data_OBS # _chem_comp.id OBS _chem_comp.name "(Z)-N^6-[(4S,5R)-5-(2-CARBOXYETHYL)-4-(CARBOXYMETHYL)-1-HYDROXYDIHYDRO-2H-THIOPYRANIUM-3(4H)-YLIDENE]-L-LYSINE" _chem_comp.type "L-PEPTIDE LINKING" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C16 H26 N2 O7 S" _chem_comp.mon_nstd_parent_comp_id LYS _chem_comp.pdbx_synonyms "2-AMINO-6-[5-(2-CARBOXY-ETHYL)-4-CARBOXYMETHYL-1-OXO-TETRAHYDRO-1LAMBDA4-THIOPYRAN-3-YLIDENEAMINO]-HEXANOIC ACID" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2005-09-11 _chem_comp.pdbx_modified_date 2023-11-03 _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 390.452 _chem_comp.one_letter_code K _chem_comp.three_letter_code OBS _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 2C16 _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.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 OBS O4 O4 O 0 1 N N N N N N 4.006 119.307 28.771 4.863 -3.247 -5.836 O4 OBS 1 OBS C11 C11 C 0 1 N N N N N N 4.519 118.357 29.393 4.513 -3.995 -4.933 C11 OBS 2 OBS O3 O3 O 0 1 N N N N N N 4.133 117.162 29.240 5.021 -5.240 -4.758 O3 OBS 3 OBS C10 C10 C 0 1 N N N N N N 5.607 118.701 30.389 3.497 -3.623 -3.881 C10 OBS 4 OBS C9 C9 C 0 1 N N N N N N 6.394 117.441 30.772 2.870 -2.265 -4.153 C9 OBS 5 OBS C8 C8 C 0 1 N N S N N N 7.460 117.687 31.868 1.836 -1.876 -3.093 C8 OBS 6 OBS C7 C7 C 0 1 N N N N N N 8.593 118.594 31.327 1.253 -0.492 -3.416 C7 OBS 7 OBS C5 C5 C 0 1 N N N N N N 10.368 117.148 33.014 0.707 -0.188 -0.813 C5 OBS 8 OBS C3 C3 C 0 1 N N R N N N 7.909 116.343 32.549 2.414 -1.970 -1.658 C3 OBS 9 OBS C2 C2 C 0 1 N N N N N N 8.226 115.232 31.537 3.700 -1.178 -1.422 C2 OBS 10 OBS C1 C1 C 0 1 N N N N N N 8.761 114.092 32.349 4.243 -1.402 -0.037 C1 OBS 11 OBS O1 O1 O 0 1 N N N N N N 8.737 112.946 31.904 5.338 -1.862 0.250 O1 OBS 12 OBS O2 O2 O 0 1 N N N N N N 9.248 114.359 33.456 3.323 -1.012 0.883 O2 OBS 13 OBS C4 C4 C 0 1 N N N N N N 9.046 116.642 33.537 1.364 -1.533 -0.643 C4 OBS 14 OBS NZ NZ N 0 1 N N N N N N 8.903 116.646 34.827 1.041 -2.278 0.363 NZ OBS 15 OBS CE CE C 0 1 N N N N N N 7.778 116.196 35.641 1.747 -3.549 0.418 CE OBS 16 OBS CD CD C 0 1 N N N N N N 7.969 116.657 37.098 1.252 -4.366 1.607 CD OBS 17 OBS CG CG C 0 1 N N N N N N 6.702 116.221 37.847 1.507 -3.665 2.946 CG OBS 18 OBS CB CB C 0 1 N N N N N N 6.731 116.762 39.288 0.984 -4.509 4.118 CB OBS 19 OBS CA CA C 0 1 N N S Y N N 5.435 116.447 40.027 1.147 -3.855 5.498 CA OBS 20 OBS N N N 0 1 N N N Y Y N 5.539 116.901 41.396 2.552 -3.596 5.806 N OBS 21 OBS C C C 0 1 N N N Y N Y 5.216 114.944 40.132 0.566 -4.708 6.608 C OBS 22 OBS O O O 0 1 N N N Y N Y 6.038 114.177 40.620 1.177 -5.168 7.562 O OBS 23 OBS OXT OXT O 0 1 N Y N Y N Y ? ? ? -0.766 -4.893 6.417 OXT OBS 24 OBS S6 S6 S 0 1 N N S N N N 10.003 118.793 32.448 -0.214 -0.174 -2.376 S6 OBS 25 OBS O5 O5 O 0 1 N N N N N N 11.469 119.152 31.490 -0.112 1.423 -2.544 O5 OBS 26 OBS H3 H3 H 0 1 N N N N N N 3.427 117.136 28.604 5.700 -5.514 -5.411 H3 OBS 27 OBS H101 H101 H 0 0 N N N N N N 5.145 119.124 31.293 3.941 -3.672 -2.881 H101 OBS 28 OBS H102 H102 H 0 0 N N N N N N 6.293 119.433 29.937 2.720 -4.397 -3.901 H102 OBS 29 OBS H9C1 H9C1 H 0 0 N N N N N N 6.926 117.103 29.871 2.368 -2.290 -5.124 H9C1 OBS 30 OBS H9C2 H9C2 H 0 0 N N N N N N 5.681 116.693 31.150 3.636 -1.487 -4.198 H9C2 OBS 31 OBS H8 H8 H 0 1 N N N N N N 7.022 118.258 32.700 1.022 -2.611 -3.166 H8 OBS 32 OBS H7C1 H7C1 H 0 0 N N N N N N 8.156 119.594 31.191 1.998 0.297 -3.267 H7C1 OBS 33 OBS H7C2 H7C2 H 0 0 N N N N N N 8.966 118.145 30.395 0.915 -0.449 -4.457 H7C2 OBS 34 OBS H5C1 H5C1 H 0 0 N N N N N N 10.779 116.510 32.218 0.002 0.003 0.001 H5C1 OBS 35 OBS H5C2 H5C2 H 0 0 N N N N N N 11.134 117.157 33.803 1.476 0.591 -0.810 H5C2 OBS 36 OBS HB HA H 0 1 N N N N N N 7.066 115.927 33.121 2.647 -3.024 -1.457 HA OBS 37 OBS H2C1 H2C1 H 0 0 N N N N N N 8.950 115.567 30.780 4.448 -1.495 -2.151 H2C1 OBS 38 OBS H2C2 H2C2 H 0 0 N N N N N N 7.320 114.931 30.990 3.489 -0.115 -1.552 H2C2 OBS 39 OBS H1 H2 H 0 1 N N N N N N 9.573 113.563 33.860 3.645 -1.144 1.800 H2 OBS 40 OBS HEC1 HEC1 H 0 0 N N N N N N 7.726 115.098 35.612 2.824 -3.369 0.488 HEC1 OBS 41 OBS HEC2 HEC2 H 0 0 N N N N N N 6.846 116.624 35.243 1.557 -4.097 -0.510 HEC2 OBS 42 OBS HDC1 HDC1 H 0 0 N N N N N N 8.118 117.745 37.159 1.767 -5.334 1.604 HDC1 OBS 43 OBS HDC2 HDC2 H 0 0 N N N N N N 8.861 116.189 37.539 0.179 -4.569 1.496 HDC2 OBS 44 OBS HGC1 HGC1 H 0 0 N N N N N N 6.658 115.122 37.874 1.018 -2.685 2.946 HGC1 OBS 45 OBS HGC2 HGC2 H 0 0 N N N N N N 5.817 116.618 37.327 2.583 -3.492 3.062 HGC2 OBS 46 OBS HBC1 HBC1 H 0 0 N N N N N N 6.850 117.855 39.246 1.502 -5.477 4.115 HBC1 OBS 47 OBS HBC2 HBC2 H 0 0 N N N N N N 7.569 116.295 39.826 -0.079 -4.729 3.952 HBC2 OBS 48 OBS HA HB H 0 1 N N N Y N N 4.621 116.935 39.471 0.619 -2.894 5.509 HB OBS 49 OBS H HN1 H 0 1 N N N Y Y N 5.073 117.781 41.492 2.783 -2.733 6.246 HN1 OBS 50 OBS H2 HN2 H 0 1 N Y N Y Y N 6.503 117.006 41.641 3.238 -4.187 5.390 HN2 OBS 51 OBS HXT HXT H 0 1 N Y N Y N Y -0.137 -0.938 0.066 -1.166 -5.433 7.132 HXT OBS 52 # 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 OBS O4 C11 DOUB N N 1 OBS C11 O3 SING N N 2 OBS C11 C10 SING N N 3 OBS O3 H3 SING N N 4 OBS C10 C9 SING N N 5 OBS C10 H101 SING N N 6 OBS C10 H102 SING N N 7 OBS C9 C8 SING N N 8 OBS C9 H9C1 SING N N 9 OBS C9 H9C2 SING N N 10 OBS C8 C7 SING N N 11 OBS C8 C3 SING N N 12 OBS C8 H8 SING N N 13 OBS C7 S6 SING N N 14 OBS C7 H7C1 SING N N 15 OBS C7 H7C2 SING N N 16 OBS C5 C4 SING N N 17 OBS C5 S6 SING N N 18 OBS C5 H5C1 SING N N 19 OBS C5 H5C2 SING N N 20 OBS C3 C2 SING N N 21 OBS C3 C4 SING N N 22 OBS C3 HB SING N N 23 OBS C2 C1 SING N N 24 OBS C2 H2C1 SING N N 25 OBS C2 H2C2 SING N N 26 OBS C1 O1 DOUB N N 27 OBS C1 O2 SING N N 28 OBS O2 H1 SING N N 29 OBS C4 NZ DOUB N E 30 OBS NZ CE SING N N 31 OBS CE CD SING N N 32 OBS CE HEC1 SING N N 33 OBS CE HEC2 SING N N 34 OBS CD CG SING N N 35 OBS CD HDC1 SING N N 36 OBS CD HDC2 SING N N 37 OBS CG CB SING N N 38 OBS CG HGC1 SING N N 39 OBS CG HGC2 SING N N 40 OBS CB CA SING N N 41 OBS CB HBC1 SING N N 42 OBS CB HBC2 SING N N 43 OBS CA N SING N N 44 OBS CA C SING N N 45 OBS CA HA SING N N 46 OBS N H SING N N 47 OBS N H2 SING N N 48 OBS C O DOUB N N 49 OBS C OXT SING N N 50 OBS OXT HXT SING N N 51 OBS S6 O5 DOUB N N 52 # 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 OBS SMILES ACDLabs 10.04 "O=S1C/C(=N/CCCCC(C(=O)O)N)C(C(CCC(=O)O)C1)CC(=O)O" OBS SMILES_CANONICAL CACTVS 3.341 "N[C@@H](CCCCN=C1C[S@@](=O)C[C@@H](CCC(O)=O)[C@H]1CC(O)=O)C(O)=O" OBS SMILES CACTVS 3.341 "N[CH](CCCCN=C1C[S](=O)C[CH](CCC(O)=O)[CH]1CC(O)=O)C(O)=O" OBS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@H]([C@H](/C(=N\CCCC[C@@H](C(=O)O)N)/C[S@]1=O)CC(=O)O)CCC(=O)O" OBS SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(C(=NCCCCC(C(=O)O)N)CS1=O)CC(=O)O)CCC(=O)O" OBS InChI InChI 1.03 "InChI=1S/C16H26N2O7S/c17-12(16(23)24)3-1-2-6-18-13-9-26(25)8-10(4-5-14(19)20)11(13)7-15(21)22/h10-12H,1-9,17H2,(H,19,20)(H,21,22)(H,23,24)/b18-13-/t10-,11-,12+,26+/m1/s1" OBS InChIKey InChI 1.03 OXEYOJPDXMYXIZ-KYPNPPHMSA-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 OBS "SYSTEMATIC NAME" ACDLabs 10.04 "(E)-N~6~-[(1S,4R,5S)-5-(2-carboxyethyl)-4-(carboxymethyl)-1-oxidodihydro-2H-thiopyran-3(4H)-ylidene]-L-lysine" OBS "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S)-2-amino-6-[[(1S,4R,5S)-5-(2-carboxyethyl)-4-(carboxymethyl)-1-oxo-thian-3-ylidene]amino]hexanoic 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 OBS "Create component" 2005-09-11 EBI OBS "Modify descriptor" 2011-06-04 RCSB OBS "Modify parent residue" 2014-01-20 EBI OBS "Modify one letter code" 2014-01-20 EBI OBS "Modify synonyms" 2021-03-01 PDBE OBS "Modify backbone" 2023-11-03 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id OBS _pdbx_chem_comp_synonyms.name "2-AMINO-6-[5-(2-CARBOXY-ETHYL)-4-CARBOXYMETHYL-1-OXO-TETRAHYDRO-1LAMBDA4-THIOPYRAN-3-YLIDENEAMINO]-HEXANOIC ACID" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? #