data_DGK # _chem_comp.id DGK _chem_comp.name "Hydrolysed Cefoperazone" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C23 H27 N5 O8 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "2-[(1~{R})-1-[[(2~{R})-2-[[4-ethyl-2,3-bis(oxidanylidene)piperazin-1-yl]carbonylamino]-2-(4-hydroxyphenyl)ethanoyl]amino]-2-oxidanylidene-ethyl]-5-methyl-5,6-dihydro-2~{H}-1,3-thiazine-4-carboxylic acid" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-03-29 _chem_comp.pdbx_modified_date 2026-04-17 _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 533.554 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DGK _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 9UJ7 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ _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_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 DGK CBK C1 C 0 1 N N N N N N 23.669 4.587 -30.609 -2.877 -2.453 0.129 CBK DGK 1 DGK OAJ O1 O 0 1 N N N N N N 23.703 3.686 -31.394 -2.270 -2.632 -0.900 OAJ DGK 2 DGK CBT C2 C 0 1 N N R N N N 22.453 5.477 -30.824 -2.648 -1.197 0.930 CBT DGK 3 DGK CBR C3 C 0 1 N N S N N N 21.327 4.971 -30.072 -3.962 -0.421 1.047 CBR DGK 4 DGK NAX N1 N 0 1 N N N N N N 21.493 3.731 -29.293 -4.502 -0.175 -0.284 NAX DGK 5 DGK SBD S1 S 0 1 N N N N N N 19.780 5.840 -29.729 -5.158 -1.395 2.011 SBD DGK 6 DGK CAV C4 C 0 1 N N N N N N 19.083 4.534 -30.787 -6.715 -0.544 1.600 CAV DGK 7 DGK CBF C5 C 0 1 N N S N N N 19.301 3.098 -30.391 -6.916 -0.641 0.086 CBF DGK 8 DGK CAA C6 C 0 1 N N N N N N 18.282 2.121 -30.647 -7.286 -2.081 -0.277 CAA DGK 9 DGK CBN C7 C 0 1 N N N N N N 20.548 2.817 -29.737 -5.686 -0.253 -0.661 CBN DGK 10 DGK CBG C8 C 0 1 N N N N N N 20.975 1.405 -29.332 -5.909 0.098 -2.084 CBG DGK 11 DGK OAM O2 O 0 1 N N N N N N 20.489 0.452 -30.007 -7.028 0.055 -2.552 OAM DGK 12 DGK OAF O3 O 0 1 N N N N N N 21.721 1.357 -28.291 -4.869 0.465 -2.858 OAF DGK 13 DGK NBB N2 N 0 1 N N N N N N 22.020 5.916 -32.126 -1.648 -0.364 0.258 NBB DGK 14 DGK CBI C9 C 0 1 N N N N N N 21.504 7.099 -32.406 -0.335 -0.584 0.471 CBI DGK 15 DGK OAH O4 O 0 1 N N N N N N 21.544 8.076 -31.625 0.018 -1.471 1.219 OAH DGK 16 DGK CBS C10 C 0 1 N N R N N N 20.922 7.147 -33.845 0.694 0.273 -0.221 CBS DGK 17 DGK CBP C11 C 0 1 Y N N N N N 19.477 6.653 -33.861 0.497 1.713 0.176 CBP DGK 18 DGK CAQ C12 C 0 1 Y N N N N N 19.126 5.489 -34.545 0.987 2.169 1.386 CAQ DGK 19 DGK CAO C13 C 0 1 Y N N N N N 17.820 4.996 -34.529 0.808 3.489 1.751 CAO DGK 20 DGK CBO C14 C 0 1 Y N N N N N 16.871 5.599 -33.719 0.135 4.358 0.904 CBO DGK 21 DGK OAN O5 O 0 1 N N N N N N 15.614 5.083 -33.672 -0.042 5.657 1.261 OAN DGK 22 DGK CAP C15 C 0 1 Y N N N N N 17.186 6.747 -33.019 -0.355 3.898 -0.310 CAP DGK 23 DGK CAR C16 C 0 1 Y N N N N N 18.482 7.273 -33.099 -0.169 2.578 -0.673 CAR DGK 24 DGK NBA N3 N 0 1 N N N N N N 21.053 8.543 -34.106 2.036 -0.163 0.173 NBA DGK 25 DGK CBJ C17 C 0 1 N N N N N N 21.294 8.950 -35.320 3.086 0.070 -0.640 CBJ DGK 26 DGK OAI O6 O 0 1 N N N N N N 21.246 8.226 -36.324 2.907 0.559 -1.738 OAI DGK 27 DGK NBV N4 N 0 1 N N N N N N 21.465 10.374 -35.325 4.333 -0.240 -0.235 NBV DGK 28 DGK CAU C18 C 0 1 N N N N N N 21.269 11.268 -34.114 4.536 -0.936 1.036 CAU DGK 29 DGK CAT C19 C 0 1 N N N N N N 21.022 12.833 -34.489 5.673 -1.947 0.918 CAT DGK 30 DGK NBU N5 N 0 1 N N N N N N 21.533 13.307 -35.800 6.869 -1.312 0.363 NBU DGK 31 DGK CAS C20 C 0 1 N N N N N N 21.245 14.764 -36.316 8.194 -1.691 0.860 CAS DGK 32 DGK CAB C21 C 0 1 N N N N N N 20.463 15.754 -35.321 8.737 -2.854 0.028 CAB DGK 33 DGK CBL C22 C 0 1 N N N N N N 22.250 12.444 -36.547 6.754 -0.380 -0.604 CBL DGK 34 DGK OAK O7 O 0 1 N N N N N N 23.205 12.696 -37.283 7.742 0.068 -1.148 OAK DGK 35 DGK CBM C23 C 0 1 N N N N N N 21.821 10.984 -36.535 5.390 0.086 -1.005 CBM DGK 36 DGK OAL O8 O 0 1 N N N N N N 21.918 10.411 -37.624 5.239 0.756 -2.005 OAL DGK 37 DGK H1 H1 H 0 1 N N N N N N 24.411 4.750 -29.841 -3.586 -3.191 0.473 H1 DGK 38 DGK H4 H4 H 0 1 N N N N N N 22.725 6.408 -30.304 -2.292 -1.461 1.926 H4 DGK 39 DGK H5 H5 H 0 1 N N N N N N 20.900 4.445 -30.939 -3.780 0.530 1.548 H5 DGK 40 DGK H7 H7 H 0 1 N N N N N N 19.515 4.664 -31.790 -7.547 -1.026 2.114 H7 DGK 41 DGK H8 H8 H 0 1 N N N N N N 17.996 4.697 -30.832 -6.654 0.503 1.898 H8 DGK 42 DGK H9 H9 H 0 1 N N N N N N 18.619 1.136 -30.291 -8.208 -2.359 0.234 H9 DGK 43 DGK H10 H10 H 0 1 N N N N N N 17.360 2.406 -30.119 -7.431 -2.158 -1.355 H10 DGK 44 DGK H11 H11 H 0 1 N N N N N N 18.085 2.072 -31.728 -6.483 -2.751 0.031 H11 DGK 45 DGK H12 H12 H 0 1 N N N N N N 21.885 0.450 -28.060 -5.063 0.684 -3.779 H12 DGK 46 DGK H13 H13 H 0 1 N N N N N N 22.119 5.270 -32.883 -1.930 0.345 -0.340 H13 DGK 47 DGK H14 H14 H 0 1 N N N N N N 21.542 6.542 -34.523 0.582 0.175 -1.300 H14 DGK 48 DGK H15 H15 H 0 1 N N N N N N 19.883 4.956 -35.101 1.511 1.493 2.045 H15 DGK 49 DGK H16 H16 H 0 1 N N N N N N 17.551 4.150 -35.144 1.191 3.845 2.697 H16 DGK 50 DGK H17 H17 H 0 1 N N N N N N 15.081 5.599 -33.079 0.671 6.244 0.975 H17 DGK 51 DGK H18 H18 H 0 1 N N N N N N 16.438 7.236 -32.413 -0.879 4.571 -0.971 H18 DGK 52 DGK H19 H19 H 0 1 N N N N N N 18.718 8.178 -32.560 -0.547 2.220 -1.619 H19 DGK 53 DGK H20 H20 H 0 1 N N N N N N 20.960 9.205 -33.362 2.169 -0.619 1.019 H20 DGK 54 DGK H21 H21 H 0 1 N N N N N N 20.397 10.904 -33.551 4.782 -0.207 1.809 H21 DGK 55 DGK H22 H22 H 0 1 N N N N N N 22.167 11.200 -33.483 3.619 -1.457 1.312 H22 DGK 56 DGK H23 H23 H 0 1 N N N N N N 21.503 13.440 -33.708 5.903 -2.346 1.906 H23 DGK 57 DGK H24 H24 H 0 1 N N N N N N 19.936 13.009 -34.474 5.363 -2.762 0.264 H24 DGK 58 DGK H25 H25 H 0 1 N N N N N N 22.214 15.229 -36.552 8.870 -0.839 0.778 H25 DGK 59 DGK H26 H26 H 0 1 N N N N N N 20.646 14.677 -37.235 8.118 -1.995 1.903 H26 DGK 60 DGK H27 H27 H 0 1 N N N N N N 20.330 16.732 -35.806 8.061 -3.706 0.110 H27 DGK 61 DGK H28 H28 H 0 1 N N N N N N 19.478 15.328 -35.079 8.813 -2.550 -1.016 H28 DGK 62 DGK H29 H29 H 0 1 N N N N N N 21.045 15.879 -34.396 9.723 -3.136 0.397 H29 DGK 63 DGK H2 H2 H 0 1 N N N N N N 19.758 2.890 -31.370 -7.733 0.019 -0.207 H2 DGK 64 # 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 DGK OAL CBM DOUB N N 1 DGK OAK CBL DOUB N N 2 DGK CBL CBM SING N N 3 DGK CBL NBU SING N N 4 DGK CBM NBV SING N N 5 DGK OAI CBJ DOUB N N 6 DGK CAS NBU SING N N 7 DGK CAS CAB SING N N 8 DGK NBU CAT SING N N 9 DGK NBV CBJ SING N N 10 DGK NBV CAU SING N N 11 DGK CBJ NBA SING N N 12 DGK CAQ CAO DOUB Y N 13 DGK CAQ CBP SING Y N 14 DGK CAO CBO SING Y N 15 DGK CAT CAU SING N N 16 DGK NBA CBS SING N N 17 DGK CBP CBS SING N N 18 DGK CBP CAR DOUB Y N 19 DGK CBS CBI SING N N 20 DGK CBO OAN SING N N 21 DGK CBO CAP DOUB Y N 22 DGK CAR CAP SING Y N 23 DGK CBI NBB SING N N 24 DGK CBI OAH DOUB N N 25 DGK NBB CBT SING N N 26 DGK OAJ CBK DOUB N N 27 DGK CBT CBK SING N N 28 DGK CBT CBR SING N N 29 DGK CAV CBF SING N N 30 DGK CAV SBD SING N N 31 DGK CAA CBF SING N N 32 DGK CBF CBN SING N N 33 DGK CBR SBD SING N N 34 DGK CBR NAX SING N N 35 DGK OAM CBG DOUB N N 36 DGK CBN CBG SING N N 37 DGK CBN NAX DOUB N N 38 DGK CBG OAF SING N N 39 DGK CBK H1 SING N N 40 DGK CBT H4 SING N N 41 DGK CBR H5 SING N N 42 DGK CAV H7 SING N N 43 DGK CAV H8 SING N N 44 DGK CAA H9 SING N N 45 DGK CAA H10 SING N N 46 DGK CAA H11 SING N N 47 DGK OAF H12 SING N N 48 DGK NBB H13 SING N N 49 DGK CBS H14 SING N N 50 DGK CAQ H15 SING N N 51 DGK CAO H16 SING N N 52 DGK OAN H17 SING N N 53 DGK CAP H18 SING N N 54 DGK CAR H19 SING N N 55 DGK NBA H20 SING N N 56 DGK CAU H21 SING N N 57 DGK CAU H22 SING N N 58 DGK CAT H23 SING N N 59 DGK CAT H24 SING N N 60 DGK CAS H25 SING N N 61 DGK CAS H26 SING N N 62 DGK CAB H27 SING N N 63 DGK CAB H28 SING N N 64 DGK CAB H29 SING N N 65 DGK CBF H2 SING N N 66 # 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 DGK InChI InChI 1.06 "InChI=1S/C23H27N5O8S/c1-3-27-8-9-28(21(33)20(27)32)23(36)26-17(13-4-6-14(30)7-5-13)18(31)24-15(10-29)19-25-16(22(34)35)12(2)11-37-19/h4-7,10,12,15,17,19,30H,3,8-9,11H2,1-2H3,(H,24,31)(H,26,36)(H,34,35)/t12-,15-,17-,19+/m1/s1" DGK InChIKey InChI 1.06 DHYCMUSKOOTWRA-XKHMPKOFSA-N DGK SMILES_CANONICAL CACTVS 3.385 "CCN1CCN(C(=O)N[C@@H](C(=O)N[C@H](C=O)[C@@H]2SC[C@@H](C)C(=N2)C(O)=O)c3ccc(O)cc3)C(=O)C1=O" DGK SMILES CACTVS 3.385 "CCN1CCN(C(=O)N[CH](C(=O)N[CH](C=O)[CH]2SC[CH](C)C(=N2)C(O)=O)c3ccc(O)cc3)C(=O)C1=O" DGK SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCN1CCN(C(=O)C1=O)C(=O)N[C@H](c2ccc(cc2)O)C(=O)N[C@H](C=O)C3N=C(C(CS3)C)C(=O)O" DGK SMILES "OpenEye OEToolkits" 2.0.7 "CCN1CCN(C(=O)C1=O)C(=O)NC(c2ccc(cc2)O)C(=O)NC(C=O)C3N=C(C(CS3)C)C(=O)O" # _pdbx_chem_comp_identifier.comp_id DGK _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-[(1~{R})-1-[[(2~{R})-2-[[4-ethyl-2,3-bis(oxidanylidene)piperazin-1-yl]carbonylamino]-2-(4-hydroxyphenyl)ethanoyl]amino]-2-oxidanylidene-ethyl]-5-methyl-5,6-dihydro-2~{H}-1,3-thiazine-4-carboxylic 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 DGK "Create component" 2012-03-29 RCSB DGK "Modify synonyms" 2012-03-30 RCSB DGK "Modify synonyms" 2021-03-13 RCSB DGK "Modify PCM" 2025-04-28 PDBJ DGK "Modify coordinates" 2026-04-15 RCSB DGK "Other modification" 2026-04-16 PDBJ DGK "Initial release" 2026-04-22 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id DGK _pdbx_chem_comp_synonyms.name "2-[(1~{R})-1-[[(2~{R})-2-[[4-ethyl-2,3-bis(oxidanylidene)piperazin-1-yl]carbonylamino]-2-(4-hydroxyphenyl)ethanoyl]amino]-2-oxidanylidene-ethyl]-5-methyl-5,6-dihydro-2~{H}-1,3-thiazine-4-carboxylic acid" _pdbx_chem_comp_synonyms.provenance AUTHOR _pdbx_chem_comp_synonyms.type ? # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id DGK _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 CBK _pdbx_chem_comp_pcm.modified_residue_id_linking_atom OG _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #