data_3I1D # _model_server_result.job_id tLjvjPXsG-lG2nsDDBudkg _model_server_result.datetime_utc '2025-04-03 22:59:53' _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 3i1d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":10}' # _entry.id 3I1D # _exptl.entry_id 3I1D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 376.453 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-[(1E)-PYRIDIN-2-YLMETHYLENE]-N-[4-(4-{[(1E)-PYRIDIN-2-YLMETHYLENE]AMINO}BENZYL)PHENYL]AMINE _entity.pdbx_number_of_molecules 9 _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 90 _cell.entry_id 3I1D _cell.length_a 74.97 _cell.length_b 74.97 _cell.length_c 74.97 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3I1D _symmetry.cell_setting ? _symmetry.Int_Tables_number 212 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 3 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? trimeric 3 author_defined_assembly 1 ? trimeric 3 author_defined_assembly 2 ? hexameric 6 author_defined_assembly 3 # 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,G,H,R 1 1,2,3 B,I,J,K,L,M,N,O,P,Q,S 2 1,4,5 A,C,D,E,F,G,H,R 3 2,6,7 B,I,J,K,L,M,N,O,P,Q,S 3 4 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S 3 1 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_564 -z+1/2,-x+1,y-1/2 0 0 -1 -1 0 0 0 1 0 37.485 74.97 -37.485 3 'crystal symmetry operation' 10_655 -y+1,z+1/2,-x+1/2 0 -1 0 0 0 1 -1 0 0 74.97 37.485 37.485 4 'crystal symmetry operation' 8_645 -z+1,x-1/2,-y+1/2 0 0 -1 1 0 0 0 -1 0 74.97 -37.485 37.485 5 'crystal symmetry operation' 11_556 y+1/2,-z+1/2,-x+1 0 1 0 0 0 -1 -1 0 0 37.485 37.485 74.97 6 'crystal symmetry operation' 18_654 -x+7/4,z+1/4,y-1/4 -1 0 0 0 0 1 0 1 0 131.1975 18.7425 -18.7425 7 'crystal symmetry operation' 21_645 z+5/4,y-1/4,-x+3/4 0 0 1 0 1 0 -1 0 0 93.7125 -18.7425 56.2275 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 G N N ? 3 H N N ? 3 L N N ? 3 M N N ? 3 N N N ? 3 O N N ? 3 P N N ? 3 Q 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 E FE FE2 . A FE2 7 1_555 O N14 NPM . B NPM 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc2 E FE FE2 . A FE2 7 1_555 O N13 NPM . B NPM 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc3 E FE FE2 . A FE2 7 1_555 P N13 NPM . B NPM 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? metalc ? metalc4 E FE FE2 . A FE2 7 1_555 P N14 NPM . B NPM 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc5 E FE FE2 . A FE2 7 1_555 Q N14 NPM . B NPM 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? metalc ? metalc6 E FE FE2 . A FE2 7 1_555 Q N13 NPM . B NPM 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc7 C FE FE2 . A FE2 101 1_555 F N14 NPM . A NPM 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc8 C FE FE2 . A FE2 101 1_555 F N13 NPM . A NPM 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc9 C FE FE2 . A FE2 101 1_555 G N13 NPM . A NPM 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? metalc ? metalc10 C FE FE2 . A FE2 101 1_555 G N14 NPM . A NPM 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc11 C FE FE2 . A FE2 101 1_555 H N13 NPM . A NPM 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? metalc ? metalc12 C FE FE2 . A FE2 101 1_555 H N14 NPM . A NPM 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? metalc ? metalc13 D FE FE2 . A FE2 102 1_555 F N11 NPM . A NPM 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? metalc ? metalc14 D FE FE2 . A FE2 102 1_555 F N12 NPM . A NPM 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc15 D FE FE2 . A FE2 102 1_555 G N12 NPM . A NPM 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc16 D FE FE2 . A FE2 102 1_555 G N11 NPM . A NPM 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? metalc ? metalc17 D FE FE2 . A FE2 102 1_555 H N12 NPM . A NPM 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc18 D FE FE2 . A FE2 102 1_555 H N11 NPM . A NPM 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc19 K FE FE2 . B FE2 7 1_555 N N12 NPM . B NPM 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc20 K FE FE2 . B FE2 7 1_555 N N11 NPM . B NPM 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc21 K FE FE2 . B FE2 7 1_555 L N11 NPM . B NPM 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc22 K FE FE2 . B FE2 7 1_555 L N12 NPM . B NPM 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc23 K FE FE2 . B FE2 7 1_555 M N12 NPM . B NPM 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc24 K FE FE2 . B FE2 7 1_555 M N11 NPM . B NPM 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc25 N N13 NPM . B NPM 8 1_555 J FE FE2 . B FE2 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc26 N N14 NPM . B NPM 8 1_555 J FE FE2 . B FE2 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc27 L N13 NPM . B NPM 9 1_555 J FE FE2 . B FE2 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc28 L N14 NPM . B NPM 9 1_555 J FE FE2 . B FE2 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc29 M N13 NPM . B NPM 10 1_555 J FE FE2 . B FE2 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc30 M N14 NPM . B NPM 10 1_555 J FE FE2 . B FE2 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc31 I FE FE2 . B FE2 102 1_555 O N11 NPM . B NPM 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? metalc ? metalc32 I FE FE2 . B FE2 102 1_555 O N12 NPM . B NPM 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc33 I FE FE2 . B FE2 102 1_555 P N12 NPM . B NPM 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? metalc ? metalc34 I FE FE2 . B FE2 102 1_555 P N11 NPM . B NPM 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc35 I FE FE2 . B FE2 102 1_555 Q N11 NPM . B NPM 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc36 I FE FE2 . B FE2 102 1_555 Q N12 NPM . B NPM 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? # _chem_comp.formula 'C25 H20 N4' _chem_comp.formula_weight 376.453 _chem_comp.id NPM _chem_comp.mon_nstd_flag . _chem_comp.name N-[(1E)-PYRIDIN-2-YLMETHYLENE]-N-[4-(4-{[(1E)-PYRIDIN-2-YLMETHYLENE]AMINO}BENZYL)PHENYL]AMINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 1,1-BIS(N-(4-PHENYL)-2-PYRIDYLCARBOXALDIMINE)METHANE # 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 N11 C1A NPM doub 152 n y N11 C1E NPM sing 153 n y N12 C1F NPM doub 154 n n N12 C1G NPM sing 155 n n N13 C1Q NPM sing 156 n n N13 C1T NPM doub 157 n n N14 C1U NPM sing 158 n y N14 C1Y NPM doub 159 n y C1A C1B NPM sing 160 n y C1A H1A NPM sing 161 n n C1B C1C NPM doub 162 n y C1B H1B NPM sing 163 n n C1C C1D NPM sing 164 n y C1C H1C NPM sing 165 n n C1D C1E NPM doub 166 n y C1D H1D NPM sing 167 n n C1E C1F NPM sing 168 n n C1F H1F NPM sing 169 n n C1G C1H NPM sing 170 n y C1G C1L NPM doub 171 n y C1H C1I NPM doub 172 n y C1H H1H NPM sing 173 n n C1I C1J NPM sing 174 n y C1I H1I NPM sing 175 n n C1J C1K NPM doub 176 n y C1J C1M NPM sing 177 n n C1K C1L NPM sing 178 n y C1K H1K NPM sing 179 n n C1L H1L NPM sing 180 n n C1M C1N NPM sing 181 n n C1M H1M1 NPM sing 182 n n C1M H1M2 NPM sing 183 n n C1N C1O NPM doub 184 n y C1N C1S NPM sing 185 n y C1O C1P NPM sing 186 n y C1O H1O NPM sing 187 n n C1P C1Q NPM doub 188 n y C1P H1P NPM sing 189 n n C1Q C1R NPM sing 190 n y C1R C1S NPM doub 191 n y C1R H1R NPM sing 192 n n C1S H1S NPM sing 193 n n C1T C1U NPM sing 194 n n C1T H1T NPM sing 195 n n C1U C1V NPM doub 196 n y C1V C1W NPM sing 197 n y C1V H1V NPM sing 198 n n C1W C1X NPM doub 199 n y C1W H1W NPM sing 200 n n C1X C1Y NPM sing 201 n y C1X H1X NPM sing 202 n n C1Y H1Y NPM sing 203 n n # _atom_sites.entry_id 3I1D _atom_sites.fract_transf_matrix[1][1] 0.013339 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013339 _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] 0.013339 _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 FE2 A 1 101 101 FE2 FE2 . D 2 FE2 A 1 102 102 FE2 FE2 . E 2 FE2 A 1 7 7 FE2 FE2 . F 3 NPM A 1 203 203 NPM NPM . G 3 NPM A 1 204 204 NPM NPM . H 3 NPM A 1 205 205 NPM NPM . I 2 FE2 B 1 102 102 FE2 FE2 . J 2 FE2 B 1 101 101 FE2 FE2 . K 2 FE2 B 1 7 7 FE2 FE2 . L 3 NPM B 1 9 9 NPM NPM . M 3 NPM B 1 10 10 NPM NPM . N 3 NPM B 1 8 8 NPM NPM . O 3 NPM B 1 203 203 NPM NPM . P 3 NPM B 1 204 204 NPM NPM . Q 3 NPM B 1 205 205 NPM NPM . R 4 HOH A 1 302 302 HOH HOH . R 4 HOH A 2 303 1 HOH HOH . R 4 HOH A 3 306 306 HOH HOH . R 4 HOH A 4 307 307 HOH HOH . S 4 HOH B 1 304 304 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 N N11 NPM . . . M 3 63.94 24.722 14.443 0.16 98.56 ? N11 NPM 10 B 1 HETATM 2 N N12 NPM . . . M 3 64.629 27.02 13.509 0.16 97.37 ? N12 NPM 10 B 1 HETATM 3 N N13 NPM . . . M 3 68.148 32.656 6.596 0.16 102.07 ? N13 NPM 10 B 1 HETATM 4 N N14 NPM . . . M 3 68.708 32.977 4.075 0.16 104.29 ? N14 NPM 10 B 1 HETATM 5 C C1A NPM . . . M 3 63.54 23.535 14.885 0.16 99.3 ? C1A NPM 10 B 1 HETATM 6 C C1B NPM . . . M 3 64.205 22.869 15.916 0.16 99.51 ? C1B NPM 10 B 1 HETATM 7 C C1C NPM . . . M 3 65.284 23.408 16.503 0.16 99.31 ? C1C NPM 10 B 1 HETATM 8 C C1D NPM . . . M 3 65.721 24.643 16.061 0.16 98.95 ? C1D NPM 10 B 1 HETATM 9 C C1E NPM . . . M 3 65.019 25.248 15.04 0.16 98.85 ? C1E NPM 10 B 1 HETATM 10 C C1F NPM . . . M 3 65.353 26.546 14.464 0.16 98.42 ? C1F NPM 10 B 1 HETATM 11 C C1G NPM . . . M 3 65.143 28.308 13.103 0.16 97.32 ? C1G NPM 10 B 1 HETATM 12 C C1H NPM . . . M 3 66.141 28.417 12.145 0.16 97.2 ? C1H NPM 10 B 1 HETATM 13 C C1I NPM . . . M 3 66.629 29.678 11.793 0.16 97.42 ? C1I NPM 10 B 1 HETATM 14 C C1J NPM . . . M 3 66.131 30.792 12.401 0.16 97.25 ? C1J NPM 10 B 1 HETATM 15 C C1K NPM . . . M 3 65.131 30.667 13.376 0.16 97.09 ? C1K NPM 10 B 1 HETATM 16 C C1L NPM . . . M 3 64.651 29.419 13.717 0.16 97.12 ? C1L NPM 10 B 1 HETATM 17 C C1M NPM . . . M 3 66.658 32.138 12.038 0.16 97.99 ? C1M NPM 10 B 1 HETATM 18 C C1N NPM . . . M 3 67.094 32.292 10.61 0.16 98.73 ? C1N NPM 10 B 1 HETATM 19 C C1O NPM . . . M 3 68.231 32.958 10.268 0.16 99.26 ? C1O NPM 10 B 1 HETATM 20 C C1P NPM . . . M 3 68.583 33.077 8.942 0.16 99.96 ? C1P NPM 10 B 1 HETATM 21 C C1Q NPM . . . M 3 67.783 32.522 7.989 0.16 100.53 ? C1Q NPM 10 B 1 HETATM 22 C C1R NPM . . . M 3 66.65 31.864 8.326 0.16 99.83 ? C1R NPM 10 B 1 HETATM 23 C C1S NPM . . . M 3 66.299 31.744 9.642 0.16 99.16 ? C1S NPM 10 B 1 HETATM 24 C C1T NPM . . . M 3 67.456 33.546 5.973 0.16 103.42 ? C1T NPM 10 B 1 HETATM 25 C C1U NPM . . . M 3 67.71 33.78 4.576 0.16 104.35 ? C1U NPM 10 B 1 HETATM 26 C C1V NPM . . . M 3 67.017 34.726 3.803 0.16 104.87 ? C1V NPM 10 B 1 HETATM 27 C C1W NPM . . . M 3 67.364 34.849 2.465 0.16 105.13 ? C1W NPM 10 B 1 HETATM 28 C C1X NPM . . . M 3 68.377 34.027 1.976 0.16 105.07 ? C1X NPM 10 B 1 HETATM 29 C C1Y NPM . . . M 3 69.016 33.118 2.796 0.16 104.81 ? C1Y NPM 10 B 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 258 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 29 #