data_8RE # _chem_comp.id 8RE _chem_comp.name 3,4-dihydroxylysine _chem_comp.type "L-peptide linking" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C6 H14 N2 O4" _chem_comp.mon_nstd_parent_comp_id LYS _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-02-28 _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 178.186 _chem_comp.one_letter_code K _chem_comp.three_letter_code 8RE _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 5N9Z _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 8RE O O1 O 0 1 N N N Y N Y 3.776 -21.097 75.759 -3.337 -0.421 -0.891 O 8RE 1 8RE C C1 C 0 1 N N N Y N Y 3.402 -21.221 76.918 -2.715 0.187 -0.052 C 8RE 2 8RE CA C2 C 0 1 N N S Y N N 4.212 -22.082 77.897 -1.426 -0.378 0.488 CA 8RE 3 8RE N N1 N 0 1 N N N Y Y N 3.850 -21.778 79.262 -1.380 -1.824 0.230 N 8RE 4 8RE CB C3 C 0 1 N N R N N N 3.879 -23.560 78.101 -0.242 0.302 -0.203 CB 8RE 5 8RE OH1 O2 O 0 1 N N N N N N 2.655 -24.009 77.540 -0.288 1.708 0.047 OH1 8RE 6 8RE CG C4 C 0 1 N N S N N N 5.065 -24.543 78.041 1.066 -0.272 0.345 CG 8RE 7 8RE OH2 O3 O 0 1 N N N N N N 4.684 -25.791 77.442 1.111 -1.678 0.095 OH2 8RE 8 8RE CD C5 C 0 1 N N N N N N 6.377 -24.010 77.461 2.250 0.408 -0.345 CD 8RE 9 8RE CE C6 C 0 1 N N N N N N 7.420 -25.073 77.789 3.556 -0.074 0.289 CE 8RE 10 8RE NZ N2 N 0 1 N N N N N N 8.699 -24.756 77.185 4.693 0.578 -0.374 NZ 8RE 11 8RE HA H2 H 0 1 N N N Y N N 5.290 -21.951 77.722 -1.373 -0.198 1.561 H2 8RE 12 8RE H H3 H 0 1 N N N Y Y N 4.387 -22.347 79.884 -2.114 -2.303 0.729 H3 8RE 13 8RE H2 H4 H 0 1 N Y N Y Y N 4.036 -20.813 79.449 -1.428 -2.016 -0.759 H4 8RE 14 8RE HB2 H6 H 0 1 N N N N N N 3.652 -23.576 79.177 -0.296 0.122 -1.277 H6 8RE 15 8RE H7 H7 H 0 1 N N N N N N 2.544 -24.935 77.722 -0.244 1.942 0.984 H7 8RE 16 8RE HG2 H8 H 0 1 N N N N N N 5.293 -24.771 79.093 1.119 -0.092 1.419 H8 8RE 17 8RE H9 H9 H 0 1 N N N N N N 3.868 -26.091 77.825 1.068 -1.912 -0.842 H9 8RE 18 8RE HD2 H10 H 0 1 N N N N N N 6.644 -23.051 77.928 2.246 0.155 -1.406 H10 8RE 19 8RE HD3 H11 H 0 1 N N N N N N 6.291 -23.876 76.372 2.167 1.488 -0.229 H11 8RE 20 8RE HE2 H12 H 0 1 N N N N N N 7.074 -26.045 77.407 3.559 0.179 1.350 H12 8RE 21 8RE HE3 H13 H 0 1 N N N N N N 7.543 -25.130 78.881 3.639 -1.155 0.174 H13 8RE 22 8RE HZ1 H14 H 0 1 N N N N N N 9.363 -25.468 77.416 4.605 1.583 -0.336 H14 8RE 23 8RE HZ2 H15 H 0 1 N N N N N N 8.595 -24.706 76.192 5.568 0.276 0.028 H15 8RE 24 8RE OXT O4 O 0 1 N Y N Y N Y 2.328 -20.578 77.377 -3.169 1.368 0.394 O1 8RE 25 8RE HXT H1 H 0 1 N Y N Y N Y 1.951 -20.053 76.681 -3.998 1.692 0.015 H1 8RE 26 # 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 8RE O C DOUB N N 1 8RE C CA SING N N 2 8RE NZ CE SING N N 3 8RE OH2 CG SING N N 4 8RE CD CE SING N N 5 8RE CD CG SING N N 6 8RE OH1 CB SING N N 7 8RE CA CB SING N N 8 8RE CA N SING N N 9 8RE CG CB SING N N 10 8RE CA HA SING N N 11 8RE N H SING N N 12 8RE N H2 SING N N 13 8RE CB HB2 SING N N 14 8RE OH1 H7 SING N N 15 8RE CG HG2 SING N N 16 8RE OH2 H9 SING N N 17 8RE CD HD2 SING N N 18 8RE CD HD3 SING N N 19 8RE CE HE2 SING N N 20 8RE CE HE3 SING N N 21 8RE NZ HZ1 SING N N 22 8RE NZ HZ2 SING N N 23 8RE C OXT SING N N 24 8RE OXT HXT SING N N 25 # 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 8RE InChI InChI 1.03 "InChI=1S/C6H14N2O4/c7-2-1-3(9)5(10)4(8)6(11)12/h3-5,9-10H,1-2,7-8H2,(H,11,12)/t3-,4-,5-/m0/s1" 8RE InChIKey InChI 1.03 ALWBRQWTMGZSIM-YUPRTTJUSA-N 8RE SMILES_CANONICAL CACTVS 3.385 "NCC[C@H](O)[C@H](O)[C@H](N)C(O)=O" 8RE SMILES CACTVS 3.385 "NCC[CH](O)[CH](O)[CH](N)C(O)=O" 8RE SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C(CN)[C@@H]([C@@H]([C@@H](C(=O)O)N)O)O" 8RE SMILES "OpenEye OEToolkits" 2.0.6 "C(CN)C(C(C(C(=O)O)N)O)O" # _pdbx_chem_comp_identifier.comp_id 8RE _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.6 _pdbx_chem_comp_identifier.identifier "(2~{S},3~{R},4~{S})-2,6-bis(azanyl)-3,4-bis(oxidanyl)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 8RE "Create component" 2017-02-28 EBI 8RE "Initial release" 2018-03-14 RCSB 8RE "Modify one letter code" 2019-05-03 EBI 8RE "Modify backbone" 2023-11-03 PDBE 8RE "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id 8RE _pdbx_chem_comp_pcm.modified_residue_id LYS _pdbx_chem_comp_pcm.type Hydroxylation _pdbx_chem_comp_pcm.category "Named protein modification" _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 ? #