data_K5L # _chem_comp.id K5L _chem_comp.name "(2~{R})-2-azanyl-3-(3-oxidanyl-3-oxidanylidene-propanoyl)oxy-propanoic acid" _chem_comp.type "L-peptide linking" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C6 H9 N O6" _chem_comp.mon_nstd_parent_comp_id SER _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-01-25 _chem_comp.pdbx_modified_date 2024-10-02 _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 191.139 _chem_comp.one_letter_code S _chem_comp.three_letter_code K5L _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 5MY0 _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 K5L O O1 O 0 1 N N N Y N Y 21.062 27.918 63.127 -4.205 0.094 0.926 O K5L 1 K5L C C1 C 0 1 N N N Y N Y 22.199 27.962 63.503 -3.554 0.293 -0.073 C K5L 2 K5L CA C2 C 0 1 N N R Y N N 22.986 26.735 63.855 -2.345 -0.557 -0.366 CA K5L 3 K5L N N1 N 0 1 N N N Y Y N 22.571 25.581 63.102 -2.431 -1.810 0.396 N K5L 4 K5L CB C3 C 0 1 N N N N N N 23.128 26.656 65.276 -1.079 0.201 0.038 CB K5L 5 K5L OAI O2 O 0 1 N N N N N N 24.908 26.560 65.576 0.090 -0.567 -0.352 OAI K5L 6 K5L CAK C4 C 0 1 N N N N N N 25.744 28.170 65.618 1.290 -0.037 -0.067 CAK K5L 7 K5L OAC O3 O 0 1 N N N N N N 26.468 28.500 64.741 1.361 1.032 0.491 OAC K5L 8 K5L CAG C5 C 0 1 N N N N N N 25.526 29.105 66.824 2.549 -0.777 -0.442 CAG K5L 9 K5L CAJ C6 C 0 1 N N N N N N 24.091 29.748 66.992 3.750 0.027 -0.014 CAJ K5L 10 K5L OAE O4 O 0 1 N N N N N N 23.791 30.988 66.923 3.599 1.090 0.539 OAE K5L 11 K5L OAB O5 O 0 1 N N N N N N 23.036 29.061 67.231 4.987 -0.440 -0.247 OAB K5L 12 K5L H2 H2 H 0 1 N N N Y N N 23.999 26.955 63.487 -2.309 -0.782 -1.432 H2 K5L 13 K5L H3 H3 H 0 1 N N N Y Y N 23.122 24.791 63.371 -2.465 -1.628 1.388 H3 K5L 14 K5L H4 H4 H 0 1 N Y N Y Y N 21.606 25.392 63.286 -3.224 -2.359 0.101 H4 K5L 15 K5L H6 H6 H 0 1 N N N N N N 22.705 27.551 65.755 -1.060 1.170 -0.460 H6 K5L 16 K5L H7 H7 H 0 1 N N N N N N 22.623 25.759 65.664 -1.073 0.348 1.118 H7 K5L 17 K5L H8 H8 H 0 1 N N N N N N 25.737 28.525 67.734 2.563 -1.746 0.057 H8 K5L 18 K5L H9 H9 H 0 1 N N N N N N 26.250 29.929 66.738 2.576 -0.924 -1.521 H9 K5L 19 K5L H10 H10 H 0 1 N N N N N N 22.288 29.642 67.299 5.726 0.111 0.046 H10 K5L 20 K5L OXT OXT O 0 1 N Y N Y N Y 22.920 29.056 63.556 -3.912 1.267 -0.924 OXT K5L 21 K5L H1 H1 H 0 1 N Y N Y N Y 22.402 29.792 63.253 -4.698 1.783 -0.695 H1 K5L 22 # 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 K5L N CA SING N N 1 K5L O C DOUB N N 2 K5L C CA SING N N 3 K5L CA CB SING N N 4 K5L OAC CAK DOUB N N 5 K5L CB OAI SING N N 6 K5L OAI CAK SING N N 7 K5L CAK CAG SING N N 8 K5L CAG CAJ SING N N 9 K5L OAE CAJ DOUB N N 10 K5L CAJ OAB SING N N 11 K5L CA H2 SING N N 12 K5L N H3 SING N N 13 K5L N H4 SING N N 14 K5L CB H6 SING N N 15 K5L CB H7 SING N N 16 K5L CAG H8 SING N N 17 K5L CAG H9 SING N N 18 K5L OAB H10 SING N N 19 K5L C OXT SING N N 20 K5L OXT H1 SING N N 21 # 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 K5L InChI InChI 1.03 "InChI=1S/C6H9NO6/c7-3(6(11)12)2-13-5(10)1-4(8)9/h3H,1-2,7H2,(H,8,9)(H,11,12)/t3-/m1/s1" K5L InChIKey InChI 1.03 IAJQGHDQMBZRHZ-GSVOUGTGSA-N K5L SMILES_CANONICAL CACTVS 3.385 "N[C@H](COC(=O)CC(O)=O)C(O)=O" K5L SMILES CACTVS 3.385 "N[CH](COC(=O)CC(O)=O)C(O)=O" K5L SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C([C@H](C(=O)O)N)OC(=O)CC(=O)O" K5L SMILES "OpenEye OEToolkits" 2.0.6 "C(C(C(=O)O)N)OC(=O)CC(=O)O" # _pdbx_chem_comp_identifier.comp_id K5L _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~{R})-2-azanyl-3-(3-oxidanyl-3-oxidanylidene-propanoyl)oxy-propanoic 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 K5L "Create component" 2017-01-25 EBI K5L "Other modification" 2017-01-26 EBI K5L "Initial release" 2018-01-24 RCSB K5L "Modify PCM" 2024-09-27 PDBE K5L "Modify backbone" 2024-10-02 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id K5L _pdbx_chem_comp_pcm.modified_residue_id DSN _pdbx_chem_comp_pcm.type Malonylation _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 ? #