data_IO8 # _chem_comp.id IO8 _chem_comp.name "2-[2-(aminomethyl)-4-(1H-indol-3-ylmethyl)-5-oxidanylidene-4H-imidazol-1-yl]ethanoic acid" _chem_comp.type "L-peptide linking" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C15 H14 N4 O3" _chem_comp.mon_nstd_parent_comp_id "GLY, TRP, GLY" _chem_comp.pdbx_synonyms "CHROMOPHORE (GLY-TRP-GLY)" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-04-01 _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 298.297 _chem_comp.one_letter_code GWG _chem_comp.three_letter_code IO8 _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 7Z7P _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # 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 IO8 C1 C1 C 0 1 N N N Y N N -13.260 26.341 -26.857 2.048 -0.999 0.376 C1 IO8 1 IO8 O2 O2 O 0 1 N N N Y N N -15.567 28.212 -25.339 1.773 2.361 0.729 O2 IO8 2 IO8 C2 C2 C 0 1 N N N Y N N -14.869 27.352 -25.857 1.646 1.158 0.580 C2 IO8 3 IO8 C3 C C 0 1 N N N Y N Y -13.123 29.728 -27.711 4.692 0.728 -0.590 C IO8 4 IO8 CD2 CD2 C 0 1 Y N N N N N -16.333 22.893 -25.501 -3.405 0.463 -0.024 CD2 IO8 5 IO8 CE3 CE3 C 0 1 Y N N N N N -15.163 22.528 -26.256 -4.080 1.678 0.049 CE3 IO8 6 IO8 CZ3 CZ3 C 0 1 Y N N N N N -14.842 21.168 -26.434 -5.451 1.706 -0.092 CZ3 IO8 7 IO8 CH2 CH2 C 0 1 Y N N N N N -15.680 20.172 -25.865 -6.156 0.531 -0.304 CH2 IO8 8 IO8 CZ2 CZ2 C 0 1 Y N N N N N -16.835 20.542 -25.121 -5.499 -0.678 -0.378 CZ2 IO8 9 IO8 CE2 CE2 C 0 1 Y N N N N N -17.168 21.895 -24.935 -4.116 -0.728 -0.233 CE2 IO8 10 IO8 NE1 NE1 N 0 1 Y N N N N N -18.216 22.540 -24.266 -3.205 -1.765 -0.256 NE1 IO8 11 IO8 CD1 CD1 C 0 1 Y N N N N N -18.068 23.909 -24.394 -1.947 -1.298 -0.073 CD1 IO8 12 IO8 CG CG C 0 1 Y N N N N N -16.913 24.154 -25.152 -1.984 0.075 0.079 CG IO8 13 IO8 CB CB C 0 1 N N N N N N -16.397 25.283 -25.513 -0.882 0.935 0.292 CB IO8 14 IO8 CA2 CA2 C 0 1 N N N Y N N -15.191 25.926 -25.982 0.398 0.414 0.366 CA2 IO8 15 IO8 N2 N2 N 0 1 N N N Y N N -14.106 25.345 -26.636 0.762 -0.899 0.254 N2 IO8 16 IO8 N3 N N 0 1 N N N Y N N -13.667 27.548 -26.414 2.623 0.225 0.575 N IO8 17 IO8 CA3 CA C 0 1 N N N Y N N -12.900 28.793 -26.546 4.054 0.481 0.753 CA IO8 18 IO8 O3 O O 0 1 N N N Y N Y -12.676 30.900 -27.604 4.019 0.694 -1.593 O IO8 19 IO8 CA1 CA1 C 0 1 N N N Y N N -11.953 26.186 -27.536 2.811 -2.298 0.313 CA1 IO8 20 IO8 N1 N1 N 0 1 N N N Y Y N -11.064 25.919 -26.299 1.872 -3.407 0.094 N1 IO8 21 IO8 OXT OXT O 0 1 N Y N Y N Y -13.572 29.259 -28.941 6.006 0.987 -0.671 OXT IO8 22 IO8 H1 H1 H 0 1 N N N N N N -14.534 23.294 -26.684 -3.533 2.594 0.215 H1 IO8 23 IO8 H12 H2 H 0 1 N N N N N N -13.966 20.885 -26.998 -5.978 2.647 -0.036 H2 IO8 24 IO8 H3 H3 H 0 1 N N N N N N -15.439 19.128 -25.998 -7.230 0.563 -0.413 H3 IO8 25 IO8 H4 H4 H 0 1 N N N N N N -17.463 19.774 -24.694 -6.058 -1.588 -0.543 H4 IO8 26 IO8 H5 H5 H 0 1 N N N N N N -18.956 22.082 -23.773 -3.434 -2.698 -0.386 H5 IO8 27 IO8 H6 H6 H 0 1 N N N N N N -18.727 24.659 -23.982 -1.054 -1.904 -0.049 H6 IO8 28 IO8 H7 H7 H 0 1 N N N N N N -17.165 26.038 -25.433 -1.039 1.998 0.396 H7 IO8 29 IO8 HA31 HA2 H 0 1 N N N Y N N -11.839 28.504 -26.576 4.522 -0.384 1.224 HA2 IO8 30 IO8 HA32 HA3 H 0 1 N N N Y N N -13.095 29.378 -25.635 4.190 1.357 1.387 HA3 IO8 31 IO8 HA1 H12 H 0 1 N N N Y N N -11.951 25.337 -28.236 3.526 -2.260 -0.509 H12 IO8 32 IO8 H13 H13 H 0 1 N N N Y N N -11.654 27.101 -28.068 3.343 -2.452 1.251 H13 IO8 33 IO8 H H14 H 0 1 N N N Y Y N -10.117 25.788 -26.591 2.360 -4.289 0.048 H14 IO8 34 IO8 H2 HN2 H 0 1 N Y N Y Y N -11.116 26.700 -25.677 1.160 -3.424 0.809 HN2 IO8 35 IO8 HXT HXT H 0 1 N Y N Y N Y -13.475 29.941 -29.595 6.370 1.139 -1.554 HXT IO8 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 IO8 C3 O3 DOUB N N 1 IO8 C3 CA3 SING N N 2 IO8 CA1 C1 SING N N 3 IO8 CA1 N1 SING N N 4 IO8 C1 N2 DOUB N N 5 IO8 C1 N3 SING N N 6 IO8 N2 CA2 SING N N 7 IO8 CA3 N3 SING N N 8 IO8 CZ3 CE3 DOUB Y N 9 IO8 CZ3 CH2 SING Y N 10 IO8 N3 C2 SING N N 11 IO8 CE3 CD2 SING Y N 12 IO8 CA2 C2 SING N N 13 IO8 CA2 CB DOUB N Z 14 IO8 CH2 CZ2 DOUB Y N 15 IO8 C2 O2 DOUB N N 16 IO8 CB CG SING N N 17 IO8 CD2 CG SING Y N 18 IO8 CD2 CE2 DOUB Y N 19 IO8 CG CD1 DOUB Y N 20 IO8 CZ2 CE2 SING Y N 21 IO8 CE2 NE1 SING Y N 22 IO8 CD1 NE1 SING Y N 23 IO8 C3 OXT SING N N 24 IO8 CE3 H1 SING N N 25 IO8 CZ3 H12 SING N N 26 IO8 CH2 H3 SING N N 27 IO8 CZ2 H4 SING N N 28 IO8 NE1 H5 SING N N 29 IO8 CD1 H6 SING N N 30 IO8 CB H7 SING N N 31 IO8 CA3 HA31 SING N N 32 IO8 CA3 HA32 SING N N 33 IO8 CA1 HA1 SING N N 34 IO8 CA1 H13 SING N N 35 IO8 N1 H SING N N 36 IO8 N1 H2 SING N N 37 IO8 OXT HXT SING N N 38 # 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 IO8 InChI InChI 1.06 "InChI=1S/C15H14N4O3/c16-6-13-18-12(15(22)19(13)8-14(20)21)5-9-7-17-11-4-2-1-3-10(9)11/h1-5,7,17H,6,8,16H2,(H,20,21)/b12-5-" IO8 InChIKey InChI 1.06 LTDNFCXBDXPOFY-XGICHPGQSA-N IO8 SMILES_CANONICAL CACTVS 3.385 "NCC1=NC(=C\c2c[nH]c3ccccc23)/C(=O)N1CC(O)=O" IO8 SMILES CACTVS 3.385 "NCC1=NC(=Cc2c[nH]c3ccccc23)C(=O)N1CC(O)=O" IO8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc2c(c1)c(c[nH]2)/C=C\3/C(=O)N(C(=N3)CN)CC(=O)O" IO8 SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc2c(c1)c(c[nH]2)C=C3C(=O)N(C(=N3)CN)CC(=O)O" # _pdbx_chem_comp_identifier.comp_id IO8 _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-(1~{H}-indol-3-ylmethylidene)-5-oxidanylidene-imidazol-1-yl]ethanoic acid" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id IO8 _pdbx_chem_comp_synonyms.name "CHROMOPHORE (GLY-TRP-GLY)" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site IO8 "Create component" 2022-04-01 PDBE IO8 "Modify parent residue" 2022-04-01 PDBE IO8 "Initial release" 2022-05-04 RCSB IO8 "Modify descriptor" 2022-08-22 RCSB IO8 "Modify backbone" 2023-11-03 PDBE #