data_A1EKM # _chem_comp.id A1EKM _chem_comp.name "[[(2~{R},3~{R},4~{S},5~{R})-4-fluoranyl-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H16 F N2 O14 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-01-22 _chem_comp.pdbx_modified_date 2026-01-16 _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 500.159 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1EKM _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 9LEB _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 A1EKM C10 C1 C 0 1 N N N N N N 120.252 114.401 117.778 -6.608 3.687 1.241 C10 A1EKM 1 A1EKM C01 C2 C 0 1 N N R N N N 117.582 111.049 121.778 -1.971 -1.763 0.831 C01 A1EKM 2 A1EKM C02 C3 C 0 1 N N R N N N 116.435 111.903 121.412 -3.249 -2.582 0.519 C02 A1EKM 3 A1EKM C03 C4 C 0 1 N N S N N N 116.711 113.192 122.027 -4.357 -1.709 1.156 C03 A1EKM 4 A1EKM C04 C5 C 0 1 N N R N N N 118.180 113.292 122.194 -3.721 -0.310 1.263 C04 A1EKM 5 A1EKM C05 C6 C 0 1 N N N N N N 117.820 110.074 120.688 -0.863 -2.083 -0.175 C05 A1EKM 6 A1EKM C06 C7 C 0 1 N N N N N N 119.727 114.797 119.152 -5.905 2.568 0.515 C06 A1EKM 7 A1EKM C07 C8 C 0 1 N N N N N N 119.229 113.866 119.982 -5.161 1.672 1.197 C07 A1EKM 8 A1EKM C08 C9 C 0 1 N N N N N N 118.735 115.643 121.713 -4.643 0.555 -0.813 C08 A1EKM 9 A1EKM C09 C10 C 0 1 N N N N N N 119.756 116.254 119.573 -6.022 2.440 -0.890 C09 A1EKM 10 A1EKM F01 F1 F 0 1 N N N N N N 116.254 114.211 121.185 -5.486 -1.672 0.331 F01 A1EKM 11 A1EKM N01 N1 N 0 1 N N N N N N 118.704 114.257 121.309 -4.529 0.662 0.523 N01 A1EKM 12 A1EKM N02 N2 N 0 1 N N N N N N 119.259 116.628 120.840 -5.384 1.431 -1.517 N02 A1EKM 13 A1EKM O01 O1 O 0 1 N N N N N N 118.740 111.957 121.894 -2.406 -0.394 0.690 O01 A1EKM 14 A1EKM O02 O2 O 0 1 N N N N N N 115.220 111.356 121.964 -3.194 -3.869 1.138 O02 A1EKM 15 A1EKM O03 O3 O 0 1 N N N N N N 118.316 115.951 122.772 -4.074 -0.350 -1.392 O03 A1EKM 16 A1EKM O04 O4 O 0 1 N N N N N N 120.193 117.073 118.843 -6.692 3.233 -1.526 O04 A1EKM 17 A1EKM O05 O5 O 0 1 N N N N N N 118.461 110.723 119.631 0.305 -1.324 0.146 O05 A1EKM 18 A1EKM O06 O6 O 0 1 N N N N N N 116.818 109.649 117.790 2.808 -0.529 0.013 O06 A1EKM 19 A1EKM O07 O7 O 0 1 N N N N N N 114.750 110.557 116.304 4.935 0.908 0.581 O07 A1EKM 20 A1EKM O08 O8 O 0 1 N N N N N N 114.042 109.398 114.112 7.447 0.882 0.337 O08 A1EKM 21 A1EKM O09 O9 O 0 1 N N N N N N 116.366 110.138 114.348 6.191 2.729 -0.839 O09 A1EKM 22 A1EKM O10 O10 O 0 1 N N N N N N 119.237 108.826 118.057 1.410 -0.848 -2.191 O10 A1EKM 23 A1EKM O11 O11 O 0 1 N N N N N N 116.241 112.146 117.660 4.773 -0.409 -1.566 O11 A1EKM 24 A1EKM O12 O12 O 0 1 N N N N N N 118.872 111.070 117.130 2.113 -2.821 -0.783 O12 A1EKM 25 A1EKM O13 O13 O 0 1 N N N N N N 114.734 110.659 118.883 5.086 -1.717 0.569 O13 A1EKM 26 A1EKM O14 O14 O 0 1 N N N N N N 115.542 108.217 115.652 6.445 2.697 1.778 O14 A1EKM 27 A1EKM P01 P1 P 0 1 N N N N N N 118.376 110.058 118.129 1.669 -1.412 -0.705 P01 A1EKM 28 A1EKM P02 P2 P 0 1 N N N N N N 115.626 110.773 117.678 4.408 -0.436 -0.132 P02 A1EKM 29 A1EKM P03 P3 P 0 1 N N N N N N 115.185 109.557 115.076 6.280 1.784 0.462 P03 A1EKM 30 A1EKM H1 H1 H 0 1 N N N N N N 120.153 113.313 117.647 -7.157 4.297 0.523 H1 A1EKM 31 A1EKM H2 H2 H 0 1 N N N N N N 119.671 114.919 117.000 -7.303 3.268 1.968 H2 A1EKM 32 A1EKM H3 H3 H 0 1 N N N N N N 121.311 114.685 117.694 -5.872 4.305 1.755 H3 A1EKM 33 A1EKM H4 H4 H 0 1 N N N N N N 117.395 110.531 122.730 -1.631 -1.955 1.849 H4 A1EKM 34 A1EKM H5 H5 H 0 1 N N N N N N 116.362 112.000 120.319 -3.398 -2.676 -0.557 H5 A1EKM 35 A1EKM H6 H6 H 0 1 N N N N N N 116.223 113.251 123.011 -4.618 -2.086 2.145 H6 A1EKM 36 A1EKM H7 H7 H 0 1 N N N N N N 118.412 113.560 123.235 -3.651 -0.014 2.310 H7 A1EKM 37 A1EKM H8 H8 H 0 1 N N N N N N 116.859 109.666 120.342 -0.629 -3.146 -0.132 H8 A1EKM 38 A1EKM H9 H9 H 0 1 N N N N N N 118.455 109.255 121.058 -1.199 -1.825 -1.179 H9 A1EKM 39 A1EKM H10 H10 H 0 1 N N N N N N 119.212 112.829 119.680 -5.064 1.751 2.270 H10 A1EKM 40 A1EKM H11 H11 H 0 1 N N N N N N 119.277 117.587 121.121 -5.458 1.336 -2.480 H11 A1EKM 41 A1EKM H12 H12 H 0 1 N N N N N N 114.486 111.910 121.725 -3.971 -4.419 0.972 H12 A1EKM 42 A1EKM H13 H13 H 0 1 N N N N N N 116.138 110.280 113.437 5.448 3.347 -0.826 H13 A1EKM 43 A1EKM H14 H14 H 0 1 N N N N N N 119.910 108.948 117.398 1.116 0.073 -2.217 H14 A1EKM 44 A1EKM H15 H15 H 0 1 N N N N N N 114.752 111.475 119.369 4.889 -1.799 1.513 H15 A1EKM 45 A1EKM H16 H16 H 0 1 N N N N N N 114.971 107.552 115.286 7.236 3.253 1.774 H16 A1EKM 46 # 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 A1EKM O08 P03 DOUB N N 1 A1EKM O09 P03 SING N N 2 A1EKM P03 O14 SING N N 3 A1EKM P03 O07 SING N N 4 A1EKM O07 P02 SING N N 5 A1EKM O12 P01 DOUB N N 6 A1EKM O11 P02 DOUB N N 7 A1EKM P02 O06 SING N N 8 A1EKM P02 O13 SING N N 9 A1EKM C10 C06 SING N N 10 A1EKM O06 P01 SING N N 11 A1EKM O10 P01 SING N N 12 A1EKM P01 O05 SING N N 13 A1EKM O04 C09 DOUB N N 14 A1EKM C06 C09 SING N N 15 A1EKM C06 C07 DOUB N N 16 A1EKM C09 N02 SING N N 17 A1EKM O05 C05 SING N N 18 A1EKM C07 N01 SING N N 19 A1EKM C05 C01 SING N N 20 A1EKM N02 C08 SING N N 21 A1EKM F01 C03 SING N N 22 A1EKM N01 C08 SING N N 23 A1EKM N01 C04 SING N N 24 A1EKM C02 C01 SING N N 25 A1EKM C02 O02 SING N N 26 A1EKM C02 C03 SING N N 27 A1EKM C08 O03 DOUB N N 28 A1EKM C01 O01 SING N N 29 A1EKM O01 C04 SING N N 30 A1EKM C03 C04 SING N N 31 A1EKM C10 H1 SING N N 32 A1EKM C10 H2 SING N N 33 A1EKM C10 H3 SING N N 34 A1EKM C01 H4 SING N N 35 A1EKM C02 H5 SING N N 36 A1EKM C03 H6 SING N N 37 A1EKM C04 H7 SING N N 38 A1EKM C05 H8 SING N N 39 A1EKM C05 H9 SING N N 40 A1EKM C07 H10 SING N N 41 A1EKM N02 H11 SING N N 42 A1EKM O02 H12 SING N N 43 A1EKM O09 H13 SING N N 44 A1EKM O10 H14 SING N N 45 A1EKM O13 H15 SING N N 46 A1EKM O14 H16 SING N N 47 # 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 A1EKM InChI InChI 1.06 "InChI=1S/C10H16FN2O14P3/c1-4-2-13(10(16)12-8(4)15)9-6(11)7(14)5(25-9)3-24-29(20,21)27-30(22,23)26-28(17,18)19/h2,5-7,9,14H,3H2,1H3,(H,20,21)(H,22,23)(H,12,15,16)(H2,17,18,19)/t5-,6+,7-,9-/m1/s1" A1EKM InChIKey InChI 1.06 RUKRVHYQIIURNV-JVZYCSMKSA-N A1EKM SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@@H]2F)C(=O)NC1=O" A1EKM SMILES CACTVS 3.385 "CC1=CN([CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2F)C(=O)NC1=O" A1EKM SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)[C@H]2[C@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)F" A1EKM SMILES "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)F" # _pdbx_chem_comp_identifier.comp_id A1EKM _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~{S},5~{R})-4-fluoranyl-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] 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 A1EKM "Create component" 2025-01-22 PDBC A1EKM "Initial release" 2026-01-21 RCSB #