data_CYJ # _chem_comp.id CYJ _chem_comp.name "(Z)-N~6~-[(4R,5S)-5-(2-CARBOXYETHYL)-4-(CARBOXYMETHYL)PIPERIDIN-3-YLIDENE]-L-LYSINE" _chem_comp.type "L-PEPTIDE LINKING" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C16 H27 N3 O6" _chem_comp.mon_nstd_parent_comp_id LYS _chem_comp.pdbx_synonyms "2-AMINO-6-(3-CARBOXY-1-[(4-CARBOXY-2-OXO-BUTYLAMINO)-METHYL]-PROPYLIDENEAMINO)-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 357.402 _chem_comp.one_letter_code K _chem_comp.three_letter_code CYJ _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 2C14 _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 CYJ O4 O4 O 0 1 N N N N N N 4.374 120.211 29.550 6.015 -4.751 -2.681 O4 CYJ 1 CYJ C11 C11 C 0 1 N N N N N N 4.887 119.299 30.214 6.376 -3.863 -1.919 C11 CYJ 2 CYJ O3 O3 O 0 1 N N N N N N 4.521 118.104 30.133 7.678 -3.588 -1.661 O3 CYJ 3 CYJ C10 C10 C 0 1 N N N N N N 6.011 119.658 31.182 5.426 -2.944 -1.192 C10 CYJ 4 CYJ C9 C9 C 0 1 N N N N N N 6.749 118.371 31.615 3.973 -3.333 -1.421 C9 CYJ 5 CYJ C8 C8 C 0 1 N N S N N N 7.829 118.609 32.695 2.997 -2.409 -0.692 C8 CYJ 6 CYJ C7 C7 C 0 1 N N N N N N 8.997 119.495 32.157 1.544 -2.834 -0.966 C7 CYJ 7 CYJ N6 N6 N 0 1 N N N N N N 10.151 119.572 33.063 0.603 -1.997 -0.216 N6 CYJ 8 CYJ C5 C5 C 0 1 N N N N N N 10.701 118.364 33.674 0.688 -0.595 -0.609 C5 CYJ 9 CYJ C3 C3 C 0 1 N N R N N N 8.343 117.294 33.358 3.231 -0.918 -1.015 C3 CYJ 10 CYJ C2 C2 C 0 1 N N N N N N 8.622 116.286 32.222 3.300 -0.578 -2.503 C2 CYJ 11 CYJ C1 C1 C 0 1 N N N N N N 9.203 114.932 32.584 3.549 0.888 -2.727 C1 CYJ 12 CYJ O1 O1 O 0 1 N N N N N N 9.899 114.338 31.711 4.231 1.064 -3.888 O1 CYJ 13 CYJ O2 O2 O 0 1 N N N N N N 9.018 114.432 33.701 3.204 1.804 -1.996 O2 CYJ 14 CYJ C4 C4 C 0 1 N N N N N N 9.470 117.738 34.299 2.103 -0.127 -0.378 C4 CYJ 15 CYJ NZ NZ N 0 1 N N N N N N 9.352 117.875 35.583 2.325 0.944 0.313 NZ CYJ 16 CYJ CE CE C 0 1 N N N N N N 8.287 117.393 36.468 3.732 1.283 0.457 CE CYJ 17 CYJ CD CD C 0 1 N N N N N N 8.374 117.918 37.889 3.879 2.525 1.331 CD CYJ 18 CYJ CG CG C 0 1 N N N N N N 7.135 117.393 38.616 3.192 3.753 0.723 CG CYJ 19 CYJ CB CB C 0 1 N N N N N N 7.103 117.979 40.022 3.349 4.979 1.635 CB CYJ 20 CYJ CA CA C 0 1 N N S Y N N 5.830 117.574 40.736 2.640 6.244 1.130 CA CYJ 21 CYJ N N N 0 1 N N N Y Y N 5.863 118.036 42.094 1.201 6.029 0.980 N CYJ 22 CYJ C C C 0 1 N N N Y N Y 5.683 116.057 40.788 3.190 6.715 -0.202 C CYJ 23 CYJ O O O 0 1 N N N Y N Y 6.474 115.305 41.339 2.563 6.827 -1.246 O CYJ 24 CYJ OXT OXT O 0 1 N Y N Y N Y ? ? ? 4.508 7.025 -0.088 OXT CYJ 25 CYJ H3 H3 H 0 1 N N N N N N 3.815 118.031 29.502 8.329 -4.152 -2.129 H3 CYJ 26 CYJ H101 H101 H 0 0 N N N N N N 5.587 120.153 32.068 5.613 -1.900 -1.467 H101 CYJ 27 CYJ H102 H102 H 0 0 N N N N N N 6.719 120.337 30.685 5.664 -3.020 -0.124 H102 CYJ 28 CYJ H9C1 H9C1 H 0 0 N N N N N N 7.261 117.976 30.725 3.815 -4.353 -1.057 H9C1 CYJ 29 CYJ H9C2 H9C2 H 0 0 N N N N N N 6.005 117.672 32.024 3.735 -3.326 -2.488 H9C2 CYJ 30 CYJ H8 H8 H 0 1 N N N N N N 7.335 119.170 33.502 3.181 -2.546 0.383 H8 CYJ 31 CYJ H7C1 H7C1 H 0 0 N N N N N N 8.603 120.516 32.050 1.316 -2.791 -2.038 H7C1 CYJ 32 CYJ H7C2 H7C2 H 0 0 N N N N N N 9.340 119.065 31.205 1.401 -3.877 -0.658 H7C2 CYJ 33 CYJ H6 H6 H 0 1 N N N N N N 10.895 119.970 32.526 0.796 -2.082 0.782 H6 CYJ 34 CYJ H5C1 H5C1 H 0 0 N N N N N N 11.508 118.563 34.395 -0.008 0.001 -0.010 H5C1 CYJ 35 CYJ H5C2 H5C2 H 0 0 N N N N N N 11.169 117.702 32.931 0.426 -0.461 -1.664 H5C2 CYJ 36 CYJ HB HA H 0 1 N N N N N N 7.653 116.729 34.002 4.177 -0.602 -0.558 HA CYJ 37 CYJ H2C1 H2C1 H 0 0 N N N N N N 9.402 116.766 31.613 4.113 -1.149 -2.958 H2C1 CYJ 38 CYJ H2C2 H2C2 H 0 0 N N N N N N 7.657 116.092 31.730 2.353 -0.852 -2.972 H2C2 CYJ 39 CYJ H1 H1 H 0 1 N N N N N N 10.214 113.514 32.063 4.411 2.012 -4.065 H1 CYJ 40 CYJ HEC1 HEC1 H 0 0 N N N N N N 8.391 116.299 36.525 4.175 1.445 -0.531 HEC1 CYJ 41 CYJ HEC2 HEC2 H 0 0 N N N N N N 7.324 117.716 36.046 4.251 0.440 0.924 HEC2 CYJ 42 CYJ HDC1 HDC1 H 0 0 N N N N N N 8.411 119.017 37.906 4.947 2.737 1.459 HDC1 CYJ 43 CYJ HDC2 HDC2 H 0 0 N N N N N N 9.291 117.558 38.379 3.466 2.327 2.327 HDC2 CYJ 44 CYJ HGC1 HGC1 H 0 0 N N N N N N 7.172 116.295 38.671 2.129 3.539 0.567 HGC1 CYJ 45 CYJ HGC2 HGC2 H 0 0 N N N N N N 6.229 117.694 38.069 3.630 3.961 -0.260 HGC2 CYJ 46 CYJ HBC1 HBC1 H 0 0 N N N N N N 7.139 119.076 39.952 4.418 5.192 1.760 HBC1 CYJ 47 CYJ HBC2 HBC2 H 0 0 N N N N N N 7.969 117.605 40.588 2.966 4.731 2.634 HBC2 CYJ 48 CYJ HA HB H 0 1 N N N Y N N 4.991 118.017 40.179 2.784 7.056 1.853 HB CYJ 49 CYJ H HN1 H 0 1 N N N Y Y N 5.393 118.916 42.158 0.855 5.797 0.075 HN1 CYJ 50 CYJ H2 HN2 H 0 1 N Y N Y Y N 6.813 118.143 42.387 0.606 6.318 1.725 HN2 CYJ 51 CYJ HXT HXT H 0 1 N Y N Y N Y -0.092 -0.945 0.032 4.883 7.344 -0.937 HXT CYJ 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 CYJ O4 C11 DOUB N N 1 CYJ C11 O3 SING N N 2 CYJ C11 C10 SING N N 3 CYJ O3 H3 SING N N 4 CYJ C10 C9 SING N N 5 CYJ C10 H101 SING N N 6 CYJ C10 H102 SING N N 7 CYJ C9 C8 SING N N 8 CYJ C9 H9C1 SING N N 9 CYJ C9 H9C2 SING N N 10 CYJ C8 C7 SING N N 11 CYJ C8 C3 SING N N 12 CYJ C8 H8 SING N N 13 CYJ C7 N6 SING N N 14 CYJ C7 H7C1 SING N N 15 CYJ C7 H7C2 SING N N 16 CYJ N6 C5 SING N N 17 CYJ N6 H6 SING N N 18 CYJ C5 C4 SING N N 19 CYJ C5 H5C1 SING N N 20 CYJ C5 H5C2 SING N N 21 CYJ C3 C2 SING N N 22 CYJ C3 C4 SING N N 23 CYJ C3 HB SING N N 24 CYJ C2 C1 SING N N 25 CYJ C2 H2C1 SING N N 26 CYJ C2 H2C2 SING N N 27 CYJ C1 O1 SING N N 28 CYJ C1 O2 DOUB N N 29 CYJ O1 H1 SING N N 30 CYJ C4 NZ DOUB N E 31 CYJ NZ CE SING N N 32 CYJ CE CD SING N N 33 CYJ CE HEC1 SING N N 34 CYJ CE HEC2 SING N N 35 CYJ CD CG SING N N 36 CYJ CD HDC1 SING N N 37 CYJ CD HDC2 SING N N 38 CYJ CG CB SING N N 39 CYJ CG HGC1 SING N N 40 CYJ CG HGC2 SING N N 41 CYJ CB CA SING N N 42 CYJ CB HBC1 SING N N 43 CYJ CB HBC2 SING N N 44 CYJ CA N SING N N 45 CYJ CA C SING N N 46 CYJ CA HA SING N N 47 CYJ N H SING N N 48 CYJ N H2 SING N N 49 CYJ C O DOUB N N 50 CYJ C OXT SING N N 51 CYJ OXT HXT SING 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 CYJ SMILES ACDLabs 10.04 "O=C(O)C(N)CCCC/N=C1/CNCC(CCC(=O)O)C1CC(=O)O" CYJ SMILES_CANONICAL CACTVS 3.341 "N[C@@H](CCCCN=C1CNC[C@@H](CCC(O)=O)[C@H]1CC(O)=O)C(O)=O" CYJ SMILES CACTVS 3.341 "N[CH](CCCCN=C1CNC[CH](CCC(O)=O)[CH]1CC(O)=O)C(O)=O" CYJ SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@H]([C@H](/C(=N\CCCC[C@@H](C(=O)O)N)/CN1)CC(=O)O)CCC(=O)O" CYJ SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(C(=NCCCCC(C(=O)O)N)CN1)CC(=O)O)CCC(=O)O" CYJ InChI InChI 1.03 "InChI=1S/C16H27N3O6/c17-12(16(24)25)3-1-2-6-19-13-9-18-8-10(4-5-14(20)21)11(13)7-15(22)23/h10-12,18H,1-9,17H2,(H,20,21)(H,22,23)(H,24,25)/b19-13-/t10-,11-,12+/m1/s1" CYJ InChIKey InChI 1.03 XKNSCWDBUODVRH-DEBZXTSDSA-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 CYJ "SYSTEMATIC NAME" ACDLabs 10.04 "(E)-N~6~-[(4R,5S)-5-(2-carboxyethyl)-4-(carboxymethyl)piperidin-3-ylidene]-L-lysine" CYJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S)-2-amino-6-[[(4R,5S)-5-(2-carboxyethyl)-4-(carboxymethyl)piperidin-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 CYJ "Create component" 2005-09-11 EBI CYJ "Modify descriptor" 2011-06-04 RCSB CYJ "Modify parent residue" 2014-01-20 EBI CYJ "Modify one letter code" 2014-01-20 EBI CYJ "Modify model coordinates code" 2014-01-20 EBI CYJ "Modify synonyms" 2020-06-05 PDBE CYJ "Modify backbone" 2023-11-03 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id CYJ _pdbx_chem_comp_synonyms.name "2-AMINO-6-(3-CARBOXY-1-[(4-CARBOXY-2-OXO-BUTYLAMINO)-METHYL]-PROPYLIDENEAMINO)-HEXANOIC ACID" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? #