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                    2024-09-27 
_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 
_chem_comp.pdbx_pcm                              Y 
# 
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 
CYJ "Modify PCM"                    2024-09-27 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         ? 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            CYJ 
_pdbx_chem_comp_pcm.modified_residue_id                LYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Non-standard residue" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               ? 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   ? 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
