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 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 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 _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 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 LYF "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id LYF _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 ? #