data_3MJ5 # _model_server_result.job_id LH0XN-QwX6jICSChisNm0w _model_server_result.datetime_utc '2024-11-22 06:46:58' _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 3mj5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":801}' # _entry.id 3MJ5 # _exptl.entry_id 3MJ5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details (R)-N-(benzo[d][1,3]dioxol-5-ylmethyl)-1-(1-(naphthalen-1-yl)ethyl)piperidine-4-carboxamide _entity.formula_weight 416.512 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-(1,3-benzodioxol-5-ylmethyl)-1-[(1R)-1-naphthalen-1-ylethyl]piperidine-4-carboxamide _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 103.02 _cell.angle_gamma 90 _cell.entry_id 3MJ5 _cell.length_a 118.397 _cell.length_b 74.129 _cell.length_c 96.895 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3MJ5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # 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 PISA dimeric 2 software_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,G 1 1 B,E,F,H 2 1 A,B,C,D,E,F,G,H 3 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 E 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 disulf ? disulf1 B SG CYS 190 B CYS 190 1_555 B SG CYS 193 B CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? metalc ? metalc1 A SG CYS 190 A CYS 190 1_555 D ZN ZN . A ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc2 A SG CYS 193 A CYS 193 1_555 D ZN ZN . A ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc3 A SG CYS 225 A CYS 225 1_555 D ZN ZN . A ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc4 A SG CYS 227 A CYS 227 1_555 D ZN ZN . A ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? metalc ? metalc5 B SG CYS 190 B CYS 190 1_555 F ZN ZN . B ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.572 ? metalc ? metalc6 B SG CYS 193 B CYS 193 1_555 F ZN ZN . B ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc7 B SG CYS 225 B CYS 225 1_555 F ZN ZN . B ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.545 ? # _chem_comp.formula 'C26 H28 N2 O3' _chem_comp.formula_weight 416.512 _chem_comp.id GRM _chem_comp.mon_nstd_flag . _chem_comp.name N-(1,3-benzodioxol-5-ylmethyl)-1-[(1R)-1-naphthalen-1-ylethyl]piperidine-4-carboxamide _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 C1 C2 GRM sing 129 n n C1 C3 GRM sing 130 n n C1 N4 GRM sing 131 n n C3 C23 GRM doub 132 n y C3 C27 GRM sing 133 n y N4 C5 GRM sing 134 n n N4 C9 GRM sing 135 n n C5 C6 GRM sing 136 n n C6 C7 GRM sing 137 n n C7 C8 GRM sing 138 n n C7 C10 GRM sing 139 n n C8 C9 GRM sing 140 n n C10 O11 GRM doub 141 n n C10 N12 GRM sing 142 n n N12 C13 GRM sing 143 n n C13 C14 GRM sing 144 n n C14 C15 GRM doub 145 n y C14 C19 GRM sing 146 n y C15 C16 GRM sing 147 n y C16 C17 GRM doub 148 n y C16 O20 GRM sing 149 n n C17 C18 GRM sing 150 n y C17 O22 GRM sing 151 n n C18 C19 GRM doub 152 n y O20 C21 GRM sing 153 n n C21 O22 GRM sing 154 n n C23 C24 GRM sing 155 n y C23 C28 GRM sing 156 n y C24 C25 GRM doub 157 n y C24 C31 GRM sing 158 n y C25 C26 GRM sing 159 n y C26 C27 GRM doub 160 n y C28 C29 GRM doub 161 n y C29 C30 GRM sing 162 n y C30 C31 GRM doub 163 n y C1 H1 GRM sing 164 n n C2 H2 GRM sing 165 n n C2 H2A GRM sing 166 n n C2 H2B GRM sing 167 n n C5 H5 GRM sing 168 n n C5 H5A GRM sing 169 n n C6 H6 GRM sing 170 n n C6 H6A GRM sing 171 n n C7 H7 GRM sing 172 n n C8 H8 GRM sing 173 n n C8 H8A GRM sing 174 n n C9 H9 GRM sing 175 n n C9 H9A GRM sing 176 n n N12 HN12 GRM sing 177 n n C13 H13 GRM sing 178 n n C13 H13A GRM sing 179 n n C15 H15 GRM sing 180 n n C18 H18 GRM sing 181 n n C19 H19 GRM sing 182 n n C21 H21 GRM sing 183 n n C21 H21A GRM sing 184 n n C25 H25 GRM sing 185 n n C26 H26 GRM sing 186 n n C27 H27 GRM sing 187 n n C28 H28 GRM sing 188 n n C29 H29 GRM sing 189 n n C30 H30 GRM sing 190 n n C31 H31 GRM sing 191 n n # _atom_sites.entry_id 3MJ5 _atom_sites.fract_transf_matrix[1][1] 0.008446 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001953 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01349 _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] 0.010593 _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 GRM A 1 801 801 GRM GRM . D 3 ZN A 1 901 901 ZN ZN . E 2 GRM B 1 801 801 GRM GRM . F 3 ZN B 1 901 901 ZN ZN . G 4 HOH A 1 317 1 HOH HOH . G 4 HOH A 2 318 2 HOH HOH . G 4 HOH A 3 319 4 HOH HOH . G 4 HOH A 4 320 6 HOH HOH . G 4 HOH A 5 321 10 HOH HOH . G 4 HOH A 6 322 12 HOH HOH . G 4 HOH A 7 323 13 HOH HOH . G 4 HOH A 8 324 14 HOH HOH . G 4 HOH A 9 325 15 HOH HOH . G 4 HOH A 10 326 20 HOH HOH . G 4 HOH A 11 327 21 HOH HOH . G 4 HOH A 12 328 22 HOH HOH . G 4 HOH A 13 329 23 HOH HOH . G 4 HOH A 14 330 26 HOH HOH . G 4 HOH A 15 331 27 HOH HOH . G 4 HOH A 16 332 29 HOH HOH . G 4 HOH A 17 333 30 HOH HOH . G 4 HOH A 18 334 35 HOH HOH . G 4 HOH A 19 335 37 HOH HOH . G 4 HOH A 20 336 38 HOH HOH . G 4 HOH A 21 337 39 HOH HOH . G 4 HOH A 22 338 44 HOH HOH . G 4 HOH A 23 339 45 HOH HOH . G 4 HOH A 24 340 46 HOH HOH . G 4 HOH A 25 341 48 HOH HOH . G 4 HOH A 26 342 51 HOH HOH . G 4 HOH A 27 343 56 HOH HOH . G 4 HOH A 28 344 57 HOH HOH . G 4 HOH A 29 345 58 HOH HOH . G 4 HOH A 30 346 59 HOH HOH . G 4 HOH A 31 347 60 HOH HOH . G 4 HOH A 32 348 62 HOH HOH . G 4 HOH A 33 349 63 HOH HOH . G 4 HOH A 34 350 65 HOH HOH . G 4 HOH A 35 351 68 HOH HOH . G 4 HOH A 36 352 70 HOH HOH . G 4 HOH A 37 353 71 HOH HOH . G 4 HOH A 38 354 73 HOH HOH . G 4 HOH A 39 355 74 HOH HOH . G 4 HOH A 40 356 75 HOH HOH . G 4 HOH A 41 357 77 HOH HOH . G 4 HOH A 42 358 81 HOH HOH . G 4 HOH A 43 359 82 HOH HOH . G 4 HOH A 44 360 83 HOH HOH . G 4 HOH A 45 361 84 HOH HOH . G 4 HOH A 46 362 85 HOH HOH . G 4 HOH A 47 363 86 HOH HOH . G 4 HOH A 48 364 87 HOH HOH . G 4 HOH A 49 365 89 HOH HOH . G 4 HOH A 50 366 90 HOH HOH . G 4 HOH A 51 367 92 HOH HOH . G 4 HOH A 52 368 93 HOH HOH . G 4 HOH A 53 369 94 HOH HOH . G 4 HOH A 54 370 95 HOH HOH . G 4 HOH A 55 371 96 HOH HOH . G 4 HOH A 56 372 97 HOH HOH . G 4 HOH A 57 373 98 HOH HOH . G 4 HOH A 58 374 99 HOH HOH . G 4 HOH A 59 375 101 HOH HOH . G 4 HOH A 60 376 112 HOH HOH . H 4 HOH B 1 317 3 HOH HOH . H 4 HOH B 2 318 5 HOH HOH . H 4 HOH B 3 319 7 HOH HOH . H 4 HOH B 4 320 8 HOH HOH . H 4 HOH B 5 321 9 HOH HOH . H 4 HOH B 6 322 11 HOH HOH . H 4 HOH B 7 323 16 HOH HOH . H 4 HOH B 8 324 17 HOH HOH . H 4 HOH B 9 325 18 HOH HOH . H 4 HOH B 10 326 19 HOH HOH . H 4 HOH B 11 327 24 HOH HOH . H 4 HOH B 12 328 25 HOH HOH . H 4 HOH B 13 329 28 HOH HOH . H 4 HOH B 14 330 31 HOH HOH . H 4 HOH B 15 331 32 HOH HOH . H 4 HOH B 16 332 33 HOH HOH . H 4 HOH B 17 333 34 HOH HOH . H 4 HOH B 18 334 36 HOH HOH . H 4 HOH B 19 335 40 HOH HOH . H 4 HOH B 20 336 41 HOH HOH . H 4 HOH B 21 337 42 HOH HOH . H 4 HOH B 22 338 43 HOH HOH . H 4 HOH B 23 339 47 HOH HOH . H 4 HOH B 24 340 49 HOH HOH . H 4 HOH B 25 341 50 HOH HOH . H 4 HOH B 26 342 52 HOH HOH . H 4 HOH B 27 343 53 HOH HOH . H 4 HOH B 28 344 54 HOH HOH . H 4 HOH B 29 345 55 HOH HOH . H 4 HOH B 30 346 61 HOH HOH . H 4 HOH B 31 347 64 HOH HOH . H 4 HOH B 32 348 66 HOH HOH . H 4 HOH B 33 349 67 HOH HOH . H 4 HOH B 34 350 69 HOH HOH . H 4 HOH B 35 351 72 HOH HOH . H 4 HOH B 36 352 76 HOH HOH . H 4 HOH B 37 353 78 HOH HOH . H 4 HOH B 38 354 79 HOH HOH . H 4 HOH B 39 355 80 HOH HOH . H 4 HOH B 40 356 88 HOH HOH . H 4 HOH B 41 357 91 HOH HOH . H 4 HOH B 42 358 100 HOH HOH . H 4 HOH B 43 359 102 HOH HOH . H 4 HOH B 44 360 103 HOH HOH . H 4 HOH B 45 361 104 HOH HOH . H 4 HOH B 46 362 105 HOH HOH . H 4 HOH B 47 363 106 HOH HOH . H 4 HOH B 48 364 107 HOH HOH . H 4 HOH B 49 365 108 HOH HOH . H 4 HOH B 50 366 109 HOH HOH . H 4 HOH B 51 367 110 HOH HOH . H 4 HOH B 52 368 111 HOH HOH . H 4 HOH B 53 369 113 HOH HOH . H 4 HOH B 54 370 114 HOH HOH . H 4 HOH B 55 371 115 HOH HOH . H 4 HOH B 56 372 116 HOH HOH . H 4 HOH B 57 373 117 HOH HOH . H 4 HOH B 58 374 118 HOH HOH . H 4 HOH B 59 375 119 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 C1 GRM . . . E 2 -12.671 36.31 -43.183 1 44.74 ? C1 GRM 801 B 1 HETATM 2 C C2 GRM . . . E 2 -11.139 36.016 -42.997 1 40.4 ? C2 GRM 801 B 1 HETATM 3 C C3 GRM . . . E 2 -13.031 37.831 -43.471 1 41.83 ? C3 GRM 801 B 1 HETATM 4 N N4 GRM . . . E 2 -13.707 35.676 -42.134 1 48.41 ? N4 GRM 801 B 1 HETATM 5 C C5 GRM . . . E 2 -14.117 36.443 -40.884 1 49.91 ? C5 GRM 801 B 1 HETATM 6 C C6 GRM . . . E 2 -15.583 36.085 -40.406 1 51.82 ? C6 GRM 801 B 1 HETATM 7 C C7 GRM . . . E 2 -15.974 34.593 -40.67 1 52.1 ? C7 GRM 801 B 1 HETATM 8 C C8 GRM . . . E 2 -14.671 33.729 -40.676 1 49.93 ? C8 GRM 801 B 1 HETATM 9 C C9 GRM . . . E 2 -13.569 34.199 -41.707 1 48.81 ? C9 GRM 801 B 1 HETATM 10 C C10 GRM . . . E 2 -16.977 34.156 -39.581 1 54.34 ? C10 GRM 801 B 1 HETATM 11 O O11 GRM . . . E 2 -16.59 34.016 -38.431 1 57.34 ? O11 GRM 801 B 1 HETATM 12 N N12 GRM . . . E 2 -18.29 33.972 -39.849 1 54.75 ? N12 GRM 801 B 1 HETATM 13 C C13 GRM . . . E 2 -19.202 33.605 -38.747 1 55.84 ? C13 GRM 801 B 1 HETATM 14 C C14 GRM . . . E 2 -20.638 33.982 -39.126 1 56.45 ? C14 GRM 801 B 1 HETATM 15 C C15 GRM . . . E 2 -20.929 35.299 -39.588 1 57.64 ? C15 GRM 801 B 1 HETATM 16 C C16 GRM . . . E 2 -22.255 35.602 -39.945 1 60.22 ? C16 GRM 801 B 1 HETATM 17 C C17 GRM . . . E 2 -23.285 34.662 -39.869 1 60.88 ? C17 GRM 801 B 1 HETATM 18 C C18 GRM . . . E 2 -23.025 33.321 -39.409 1 59.3 ? C18 GRM 801 B 1 HETATM 19 C C19 GRM . . . E 2 -21.674 32.996 -39.044 1 57.59 ? C19 GRM 801 B 1 HETATM 20 O O20 GRM . . . E 2 -22.691 36.818 -40.411 1 62.88 ? O20 GRM 801 B 1 HETATM 21 C C21 GRM . . . E 2 -24.111 36.531 -40.688 1 62.12 ? C21 GRM 801 B 1 HETATM 22 O O22 GRM . . . E 2 -24.516 35.189 -40.282 1 61.78 ? O22 GRM 801 B 1 HETATM 23 C C23 GRM . . . E 2 -13.948 38.327 -44.483 1 39.45 ? C23 GRM 801 B 1 HETATM 24 C C24 GRM . . . E 2 -14.177 39.768 -44.615 1 38.21 ? C24 GRM 801 B 1 HETATM 25 C C25 GRM . . . E 2 -13.537 40.669 -43.753 1 38.15 ? C25 GRM 801 B 1 HETATM 26 C C26 GRM . . . E 2 -12.651 40.188 -42.77 1 40.23 ? C26 GRM 801 B 1 HETATM 27 C C27 GRM . . . E 2 -12.392 38.811 -42.622 1 41.24 ? C27 GRM 801 B 1 HETATM 28 C C28 GRM . . . E 2 -14.656 37.487 -45.388 1 39.37 ? C28 GRM 801 B 1 HETATM 29 C C29 GRM . . . E 2 -15.533 38.03 -46.369 1 37.74 ? C29 GRM 801 B 1 HETATM 30 C C30 GRM . . . E 2 -15.73 39.428 -46.459 1 38.65 ? C30 GRM 801 B 1 HETATM 31 C C31 GRM . . . E 2 -15.058 40.307 -45.584 1 37.89 ? C31 GRM 801 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #