data_XD2 # _chem_comp.id XD2 _chem_comp.name "(2R)-2-[(1R)-1-{[(2R)-2-hydroxy-2-phenylacetyl]amino}-2-oxoethyl]-5-{[(1-methyl-1H-tetrazol-5-yl)sulfanyl]methyl}-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H20 N6 O5 S2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "Cefamandole, bound form" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-06-09 _chem_comp.pdbx_modified_date 2021-03-13 _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 464.519 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XD2 _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 3N8S _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # 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 XD2 CAA CAA C 0 1 N N N -5.499 -4.252 0.908 -6.383 3.190 0.844 CAA XD2 1 XD2 OAB OAB O 0 1 N N N -11.209 -7.040 5.265 -2.998 -3.195 1.012 OAB XD2 2 XD2 OAC OAC O 0 1 N N N -9.009 -13.684 3.664 4.886 -1.725 1.011 OAC XD2 3 XD2 OAD OAD O 0 1 N N N -12.521 -10.681 4.442 2.976 -3.142 -1.310 OAD XD2 4 XD2 OAE OAE O 0 1 N N N -10.433 -6.282 3.617 -2.804 -1.449 2.370 OAE XD2 5 XD2 OAF OAF O 0 1 N N N -9.916 -14.644 1.239 6.988 -0.504 0.066 OAF XD2 6 XD2 CAG CAG C 0 1 Y N N -7.456 -11.105 -1.215 5.086 4.029 0.513 CAG XD2 7 XD2 CAH CAH C 0 1 Y N N -8.798 -10.939 -1.196 4.631 3.524 -0.690 CAH XD2 8 XD2 CAI CAI C 0 1 Y N N -6.926 -12.002 -0.330 5.751 3.205 1.402 CAI XD2 9 XD2 CAJ CAJ C 0 1 Y N N -9.635 -11.620 -0.306 4.838 2.194 -1.004 CAJ XD2 10 XD2 CAK CAK C 0 1 Y N N -7.758 -12.702 0.539 5.958 1.875 1.087 CAK XD2 11 XD2 CAL CAL C 0 1 N N N -11.704 -11.101 5.470 2.214 -2.901 -0.405 CAL XD2 12 XD2 CAM CAM C 0 1 N N N -8.714 -7.292 2.273 -3.422 -0.489 -0.614 CAM XD2 13 XD2 CAN CAN C 0 1 N N N -8.066 -9.731 2.907 -1.095 0.136 -1.500 CAN XD2 14 XD2 NAO NAO N 0 1 Y N N -5.885 -4.466 4.347 -7.592 0.216 -0.758 NAO XD2 15 XD2 NAP NAP N 0 1 Y N N -6.403 -5.555 4.130 -6.331 -0.021 -0.727 NAP XD2 16 XD2 NAQ NAQ N 0 1 Y N N -5.521 -3.882 3.346 -7.846 1.362 -0.225 NAQ XD2 17 XD2 NAR NAR N 0 1 N N N -10.483 -11.977 3.501 3.357 -0.764 -0.277 NAR XD2 18 XD2 NAS NAS N 0 1 N N N -10.004 -9.325 5.060 -0.128 -1.650 0.750 NAS XD2 19 XD2 SAT SAT S 0 1 N N N -6.985 -7.024 1.771 -3.949 1.089 0.099 SAT XD2 20 XD2 SAU SAU S 0 1 N N N -7.754 -10.698 4.407 0.558 -0.616 -1.601 SAU XD2 21 XD2 CAV CAV C 0 1 N N N -10.497 -7.115 4.387 -2.461 -2.004 1.345 CAV XD2 22 XD2 CAW CAW C 0 1 N N N -9.733 -12.959 2.999 4.627 -0.916 0.146 CAW XD2 23 XD2 CAX CAX C 0 1 N N N -8.878 -8.459 3.194 -1.925 -0.616 -0.500 CAX XD2 24 XD2 CAY CAY C 0 1 N N N -9.796 -8.380 4.209 -1.459 -1.375 0.465 CAY XD2 25 XD2 CAZ CAZ C 0 1 Y N N -9.112 -12.512 0.569 5.502 1.369 -0.116 CAZ XD2 26 XD2 CBA CBA C 0 1 Y N N -6.364 -5.664 2.817 -5.688 0.977 -0.161 CBA XD2 27 XD2 CBB CBB C 0 1 N N R -9.992 -13.280 1.512 5.727 -0.081 -0.458 CBB XD2 28 XD2 CBC CBC C 0 1 N N R -10.428 -11.619 4.914 2.288 -1.576 0.309 CBC XD2 29 XD2 CBD CBD C 0 1 N N R -9.374 -10.597 5.142 0.952 -0.843 0.164 CBD XD2 30 XD2 NBE NBE N 0 1 Y N N -5.762 -4.571 2.379 -6.615 1.902 0.185 NBE XD2 31 XD2 H1 H1 H 0 1 N N N -5.035 -3.258 0.825 -6.219 3.959 0.090 H1 XD2 32 XD2 H2 H2 H 0 1 N N N -4.823 -5.009 0.484 -7.253 3.451 1.446 H2 XD2 33 XD2 H3 H3 H 0 1 N N N -6.450 -4.259 0.356 -5.505 3.116 1.486 H3 XD2 34 XD2 H4 H4 H 0 1 N N N -11.685 -6.219 5.218 -3.651 -3.568 1.620 H4 XD2 35 XD2 H6 H6 H 0 1 N N N -9.532 -15.095 1.982 7.062 -0.422 1.026 H6 XD2 36 XD2 H7 H7 H 0 1 N N N -6.830 -10.553 -1.900 4.928 5.069 0.757 H7 XD2 37 XD2 H8 H8 H 0 1 N N N -9.243 -10.250 -1.899 4.111 4.168 -1.384 H8 XD2 38 XD2 H9 H9 H 0 1 N N N -5.859 -12.168 -0.305 6.108 3.599 2.342 H9 XD2 39 XD2 H10 H10 H 0 1 N N N -10.699 -11.435 -0.316 4.482 1.799 -1.944 H10 XD2 40 XD2 H11 H11 H 0 1 N N N -7.318 -13.421 1.214 6.477 1.230 1.782 H11 XD2 41 XD2 H12 H12 H 0 1 N N N -11.954 -11.060 6.520 1.480 -3.635 -0.107 H12 XD2 42 XD2 H14 H14 H 0 1 N N N -9.075 -6.388 2.784 -3.898 -1.308 -0.075 H14 XD2 43 XD2 H15 H15 H 0 1 N N N -9.318 -7.469 1.371 -3.711 -0.528 -1.664 H15 XD2 44 XD2 H16 H16 H 0 1 N N N -8.625 -10.354 2.194 -1.003 1.176 -1.188 H16 XD2 45 XD2 H17 H17 H 0 1 N N N -7.101 -9.443 2.464 -1.575 0.091 -2.478 H17 XD2 46 XD2 H18 H18 H 0 1 N N N -11.098 -11.474 2.894 3.150 -0.117 -0.970 H18 XD2 47 XD2 H20 H20 H 0 1 N N N -11.023 -12.955 1.308 5.724 -0.204 -1.541 H20 XD2 48 XD2 H21 H21 H 0 1 N N N -10.153 -12.518 5.485 2.497 -1.744 1.366 H21 XD2 49 XD2 H22 H22 H 0 1 N N N -9.133 -10.709 6.209 1.003 0.125 0.661 H22 XD2 50 XD2 H5 H5 H 0 1 N N N -9.833 -8.903 5.950 0.092 -2.385 1.344 H5 XD2 51 # # 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 XD2 CAG CAH DOUB Y N 1 XD2 CAG CAI SING Y N 2 XD2 CAH CAJ SING Y N 3 XD2 CAI CAK DOUB Y N 4 XD2 CAJ CAZ DOUB Y N 5 XD2 CAK CAZ SING Y N 6 XD2 CAZ CBB SING N N 7 XD2 CAA NBE SING N N 8 XD2 OAF CBB SING N N 9 XD2 CBB CAW SING N N 10 XD2 SAT CAM SING N N 11 XD2 SAT CBA SING N N 12 XD2 CAM CAX SING N N 13 XD2 NBE CBA SING Y N 14 XD2 NBE NAQ SING Y N 15 XD2 CBA NAP DOUB Y N 16 XD2 CAN CAX SING N N 17 XD2 CAN SAU SING N N 18 XD2 CAW NAR SING N N 19 XD2 CAW OAC DOUB N N 20 XD2 CAX CAY DOUB N N 21 XD2 NAQ NAO DOUB Y N 22 XD2 NAR CBC SING N N 23 XD2 OAE CAV DOUB N N 24 XD2 NAP NAO SING Y N 25 XD2 CAY CAV SING N N 26 XD2 CAY NAS SING N N 27 XD2 CAV OAB SING N N 28 XD2 SAU CBD SING N N 29 XD2 OAD CAL DOUB N N 30 XD2 CBC CBD SING N N 31 XD2 CBC CAL SING N N 32 XD2 NAS CBD SING N N 33 XD2 CAA H1 SING N N 34 XD2 CAA H2 SING N N 35 XD2 CAA H3 SING N N 36 XD2 OAB H4 SING N N 37 XD2 OAF H6 SING N N 38 XD2 CAG H7 SING N N 39 XD2 CAH H8 SING N N 40 XD2 CAI H9 SING N N 41 XD2 CAJ H10 SING N N 42 XD2 CAK H11 SING N N 43 XD2 CAL H12 SING N N 44 XD2 CAM H14 SING N N 45 XD2 CAM H15 SING N N 46 XD2 CAN H16 SING N N 47 XD2 CAN H17 SING N N 48 XD2 NAR H18 SING N N 49 XD2 CBB H20 SING N N 50 XD2 CBC H21 SING N N 51 XD2 CBD H22 SING N N 52 XD2 NAS H5 SING N N 53 # # 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 XD2 SMILES ACDLabs 12.01 "O=CC(NC(=O)C(O)c1ccccc1)C2SCC(=C(N2)C(=O)O)CSc3nnnn3C" XD2 InChI InChI 1.03 "InChI=1S/C18H20N6O5S2/c1-24-18(21-22-23-24)31-9-11-8-30-16(20-13(11)17(28)29)12(7-25)19-15(27)14(26)10-5-3-2-4-6-10/h2-7,12,14,16,20,26H,8-9H2,1H3,(H,19,27)(H,28,29)/t12-,14-,16-/m1/s1" XD2 InChIKey InChI 1.03 CTWPBVTUYYLUGC-XNRPHZJLSA-N XD2 SMILES_CANONICAL CACTVS 3.370 "Cn1nnnc1SCC2=C(N[C@H](SC2)[C@H](NC(=O)[C@H](O)c3ccccc3)C=O)C(O)=O" XD2 SMILES CACTVS 3.370 "Cn1nnnc1SCC2=C(N[CH](SC2)[CH](NC(=O)[CH](O)c3ccccc3)C=O)C(O)=O" XD2 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "Cn1c(nnn1)SCC2=C(N[C@H](SC2)[C@@H](C=O)NC(=O)[C@@H](c3ccccc3)O)C(=O)O" XD2 SMILES "OpenEye OEToolkits" 1.7.6 "Cn1c(nnn1)SCC2=C(NC(SC2)C(C=O)NC(=O)C(c3ccccc3)O)C(=O)O" # # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier XD2 "SYSTEMATIC NAME" ACDLabs 12.01 "(2R)-2-[(1R)-1-{[(2R)-2-hydroxy-2-phenylacetyl]amino}-2-oxoethyl]-5-{[(1-methyl-1H-tetrazol-5-yl)sulfanyl]methyl}-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid" XD2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2R)-5-[(1-methyl-1,2,3,4-tetrazol-5-yl)sulfanylmethyl]-2-[(1R)-2-oxidanylidene-1-[[(2R)-2-oxidanyl-2-phenyl-ethanoyl]amino]ethyl]-3,6-dihydro-2H-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 XD2 "Create component" 2010-06-09 RCSB XD2 "Modify aromatic_flag" 2011-06-04 RCSB XD2 "Modify descriptor" 2011-06-04 RCSB XD2 "Other modification" 2012-05-16 RCSB XD2 "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id XD2 _pdbx_chem_comp_synonyms.name "Cefamandole, bound form" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##