N N N N N N 21.343 18.975 -34.255 -12.111 0.411 0.517 H22 A1ESM 57 # 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 A1ESM O27 C26 DOUB N N 1 A1ESM O11 P10 DOUB N N 2 A1ESM C25 C26 SING N N 3 A1ESM C25 C24 SING N N 4 A1ESM C26 O28 SING N N 5 A1ESM O13 P10 SING N N 6 A1ESM P10 O12 SING N N 7 A1ESM P10 O9 SING N N 8 A1ESM C23 C24 DOUB Y N 9 A1ESM C23 C22 SING Y N 10 A1ESM C24 C29 SING Y N 11 A1ESM O9 C8 SING N N 12 A1ESM C22 C21 DOUB Y N 13 A1ESM C29 C30 DOUB Y N 14 A1ESM C8 C7 SING N N 15 A1ESM C21 C30 SING Y N 16 A1ESM C21 C20 SING N N 17 A1ESM O1 C2 SING N N 18 A1ESM C7 C2 SING N N 19 A1ESM C7 O6 SING N N 20 A1ESM C2 C3 SING N N 21 A1ESM C20 C18 SING N N 22 A1ESM O6 C5 SING N N 23 A1ESM N17 C18 SING N N 24 A1ESM N17 C16 SING N N 25 A1ESM C3 C5 SING N N 26 A1ESM C3 O4 SING N N 27 A1ESM C18 O19 DOUB N N 28 A1ESM C15 C16 DOUB N N 29 A1ESM C15 N14 SING N N 30 A1ESM C5 N14 SING N N 31 A1ESM C16 C31 SING N N 32 A1ESM N14 C34 SING N N 33 A1ESM C31 O32 DOUB N N 34 A1ESM C31 N33 SING N N 35 A1ESM C34 N33 SING N N 36 A1ESM C34 O35 DOUB N N 37 A1ESM C5 H1 SING N N 38 A1ESM C3 H2 SING N N 39 A1ESM O4 H3 SING N N 40 A1ESM C7 H4 SING N N 41 A1ESM C8 H5 SING N N 42 A1ESM C8 H6 SING N N 43 A1ESM O13 H7 SING N N 44 A1ESM O12 H8 SING N N 45 A1ESM C2 H9 SING N N 46 A1ESM O1 H10 SING N N 47 A1ESM N33 H11 SING N N 48 A1ESM C15 H12 SING N N 49 A1ESM N17 H13 SING N N 50 A1ESM C20 H14 SING N N 51 A1ESM C20 H15 SING N N 52 A1ESM C30 H16 SING N N 53 A1ESM C29 H17 SING N N 54 A1ESM C23 H18 SING N N 55 A1ESM C22 H19 SING N N 56 A1ESM C25 H20 SING N N 57 A1ESM C25 H21 SING N N 58 A1ESM O28 H22 SING N N 59 # 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 A1ESM InChI InChI 1.06 "InChI=1S/C19H22N3O12P/c23-13(5-9-1-3-10(4-2-9)6-14(24)25)20-11-7-22(19(29)21-17(11)28)18-16(27)15(26)12(34-18)8-33-35(30,31)32/h1-4,7,12,15-16,18,26-27H,5-6,8H2,(H,20,23)(H,24,25)(H,21,28,29)(H2,30,31,32)/t12-,15-,16-,18-/m1/s1" A1ESM InChIKey InChI 1.06 ITRLCXLCPJFIHZ-HALQFCHDSA-N A1ESM SMILES_CANONICAL CACTVS 3.385 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(NC(=O)Cc3ccc(CC(O)=O)cc3)C(=O)NC2=O" A1ESM SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=C(NC(=O)Cc3ccc(CC(O)=O)cc3)C(=O)NC2=O" A1ESM SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(ccc1CC(=O)NC2=CN(C(=O)NC2=O)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)CC(=O)O" A1ESM SMILES "OpenEye OEToolkits" 2.0.7 "c1cc(ccc1CC(=O)NC2=CN(C(=O)NC2=O)C3C(C(C(O3)COP(=O)(O)O)O)O)CC(=O)O" # _pdbx_chem_comp_identifier.comp_id A1ESM _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-[4-[2-[[1-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-2,4-bis(oxidanylidene)pyrimidin-5-yl]amino]-2-oxidanylidene-ethyl]phenyl]ethanoic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1ESM "Create component" 2025-06-27 PDBC A1ESM "Initial release" 2026-07-01 RCSB #