data_LGY # _chem_comp.id LGY _chem_comp.name "(E)-N~6~-(4-oxobutylidene)-L-lysine" _chem_comp.type "L-PEPTIDE LINKING" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C10 H18 N2 O3" _chem_comp.mon_nstd_parent_comp_id LYS _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-07-16 _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 214.262 _chem_comp.one_letter_code ? _chem_comp.three_letter_code LGY _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 3NX8 _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 LGY OXT OXT O 0 1 N Y N Y N Y 33.816 -18.826 5.714 4.846 2.033 -0.800 OXT LGY 1 LGY C C C 0 1 N N N Y N Y 34.400 -17.819 5.070 4.828 0.926 -0.040 C LGY 2 LGY N N N 0 1 N N N Y Y N 32.649 -16.418 6.062 4.350 -1.437 0.262 N LGY 3 LGY O O O 0 1 N N N Y N Y 35.337 -17.959 4.298 5.576 0.830 0.904 O LGY 4 LGY N1 N1 N 0 1 N N N N N N 38.284 -12.552 7.738 -2.228 -1.343 0.337 N1 LGY 5 LGY C3 C3 C 0 1 N N N N N N 39.797 -10.982 8.784 -4.547 -0.733 0.047 C3 LGY 6 LGY C4 C4 C 0 1 N N N N N N 40.539 -9.854 8.019 -4.988 0.622 -0.511 C4 LGY 7 LGY C5 C5 C 0 1 N N N N N N 40.505 -8.543 8.773 -6.360 0.959 0.014 C5 LGY 8 LGY O6 O6 O 0 1 N N N N N N 41.133 -7.584 8.341 -6.546 2.002 0.593 O6 LGY 9 LGY CA CA C 0 1 N N S Y N N 33.991 -16.421 5.489 3.877 -0.196 -0.366 CA LGY 10 LGY CB CB C 0 1 N N N N N N 35.022 -15.926 6.538 2.484 0.146 0.168 CB LGY 11 LGY CD CD C 0 1 N N N N N N 36.606 -13.944 6.624 0.098 -0.591 0.264 CD LGY 12 LGY CE CE C 0 1 N N N N N N 36.866 -12.891 7.710 -0.894 -1.671 -0.174 CE LGY 13 LGY CG CG C 0 1 N N N N N N 35.133 -14.397 6.629 1.491 -0.933 -0.270 CG LGY 14 LGY C11 C11 C 0 1 N N N N N N 38.491 -11.360 8.143 -3.175 -1.070 -0.478 C11 LGY 15 LGY H HN H 0 1 N N N Y Y N 32.403 -15.487 6.330 4.403 -1.338 1.265 HN LGY 16 LGY H2 HNA H 0 1 N Y N Y Y N 31.996 -16.753 5.383 3.765 -2.218 0.006 HNA LGY 17 LGY H3 H3 H 0 1 N N N N N N 40.444 -11.871 8.803 -4.518 -0.686 1.135 H3 LGY 18 LGY H3A H3A H 0 1 N N N N N N 39.593 -10.631 9.806 -5.254 -1.502 -0.265 H3A LGY 19 LGY H4 H4 H 0 1 N N N N N N 41.588 -10.154 7.881 -4.281 1.391 -0.199 H4 LGY 20 LGY H4A H4A H 0 1 N N N N N N 40.052 -9.711 7.043 -5.017 0.575 -1.599 H4A LGY 21 LGY H5 H5 H 0 1 N N N N N N 39.932 -8.453 9.684 -7.177 0.267 -0.127 H5 LGY 22 LGY HA HA H 0 1 N N N Y N N 33.975 -15.756 4.613 3.829 -0.331 -1.446 HA LGY 23 LGY HB HB H 0 1 N N N N N N 34.713 -16.304 7.524 2.513 0.193 1.256 HB LGY 24 LGY HBA HBA H 0 1 N N N N N N 36.009 -16.323 6.258 2.170 1.111 -0.229 HBA LGY 25 LGY HD HD H 0 1 N N N N N N 36.842 -13.509 5.642 -0.216 0.374 -0.134 HD LGY 26 LGY HDA HDA H 0 1 N N N N N N 37.248 -14.817 6.813 0.128 -0.544 1.352 HDA LGY 27 LGY HE HE H 0 1 N N N N N N 36.568 -13.295 8.689 -0.580 -2.636 0.223 HE LGY 28 LGY HEA HEA H 0 1 N N N N N N 36.279 -11.987 7.490 -0.923 -1.718 -1.263 HEA LGY 29 LGY HG HG H 0 1 N N N N N N 34.620 -13.950 5.765 1.462 -0.980 -1.358 HG LGY 30 LGY HGA HGA H 0 1 N N N N N N 34.660 -14.060 7.563 1.806 -1.898 0.127 HGA LGY 31 LGY H11 H11 H 0 1 N N N N N N 37.719 -10.614 8.024 -2.992 -1.080 -1.543 H11 LGY 32 LGY HXT HOXT H 0 0 N Y N Y N Y 34.240 -19.642 5.477 5.473 2.725 -0.552 HOXT LGY 33 # 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 LGY OXT C SING N N 1 LGY C O DOUB N N 2 LGY C CA SING N N 3 LGY N CA SING N N 4 LGY N1 CE SING N N 5 LGY N1 C11 DOUB N N 6 LGY C3 C4 SING N N 7 LGY C3 C11 SING N N 8 LGY C4 C5 SING N N 9 LGY C5 O6 DOUB N N 10 LGY CA CB SING N N 11 LGY CB CG SING N N 12 LGY CD CE SING N N 13 LGY CD CG SING N N 14 LGY N H SING N N 15 LGY N H2 SING N N 16 LGY C3 H3 SING N N 17 LGY C3 H3A SING N N 18 LGY C4 H4 SING N N 19 LGY C4 H4A SING N N 20 LGY C5 H5 SING N N 21 LGY CA HA SING N N 22 LGY CB HB SING N N 23 LGY CB HBA SING N N 24 LGY CD HD SING N N 25 LGY CD HDA SING N N 26 LGY CE HE SING N N 27 LGY CE HEA SING N N 28 LGY CG HG SING N N 29 LGY CG HGA SING N N 30 LGY C11 H11 SING N N 31 LGY OXT HXT SING N N 32 # 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 LGY SMILES ACDLabs 12.01 "O=C(O)C(N)CCCC/N=C/CCC=O" LGY SMILES_CANONICAL CACTVS 3.370 "N[C@@H](CCCCN=CCCC=O)C(O)=O" LGY SMILES CACTVS 3.370 "N[CH](CCCCN=CCCC=O)C(O)=O" LGY SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C(CC/N=C/CCC=O)C[C@@H](C(=O)O)N" LGY SMILES "OpenEye OEToolkits" 1.7.0 "C(CCN=CCCC=O)CC(C(=O)O)N" LGY InChI InChI 1.03 "InChI=1S/C10H18N2O3/c11-9(10(14)15)5-1-2-6-12-7-3-4-8-13/h7-9H,1-6,11H2,(H,14,15)/b12-7+/t9-/m0/s1" LGY InChIKey InChI 1.03 QHNKFGZIDRMVOP-SZUMLMDFSA-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 LGY "SYSTEMATIC NAME" ACDLabs 12.01 "(E)-N~6~-(4-oxobutylidene)-L-lysine" LGY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "(2S)-2-azanyl-6-[(E)-4-oxobutylideneamino]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 LGY "Create component" 2010-07-16 RCSB LGY "Modify descriptor" 2011-06-04 RCSB LGY "Modify backbone" 2023-11-03 PDBE LGY "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id LGY _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 ? #