data_A1KN5 # _chem_comp.id A1KN5 _chem_comp.name "Prechlororaphen thiolopyrophosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H32 O6 P2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "[(~{E})-5-[(1~{S},4~{R},5~{R})-3-ethyl-1,2,4,5-tetramethyl-cyclopent-2-en-1-yl]-3-methyl-pent-2-enyl]sulfanyl-phosphonooxy-phosphinic acid" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2026-08-24 _chem_comp.pdbx_modified_date 2026-09-25 _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 426.445 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1KN5 _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 33CV _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE _chem_comp.pdbx_pcm ? _chem_comp.pdbx_comp_type ? # 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 A1KN5 C4 C1 C 0 1 N N N N N N 0.738 -5.238 -1.757 1.293 -4.146 0.856 C4 A1KN5 1 A1KN5 C5 C2 C 0 1 N N N N N N 1.591 -3.198 -3.202 2.333 -2.282 -0.647 C5 A1KN5 2 A1KN5 C6 C3 C 0 1 N N N N N N 2.760 -3.741 -4.041 2.832 -1.230 0.346 C6 A1KN5 3 A1KN5 C7 C4 C 0 1 N N S N N N 4.115 -3.729 -3.299 3.977 -0.436 -0.285 C7 A1KN5 4 A1KN5 C8 C5 C 0 1 N N R N N N 4.311 -2.505 -2.416 3.447 0.453 -1.434 C8 A1KN5 5 A1KN5 C10 C6 C 0 1 N N N N N N 5.102 -1.431 -3.161 4.497 0.614 -2.534 C10 A1KN5 6 A1KN5 C13 C7 C 0 1 N N N N N N 4.216 -4.792 -2.421 4.559 0.535 0.715 C13 A1KN5 7 A1KN5 C15 C8 C 0 1 N N N N N N 3.751 -6.206 -2.726 5.502 0.151 1.827 C15 A1KN5 8 A1KN5 C26 C9 C 0 1 N N N N N N 6.089 -6.453 -0.628 5.711 3.661 0.642 C26 A1KN5 9 A1KN5 O2B O1 O 0 1 N N N N N N 2.054 -8.588 -1.276 -5.755 1.202 -0.978 O2B A1KN5 10 A1KN5 PB P1 P 0 1 N N N N N N 1.045 -8.401 -0.091 -4.817 1.693 0.056 PB A1KN5 11 A1KN5 O1B O2 O 0 1 N N N N N N 1.578 -9.358 0.985 -3.880 2.842 -0.572 O1B A1KN5 12 A1KN5 O3B O3 O 0 1 N N N N N N -0.267 -8.865 -0.512 -5.650 2.296 1.294 O3B A1KN5 13 A1KN5 O3A O4 O 0 1 N N N N N N 1.177 -6.872 0.351 -3.899 0.474 0.569 O3A A1KN5 14 A1KN5 PA P2 P 0 1 N N N N N N 0.408 -6.152 1.551 -3.096 -0.710 -0.170 PA A1KN5 15 A1KN5 O1A O5 O 0 1 N N N N N N 1.231 -6.530 2.785 -2.001 -0.076 -1.165 O1A A1KN5 16 A1KN5 O2A O6 O 0 1 N N N N N N -0.960 -6.578 1.757 -4.045 -1.541 -0.945 O2A A1KN5 17 A1KN5 S1 S1 S 0 1 N N N N N N 0.519 -4.182 1.271 -2.122 -1.915 1.278 S1 A1KN5 18 A1KN5 C1 C10 C 0 1 N N N N N N 2.213 -4.118 0.639 -1.287 -3.170 0.270 C1 A1KN5 19 A1KN5 C2 C11 C 0 1 N N N N N N 2.235 -3.343 -0.665 -0.080 -2.560 -0.394 C2 A1KN5 20 A1KN5 C3 C12 C 0 1 N N N N N N 1.524 -3.940 -1.874 1.122 -2.975 -0.078 C3 A1KN5 21 A1KN5 C14 C13 C 0 1 N N N N N N 5.268 -3.805 -4.301 5.062 -1.385 -0.800 C14 A1KN5 22 A1KN5 C9 C14 C 0 1 N N R N N N 5.159 -3.092 -1.286 3.205 1.792 -0.697 C9 A1KN5 23 A1KN5 C11 C15 C 0 1 N N N N N N 4.837 -2.443 0.066 1.752 1.888 -0.231 C11 A1KN5 24 A1KN5 C12 C16 C 0 1 N N N N N N 4.798 -4.437 -1.283 4.138 1.750 0.491 C12 A1KN5 25 A1KN5 C25 C17 C 0 1 N N N N N N 5.066 -5.421 -0.151 4.530 2.953 1.309 C25 A1KN5 26 A1KN5 H1 H1 H 0 1 N N N N N N 0.809 -5.619 -0.727 2.350 -4.398 0.932 H1 A1KN5 27 A1KN5 H2 H2 H 0 1 N N N N N N -0.317 -5.051 -2.007 0.909 -3.884 1.842 H2 A1KN5 28 A1KN5 H3 H3 H 0 1 N N N N N N 1.153 -5.982 -2.453 0.742 -5.003 0.468 H3 A1KN5 29 A1KN5 H4 H4 H 0 1 N N N N N N 1.743 -2.125 -3.014 2.066 -1.798 -1.586 H4 A1KN5 30 A1KN5 H5 H5 H 0 1 N N N N N N 0.649 -3.344 -3.750 3.120 -3.015 -0.826 H5 A1KN5 31 A1KN5 H6 H6 H 0 1 N N N N N N 2.854 -3.123 -4.946 2.016 -0.553 0.599 H6 A1KN5 32 A1KN5 H7 H7 H 0 1 N N N N N N 2.530 -4.778 -4.327 3.188 -1.724 1.250 H7 A1KN5 33 A1KN5 H8 H8 H 0 1 N N N N N N 3.353 -2.116 -2.042 2.516 0.056 -1.839 H8 A1KN5 34 A1KN5 H9 H9 H 0 1 N N N N N N 5.235 -0.555 -2.510 4.751 -0.366 -2.940 H9 A1KN5 35 A1KN5 H10 H10 H 0 1 N N N N N N 6.087 -1.831 -3.443 4.098 1.244 -3.329 H10 A1KN5 36 A1KN5 H11 H11 H 0 1 N N N N N N 4.554 -1.135 -4.067 5.392 1.077 -2.118 H11 A1KN5 37 A1KN5 H12 H12 H 0 1 N N N N N N 3.948 -6.853 -1.858 6.524 0.143 1.449 H12 A1KN5 38 A1KN5 H13 H13 H 0 1 N N N N N N 2.672 -6.199 -2.940 5.419 0.874 2.638 H13 A1KN5 39 A1KN5 H14 H14 H 0 1 N N N N N N 4.296 -6.590 -3.601 5.243 -0.841 2.196 H14 A1KN5 40 A1KN5 H15 H15 H 0 1 N N N N N N 6.292 -7.170 0.181 6.556 2.975 0.576 H15 A1KN5 41 A1KN5 H16 H16 H 0 1 N N N N N N 5.689 -6.989 -1.501 5.424 3.980 -0.360 H16 A1KN5 42 A1KN5 H17 H17 H 0 1 N N N N N N 7.022 -5.942 -0.907 5.995 4.531 1.234 H17 A1KN5 43 A1KN5 H18 H18 H 0 1 N N N N N N 2.355 -9.799 0.661 -3.239 3.210 0.051 H18 A1KN5 44 A1KN5 H19 H19 H 0 1 N N N N N N -0.221 -9.177 -1.408 -6.226 3.036 1.058 H19 A1KN5 45 A1KN5 H20 H20 H 0 1 N N N N N N 0.671 -6.961 3.420 -1.345 0.481 -0.724 H20 A1KN5 46 A1KN5 H21 H21 H 0 1 N N N N N N 2.579 -5.141 0.464 -0.973 -3.997 0.906 H21 A1KN5 47 A1KN5 H22 H22 H 0 1 N N N N N N 2.860 -3.618 1.374 -1.973 -3.539 -0.493 H22 A1KN5 48 A1KN5 H23 H23 H 0 1 N N N N N N 2.742 -2.392 -0.735 -0.205 -1.780 -1.130 H23 A1KN5 49 A1KN5 H24 H24 H 0 1 N N N N N N 6.226 -3.796 -3.760 4.639 -2.043 -1.559 H24 A1KN5 50 A1KN5 H25 H25 H 0 1 N N N N N N 5.186 -4.734 -4.885 5.875 -0.804 -1.236 H25 A1KN5 51 A1KN5 H26 H26 H 0 1 N N N N N N 5.222 -2.940 -4.979 5.444 -1.982 0.027 H26 A1KN5 52 A1KN5 H27 H27 H 0 1 N N N N N N 6.226 -2.958 -1.516 3.454 2.632 -1.346 H27 A1KN5 53 A1KN5 H28 H28 H 0 1 N N N N N N 5.467 -2.892 0.848 1.532 1.065 0.449 H28 A1KN5 54 A1KN5 H29 H29 H 0 1 N N N N N N 5.036 -1.363 0.011 1.598 2.836 0.286 H29 A1KN5 55 A1KN5 H30 H30 H 0 1 N N N N N N 3.777 -2.608 0.309 1.088 1.834 -1.094 H30 A1KN5 56 A1KN5 H31 H31 H 0 1 N N N N N N 5.464 -4.882 0.721 4.817 2.633 2.311 H31 A1KN5 57 A1KN5 H32 H32 H 0 1 N N N N N N 4.131 -5.929 0.127 3.685 3.639 1.375 H32 A1KN5 58 # 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 A1KN5 C14 C7 SING N N 1 A1KN5 C6 C7 SING N N 2 A1KN5 C6 C5 SING N N 3 A1KN5 C7 C13 SING N N 4 A1KN5 C7 C8 SING N N 5 A1KN5 C5 C3 SING N N 6 A1KN5 C10 C8 SING N N 7 A1KN5 C15 C13 SING N N 8 A1KN5 C13 C12 DOUB N N 9 A1KN5 C8 C9 SING N N 10 A1KN5 C3 C4 SING N N 11 A1KN5 C3 C2 DOUB N E 12 A1KN5 C9 C12 SING N N 13 A1KN5 C9 C11 SING N N 14 A1KN5 C12 C25 SING N N 15 A1KN5 O2B PB DOUB N N 16 A1KN5 C2 C1 SING N N 17 A1KN5 C26 C25 SING N N 18 A1KN5 O3B PB SING N N 19 A1KN5 PB O3A SING N N 20 A1KN5 PB O1B SING N N 21 A1KN5 O3A PA SING N N 22 A1KN5 C1 S1 SING N N 23 A1KN5 S1 PA SING N N 24 A1KN5 PA O2A DOUB N N 25 A1KN5 PA O1A SING N N 26 A1KN5 C4 H1 SING N N 27 A1KN5 C4 H2 SING N N 28 A1KN5 C4 H3 SING N N 29 A1KN5 C5 H4 SING N N 30 A1KN5 C5 H5 SING N N 31 A1KN5 C6 H6 SING N N 32 A1KN5 C6 H7 SING N N 33 A1KN5 C8 H8 SING N N 34 A1KN5 C10 H9 SING N N 35 A1KN5 C10 H10 SING N N 36 A1KN5 C10 H11 SING N N 37 A1KN5 C15 H12 SING N N 38 A1KN5 C15 H13 SING N N 39 A1KN5 C15 H14 SING N N 40 A1KN5 C26 H15 SING N N 41 A1KN5 C26 H16 SING N N 42 A1KN5 C26 H17 SING N N 43 A1KN5 O1B H18 SING N N 44 A1KN5 O3B H19 SING N N 45 A1KN5 O1A H20 SING N N 46 A1KN5 C1 H21 SING N N 47 A1KN5 C1 H22 SING N N 48 A1KN5 C2 H23 SING N N 49 A1KN5 C14 H24 SING N N 50 A1KN5 C14 H25 SING N N 51 A1KN5 C14 H26 SING N N 52 A1KN5 C9 H27 SING N N 53 A1KN5 C11 H28 SING N N 54 A1KN5 C11 H29 SING N N 55 A1KN5 C11 H30 SING N N 56 A1KN5 C25 H31 SING N N 57 A1KN5 C25 H32 SING N N 58 # 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 A1KN5 InChI InChI 1.06 "InChI=1S/C17H32O6P2S/c1-7-16-13(3)14(4)17(6,15(16)5)10-8-12(2)9-11-26-25(21,22)23-24(18,19)20/h9,13-14H,7-8,10-11H2,1-6H3,(H,21,22)(H2,18,19,20)/b12-9+/t13-,14-,17+/m1/s1" A1KN5 InChIKey InChI 1.06 RXPAJCUBXSGOCG-PQLSEBNVSA-N A1KN5 SMILES_CANONICAL CACTVS 3.385 "CCC1=C(C)[C@@](C)(CCC(/C)=C/CS[P](O)(=O)O[P](O)(O)=O)[C@H](C)[C@H]1C" A1KN5 SMILES CACTVS 3.385 "CCC1=C(C)[C](C)(CCC(C)=CCS[P](O)(=O)O[P](O)(O)=O)[CH](C)[CH]1C" A1KN5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCC1=C([C@@]([C@@H]([C@H]1C)C)(C)CC/C(=C/CSP(=O)(O)OP(=O)(O)O)/C)C" A1KN5 SMILES "OpenEye OEToolkits" 2.0.7 "CCC1=C(C(C(C1C)C)(C)CCC(=CCSP(=O)(O)OP(=O)(O)O)C)C" # _pdbx_chem_comp_identifier.comp_id A1KN5 _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 "[(~{E})-5-[(1~{S},4~{R},5~{R})-3-ethyl-1,2,4,5-tetramethyl-cyclopent-2-en-1-yl]-3-methyl-pent-2-enyl]sulfanyl-phosphonooxy-phosphinic 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 A1KN5 "Create component" 2026-08-24 PDBE A1KN5 "Initial release" 2026-09-30 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id A1KN5 _pdbx_chem_comp_synonyms.name "[(~{E})-5-[(1~{S},4~{R},5~{R})-3-ethyl-1,2,4,5-tetramethyl-cyclopent-2-en-1-yl]-3-methyl-pent-2-enyl]sulfanyl-phosphonooxy-phosphinic acid" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? #