data_NEF # _chem_comp.id NEF _chem_comp.name "Nitrocefin - open form" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C21 H18 N4 O9 S2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "(2R)-5-[(E)-2-(2,4-dinitrophenyl)ethenyl]-2-[(1R)-2-oxidanyl-2-oxidanylidene-1-(2-thiophen-2-ylethanoylamino)ethyl]-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-09-26 _chem_comp.pdbx_modified_date 2021-09-06 _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 534.519 _chem_comp.one_letter_code ? _chem_comp.three_letter_code NEF _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 6HR9 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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.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 NEF C2 C1 C 0 1 N N N -3.323 0.475 16.773 0.621 0.899 0.161 C2 NEF 1 NEF C3 C2 C 0 1 N N R -5.723 2.833 17.157 -3.220 -0.803 0.131 C3 NEF 2 NEF C4 C3 C 0 1 N N N -2.589 1.309 16.059 1.165 -0.475 -0.107 C4 NEF 3 NEF C6 C4 C 0 1 N N N -1.727 0.677 15.058 2.568 -0.615 -0.168 C6 NEF 4 NEF C7 C5 C 0 1 N N N -7.455 0.163 15.115 -6.215 1.575 -0.054 C7 NEF 5 NEF C8 C6 C 0 1 Y N N -6.526 -0.990 15.003 -7.665 1.203 -0.229 C8 NEF 6 NEF C11 C7 C 0 1 Y N N -4.793 -2.543 14.039 -9.992 0.620 -0.961 C11 NEF 7 NEF C13 C8 C 0 1 N N R -4.452 2.488 17.901 -1.795 -0.467 -0.312 C13 NEF 8 NEF C14 C9 C 0 1 Y N N 0.224 -0.770 14.761 4.823 0.331 -0.155 C14 NEF 9 NEF C15 C10 C 0 1 N N N -2.627 2.782 16.234 0.428 -1.578 -0.291 C15 NEF 10 NEF C16 C11 C 0 1 N N N -1.348 3.579 16.067 1.160 -2.817 -0.569 C16 NEF 11 NEF C17 C12 C 0 1 Y N N 0.130 -0.708 13.381 5.394 -0.924 -0.387 C17 NEF 12 NEF S19 S1 S 0 1 N N N -4.044 0.818 18.188 -1.069 0.763 0.819 S19 NEF 13 NEF C1 C13 C 0 1 N N N -5.590 4.271 16.736 -3.192 -1.368 1.528 C1 NEF 14 NEF O2 O1 O 0 1 N N N -5.533 4.585 15.590 -3.793 -0.812 2.417 O2 NEF 15 NEF N4 N1 N 0 1 N N N -6.084 1.931 16.109 -4.038 0.413 0.112 N4 NEF 16 NEF C5 C14 C 0 1 N N N -6.956 0.951 16.309 -5.374 0.324 -0.035 C5 NEF 17 NEF O6 O2 O 0 1 N N N -7.341 0.662 17.408 -5.901 -0.762 -0.152 O6 NEF 18 NEF C9 C15 C 0 1 Y N N -6.180 -2.007 15.862 -8.520 0.952 0.763 C9 NEF 19 NEF C10 C16 C 0 1 Y N N -5.231 -2.844 15.303 -9.804 0.631 0.359 C10 NEF 20 NEF S12 S2 S 0 1 Y N N -5.655 -1.144 13.542 -8.490 1.041 -1.774 S12 NEF 21 NEF N14 N2 N 0 1 N N N -3.312 3.245 17.424 -0.954 -1.670 -0.247 N14 NEF 22 NEF O17 O3 O 0 1 N N N -0.559 3.340 15.178 1.426 -3.123 -1.716 O17 NEF 23 NEF O18 O4 O 0 1 N N N -1.139 4.501 16.844 1.539 -3.619 0.448 O18 NEF 24 NEF C12 C17 C 0 1 N N N -0.756 -0.039 15.562 3.361 0.478 -0.091 C12 NEF 25 NEF C18 C18 C 0 1 Y N N 1.017 -1.388 12.593 6.766 -1.054 -0.440 C18 NEF 26 NEF C19 C19 C 0 1 Y N N 1.996 -2.143 13.197 7.577 0.053 -0.264 C19 NEF 27 NEF C20 C20 C 0 1 Y N N 2.108 -2.212 14.571 7.019 1.299 -0.034 C20 NEF 28 NEF C21 C21 C 0 1 Y N N 1.232 -1.510 15.382 5.650 1.446 0.022 C21 NEF 29 NEF N22 N3 N 1 1 N N N 1.383 -1.662 16.778 5.056 2.778 0.274 N22 NEF 30 NEF N23 N4 N 1 1 N N N 2.889 -2.831 12.404 9.049 -0.095 -0.322 N23 NEF 31 NEF O24 O5 O -1 1 N N N 1.384 -0.624 17.695 5.576 3.535 1.075 O24 NEF 32 NEF O25 O6 O 0 1 N N N 1.540 -2.967 17.255 4.047 3.118 -0.318 O25 NEF 33 NEF O26 O7 O -1 1 N N N 2.747 -2.715 11.042 9.766 0.877 -0.168 O26 NEF 34 NEF O27 O8 O 0 1 N N N 3.880 -3.618 12.988 9.543 -1.190 -0.524 O27 NEF 35 NEF H1 H1 H 0 1 N N N -4.136 0.158 16.103 1.255 1.406 0.888 H1 NEF 36 NEF H2 H2 H 0 1 N N N -2.666 -0.382 16.983 0.605 1.471 -0.767 H2 NEF 37 NEF H3 H3 H 0 1 N N N -6.531 2.804 17.902 -3.648 -1.539 -0.550 H3 NEF 38 NEF H5 H5 H 0 1 N N N -1.880 0.792 13.995 3.008 -1.595 -0.277 H5 NEF 39 NEF H7 H7 H 0 1 N N N -7.420 0.778 14.204 -5.900 2.211 -0.881 H7 NEF 40 NEF H8 H8 H 0 1 N N N -8.485 -0.185 15.284 -6.089 2.112 0.886 H8 NEF 41 NEF H9 H9 H 0 1 N N N -4.051 -3.081 13.468 -10.925 0.392 -1.456 H9 NEF 42 NEF H10 H10 H 0 1 N N N -4.629 2.862 18.920 -1.806 -0.075 -1.329 H10 NEF 43 NEF H12 H12 H 0 1 N N N -0.650 -0.118 12.923 4.763 -1.790 -0.524 H12 NEF 44 NEF H14 H14 H 0 1 N N N -5.670 2.041 15.205 -3.616 1.282 0.206 H14 NEF 45 NEF H15 H15 H 0 1 N N N -6.597 -2.136 16.850 -8.232 0.997 1.803 H15 NEF 46 NEF H16 H16 H 0 1 N N N -4.850 -3.700 15.840 -10.593 0.402 1.060 H16 NEF 47 NEF H19 H19 H 0 1 N N N -0.322 4.928 16.617 2.016 -4.412 0.167 H19 NEF 48 NEF H20 H20 H 0 1 N N N -0.673 -0.094 16.637 2.921 1.458 0.018 H20 NEF 49 NEF H22 H22 H 0 1 N N N 0.950 -1.333 11.516 7.209 -2.023 -0.619 H22 NEF 50 NEF H23 H23 H 0 1 N N N 2.884 -2.817 15.016 7.659 2.159 0.102 H23 NEF 51 NEF OXY OXY O 0 1 N Y N ? ? ? -2.499 -2.489 1.785 OXY NEF 52 NEF HXY HXY H 0 1 N Y N ? ? ? -2.511 -2.812 2.696 HXY NEF 53 NEF H4 H4 H 0 1 N N N -2.639 3.264 18.164 -1.372 -2.542 -0.172 H4 NEF 54 # # 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 NEF O26 N23 SING N N 1 NEF N23 O27 DOUB N N 2 NEF N23 C19 SING N N 3 NEF C18 C19 DOUB Y N 4 NEF C18 C17 SING Y N 5 NEF C19 C20 SING Y N 6 NEF C17 C14 DOUB Y N 7 NEF S12 C11 SING Y N 8 NEF S12 C8 SING Y N 9 NEF C11 C10 DOUB Y N 10 NEF C20 C21 DOUB Y N 11 NEF C14 C21 SING Y N 12 NEF C14 C12 SING N N 13 NEF C8 C7 SING N N 14 NEF C8 C9 DOUB Y N 15 NEF C6 C12 DOUB N E 16 NEF C6 C4 SING N N 17 NEF C7 C5 SING N N 18 NEF O17 C16 DOUB N N 19 NEF C10 C9 SING Y N 20 NEF C21 N22 SING N N 21 NEF O2 C1 DOUB N N 22 NEF C4 C15 DOUB N N 23 NEF C4 C2 SING N N 24 NEF C16 C15 SING N N 25 NEF C16 O18 SING N N 26 NEF N4 C5 SING N N 27 NEF N4 C3 SING N N 28 NEF C15 N14 SING N N 29 NEF C5 O6 DOUB N N 30 NEF C1 C3 SING N N 31 NEF C2 S19 SING N N 32 NEF N22 O25 DOUB N N 33 NEF N22 O24 SING N N 34 NEF C3 C13 SING N N 35 NEF N14 C13 SING N N 36 NEF C13 S19 SING N N 37 NEF C2 H1 SING N N 38 NEF C2 H2 SING N N 39 NEF C3 H3 SING N N 40 NEF C6 H5 SING N N 41 NEF C7 H7 SING N N 42 NEF C7 H8 SING N N 43 NEF C11 H9 SING N N 44 NEF C13 H10 SING N N 45 NEF C17 H12 SING N N 46 NEF N4 H14 SING N N 47 NEF C9 H15 SING N N 48 NEF C10 H16 SING N N 49 NEF O18 H19 SING N N 50 NEF C12 H20 SING N N 51 NEF C18 H22 SING N N 52 NEF C20 H23 SING N N 53 NEF C1 OXY SING N N 54 NEF OXY HXY SING N N 55 NEF N14 H4 SING N N 56 # # 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 NEF InChI InChI 1.03 "InChI=1S/C21H18N4O9S2/c26-16(9-14-2-1-7-35-14)22-18(21(29)30)19-23-17(20(27)28)12(10-36-19)4-3-11-5-6-13(24(31)32)8-15(11)25(33)34/h1-8,18-19,23H,9-10H2,(H,22,26)(H,27,28)(H,29,30)/b4-3+/t18-,19+/m0/s1" NEF InChIKey InChI 1.03 PYBZXZZHQKFSGC-CZHQAMEJSA-N NEF SMILES_CANONICAL CACTVS 3.385 "OC(=O)[C@@H](NC(=O)Cc1sccc1)[C@@H]2NC(=C(CS2)\C=C\c3ccc(cc3[N+]([O-])=O)[N+]([O-])=O)C(O)=O" NEF SMILES CACTVS 3.385 "OC(=O)[CH](NC(=O)Cc1sccc1)[CH]2NC(=C(CS2)C=Cc3ccc(cc3[N+]([O-])=O)[N+]([O-])=O)C(O)=O" NEF SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(sc1)CC(=O)N[C@@H]([C@@H]2NC(=C(CS2)/C=C/c3ccc(cc3[N+](=O)[O-])[N+](=O)[O-])C(=O)O)C(=O)O" NEF SMILES "OpenEye OEToolkits" 2.0.7 "c1cc(sc1)CC(=O)NC(C2NC(=C(CS2)C=Cc3ccc(cc3[N+](=O)[O-])[N+](=O)[O-])C(=O)O)C(=O)O" # _pdbx_chem_comp_identifier.comp_id NEF _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})-5-[(~{E})-2-(2,4-dinitrophenyl)ethenyl]-2-[(1~{R})-2-oxidanyl-2-oxidanylidene-1-(2-thiophen-2-ylethanoylamino)ethyl]-3,6-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 NEF "Create component" 2018-09-26 EBI NEF "Other modification" 2018-09-27 EBI NEF "Initial release" 2019-10-23 RCSB NEF "Modify leaving atom flag" 2021-08-24 PDBE NEF "Modify aromatic_flag" 2021-09-06 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id NEF _pdbx_chem_comp_synonyms.name "(2R)-5-[(E)-2-(2,4-dinitrophenyl)ethenyl]-2-[(1R)-2-oxidanyl-2-oxidanylidene-1-(2-thiophen-2-ylethanoylamino)ethyl]-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##