data_LYF
# 
_chem_comp.id                                    LYF 
_chem_comp.name                                  "(2E,4S)-2-{[(5S)-5-amino-5-carboxypentyl]imino}-4-hydroxyheptanedioic acid" 
_chem_comp.type                                  "L-PEPTIDE LINKING" 
_chem_comp.pdbx_type                             ATOMP 
_chem_comp.formula                               "C13 H22 N2 O7" 
_chem_comp.mon_nstd_parent_comp_id               LYS 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2011-10-25 
_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                        318.323 
_chem_comp.one_letter_code                       K 
_chem_comp.three_letter_code                     LYF 
_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        3UBS 
_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.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 
LYF C    C    C 0 1 N N N Y N Y -93.219 13.787 32.963 -6.432 -0.738 0.027  C    LYF 1  
LYF N    N    N 0 1 N N N Y Y N -94.565 15.676 33.459 -4.533 -2.164 -0.488 N    LYF 2  
LYF O    O    O 0 1 N N N Y N Y -92.061 14.189 33.160 -6.949 -1.174 -0.975 O    LYF 3  
LYF CA   CA   C 0 1 N N S Y N N -94.269 14.710 32.403 -4.974 -1.005 0.300  CA   LYF 4  
LYF CB   CB   C 0 1 N N N N N N -93.809 15.417 31.125 -4.148 0.222  -0.091 CB   LYF 5  
LYF CD   CD   C 0 1 N N N N N N -92.794 15.242 28.823 -1.860 1.226  -0.090 CD   LYF 6  
LYF CE   CE   C 0 1 N N N N N N -92.406 14.292 27.697 -0.398 1.003  0.302  CE   LYF 7  
LYF CG   CG   C 0 1 N N N N N N -93.291 14.472 30.048 -2.686 -0.002 0.301  CG   LYF 8  
LYF NZ   NZ   N 0 1 N N N N N N -91.668 15.073 26.702 0.392  2.177  -0.072 NZ   LYF 9  
LYF C11  C11  C 0 1 N N N N N N -91.969 13.552 24.848 2.306  1.064  0.897  C11  LYF 10 
LYF C12  C12  C 0 1 N N S N N N -91.159 12.295 25.062 2.786  0.093  -0.184 C12  LYF 11 
LYF C13  C13  C 0 1 N N N N N N -89.748 12.415 24.470 3.359  -1.162 0.477  C13  LYF 12 
LYF C14  C14  C 0 1 N N N N N N -90.646 15.725 24.651 2.399  3.483  -0.020 C14  LYF 13 
LYF O15  O15  O 0 1 N N N N N N -90.403 16.868 25.095 1.796  4.538  -0.600 O15  LYF 14 
LYF O16  O16  O 0 1 N N N N N N -90.260 15.361 23.506 3.573  3.547  0.283  O16  LYF 15 
LYF O17  O17  O 0 1 N N N N N N -91.931 11.292 24.367 3.798  0.721  -0.973 O17  LYF 16 
LYF C18  C18  C 0 1 N N N N N N -89.061 11.063 24.363 3.724  -2.184 -0.602 C18  LYF 17 
LYF C20  C20  C 0 1 N N N N N N -87.554 11.190 24.457 4.289  -3.421 0.049  C20  LYF 18 
LYF O21  O21  O 0 1 N N N N N N -87.043 11.341 25.588 4.681  -4.458 -0.708 O21  LYF 19 
LYF O22  O22  O 0 1 N N N N N N -86.879 11.128 23.405 4.389  -3.478 1.251  O22  LYF 20 
LYF C41  C41  C 0 1 N N N N N N -91.414 14.799 25.483 1.630  2.244  0.248  C41  LYF 21 
LYF OXT  OXT  O 0 1 N Y N Y N Y -93.618 12.548 33.244 -7.155 -0.010 0.893  OXT  LYF 22 
LYF H    HN   H 0 1 N N N Y Y N -95.262 16.318 33.138 -5.019 -3.001 -0.202 HN   LYF 23 
LYF H2   HNA  H 0 1 N Y N Y Y N -94.903 15.193 34.267 -4.651 -1.996 -1.475 HNA  LYF 24 
LYF HA   HA   H 0 1 N N N Y N N -95.162 14.138 32.111 -4.836 -1.213 1.361  HA   LYF 25 
LYF HB   HB   H 0 1 N N N N N N -94.668 15.965 30.712 -4.216 0.377  -1.168 HB   LYF 26 
LYF HBA  HBA  H 0 1 N N N N N N -92.995 16.107 31.392 -4.534 1.099  0.428  HBA  LYF 27 
LYF HD   HD   H 0 1 N N N N N N -91.913 15.836 29.108 -2.246 2.103  0.429  HD   LYF 28 
LYF HDA  HDA  H 0 1 N N N N N N -93.597 15.906 28.469 -1.928 1.381  -1.167 HDA  LYF 29 
LYF HE   HE   H 0 1 N N N N N N -91.775 13.480 28.086 -0.331 0.847  1.379  HE   LYF 30 
LYF HEA  HEA  H 0 1 N N N N N N -93.307 13.853 27.243 -0.013 0.125  -0.216 HEA  LYF 31 
LYF HG   HG   H 0 1 N N N N N N -92.457 13.885 30.461 -2.619 -0.157 1.378  HG   LYF 32 
LYF HGA  HGA  H 0 1 N N N N N N -94.108 13.803 29.740 -2.301 -0.879 -0.217 HGA  LYF 33 
LYF H11  H11  H 0 1 N N N N N N -92.023 13.729 23.764 1.599  0.557  1.553  H11  LYF 34 
LYF H11A H11A H 0 0 N N N N N N -92.967 13.379 25.277 3.159  1.409  1.480  H11A LYF 35 
LYF H12  H12  H 0 1 N N N N N N -90.999 12.067 26.126 1.947  -0.183 -0.822 H12  LYF 36 
LYF H13  H13  H 0 1 N N N N N N -89.825 12.852 23.463 4.251  -0.899 1.044  H13  LYF 37 
LYF H13A H13A H 0 0 N N N N N N -89.146 13.065 25.123 2.615  -1.592 1.148  H13A LYF 38 
LYF HO15 HO15 H 0 0 N N N N N N -89.911 17.361 24.449 2.338  5.324  -0.755 HO15 LYF 39 
LYF HO17 HO17 H 0 0 N N N N N N -91.498 10.450 24.443 4.577  0.994  -0.468 HO17 LYF 40 
LYF H18  H18  H 0 1 N N N N N N -89.413 10.422 25.185 2.832  -2.448 -1.169 H18  LYF 41 
LYF H18A H18A H 0 0 N N N N N N -89.317 10.612 23.393 4.468  -1.755 -1.273 H18A LYF 42 
LYF HO21 HO21 H 0 0 N N N N N N -86.098 11.397 25.504 5.036  -5.229 -0.246 HO21 LYF 43 
LYF HXT  HXT  H 0 1 N Y N Y N Y -92.890 12.055 33.604 -8.085 0.138  0.673  HXT  LYF 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 
LYF CA  C    SING N N 1  
LYF C   O    DOUB N N 2  
LYF C   OXT  SING N N 3  
LYF CA  N    SING N N 4  
LYF N   H    SING N N 5  
LYF N   H2   SING N N 6  
LYF CB  CA   SING N N 7  
LYF CA  HA   SING N N 8  
LYF CG  CB   SING N N 9  
LYF CB  HB   SING N N 10 
LYF CB  HBA  SING N N 11 
LYF CE  CD   SING N N 12 
LYF CD  CG   SING N N 13 
LYF CD  HD   SING N N 14 
LYF CD  HDA  SING N N 15 
LYF NZ  CE   SING N N 16 
LYF CE  HE   SING N N 17 
LYF CE  HEA  SING N N 18 
LYF CG  HG   SING N N 19 
LYF CG  HGA  SING N N 20 
LYF C41 NZ   DOUB N N 21 
LYF C11 C12  SING N N 22 
LYF C11 C41  SING N N 23 
LYF C11 H11  SING N N 24 
LYF C11 H11A SING N N 25 
LYF O17 C12  SING N N 26 
LYF C13 C12  SING N N 27 
LYF C12 H12  SING N N 28 
LYF C18 C13  SING N N 29 
LYF C13 H13  SING N N 30 
LYF C13 H13A SING N N 31 
LYF O16 C14  DOUB N N 32 
LYF C14 O15  SING N N 33 
LYF C14 C41  SING N N 34 
LYF O15 HO15 SING N N 35 
LYF O17 HO17 SING N N 36 
LYF C18 C20  SING N N 37 
LYF C18 H18  SING N N 38 
LYF C18 H18A SING N N 39 
LYF O22 C20  DOUB N N 40 
LYF C20 O21  SING N N 41 
LYF O21 HO21 SING N N 42 
LYF OXT HXT  SING N N 43 
# 
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 
LYF SMILES           ACDLabs              12.01 "O=C(O)C(N)CCCC/N=C(/C(=O)O)CC(O)CCC(=O)O"                                                                                                         
LYF InChI            InChI                1.03  "InChI=1S/C13H22N2O7/c14-9(12(19)20)3-1-2-6-15-10(13(21)22)7-8(16)4-5-11(17)18/h8-9,16H,1-7,14H2,(H,17,18)(H,19,20)(H,21,22)/b15-10+/t8-,9-/m0/s1" 
LYF InChIKey         InChI                1.03  SZZIBLQGBUJBOW-GLLKNPCHSA-N                                                                                                                        
LYF SMILES_CANONICAL CACTVS               3.370 "N[C@@H](CCCCN=C(C[C@@H](O)CCC(O)=O)C(O)=O)C(O)=O"                                                                                                 
LYF SMILES           CACTVS               3.370 "N[CH](CCCCN=C(C[CH](O)CCC(O)=O)C(O)=O)C(O)=O"                                                                                                     
LYF SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "C(CC/N=C(\C[C@H](CCC(=O)O)O)/C(=O)O)C[C@@H](C(=O)O)N"                                                                                             
LYF SMILES           "OpenEye OEToolkits" 1.7.2 "C(CCN=C(CC(CCC(=O)O)O)C(=O)O)CC(C(=O)O)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 
LYF "SYSTEMATIC NAME" ACDLabs              12.01 "(2E,4S)-2-{[(5S)-5-amino-5-carboxypentyl]imino}-4-hydroxyheptanedioic acid"                   
LYF "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "(2E,4S)-2-[(5S)-5-azanyl-6-oxidanyl-6-oxidanylidene-hexyl]imino-4-oxidanyl-heptanedioic 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 
LYF "Create component" 2011-10-25 RCSB 
LYF "Modify backbone"  2023-11-03 PDBE 
# 
