data_JBY # _chem_comp.id JBY _chem_comp.name "(2S)-2-{(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}propanoic acid" _chem_comp.type "L-peptide linking" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C14 H15 N3 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "Gly-Ala-Try Chromophore" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-08-29 _chem_comp.pdbx_modified_date 2023-11-03 _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 289.287 _chem_comp.one_letter_code ? _chem_comp.three_letter_code JBY _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 6M9X _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # 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 JBY C1 C1 C 0 1 N N N Y N N 2.397 14.476 24.130 1.102 -1.200 -0.152 C1 JBY 1 JBY C2 C2 C 0 1 N N N Y N N 0.470 14.522 25.081 1.336 0.986 -0.304 C2 JBY 2 JBY N2 N2 N 0 1 N N N Y N N 2.666 14.852 25.406 -0.106 -0.743 -0.052 N2 JBY 3 JBY N3 N3 N 0 1 N N N Y N N 1.076 14.239 23.960 2.006 -0.187 -0.306 N3 JBY 4 JBY O2 O2 O 0 1 N N N Y N N -0.812 14.429 25.331 1.803 2.105 -0.417 O2 JBY 5 JBY O3 O O 0 1 N N N Y N Y -0.298 12.557 21.055 3.506 0.962 1.511 O JBY 6 JBY C3 C C 0 1 N N N Y N Y 0.395 12.628 22.068 4.153 0.376 0.676 C JBY 7 JBY CA3 CA3 C 0 1 N N S Y N N 0.266 13.949 22.761 3.456 -0.346 -0.448 CA3 JBY 8 JBY CB3 CB3 C 0 1 N N N N N N 0.547 15.088 21.770 3.904 0.243 -1.788 CB3 JBY 9 JBY CA1 CA1 C 0 1 N N N Y N N 3.452 14.389 23.073 1.465 -2.662 -0.099 CA1 JBY 10 JBY N1 N N 0 1 N N N Y Y N 3.700 15.764 22.620 0.246 -3.463 0.080 N JBY 11 JBY CA2 CA2 C 0 1 N N N Y N N 1.463 14.875 26.054 -0.082 0.622 -0.134 CA2 JBY 12 JBY CB2 CB2 C 0 1 N N N N N N 1.112 15.248 27.414 -1.159 1.479 -0.070 CB2 JBY 13 JBY CG2 CG2 C 0 1 Y N N N N N 1.948 15.718 28.529 -2.520 0.941 -0.012 CG2 JBY 14 JBY CD2 CD2 C 0 1 Y N N N N N 1.297 15.990 29.681 -2.726 -0.441 0.105 CD2 JBY 15 JBY CE2 CE2 C 0 1 Y N N N N N 1.917 16.440 30.807 -4.003 -0.939 0.160 CE2 JBY 16 JBY CZ CZ C 0 1 Y N N N N N 3.276 16.767 30.744 -5.092 -0.075 0.098 CZ JBY 17 JBY OH O3 O 0 1 N N N N N N 3.794 17.229 31.783 -6.353 -0.574 0.152 O3 JBY 18 JBY CE1 CE1 C 0 1 Y N N N N N 3.943 16.610 29.546 -4.893 1.296 -0.018 CE1 JBY 19 JBY CD1 CD1 C 0 1 Y N N N N N 3.304 16.092 28.419 -3.622 1.806 -0.068 CD1 JBY 20 JBY HA31 H4 H 0 1 N N N Y N N -0.789 14.050 23.055 3.711 -1.405 -0.414 H4 JBY 21 JBY H5 H5 H 0 1 N N N N N N 0.451 16.055 22.285 3.399 -0.279 -2.601 H5 JBY 22 JBY H6 H6 H 0 1 N N N N N N 1.567 14.985 21.372 3.649 1.302 -1.823 H6 JBY 23 JBY H7 H7 H 0 1 N N N N N N -0.176 15.040 20.942 4.982 0.125 -1.894 H7 JBY 24 JBY HA1 H8 H 0 1 N N N Y N N 3.100 13.770 22.235 1.954 -2.949 -1.030 H8 JBY 25 JBY HA2 H9 H 0 1 N N N Y N N 4.373 13.954 23.489 2.142 -2.839 0.737 H9 JBY 26 JBY H H1 H 0 1 N N N Y Y N 4.403 15.759 21.908 0.463 -4.447 0.118 H1 JBY 27 JBY H2 H2 H 0 1 N Y N Y Y N 2.855 16.151 22.251 -0.260 -3.171 0.903 H2 JBY 28 JBY H13 H13 H 0 1 N N N N N N 0.060 15.166 27.645 -0.999 2.547 -0.062 H13 JBY 29 JBY H14 H14 H 0 1 N N N N N N 0.228 15.843 29.711 -1.882 -1.112 0.152 H14 JBY 30 JBY H16 H16 H 0 1 N N N N N N 1.369 16.543 31.732 -4.163 -2.003 0.250 H16 JBY 31 JBY H17 H17 H 0 1 N N N N N N 4.983 16.894 29.479 -5.743 1.962 -0.065 H17 JBY 32 JBY H18 H18 H 0 1 N N N N N N 3.835 15.980 27.485 -3.469 2.872 -0.154 H18 JBY 33 JBY OXT OXT O 0 1 N Y N Y N Y 1.152 11.646 22.634 5.493 0.367 0.750 OXT JBY 34 JBY HXT HXT H 0 1 N Y N Y N Y 1.075 10.851 22.120 5.895 0.844 1.489 HXT JBY 35 JBY HOH H3 H 0 1 N N N N N N 3.148 17.244 32.480 -6.710 -0.645 1.048 H3 JBY 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 JBY O3 C3 DOUB N N 1 JBY CB3 CA3 SING N N 2 JBY C3 CA3 SING N N 3 JBY N1 CA1 SING N N 4 JBY CA3 N3 SING N N 5 JBY CA1 C1 SING N N 6 JBY N3 C1 SING N N 7 JBY N3 C2 SING N N 8 JBY C1 N2 DOUB N N 9 JBY C2 O2 DOUB N N 10 JBY C2 CA2 SING N N 11 JBY N2 CA2 SING N N 12 JBY CA2 CB2 DOUB N Z 13 JBY CB2 CG2 SING N N 14 JBY CD1 CG2 SING Y N 15 JBY CD1 CE1 DOUB Y N 16 JBY CG2 CD2 DOUB Y N 17 JBY CE1 CZ SING Y N 18 JBY CD2 CE2 SING Y N 19 JBY CZ CE2 DOUB Y N 20 JBY CZ OH SING N N 21 JBY CA3 HA31 SING N N 22 JBY CB3 H5 SING N N 23 JBY CB3 H6 SING N N 24 JBY CB3 H7 SING N N 25 JBY CA1 HA1 SING N N 26 JBY CA1 HA2 SING N N 27 JBY N1 H SING N N 28 JBY N1 H2 SING N N 29 JBY CB2 H13 SING N N 30 JBY CD2 H14 SING N N 31 JBY CE2 H16 SING N N 32 JBY CE1 H17 SING N N 33 JBY CD1 H18 SING N N 34 JBY C3 OXT SING N N 35 JBY OXT HXT SING N N 36 JBY OH HOH SING N N 37 # 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 JBY SMILES ACDLabs 12.01 "C1(=NC(\C(=O)N1C(C(=O)O)C)=C/c2ccc(O)cc2)CN" JBY InChI InChI 1.03 "InChI=1S/C14H15N3O4/c1-8(14(20)21)17-12(7-15)16-11(13(17)19)6-9-2-4-10(18)5-3-9/h2-6,8,18H,7,15H2,1H3,(H,20,21)/b11-6-/t8-/m0/s1" JBY InChIKey InChI 1.03 KZUMQCZIDYKIEK-OITNDJBGSA-N JBY SMILES_CANONICAL CACTVS 3.385 "C[C@H](N1C(=NC(=C\c2ccc(O)cc2)/C1=O)CN)C(O)=O" JBY SMILES CACTVS 3.385 "C[CH](N1C(=NC(=Cc2ccc(O)cc2)C1=O)CN)C(O)=O" JBY SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C[C@@H](C(=O)O)N1C(=N/C(=C\c2ccc(cc2)O)/C1=O)CN" JBY SMILES "OpenEye OEToolkits" 2.0.6 "CC(C(=O)O)N1C(=NC(=Cc2ccc(cc2)O)C1=O)CN" # 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 JBY "SYSTEMATIC NAME" ACDLabs 12.01 "(2S)-2-{(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}propanoic acid" JBY "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "(2~{S})-2-[(4~{Z})-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxidanylidene-imidazol-1-yl]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 JBY "Create component" 2018-08-29 RCSB JBY "Initial release" 2019-03-13 RCSB JBY "Modify synonyms" 2021-03-01 PDBE JBY "Modify backbone" 2023-11-03 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id JBY _pdbx_chem_comp_synonyms.name "Gly-Ala-Try Chromophore" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? #