data_5EYM # _model_server_result.job_id wrsW_gd7zeu7bi2mtKw2FA _model_server_result.datetime_utc '2024-10-10 23:34:03' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 5eym # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 5EYM # _exptl.entry_id 5EYM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 464.558 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-[(3~{Z})-3-[[[4-[(dimethylamino)methyl]phenyl]amino]-phenyl-methylidene]-2-oxidanylidene-1~{H}-indol-6-yl]-~{N}-ethyl-prop-2-ynamide _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 5EYM _cell.length_a 78.76 _cell.length_b 78.76 _cell.length_c 223.412 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EYM _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,H 1 1 B,G,I 2 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 G N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A OD1 ASP 31 A ASP 65 1_555 D CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? metalc ? metalc2 A OD2 ASP 31 A ASP 65 1_555 D CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.018 ? metalc ? metalc3 A OD2 ASP 31 A ASP 65 1_555 E CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc4 A OD1 ASP 32 A ASP 66 1_555 E CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? metalc ? metalc5 A OD2 ASP 32 A ASP 66 1_555 F CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc6 D CA CA . A CA 402 1_555 H O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.737 ? metalc ? metalc7 D CA CA . A CA 402 1_555 H O HOH . A HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.189 ? metalc ? metalc8 D CA CA . A CA 402 1_555 B OD2 ASP 32 B ASP 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc9 E CA CA . A CA 403 1_555 H O HOH . A HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? metalc ? metalc10 E CA CA . A CA 403 1_555 B OD2 ASP 31 B ASP 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc11 E CA CA . A CA 403 1_555 B OD1 ASP 32 B ASP 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc12 E CA CA . A CA 403 1_555 I O HOH . B HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.799 ? metalc ? metalc13 F CA CA . A CA 404 1_555 B OD1 ASP 31 B ASP 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.737 ? metalc ? metalc14 F CA CA . A CA 404 1_555 B OD2 ASP 31 B ASP 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.136 ? metalc ? metalc15 F CA CA . A CA 404 1_555 I O HOH . B HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.08 ? metalc ? metalc16 F CA CA . A CA 404 1_555 I O HOH . B HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.781 ? # _chem_comp.formula 'C29 H28 N4 O2' _chem_comp.formula_weight 464.558 _chem_comp.id 5U5 _chem_comp.mon_nstd_flag . _chem_comp.name 3-[(3~{Z})-3-[[[4-[(dimethylamino)methyl]phenyl]amino]-phenyl-methylidene]-2-oxidanylidene-1~{H}-indol-6-yl]-~{N}-ethyl-prop-2-ynamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C34 C35 5U5 sing 1 n n C18 C17 5U5 doub 2 n y C18 C13 5U5 sing 3 n y C17 C16 5U5 sing 4 n y C32 N31 5U5 sing 5 n n O28 C27 5U5 doub 6 n n C27 C26 5U5 sing 7 n n C27 N29 5U5 sing 8 n n C26 C25 5U5 trip 9 n n C25 C2 5U5 sing 10 n n C2 C3 5U5 doub 11 n y C2 C1 5U5 sing 12 n y C3 C6 5U5 sing 13 n y C1 C4 5U5 doub 14 n y C35 N29 5U5 sing 15 n n C6 C5 5U5 doub 16 n y C6 N7 5U5 sing 17 n n C4 C5 5U5 sing 18 n y C5 C9 5U5 sing 19 n n N7 C8 5U5 sing 20 n n C8 C9 5U5 sing 21 n n C8 O10 5U5 doub 22 n n C9 C11 5U5 doub 23 z n C11 C13 5U5 sing 24 n n C11 N12 5U5 sing 25 n n C13 C14 5U5 doub 26 n y C16 C15 5U5 doub 27 n y N12 C19 5U5 sing 28 n n C24 C23 5U5 doub 29 n y C24 C19 5U5 sing 30 n y C23 C22 5U5 sing 31 n y C19 C20 5U5 doub 32 n y C20 C21 5U5 sing 33 n y C22 C21 5U5 doub 34 n y C22 C30 5U5 sing 35 n n C30 N31 5U5 sing 36 n n N31 C33 5U5 sing 37 n n C14 C15 5U5 sing 38 n y C4 H1 5U5 sing 39 n n C15 H2 5U5 sing 40 n n C17 H3 5U5 sing 41 n n C20 H4 5U5 sing 42 n n C21 H5 5U5 sing 43 n n C24 H6 5U5 sing 44 n n N29 H7 5U5 sing 45 n n C35 H8 5U5 sing 46 n n C35 H9 5U5 sing 47 n n C34 H10 5U5 sing 48 n n C34 H11 5U5 sing 49 n n C34 H12 5U5 sing 50 n n C3 H13 5U5 sing 51 n n N7 H14 5U5 sing 52 n n C1 H16 5U5 sing 53 n n C18 H17 5U5 sing 54 n n C16 H18 5U5 sing 55 n n C14 H19 5U5 sing 56 n n C23 H20 5U5 sing 57 n n C30 H21 5U5 sing 58 n n C30 H22 5U5 sing 59 n n C33 H24 5U5 sing 60 n n C33 H25 5U5 sing 61 n n C33 H26 5U5 sing 62 n n C32 H27 5U5 sing 63 n n C32 H28 5U5 sing 64 n n C32 H29 5U5 sing 65 n n N12 H30 5U5 sing 66 n n # _atom_sites.entry_id 5EYM _atom_sites.fract_transf_matrix[1][1] 0.012697 _atom_sites.fract_transf_matrix[1][2] 0.007331 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014661 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.004476 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 5U5 A 1 401 1 5U5 LIG . D 3 CA A 1 402 1 CA CA . E 3 CA A 1 403 2 CA CA . F 3 CA A 1 404 3 CA CA . G 2 5U5 B 1 401 2 5U5 LIG . H 4 HOH A 1 501 3 HOH HOH . H 4 HOH A 2 502 13 HOH HOH . H 4 HOH A 3 503 15 HOH HOH . H 4 HOH A 4 504 1 HOH HOH . H 4 HOH A 5 505 16 HOH HOH . H 4 HOH A 6 506 14 HOH HOH . H 4 HOH A 7 507 2 HOH HOH . H 4 HOH A 8 508 12 HOH HOH . H 4 HOH A 9 509 17 HOH HOH . I 4 HOH B 1 501 4 HOH HOH . I 4 HOH B 2 502 11 HOH HOH . I 4 HOH B 3 503 10 HOH HOH . I 4 HOH B 4 504 5 HOH HOH . I 4 HOH B 5 505 7 HOH HOH . I 4 HOH B 6 506 6 HOH HOH . I 4 HOH B 7 507 9 HOH HOH . I 4 HOH B 8 508 8 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C4 5U5 . . . C 2 -62.933 -30.545 76.907 1 45.96 ? C4 5U5 401 A 1 HETATM 2 C C5 5U5 . . . C 2 -63.54 -31.792 76.94 1 44.8 ? C5 5U5 401 A 1 HETATM 3 C C6 5U5 . . . C 2 -62.78 -32.945 76.902 1 43.88 ? C6 5U5 401 A 1 HETATM 4 C C8 5U5 . . . C 2 -64.898 -33.636 77.007 1 39.69 ? C8 5U5 401 A 1 HETATM 5 N N12 5U5 . . . C 2 -67.26 -32.193 77.148 1 39.17 ? N12 5U5 401 A 1 HETATM 6 C C13 5U5 . . . C 2 -66.06 -29.972 77.078 1 42.8 ? C13 5U5 401 A 1 HETATM 7 C C15 5U5 . . . C 2 -66.098 -27.891 78.281 1 47.55 ? C15 5U5 401 A 1 HETATM 8 C C17 5U5 . . . C 2 -66.022 -27.889 75.887 1 47.96 ? C17 5U5 401 A 1 HETATM 9 C C20 5U5 . . . C 2 -69.545 -32.951 77.247 1 49.78 ? C20 5U5 401 A 1 HETATM 10 C C21 5U5 . . . C 2 -70.91 -32.739 77.281 1 48.35 ? C21 5U5 401 A 1 HETATM 11 C C22 5U5 . . . C 2 -71.407 -31.454 77.252 1 47.39 ? C22 5U5 401 A 1 HETATM 12 C C24 5U5 . . . C 2 -69.149 -30.594 77.154 1 43.98 ? C24 5U5 401 A 1 HETATM 13 C C26 5U5 . . . C 2 -58.158 -31.293 76.649 1 57.96 ? C26 5U5 401 A 1 HETATM 14 O O28 5U5 . . . C 2 -56.374 -29.931 76.232 1 61.91 ? O28 5U5 401 A 1 HETATM 15 C C27 5U5 . . . C 2 -56.752 -31.032 76.581 1 61.23 ? C27 5U5 401 A 1 HETATM 16 N N29 5U5 . . . C 2 -55.823 -31.995 76.918 1 59.73 ? N29 5U5 401 A 1 HETATM 17 C C35 5U5 . . . C 2 -54.366 -31.803 76.875 1 58.89 ? C35 5U5 401 A 1 HETATM 18 C C34 5U5 . . . C 2 -53.862 -31.675 75.456 0 59.41 ? C34 5U5 401 A 1 HETATM 19 C C25 5U5 . . . C 2 -59.354 -31.483 76.715 1 53.6 ? C25 5U5 401 A 1 HETATM 20 C C2 5U5 . . . C 2 -60.774 -31.663 76.784 1 51.34 ? C2 5U5 401 A 1 HETATM 21 C C3 5U5 . . . C 2 -61.393 -32.913 76.826 1 47.07 ? C3 5U5 401 A 1 HETATM 22 N N7 5U5 . . . C 2 -63.593 -34.097 76.943 1 42.83 ? N7 5U5 401 A 1 HETATM 23 O O10 5U5 . . . C 2 -65.877 -34.348 77.06 1 43.52 ? O10 5U5 401 A 1 HETATM 24 C C9 5U5 . . . C 2 -64.94 -32.177 77.014 1 40.65 ? C9 5U5 401 A 1 HETATM 25 C C1 5U5 . . . C 2 -61.546 -30.496 76.831 1 47.62 ? C1 5U5 401 A 1 HETATM 26 C C11 5U5 . . . C 2 -66.081 -31.449 77.075 1 40.49 ? C11 5U5 401 A 1 HETATM 27 C C18 5U5 . . . C 2 -66.025 -29.275 75.885 1 46.15 ? C18 5U5 401 A 1 HETATM 28 C C16 5U5 . . . C 2 -66.058 -27.197 77.086 1 48.76 ? C16 5U5 401 A 1 HETATM 29 C C14 5U5 . . . C 2 -66.098 -29.277 78.276 1 47.5 ? C14 5U5 401 A 1 HETATM 30 C C19 5U5 . . . C 2 -68.646 -31.89 77.197 1 43.84 ? C19 5U5 401 A 1 HETATM 31 C C23 5U5 . . . C 2 -70.521 -30.381 77.189 1 44.49 ? C23 5U5 401 A 1 HETATM 32 C C30 5U5 . . . C 2 -72.907 -31.285 77.298 1 50.82 ? C30 5U5 401 A 1 HETATM 33 N N31 5U5 . . . C 2 -73.308 -29.877 77.432 1 53.49 ? N31 5U5 401 A 1 HETATM 34 C C33 5U5 . . . C 2 -74.577 -29.8 78.173 1 53.75 ? C33 5U5 401 A 1 HETATM 35 C C32 5U5 . . . C 2 -73.432 -29.199 76.124 1 52.35 ? C32 5U5 401 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 35 #