data_LKE # _chem_comp.id LKE _chem_comp.name "2-[(4~{Z})-2-(aminomethyl)-4-[(4-azidophenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic acid" _chem_comp.type "L-peptide linking" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C13 H12 N6 O3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-08-21 _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 300.273 _chem_comp.one_letter_code GYG _chem_comp.three_letter_code LKE _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 6SM0 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE _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 LKE CA1 CA1 C 0 1 N N N Y N N 24.466 4.990 0.823 2.491 2.363 -0.306 CA1 LKE 1 LKE N1 N1 N 0 1 N N N Y Y N 25.528 4.111 0.441 1.350 3.261 -0.086 N1 LKE 2 LKE C1 C1 C 0 1 N N N Y N N 23.960 4.347 2.066 2.006 0.937 -0.348 C1 LKE 3 LKE N2 N2 N 0 1 N N N Y N N 22.857 3.579 2.106 0.763 0.580 -0.209 N2 LKE 4 LKE N3 N3 N 0 1 N N N Y N N 24.610 4.389 3.234 2.813 -0.145 -0.543 N3 LKE 5 LKE CA3 CA3 C 0 1 N N N Y N N 25.818 5.038 3.655 4.265 -0.109 -0.740 CA3 LKE 6 LKE C3 C3 C 0 1 N N N Y N Y 25.329 6.472 3.791 4.955 -0.205 0.596 C3 LKE 7 LKE O3 O3 O 0 1 N N N Y N Y 24.142 6.947 3.328 4.302 -0.295 1.609 O3 LKE 8 LKE C2 C2 C 0 1 N N N Y N N 23.876 3.766 4.063 2.043 -1.256 -0.522 C2 LKE 9 LKE O2 O2 O 0 1 N N N Y N N 24.268 3.570 5.472 2.406 -2.409 -0.661 O2 LKE 10 LKE CA2 CA2 C 0 1 N N N Y N N 22.751 3.190 3.394 0.666 -0.767 -0.298 CA2 LKE 11 LKE CB2 CB2 C 0 1 N N N N N N 21.858 2.345 4.166 -0.488 -1.532 -0.202 CB2 LKE 12 LKE CG2 CG2 C 0 1 Y N N N N N 20.721 1.737 3.476 -1.747 -0.902 -0.127 CG2 LKE 13 LKE CD2 CD2 C 0 1 Y N N N N N 19.843 1.095 4.318 -1.836 0.489 -0.339 CD2 LKE 14 LKE CE2 CE2 C 0 1 Y N N N N N 18.703 0.500 3.799 -3.031 1.123 -0.273 CE2 LKE 15 LKE CZ CZ C 0 1 Y N N N N N 18.455 0.489 2.434 -4.240 0.346 0.021 CZ LKE 16 LKE CE1 CE1 C 0 1 Y N N N N N 19.336 1.191 1.624 -4.113 -1.100 0.236 CE1 LKE 17 LKE CD1 CD1 C 0 1 Y N N N N N 20.481 1.793 2.143 -2.891 -1.677 0.152 CD1 LKE 18 LKE NW NW N 0 1 N N N N N N 17.264 0.002 2.006 -5.418 0.936 0.091 NW LKE 19 LKE NX NX N 1 1 N N N N N N 16.551 0.527 0.867 -6.338 0.329 0.317 NX LKE 20 LKE NY NY N -1 1 N N N N N N 15.913 0.977 -0.086 -7.257 -0.277 0.544 NY LKE 21 LKE OXT OXT O 0 1 N Y N Y N Y 26.134 7.381 4.575 6.296 -0.192 0.661 OXT LKE 22 LKE HA1 H1 H 0 1 N N N Y N N 24.840 6.005 1.023 2.972 2.611 -1.252 H1 LKE 23 LKE HA2 H2 H 0 1 N N N Y N N 23.685 5.033 0.049 3.207 2.479 0.508 H2 LKE 24 LKE H H3 H 0 1 N N N Y Y N 25.953 4.447 -0.399 0.848 3.010 0.753 H3 LKE 25 LKE H2 H4 H 0 1 N Y N Y Y N 26.212 4.078 1.170 1.649 4.225 -0.053 H4 LKE 26 LKE HA31 H6 H 0 1 N N N Y N N 26.180 4.640 4.614 4.567 -0.948 -1.366 H6 LKE 27 LKE HA32 H7 H 0 1 N N N Y N N 26.612 4.950 2.898 4.542 0.826 -1.226 H7 LKE 28 LKE H8 H8 H 0 1 N N N N N N 22.028 2.171 5.218 -0.421 -2.610 -0.185 H8 LKE 29 LKE H9 H9 H 0 1 N N N N N N 20.041 1.054 5.379 -0.942 1.055 -0.555 H9 LKE 30 LKE H10 H10 H 0 1 N N N N N N 17.995 0.036 4.470 -3.093 2.189 -0.436 H10 LKE 31 LKE H11 H11 H 0 1 N N N N N N 19.130 1.273 0.567 -4.986 -1.699 0.450 H11 LKE 32 LKE H12 H12 H 0 1 N N N N N N 21.173 2.301 1.487 -2.790 -2.741 0.309 H12 LKE 33 LKE HXT H14 H 0 1 N Y N Y N Y 25.687 8.216 4.651 6.693 -0.256 1.541 H14 LKE 34 # 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 LKE NY NX DOUB N N 1 LKE N1 CA1 SING N N 2 LKE CA1 C1 SING N N 3 LKE NX NW DOUB N N 4 LKE CE1 CD1 DOUB Y N 5 LKE CE1 CZ SING Y N 6 LKE NW CZ SING N N 7 LKE C1 N2 DOUB N N 8 LKE C1 N3 SING N N 9 LKE N2 CA2 SING N N 10 LKE CD1 CG2 SING Y N 11 LKE CZ CE2 DOUB Y N 12 LKE N3 CA3 SING N N 13 LKE N3 C2 SING N N 14 LKE O3 C3 DOUB N N 15 LKE CA2 C2 SING N N 16 LKE CA2 CB2 DOUB N Z 17 LKE CG2 CB2 SING N N 18 LKE CG2 CD2 DOUB Y N 19 LKE CA3 C3 SING N N 20 LKE CE2 CD2 SING Y N 21 LKE C2 O2 DOUB N N 22 LKE C3 OXT SING N N 23 LKE CA1 HA1 SING N N 24 LKE CA1 HA2 SING N N 25 LKE N1 H SING N N 26 LKE N1 H2 SING N N 27 LKE CA3 HA31 SING N N 28 LKE CA3 HA32 SING N N 29 LKE CB2 H8 SING N N 30 LKE CD2 H9 SING N N 31 LKE CE2 H10 SING N N 32 LKE CE1 H11 SING N N 33 LKE CD1 H12 SING N N 34 LKE 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 LKE InChI InChI 1.03 "InChI=1S/C13H12N6O3/c14-6-11-16-10(13(22)19(11)7-12(20)21)5-8-1-3-9(4-2-8)17-18-15/h1-5H,6-7,14H2,(H,20,21)/b10-5-" LKE InChIKey InChI 1.03 LLZZHPRLBAOKOQ-YHYXMXQVSA-N LKE SMILES_CANONICAL CACTVS 3.385 "NCC1=N\C(=C/c2ccc(cc2)N=[N+]=[N-])C(=O)N1CC(O)=O" LKE SMILES CACTVS 3.385 "NCC1=NC(=Cc2ccc(cc2)N=[N+]=[N-])C(=O)N1CC(O)=O" LKE SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(ccc1/C=C\2/C(=O)N(C(=N2)CN)CC(=O)O)N=[N+]=[N-]" LKE SMILES "OpenEye OEToolkits" 2.0.7 "c1cc(ccc1C=C2C(=O)N(C(=N2)CN)CC(=O)O)N=[N+]=[N-]" # _pdbx_chem_comp_identifier.comp_id LKE _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-[(4~{Z})-2-(aminomethyl)-4-[(4-azidophenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]ethanoic 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 LKE "Create component" 2019-08-21 PDBE LKE "Initial release" 2021-02-17 RCSB LKE "Modify backbone" 2023-11-03 PDBE LKE "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id LKE _pdbx_chem_comp_pcm.modified_residue_id "GLY, TYR, GLY" _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category Chromophore/chromophore-like _pdbx_chem_comp_pcm.position "Amino-acid side chain and backbone" _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 ? #