data_J8W # _chem_comp.id J8W _chem_comp.name "(2~{S})-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 2019-02-11 _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 191.139 _chem_comp.one_letter_code S _chem_comp.three_letter_code J8W _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 6QL9 _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 J8W N N N 0 1 N N N Y Y N 89.655 -78.248 20.184 2.435 1.816 -0.392 N J8W 1 J8W CA CA C 0 1 N N S Y N N 89.428 -78.931 21.449 2.352 0.562 0.368 CA J8W 2 J8W CB CB C 0 1 N N N N N N 90.057 -78.087 22.571 1.088 -0.198 -0.038 CB J8W 3 J8W OG OG O 0 1 N N N N N N 89.098 -77.693 23.577 -0.083 0.566 0.353 OG J8W 4 J8W C C C 0 1 N N N Y N Y 87.943 -79.299 21.575 3.564 -0.285 0.073 C J8W 5 J8W O O O 0 1 N N N Y N Y 87.483 -80.209 20.900 4.214 -0.083 -0.925 O J8W 6 J8W C1 C1 C 0 1 N N N N N N 89.563 -78.001 26.037 -2.542 0.770 0.443 C1 J8W 7 J8W C2 C2 C 0 1 N N N N N N 89.281 -77.067 24.898 -1.282 0.034 0.067 C2 J8W 8 J8W C3 C3 C 0 1 N N N N N N 88.674 -79.215 25.904 -3.741 -0.035 0.014 C3 J8W 9 J8W O7 O7 O 0 1 N N N N N N 89.122 -75.864 25.075 -1.350 -1.035 -0.492 O7 J8W 10 J8W O8 O8 O 0 1 N N N N N N 87.450 -79.081 26.080 -4.979 0.428 0.247 O8 J8W 11 J8W O9 O9 O 0 1 N N N N N N 89.103 -80.351 25.548 -3.588 -1.098 -0.541 O9 J8W 12 J8W H H1 H 0 1 N N N Y Y N 90.623 -78.009 20.103 2.470 1.636 -1.385 H1 J8W 13 J8W H2 H2 H 0 1 N Y N Y Y N 89.396 -78.850 19.429 1.667 2.429 -0.163 H2 J8W 14 J8W HA H4 H 0 1 N N N Y N N 89.986 -79.879 21.419 2.315 0.785 1.434 H4 J8W 15 J8W H5 H5 H 0 1 N N N N N N 90.850 -78.677 23.053 1.082 -0.343 -1.118 H5 J8W 16 J8W H6 H6 H 0 1 N N N N N N 90.493 -77.180 22.127 1.071 -1.168 0.459 H6 J8W 17 J8W H8 H8 H 0 1 N N N N N N 90.618 -78.311 26.008 -2.569 0.915 1.523 H8 J8W 18 J8W H9 H9 H 0 1 N N N N N N 89.356 -77.494 26.991 -2.558 1.740 -0.054 H9 J8W 19 J8W H10 H10 H 0 1 N N N N N N 87.013 -79.906 25.907 -5.717 -0.124 -0.046 H10 J8W 20 J8W OXT OXT O 0 1 N Y N Y N Y 87.186 -78.551 22.388 3.920 -1.263 0.920 OXT J8W 21 J8W HXT H3 H 0 1 N Y N Y N Y 86.284 -78.845 22.341 4.705 -1.780 0.689 H3 J8W 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 J8W N CA SING N N 1 J8W O C DOUB N N 2 J8W CA C SING N N 3 J8W CA CB SING N N 4 J8W CB OG SING N N 5 J8W OG C2 SING N N 6 J8W C2 O7 DOUB N N 7 J8W C2 C1 SING N N 8 J8W O9 C3 DOUB N N 9 J8W C3 C1 SING N N 10 J8W C3 O8 SING N N 11 J8W N H SING N N 12 J8W N H2 SING N N 13 J8W CA HA SING N N 14 J8W CB H5 SING N N 15 J8W CB H6 SING N N 16 J8W C1 H8 SING N N 17 J8W C1 H9 SING N N 18 J8W O8 H10 SING N N 19 J8W C OXT SING N N 20 J8W OXT HXT 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 J8W 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-/m0/s1" J8W InChIKey InChI 1.03 IAJQGHDQMBZRHZ-VKHMYHEASA-N J8W SMILES_CANONICAL CACTVS 3.385 "N[C@@H](COC(=O)CC(O)=O)C(O)=O" J8W SMILES CACTVS 3.385 "N[CH](COC(=O)CC(O)=O)C(O)=O" J8W SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C([C@@H](C(=O)O)N)OC(=O)CC(=O)O" J8W SMILES "OpenEye OEToolkits" 2.0.7 "C(C(C(=O)O)N)OC(=O)CC(=O)O" # _pdbx_chem_comp_identifier.comp_id J8W _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "(2~{S})-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 J8W "Create component" 2019-02-11 RCSB J8W "Initial release" 2020-03-18 RCSB J8W "Modify backbone" 2023-11-03 PDBE J8W "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id J8W _pdbx_chem_comp_pcm.modified_residue_id SER _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 ? #