data_LYZ # _chem_comp.id LYZ _chem_comp.name 5-HYDROXYLYSINE _chem_comp.type "L-PEPTIDE LINKING" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C6 H14 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 1999-07-08 _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 162.187 _chem_comp.one_letter_code K _chem_comp.three_letter_code LYZ _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1QGW _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 LYZ N N N 0 1 N N N Y Y N 17.961 47.415 21.951 -1.859 0.261 -1.666 N LYZ 1 LYZ CA CA C 0 1 N N S Y N N 16.666 47.930 22.340 -0.411 0.504 -1.613 CA LYZ 2 LYZ C C C 0 1 N N N Y N Y 15.596 47.795 21.264 0.237 -0.061 -2.849 C LYZ 3 LYZ O O O 0 1 N N N Y N Y 14.487 48.310 21.421 -0.243 -1.025 -3.397 O LYZ 4 LYZ CB CB C 0 1 N N N N N N 16.752 49.385 22.839 0.174 -0.172 -0.373 CB LYZ 5 LYZ CG CG C 0 1 N N N N N N 17.680 49.561 24.034 -0.485 0.402 0.881 CG LYZ 6 LYZ CD CD C 0 1 N N R N N N 18.168 50.988 24.182 0.100 -0.275 2.121 CD LYZ 7 LYZ CE CE C 0 1 N N N N N N 19.047 51.131 25.418 -0.558 0.300 3.376 CE LYZ 8 LYZ NZ NZ N 0 1 N N N N N N 19.374 52.580 25.620 0.003 -0.350 4.567 NZ LYZ 9 LYZ OH OH O 0 1 N N N N N N 16.932 51.595 24.631 1.509 -0.038 2.173 OH LYZ 10 LYZ OXT OXT O 0 1 N Y N Y N Y 15.840 47.022 20.208 1.350 0.504 -3.342 OXT LYZ 11 LYZ H H H 0 1 N N N Y Y N 18.677 47.505 22.671 -2.236 0.561 -0.779 H LYZ 12 LYZ H2 HN2 H 0 1 N Y N Y Y N 18.271 47.847 21.081 -1.984 -0.738 -1.711 H2 LYZ 13 LYZ HA HA H 0 1 N N N Y N N 16.343 47.280 23.186 -0.225 1.577 -1.564 HA LYZ 14 LYZ HB2 1HB H 0 1 N N N N N N 17.041 50.071 22.009 1.248 0.007 -0.334 HB2 LYZ 15 LYZ HB3 2HB H 0 1 N N N N N N 15.736 49.786 23.064 -0.012 -1.245 -0.422 HB3 LYZ 16 LYZ HG2 1HG H 0 1 N N N N N N 17.198 49.201 24.973 -1.559 0.222 0.842 HG2 LYZ 17 LYZ HG3 2HG H 0 1 N N N N N N 18.535 48.846 23.987 -0.298 1.475 0.931 HG3 LYZ 18 LYZ HD HD H 0 1 N N N N N N 18.697 51.367 23.276 -0.086 -1.347 2.072 HD LYZ 19 LYZ HE2 1HE H 0 1 N N N N N N 18.585 50.669 26.322 -1.633 0.119 3.337 HE2 LYZ 20 LYZ HE3 2HE H 0 1 N N N N N N 19.960 50.493 25.365 -0.372 1.372 3.426 HE3 LYZ 21 LYZ HZ1 1HZ H 0 1 N N N N N N 19.962 52.675 26.447 -0.457 0.058 5.366 HZ1 LYZ 22 LYZ HZ2 2HZ H 0 1 N N N N N N 18.538 53.163 25.667 -0.280 -1.317 4.531 HZ2 LYZ 23 LYZ HH HO H 0 1 N N N N N N 17.237 52.489 24.723 1.630 0.920 2.215 HH LYZ 24 LYZ HXT HXT H 0 1 N Y N Y N Y 15.172 46.937 19.537 1.767 0.140 -4.135 HXT LYZ 25 # 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 LYZ N CA SING N N 1 LYZ N H SING N N 2 LYZ N H2 SING N N 3 LYZ CA C SING N N 4 LYZ CA CB SING N N 5 LYZ CA HA SING N N 6 LYZ C O DOUB N N 7 LYZ C OXT SING N N 8 LYZ CB CG SING N N 9 LYZ CB HB2 SING N N 10 LYZ CB HB3 SING N N 11 LYZ CG CD SING N N 12 LYZ CG HG2 SING N N 13 LYZ CG HG3 SING N N 14 LYZ CD CE SING N N 15 LYZ CD OH SING N N 16 LYZ CD HD SING N N 17 LYZ CE NZ SING N N 18 LYZ CE HE2 SING N N 19 LYZ CE HE3 SING N N 20 LYZ NZ HZ1 SING N N 21 LYZ NZ HZ2 SING N N 22 LYZ OH HH SING N N 23 LYZ OXT HXT SING N N 24 # 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 LYZ SMILES ACDLabs 10.04 "O=C(O)C(N)CCC(O)CN" LYZ SMILES_CANONICAL CACTVS 3.341 "NC[C@H](O)CC[C@H](N)C(O)=O" LYZ SMILES CACTVS 3.341 "NC[CH](O)CC[CH](N)C(O)=O" LYZ SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C(C[C@@H](C(=O)O)N)[C@H](CN)O" LYZ SMILES "OpenEye OEToolkits" 1.5.0 "C(CC(C(=O)O)N)C(CN)O" LYZ InChI InChI 1.03 "InChI=1S/C6H14N2O3/c7-3-4(9)1-2-5(8)6(10)11/h4-5,9H,1-3,7-8H2,(H,10,11)/t4-,5+/m1/s1" LYZ InChIKey InChI 1.03 YSMODUONRAFBET-UHNVWZDZSA-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 LYZ "SYSTEMATIC NAME" ACDLabs 10.04 "(5R)-5-hydroxy-L-lysine" LYZ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S,5R)-2,6-diamino-5-hydroxy-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 LYZ "Create component" 1999-07-08 RCSB LYZ "Modify descriptor" 2011-06-04 RCSB LYZ "Modify backbone" 2023-11-03 PDBE #