data_XY5 # _chem_comp.id XY5 _chem_comp.name "2-[[(5~{Z})-8-azanyl-11,12-dihydrobenzo[c][1,2]benzodiazocin-3-yl]amino]ethanal" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H16 N4 O2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-11-27 _chem_comp.pdbx_modified_date 2024-06-28 _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 296.324 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XY5 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 6IAM _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_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 XY5 CA CA C 0 1 N N N N Y N -19.458 14.864 -24.969 -4.709 -0.132 -0.525 CA XY5 1 XY5 C C C 0 1 N N N N Y Y -19.787 13.303 -25.000 -5.905 0.784 -0.543 C XY5 2 XY5 O O O 0 1 N N N N Y Y -19.512 12.623 -25.967 -5.840 1.873 -0.024 O XY5 3 XY5 CB1 CB1 C 0 1 Y N N N Y N -18.873 16.041 -29.185 -0.118 -0.184 1.120 CB1 XY5 4 XY5 NB1 NB1 N 0 1 N N N N Y N -18.120 15.206 -30.119 0.946 0.354 1.772 NB1 XY5 5 XY5 CB2 CB2 C 0 1 Y N N N Y N -19.269 15.513 -27.908 -1.331 0.486 0.986 CB2 XY5 6 XY5 NB2 NB2 N 0 1 N N N N Y N -20.386 15.753 -25.724 -3.602 0.523 0.176 NB2 XY5 7 XY5 CB3 CB3 C 0 1 Y N N N Y N -19.986 16.302 -27.040 -2.379 -0.136 0.322 CB3 XY5 8 XY5 CA1 CA1 C 0 1 Y N N N Y N -16.119 16.609 -29.566 3.009 0.260 0.447 CA1 XY5 9 XY5 CA2 CA2 C 0 1 Y N N N N N -16.372 17.935 -29.893 3.109 -0.773 -0.473 CA2 XY5 10 XY5 CA3 CA3 C 0 1 Y N N N N N -15.733 18.981 -29.170 4.146 -0.782 -1.401 CA3 XY5 11 XY5 CA4 CA4 C 0 1 Y N N N N N -14.861 18.655 -28.115 5.084 0.224 -1.444 CA4 XY5 12 XY5 CA5 CA5 C 0 1 Y N N N Y N -14.642 17.330 -27.803 4.996 1.276 -0.539 CA5 XY5 13 XY5 CA6 CA6 C 0 1 Y N N N Y N -15.244 16.296 -28.518 3.979 1.293 0.388 CA6 XY5 14 XY5 CA7 CA7 C 0 1 N N N N N N -17.315 18.272 -31.063 2.148 -1.935 -0.582 CA7 XY5 15 XY5 CB4 CB4 C 0 1 Y N N N N N -20.336 17.615 -27.409 -2.213 -1.415 -0.200 CB4 XY5 16 XY5 CB5 CB5 C 0 1 Y N N N N N -19.952 18.128 -28.656 -1.004 -2.075 -0.067 CB5 XY5 17 XY5 CB6 CB6 C 0 1 Y N N N N N -19.232 17.333 -29.543 0.042 -1.461 0.585 CB6 XY5 18 XY5 CB7 CB7 C 0 1 N N N N N N -18.816 17.926 -30.897 1.382 -2.146 0.720 CB7 XY5 19 XY5 NA1 NA1 N 0 1 N N N N Y N -16.723 15.452 -30.274 2.112 0.412 1.416 NA1 XY5 20 XY5 N NA2 N 0 1 N N N Y Y N -13.734 16.946 -26.724 5.935 2.309 -0.570 N XY5 21 XY5 HA2 HA2 H 0 1 N N N N Y N -18.450 15.002 -25.386 -4.968 -1.057 -0.009 HA2 XY5 22 XY5 HA3 HA3 H 0 1 N N N N Y N -19.467 15.187 -23.917 -4.409 -0.358 -1.548 HA3 XY5 23 XY5 HB21 HB21 H 0 0 N N N N Y N -19.005 14.503 -27.632 -1.455 1.478 1.394 HB21 XY5 24 XY5 HB22 HB22 H 0 0 N N N N Y N -20.580 16.536 -25.132 -3.719 1.415 0.539 HB22 XY5 25 XY5 HA31 HA31 H 0 0 N N N N N N -15.915 20.014 -29.428 4.216 -1.599 -2.105 HA31 XY5 26 XY5 HA41 HA41 H 0 0 N N N N N N -14.368 19.436 -27.555 5.881 0.196 -2.173 HA41 XY5 27 XY5 HA61 HA61 H 0 0 N N N N Y N -15.038 15.266 -28.267 3.918 2.113 1.088 HA61 XY5 28 XY5 HA72 HA72 H 0 0 N N N N N N -16.948 17.731 -31.948 1.439 -1.737 -1.386 HA72 XY5 29 XY5 HA71 HA71 H 0 0 N N N N N N -17.245 19.355 -31.241 2.709 -2.840 -0.817 HA71 XY5 30 XY5 HB41 HB41 H 0 0 N N N N N N -20.904 18.231 -26.727 -3.034 -1.896 -0.711 HB41 XY5 31 XY5 HB51 HB51 H 0 0 N N N N N N -20.215 19.140 -28.928 -0.882 -3.069 -0.473 HB51 XY5 32 XY5 HB72 HB72 H 0 0 N N N N N N -19.392 18.851 -31.049 1.236 -3.212 0.894 HB72 XY5 33 XY5 HB71 HB71 H 0 0 N N N N N N -19.080 17.197 -31.677 1.938 -1.709 1.550 HB71 XY5 34 XY5 H HA21 H 0 1 N N N Y Y N -13.367 17.768 -26.288 6.651 2.295 -1.224 H XY5 35 XY5 H2 H2 H 0 1 N Y N Y Y N -14.232 16.404 -26.047 5.871 3.042 0.063 H2 XY5 36 XY5 OXT OXT O 0 1 N Y N N Y Y ? ? ? -7.043 0.391 -1.136 O1 XY5 37 XY5 HXT HXT H 0 1 N Y N N Y Y ? ? ? -7.783 1.013 -1.123 H1 XY5 38 # 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 XY5 CA7 CB7 SING N N 1 XY5 CA7 CA2 SING N N 2 XY5 CB7 CB6 SING N N 3 XY5 NA1 NB1 DOUB N N 4 XY5 NA1 CA1 SING N N 5 XY5 NB1 CB1 SING N N 6 XY5 CA2 CA1 DOUB Y N 7 XY5 CA2 CA3 SING Y N 8 XY5 CA1 CA6 SING Y N 9 XY5 CB6 CB1 DOUB Y N 10 XY5 CB6 CB5 SING Y N 11 XY5 CB1 CB2 SING Y N 12 XY5 CA3 CA4 DOUB Y N 13 XY5 CB5 CB4 DOUB Y N 14 XY5 CA6 CA5 DOUB Y N 15 XY5 CA4 CA5 SING Y N 16 XY5 CB2 CB3 DOUB Y N 17 XY5 CA5 N SING N N 18 XY5 CB4 CB3 SING Y N 19 XY5 CB3 NB2 SING N N 20 XY5 O C DOUB N N 21 XY5 NB2 CA SING N N 22 XY5 C CA SING N N 23 XY5 CA HA2 SING N N 24 XY5 CA HA3 SING N N 25 XY5 CB2 HB21 SING N N 26 XY5 NB2 HB22 SING N N 27 XY5 CA3 HA31 SING N N 28 XY5 CA4 HA41 SING N N 29 XY5 CA6 HA61 SING N N 30 XY5 CA7 HA72 SING N N 31 XY5 CA7 HA71 SING N N 32 XY5 CB4 HB41 SING N N 33 XY5 CB5 HB51 SING N N 34 XY5 CB7 HB72 SING N N 35 XY5 CB7 HB71 SING N N 36 XY5 N H SING N N 37 XY5 N H2 SING N N 38 XY5 C OXT SING N N 39 XY5 OXT HXT SING N N 40 # 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 XY5 InChI InChI 1.06 "InChI=1S/C16H16N4O2/c17-12-5-3-10-1-2-11-4-6-13(18-9-16(21)22)8-15(11)20-19-14(10)7-12/h3-8,18H,1-2,9,17H2,(H,21,22)/b20-19-" XY5 InChIKey InChI 1.06 IKRVZASJFAMVAN-VXPUYCOJSA-N XY5 SMILES_CANONICAL CACTVS 3.385 "Nc1ccc2CCc3ccc(NCC(O)=O)cc3N=Nc2c1" XY5 SMILES CACTVS 3.385 "Nc1ccc2CCc3ccc(NCC(O)=O)cc3N=Nc2c1" XY5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc2c(cc1N)/N=N\c3cc(ccc3CC2)NCC(=O)O" XY5 SMILES "OpenEye OEToolkits" 2.0.7 "c1cc2c(cc1N)N=Nc3cc(ccc3CC2)NCC(=O)O" # _pdbx_chem_comp_identifier.comp_id XY5 _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-[[(5~{Z})-8-azanyl-11,12-dihydrobenzo[c][1,2]benzodiazocin-3-yl]amino]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 XY5 "Create component" 2018-11-27 EBI XY5 "Initial release" 2019-02-06 RCSB XY5 "Modify backbone" 2023-11-03 PDBE XY5 "Other modification" 2024-06-28 PDBE #