data_KHB # _chem_comp.id KHB _chem_comp.name "N~6~-[(3S)-3-hydroxybutanoyl]-L-lysine" _chem_comp.type "L-peptide linking" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C10 H20 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 2018-02-05 _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 232.277 _chem_comp.one_letter_code ? _chem_comp.three_letter_code KHB _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 5Z94 _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 KHB N N N 0 1 N N N Y Y N -12.125 11.395 -6.960 4.278 1.772 -0.200 N KHB 1 KHB CA CA C 0 1 N N S Y N N -11.096 11.089 -6.042 4.262 0.416 0.365 CA KHB 2 KHB C C C 0 1 N N N Y N Y -10.025 12.173 -6.084 5.519 -0.311 -0.037 C KHB 3 KHB O O O 0 1 N N N Y N Y -9.460 12.475 -7.170 6.160 0.072 -0.987 O KHB 4 KHB CB CB C 0 1 N N N N N N -10.532 9.749 -6.469 3.043 -0.342 -0.163 CB KHB 5 KHB CG CG C 0 1 N N N N N N -9.313 9.382 -5.621 1.765 0.326 0.350 CG KHB 6 KHB CD CD C 0 1 N N N N N N -8.860 7.942 -5.925 0.546 -0.433 -0.178 CD KHB 7 KHB CE CE C 0 1 N N N N N N -7.486 7.653 -5.327 -0.732 0.235 0.335 CE KHB 8 KHB C1 C1 C 0 1 N N N N N N -6.160 5.604 -4.905 -3.141 -0.080 0.154 C1 KHB 9 KHB C2 C2 C 0 1 N N N N N N -5.795 4.173 -5.282 -4.342 -0.827 -0.367 C2 KHB 10 KHB C3 C3 C 0 1 N N S N N N -5.637 3.364 -4.011 -5.619 -0.160 0.146 C3 KHB 11 KHB C4 C4 C 0 1 N N N N N N -5.421 1.907 -4.362 -6.834 -0.988 -0.278 C4 KHB 12 KHB NZ NZ N 0 1 N N N N N N -7.135 6.298 -5.688 -1.899 -0.491 -0.171 NZ KHB 13 KHB O2 O2 O 0 1 N N N N N N -6.806 3.506 -3.249 -5.724 1.155 -0.405 O2 KHB 14 KHB O1 O1 O 0 1 N N N N N N -5.649 6.166 -3.955 -3.292 0.891 0.865 O1 KHB 15 KHB OXT OXT O 0 1 N Y N Y N Y -9.741 12.766 -4.930 5.926 -1.384 0.659 OXT KHB 16 KHB H H H 0 1 N N N Y Y N -12.534 12.276 -6.722 4.327 1.743 -1.207 H KHB 17 KHB H2 HN2 H 0 1 N Y N Y Y N -11.744 11.443 -7.883 3.477 2.302 0.109 HN2 KHB 18 KHB HA HA H 0 1 N N N Y N N -11.493 11.010 -5.019 4.209 0.477 1.452 HA KHB 19 KHB HB2 HB2 H 0 1 N N N N N N -11.304 8.976 -6.345 3.049 -0.326 -1.253 HB2 KHB 20 KHB HB3 HB3 H 0 1 N N N N N N -10.234 9.803 -7.526 3.078 -1.374 0.185 HB3 KHB 21 KHB HG2 HG2 H 0 1 N N N N N N -8.491 10.076 -5.849 1.759 0.309 1.440 HG2 KHB 22 KHB HG3 HG3 H 0 1 N N N N N N -9.575 9.462 -4.556 1.730 1.358 0.002 HG3 KHB 23 KHB HD2 HD2 H 0 1 N N N N N N -9.591 7.239 -5.499 0.552 -0.416 -1.268 HD2 KHB 24 KHB HD3 HD3 H 0 1 N N N N N N -8.812 7.804 -7.015 0.581 -1.465 0.170 HD3 KHB 25 KHB HE2 HE2 H 0 1 N N N N N N -6.743 8.355 -5.734 -0.738 0.219 1.424 HE2 KHB 26 KHB HE3 HE3 H 0 1 N N N N N N -7.524 7.753 -4.232 -0.767 1.267 -0.013 HE3 KHB 27 KHB H22 H22 H 0 1 N N N N N N -6.593 3.738 -5.901 -4.336 -0.811 -1.457 H22 KHB 28 KHB H23 H23 H 0 1 N N N N N N -4.850 4.168 -5.845 -4.307 -1.860 -0.019 H23 KHB 29 KHB H32 H32 H 0 1 N N N N N N -4.763 3.734 -3.455 -5.585 -0.096 1.234 H32 KHB 30 KHB H41 H41 H 0 1 N N N N N N -5.306 1.320 -3.439 -6.754 -1.991 0.142 H41 KHB 31 KHB H42 H42 H 0 1 N N N N N N -6.287 1.534 -4.928 -7.744 -0.512 0.087 H42 KHB 32 KHB H43 H43 H 0 1 N N N N N N -4.513 1.808 -4.974 -6.868 -1.051 -1.366 H43 KHB 33 KHB H19 H19 H 0 1 N N N N N N -7.567 5.853 -6.473 -1.778 -1.267 -0.740 H19 KHB 34 KHB HO2 HO2 H 0 1 N N N N N N -6.987 4.429 -3.115 -6.512 1.638 -0.122 HO2 KHB 35 KHB HXT HXT H 0 1 N Y N Y N Y -9.070 13.424 -5.068 6.738 -1.817 0.363 HXT KHB 36 # 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 KHB O C DOUB N N 1 KHB N CA SING N N 2 KHB CB CA SING N N 3 KHB CB CG SING N N 4 KHB C CA SING N N 5 KHB CD CG SING N N 6 KHB CD CE SING N N 7 KHB NZ CE SING N N 8 KHB NZ C1 SING N N 9 KHB C2 C1 SING N N 10 KHB C2 C3 SING N N 11 KHB C1 O1 DOUB N N 12 KHB C4 C3 SING N N 13 KHB C3 O2 SING N N 14 KHB C OXT SING N N 15 KHB N H SING N N 16 KHB N H2 SING N N 17 KHB CA HA SING N N 18 KHB CB HB2 SING N N 19 KHB CB HB3 SING N N 20 KHB CG HG2 SING N N 21 KHB CG HG3 SING N N 22 KHB CD HD2 SING N N 23 KHB CD HD3 SING N N 24 KHB CE HE2 SING N N 25 KHB CE HE3 SING N N 26 KHB C2 H22 SING N N 27 KHB C2 H23 SING N N 28 KHB C3 H32 SING N N 29 KHB C4 H41 SING N N 30 KHB C4 H42 SING N N 31 KHB C4 H43 SING N N 32 KHB NZ H19 SING N N 33 KHB O2 HO2 SING N N 34 KHB OXT HXT SING N N 35 # 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 KHB SMILES ACDLabs 12.01 "NC(C(O)=O)CCCCNC(=O)CC(O)C" KHB InChI InChI 1.03 "InChI=1S/C10H20N2O4/c1-7(13)6-9(14)12-5-3-2-4-8(11)10(15)16/h7-8,13H,2-6,11H2,1H3,(H,12,14)(H,15,16)/t7-,8-/m0/s1" KHB InChIKey InChI 1.03 NFPICWYWQOLZEW-YUMQZZPRSA-N KHB SMILES_CANONICAL CACTVS 3.385 "C[C@H](O)CC(=O)NCCCC[C@H](N)C(O)=O" KHB SMILES CACTVS 3.385 "C[CH](O)CC(=O)NCCCC[CH](N)C(O)=O" KHB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C[C@@H](CC(=O)NCCCC[C@@H](C(=O)O)N)O" KHB SMILES "OpenEye OEToolkits" 2.0.6 "CC(CC(=O)NCCCCC(C(=O)O)N)O" # 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 KHB "SYSTEMATIC NAME" ACDLabs 12.01 "N~6~-[(3S)-3-hydroxybutanoyl]-L-lysine" KHB "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "(2~{S})-2-azanyl-6-[[(3~{S})-3-oxidanylbutanoyl]amino]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 KHB "Create component" 2018-02-05 RCSB KHB "Initial release" 2019-02-06 RCSB KHB "Modify backbone" 2023-11-03 PDBE KHB "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id KHB _pdbx_chem_comp_pcm.modified_residue_id LYS _pdbx_chem_comp_pcm.type Beta-hydroxybutyrylation _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 ? #