data_A5S # _chem_comp.id A5S _chem_comp.name "~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] 3-oxidanylidenebutanethioate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H27 N2 O9 P S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-07-17 _chem_comp.pdbx_modified_date 2024-09-27 _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 442.422 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A5S _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 8PRV _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE _chem_comp.pdbx_pcm Y # 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_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_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 A5S C1 C1 C 0 1 N N N N N N 126.206 163.477 166.192 -8.270 0.442 -0.177 C1 A5S 1 A5S C2 C2 C 0 1 N N N N N N 127.512 163.562 166.955 -9.727 0.351 -0.552 C2 A5S 2 A5S C3 C3 C 0 1 N N N N N N 127.745 164.995 167.380 -10.486 1.473 0.108 C3 A5S 3 A5S C4 C4 C 0 1 N N N N N N 128.526 165.934 166.488 -11.972 1.607 -0.107 C4 A5S 4 A5S O1 O1 O 0 1 N N N N N N 127.282 165.360 168.447 -9.904 2.265 0.810 O1 A5S 5 A5S O5 O2 O 0 1 N N N N N N 125.551 164.495 165.990 -7.886 1.331 0.554 O5 A5S 6 A5S O40 O3 O 0 1 N N N N N N 124.513 162.748 160.638 -2.042 -2.146 -0.732 O40 A5S 7 A5S C39 C5 C 0 1 N N N N N N 123.508 163.056 161.259 -2.067 -1.161 -0.024 C39 A5S 8 A5S N41 N1 N 0 1 N N N N N N 123.437 163.177 162.578 -3.231 -0.518 0.194 N41 A5S 9 A5S C42 C6 C 0 1 N N N N N N 124.577 162.882 163.427 -4.466 -1.009 -0.422 C42 A5S 10 A5S C43 C7 C 0 1 N N N N N N 124.194 162.090 164.684 -5.633 -0.107 -0.016 C43 A5S 11 A5S S44 S1 S 0 1 N N N N N N 125.652 161.979 165.646 -7.158 -0.713 -0.778 S44 A5S 12 A5S C38 C8 C 0 1 N N N N N N 122.221 163.226 160.513 -0.797 -0.656 0.610 C38 A5S 13 A5S C37 C9 C 0 1 N N N N N N 121.663 161.803 160.366 0.370 -1.559 0.204 C37 A5S 14 A5S N36 N2 N 0 1 N N N N N N 122.220 161.115 159.204 1.605 -1.068 0.820 N36 A5S 15 A5S C34 C10 C 0 1 N N N N N N 121.599 161.070 158.022 2.769 -1.711 0.601 C34 A5S 16 A5S O35 O4 O 0 1 N N N N N N 120.486 161.544 157.815 2.781 -2.747 -0.029 O35 A5S 17 A5S C32 C11 C 0 1 N N R N N N 122.318 160.447 156.858 4.057 -1.142 1.140 C32 A5S 18 A5S O33 O5 O 0 1 N N N N N N 123.081 159.293 157.311 3.764 -0.091 2.062 O33 A5S 19 A5S C29 C12 C 0 1 N N N N N N 123.139 161.514 156.047 4.893 -0.589 -0.016 C29 A5S 20 A5S C31 C13 C 0 1 N N N N N N 122.377 162.831 155.797 5.331 -1.740 -0.924 C31 A5S 21 A5S C30 C14 C 0 1 N N N N N N 124.465 161.819 156.745 4.054 0.405 -0.822 C30 A5S 22 A5S C28 C15 C 0 1 N N N N N N 123.359 160.954 154.639 6.128 0.119 0.541 C28 A5S 23 A5S O27 O6 O 0 1 N N N N N N 123.709 159.553 154.576 6.909 0.636 -0.538 O27 A5S 24 A5S P24 P1 P 0 1 N N N N N N 123.877 158.907 153.107 8.284 1.444 -0.318 P24 A5S 25 A5S O23 O7 O 0 1 N N N N N N 122.668 157.970 152.710 8.821 1.986 -1.736 O23 A5S 26 A5S O25 O8 O 0 1 N N N N N N 123.765 160.004 152.042 8.044 2.589 0.589 O25 A5S 27 A5S O26 O9 O 0 1 N N N N N N 125.178 158.141 153.074 9.384 0.465 0.334 O26 A5S 28 A5S H1 H1 H 0 1 N N N N N N 127.461 162.918 167.845 -9.830 0.430 -1.634 H1 A5S 29 A5S H2 H2 H 0 1 N N N N N N 128.338 163.230 166.309 -10.129 -0.605 -0.218 H2 A5S 30 A5S H3 H3 H 0 1 N N N N N N 128.584 166.926 166.960 -12.502 1.042 0.658 H3 A5S 31 A5S H4 H4 H 0 1 N N N N N N 129.542 165.539 166.340 -12.254 2.658 -0.045 H4 A5S 32 A5S H5 H5 H 0 1 N N N N N N 128.021 166.020 165.515 -12.232 1.219 -1.092 H5 A5S 33 A5S H6 H6 H 0 1 N N N N N N 122.580 163.478 162.996 -3.251 0.269 0.760 H6 A5S 34 A5S H7 H7 H 0 1 N N N N N N 125.303 162.292 162.848 -4.359 -0.999 -1.507 H7 A5S 35 A5S H8 H8 H 0 1 N N N N N N 125.039 163.831 163.737 -4.660 -2.028 -0.086 H8 A5S 36 A5S H9 H9 H 0 1 N N N N N N 123.406 162.617 165.243 -5.739 -0.117 1.069 H9 A5S 37 A5S H10 H10 H 0 1 N N N N N N 123.839 161.085 164.410 -5.438 0.912 -0.352 H10 A5S 38 A5S H11 H11 H 0 1 N N N N N N 122.402 163.675 159.525 -0.602 0.362 0.274 H11 A5S 39 A5S H12 H12 H 0 1 N N N N N N 121.524 163.859 161.082 -0.903 -0.667 1.695 H12 A5S 40 A5S H13 H13 H 0 1 N N N N N N 120.570 161.860 160.255 0.176 -2.578 0.540 H13 A5S 41 A5S H14 H14 H 0 1 N N N N N N 121.911 161.229 161.271 0.477 -1.549 -0.881 H14 A5S 42 A5S H15 H15 H 0 1 N N N N N N 123.104 160.658 159.297 1.585 -0.281 1.386 H15 A5S 43 A5S H16 H16 H 0 1 N N N N N N 121.543 160.076 156.171 4.616 -1.927 1.649 H16 A5S 44 A5S H17 H17 H 0 1 N N N N N N 122.510 158.703 157.789 3.267 0.644 1.676 H17 A5S 45 A5S H18 H18 H 0 1 N N N N N N 122.166 163.321 156.759 5.990 -1.357 -1.703 H18 A5S 46 A5S H19 H19 H 0 1 N N N N N N 122.991 163.497 155.173 5.862 -2.487 -0.334 H19 A5S 47 A5S H20 H20 H 0 1 N N N N N N 121.430 162.614 155.280 4.454 -2.196 -1.383 H20 A5S 48 A5S H21 H21 H 0 1 N N N N N N 124.267 162.218 157.751 3.742 1.225 -0.175 H21 A5S 49 A5S H22 H22 H 0 1 N N N N N N 125.057 160.895 156.827 4.650 0.799 -1.645 H22 A5S 50 A5S H23 H23 H 0 1 N N N N N N 125.025 162.563 156.159 3.174 -0.100 -1.219 H23 A5S 51 A5S H24 H24 H 0 1 N N N N N N 124.171 161.528 154.169 5.816 0.939 1.189 H24 A5S 52 A5S H25 H25 H 0 1 N N N N N N 122.430 161.098 154.068 6.726 -0.589 1.115 H25 A5S 53 A5S H26 H26 H 0 1 N N N N N N 122.223 158.330 151.952 9.649 2.483 -1.679 H26 A5S 54 A5S H27 H27 H 0 1 N N N N N N 125.727 158.478 152.376 9.591 -0.309 -0.207 H27 A5S 55 # 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 A5S O25 P24 DOUB N N 1 A5S O23 P24 SING N N 2 A5S O26 P24 SING N N 3 A5S P24 O27 SING N N 4 A5S O27 C28 SING N N 5 A5S C28 C29 SING N N 6 A5S C31 C29 SING N N 7 A5S C29 C30 SING N N 8 A5S C29 C32 SING N N 9 A5S C32 O33 SING N N 10 A5S C32 C34 SING N N 11 A5S O35 C34 DOUB N N 12 A5S C34 N36 SING N N 13 A5S N36 C37 SING N N 14 A5S C37 C38 SING N N 15 A5S C38 C39 SING N N 16 A5S O40 C39 DOUB N N 17 A5S C39 N41 SING N N 18 A5S N41 C42 SING N N 19 A5S C42 C43 SING N N 20 A5S C43 S44 SING N N 21 A5S S44 C1 SING N N 22 A5S O5 C1 DOUB N N 23 A5S C1 C2 SING N N 24 A5S C4 C3 SING N N 25 A5S C2 C3 SING N N 26 A5S C3 O1 DOUB N N 27 A5S C2 H1 SING N N 28 A5S C2 H2 SING N N 29 A5S C4 H3 SING N N 30 A5S C4 H4 SING N N 31 A5S C4 H5 SING N N 32 A5S N41 H6 SING N N 33 A5S C42 H7 SING N N 34 A5S C42 H8 SING N N 35 A5S C43 H9 SING N N 36 A5S C43 H10 SING N N 37 A5S C38 H11 SING N N 38 A5S C38 H12 SING N N 39 A5S C37 H13 SING N N 40 A5S C37 H14 SING N N 41 A5S N36 H15 SING N N 42 A5S C32 H16 SING N N 43 A5S O33 H17 SING N N 44 A5S C31 H18 SING N N 45 A5S C31 H19 SING N N 46 A5S C31 H20 SING N N 47 A5S C30 H21 SING N N 48 A5S C30 H22 SING N N 49 A5S C30 H23 SING N N 50 A5S C28 H24 SING N N 51 A5S C28 H25 SING N N 52 A5S O23 H26 SING N N 53 A5S O26 H27 SING N N 54 # 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 A5S InChI InChI 1.06 "InChI=1S/C15H27N2O9PS/c1-10(18)8-12(20)28-7-6-16-11(19)4-5-17-14(22)13(21)15(2,3)9-26-27(23,24)25/h13,21H,4-9H2,1-3H3,(H,16,19)(H,17,22)(H2,23,24,25)/t13-/m0/s1" A5S InChIKey InChI 1.06 YNABGOTVLHSZGL-ZDUSSCGKSA-N A5S SMILES_CANONICAL CACTVS 3.385 "CC(=O)CC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(O)=O" A5S SMILES CACTVS 3.385 "CC(=O)CC(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(O)=O" A5S SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(=O)CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)O)O" A5S SMILES "OpenEye OEToolkits" 2.0.7 "CC(=O)CC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)O)O" # _pdbx_chem_comp_identifier.comp_id A5S _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 "~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] 3-oxidanylidenebutanethioate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A5S "Create component" 2023-07-17 PDBE A5S "Initial release" 2023-11-22 RCSB A5S "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id A5S _pdbx_chem_comp_pcm.modified_residue_id SER _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom O23 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom CB _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #