data_PNK # _chem_comp.id PNK _chem_comp.name "(2R,4S)-2-{(R)-carboxy[(phenylacetyl)amino]methyl}-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAD _chem_comp.formula "C16 H20 N2 O5 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "Penicillin, hydroxylated form" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2009-06-22 _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 352.405 _chem_comp.one_letter_code ? _chem_comp.three_letter_code PNK _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 3HUO _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # 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 PNK C1 C1 C 0 1 N N R 52.098 15.372 -18.847 0.157 -0.920 0.028 C1 PNK 1 PNK C2 C2 C 0 1 N N N 51.806 13.869 -18.966 0.041 -2.322 0.570 C2 PNK 2 PNK C3 C3 C 0 1 Y N N 56.578 19.028 -18.280 -5.313 -0.113 0.750 C3 PNK 3 PNK C4 C4 C 0 1 N N R 51.530 16.217 -20.027 1.579 -0.403 0.253 C4 PNK 4 PNK C5 C5 C 0 1 N N S 49.422 16.490 -21.234 3.178 1.253 -0.542 C5 PNK 5 PNK C6 C6 C 0 1 N N N 50.194 15.632 -22.328 4.015 -0.000 -0.864 C6 PNK 6 PNK C7 C7 C 0 1 Y N N 57.070 20.063 -19.066 -6.548 -0.198 0.134 C7 PNK 7 PNK C8 C8 C 0 1 Y N N 56.980 19.980 -20.447 -6.866 0.663 -0.899 C8 PNK 8 PNK C9 C9 C 0 1 N N N 49.349 17.958 -21.549 3.723 1.893 0.709 C9 PNK 9 PNK C10 C10 C 0 1 Y N N 56.405 18.868 -21.046 -5.949 1.609 -1.317 C10 PNK 10 PNK C11 C11 C 0 1 Y N N 55.916 17.834 -20.254 -4.714 1.694 -0.702 C11 PNK 11 PNK C12 C12 C 0 1 N N N 49.578 14.242 -22.411 4.578 0.079 -2.284 C12 PNK 12 PNK N1 N1 N 0 1 N N N 50.045 16.230 -19.905 1.758 0.953 -0.339 N1 PNK 13 PNK O1 O1 O 0 1 N N N 48.389 18.328 -22.260 4.816 2.671 0.643 O1 PNK 14 PNK O2 O2 O 0 1 N N N 50.207 18.700 -21.051 3.177 1.707 1.770 O2 PNK 15 PNK O3 O3 O 0 1 N N N 52.764 13.079 -18.708 0.369 -3.369 -0.203 O3 PNK 16 PNK O4 O4 O 0 1 N N N 50.638 13.540 -19.249 -0.348 -2.502 1.699 O4 PNK 17 PNK O5 O5 O 0 1 N N N 53.244 17.624 -17.691 -2.430 -0.621 -0.667 O5 PNK 18 PNK C16 C16 C 0 1 Y N N 56.000 17.918 -18.875 -4.396 0.834 0.332 C16 PNK 19 PNK C15 C15 C 0 1 N N N 55.477 16.788 -18.006 -3.050 0.927 1.003 C15 PNK 20 PNK C14 C14 C 0 1 N N N 53.968 16.710 -18.113 -2.071 0.030 0.291 C14 PNK 21 PNK N2 N2 N 0 1 N N N 53.522 15.610 -18.683 -0.795 -0.048 0.720 N2 PNK 22 PNK S1 S1 S 0 1 N N N 51.895 15.532 -21.679 2.802 -1.373 -0.724 S1 PNK 23 PNK C13 C13 C 0 1 N N N 50.166 16.333 -23.693 5.144 -0.170 0.154 C13 PNK 24 PNK H1 H1 H 0 1 N N N 51.567 15.712 -17.946 -0.063 -0.924 -1.040 H1 PNK 25 PNK H3 H3 H 0 1 N N N 56.646 19.089 -17.204 -5.066 -0.782 1.561 H3 PNK 26 PNK H4 H4 H 0 1 N N N 52.001 17.208 -19.955 1.832 -0.405 1.313 H4 PNK 27 PNK H5 H5 H 0 1 N N N 48.371 16.167 -21.227 3.271 1.959 -1.367 H5 PNK 28 PNK H7 H7 H 0 1 N N N 57.521 20.928 -18.603 -7.264 -0.938 0.461 H7 PNK 29 PNK H8 H8 H 0 1 N N N 57.359 20.785 -21.060 -7.830 0.595 -1.381 H8 PNK 30 PNK H10 H10 H 0 1 N N N 56.337 18.806 -22.122 -6.198 2.282 -2.125 H10 PNK 31 PNK H11 H11 H 0 1 N N N 55.471 16.965 -20.716 -3.998 2.434 -1.029 H11 PNK 32 PNK H12 H12 H 0 1 N N N 49.429 13.969 -23.466 5.214 0.960 -2.374 H12 PNK 33 PNK H12A H12A H 0 0 N N N 50.251 13.514 -21.935 5.166 -0.816 -2.492 H12A PNK 34 PNK H12B H12B H 0 0 N N N 48.608 14.239 -21.892 3.757 0.148 -2.997 H12B PNK 35 PNK HN1 HN1 H 0 1 N N N 49.735 15.343 -19.564 1.242 1.041 -1.202 HN1 PNK 36 PNK HO1 HO1 H 0 1 N N N 48.416 19.272 -22.363 5.128 3.059 1.472 HO1 PNK 37 PNK HO3 HO3 H 0 1 N N N 52.458 12.181 -18.762 0.278 -4.249 0.189 HO3 PNK 38 PNK H15 H15 H 0 1 N N N 55.915 15.837 -18.343 -2.695 1.957 0.964 H15 PNK 39 PNK H15A H15A H 0 0 N N N 55.756 16.977 -16.959 -3.141 0.614 2.043 H15A PNK 40 PNK HN2 HN2 H 0 1 N N N 54.175 14.926 -19.009 -0.508 0.472 1.486 HN2 PNK 41 PNK H13 H13 H 0 1 N N N 50.159 17.423 -23.546 4.721 -0.275 1.153 H13 PNK 42 PNK H13A H13A H 0 0 N N N 51.057 16.047 -24.270 5.723 -1.060 -0.091 H13A PNK 43 PNK H13B H13B H 0 0 N N N 49.261 16.032 -24.241 5.794 0.705 0.125 H13B PNK 44 # # 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 PNK C1 C2 SING N N 1 PNK C1 C4 SING N N 2 PNK C1 N2 SING N N 3 PNK C2 O3 SING N N 4 PNK C2 O4 DOUB N N 5 PNK C3 C7 DOUB Y N 6 PNK C3 C16 SING Y N 7 PNK C4 N1 SING N N 8 PNK C4 S1 SING N N 9 PNK C5 C6 SING N N 10 PNK C5 C9 SING N N 11 PNK C5 N1 SING N N 12 PNK C6 C12 SING N N 13 PNK C6 S1 SING N N 14 PNK C6 C13 SING N N 15 PNK C7 C8 SING Y N 16 PNK C8 C10 DOUB Y N 17 PNK C9 O1 SING N N 18 PNK C9 O2 DOUB N N 19 PNK C10 C11 SING Y N 20 PNK C11 C16 DOUB Y N 21 PNK O5 C14 DOUB N N 22 PNK C16 C15 SING N N 23 PNK C15 C14 SING N N 24 PNK C14 N2 SING N N 25 PNK C1 H1 SING N N 26 PNK C3 H3 SING N N 27 PNK C4 H4 SING N N 28 PNK C5 H5 SING N N 29 PNK C7 H7 SING N N 30 PNK C8 H8 SING N N 31 PNK C10 H10 SING N N 32 PNK C11 H11 SING N N 33 PNK C12 H12 SING N N 34 PNK C12 H12A SING N N 35 PNK C12 H12B SING N N 36 PNK N1 HN1 SING N N 37 PNK O1 HO1 SING N N 38 PNK O3 HO3 SING N N 39 PNK C15 H15 SING N N 40 PNK C15 H15A SING N N 41 PNK N2 HN2 SING N N 42 PNK C13 H13 SING N N 43 PNK C13 H13A SING N N 44 PNK C13 H13B SING N N 45 # # 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 PNK SMILES ACDLabs 10.04 "O=C(NC(C(=O)O)C1SC(C(N1)C(=O)O)(C)C)Cc2ccccc2" PNK SMILES_CANONICAL CACTVS 3.341 "CC1(C)S[C@@H](N[C@H]1C(O)=O)[C@H](NC(=O)Cc2ccccc2)C(O)=O" PNK SMILES CACTVS 3.341 "CC1(C)S[CH](N[CH]1C(O)=O)[CH](NC(=O)Cc2ccccc2)C(O)=O" PNK SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1([C@@H](N[C@H](S1)[C@@H](C(=O)O)NC(=O)Cc2ccccc2)C(=O)O)C" PNK SMILES "OpenEye OEToolkits" 1.5.0 "CC1(C(NC(S1)C(C(=O)O)NC(=O)Cc2ccccc2)C(=O)O)C" PNK InChI InChI 1.03 "InChI=1S/C16H20N2O5S/c1-16(2)12(15(22)23)18-13(24-16)11(14(20)21)17-10(19)8-9-6-4-3-5-7-9/h3-7,11-13,18H,8H2,1-2H3,(H,17,19)(H,20,21)(H,22,23)/t11-,12-,13+/m0/s1" PNK InChIKey InChI 1.03 HCYWNSXLUZRKJX-RWMBFGLXSA-N # # 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 PNK "SYSTEMATIC NAME" ACDLabs 10.04 "(2R,4S)-2-{(R)-carboxy[(phenylacetyl)amino]methyl}-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid" PNK "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R,4S)-2-[(1R)-2-hydroxy-2-oxo-1-(2-phenylethanoylamino)ethyl]-5,5-dimethyl-1,3-thiazolidine-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 PNK "Create component" 2009-06-22 PDBJ PNK "Modify aromatic_flag" 2011-06-04 RCSB PNK "Modify descriptor" 2011-06-04 RCSB PNK "Modify synonyms" 2012-05-10 RCSB PNK "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id PNK _pdbx_chem_comp_synonyms.name "Penicillin, hydroxylated form" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##