data_4NYI # _model_server_result.job_id D8-6owHOm8boO6XiNrHlMA _model_server_result.datetime_utc '2024-11-26 14:12:27' _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 4nyi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1101}' # _entry.id 4NYI # _exptl.entry_id 4NYI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 429.557 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-{1-[(5-methyl-1H-indol-3-yl)methyl]piperidin-4-yl}-L-tryptophanamide _entity.pdbx_number_of_molecules 1 _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 4NYI _cell.length_a 183.285 _cell.length_b 183.285 _cell.length_c 177.86 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NYI _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 4 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 OG SER 18 Q SER 17 1_555 D MG MG . Q MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc2 A OG1 THR 36 Q THR 35 1_555 D MG MG . Q MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc3 D MG MG . Q MG 201 1_555 E O1G GNP . Q GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc4 D MG MG . Q MG 201 1_555 E O1B GNP . Q GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc5 D MG MG . Q MG 201 1_555 G O HOH . Q HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc6 D MG MG . Q MG 201 1_555 G O HOH . Q HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? # _chem_comp.formula 'C26 H31 N5 O' _chem_comp.formula_weight 429.557 _chem_comp.id 2PX _chem_comp.mon_nstd_flag . _chem_comp.name N-{1-[(5-methyl-1H-indol-3-yl)methyl]piperidin-4-yl}-L-tryptophanamide _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 C17 C18 2PX sing 1 n n C17 C16 2PX sing 2 n n O01 C02 2PX doub 3 n n C11 C10 2PX doub 4 n y C11 C12 2PX sing 5 n y C18 N21 2PX sing 6 n n C10 C09 2PX sing 7 n y C16 N15 2PX sing 8 n n C16 C19 2PX sing 9 n n C02 N15 2PX sing 10 n n C02 C03 2PX sing 11 n n C12 C13 2PX doub 12 n y N21 C22 2PX sing 13 n n N21 C20 2PX sing 14 n n C22 C23 2PX sing 15 n n C04 C03 2PX sing 16 n n C04 C05 2PX sing 17 n n C19 C20 2PX sing 18 n n C09 C05 2PX sing 19 n y C09 C08 2PX doub 20 n y N14 C03 2PX sing 21 n n C24 C23 2PX doub 22 n y C24 N25 2PX sing 23 n y C05 C06 2PX doub 24 n y C23 C27 2PX sing 25 n y C13 C08 2PX sing 26 n y C08 N07 2PX sing 27 n y N25 C26 2PX sing 28 n y C06 N07 2PX sing 29 n y C27 C26 2PX doub 30 n y C27 C28 2PX sing 31 n y C26 C32 2PX sing 32 n y C28 C29 2PX doub 33 n y C32 C31 2PX doub 34 n y C29 C31 2PX sing 35 n y C29 C30 2PX sing 36 n n C03 H1 2PX sing 37 n n C04 H2 2PX sing 38 n n C04 H3 2PX sing 39 n n C06 H4 2PX sing 40 n n N07 H5 2PX sing 41 n n C10 H6 2PX sing 42 n n C11 H7 2PX sing 43 n n C12 H8 2PX sing 44 n n C13 H9 2PX sing 45 n n N14 H10 2PX sing 46 n n N14 H11 2PX sing 47 n n N15 H13 2PX sing 48 n n C16 H14 2PX sing 49 n n C17 H15 2PX sing 50 n n C17 H16 2PX sing 51 n n C18 H17 2PX sing 52 n n C18 H18 2PX sing 53 n n C19 H19 2PX sing 54 n n C19 H20 2PX sing 55 n n C20 H21 2PX sing 56 n n C20 H22 2PX sing 57 n n C22 H24 2PX sing 58 n n C22 H25 2PX sing 59 n n C24 H26 2PX sing 60 n n N25 H27 2PX sing 61 n n C28 H28 2PX sing 62 n n C30 H29 2PX sing 63 n n C30 H30 2PX sing 64 n n C30 H31 2PX sing 65 n n C31 H32 2PX sing 66 n n C32 H33 2PX sing 67 n n # _atom_sites.entry_id 4NYI _atom_sites.fract_transf_matrix[1][1] 0.005456 _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] 0.005456 _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] 0.005622 _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 D 4 MG Q 1 201 1002 MG MG . E 5 GNP Q 1 202 1001 GNP GNP . F 6 2PX S 1 1101 1 2PX LIG . G 7 HOH Q 1 301 1 HOH HOH . G 7 HOH Q 2 302 6 HOH HOH . G 7 HOH Q 3 303 13 HOH HOH . G 7 HOH Q 4 304 15 HOH HOH . G 7 HOH Q 5 305 23 HOH HOH . G 7 HOH Q 6 306 31 HOH HOH . G 7 HOH Q 7 307 33 HOH HOH . G 7 HOH Q 8 308 36 HOH HOH . G 7 HOH Q 9 309 50 HOH HOH . G 7 HOH Q 10 310 56 HOH HOH . G 7 HOH Q 11 311 58 HOH HOH . G 7 HOH Q 12 312 60 HOH HOH . G 7 HOH Q 13 313 63 HOH HOH . G 7 HOH Q 14 314 64 HOH HOH . G 7 HOH Q 15 315 66 HOH HOH . G 7 HOH Q 16 316 73 HOH HOH . G 7 HOH Q 17 317 94 HOH HOH . G 7 HOH Q 18 318 122 HOH HOH . G 7 HOH Q 19 319 123 HOH HOH . G 7 HOH Q 20 320 127 HOH HOH . G 7 HOH Q 21 321 134 HOH HOH . G 7 HOH Q 22 322 149 HOH HOH . G 7 HOH Q 23 323 151 HOH HOH . G 7 HOH Q 24 324 156 HOH HOH . H 7 HOH R 1 201 7 HOH HOH . H 7 HOH R 2 202 10 HOH HOH . H 7 HOH R 3 203 16 HOH HOH . H 7 HOH R 4 204 17 HOH HOH . H 7 HOH R 5 205 21 HOH HOH . H 7 HOH R 6 206 38 HOH HOH . H 7 HOH R 7 207 40 HOH HOH . H 7 HOH R 8 208 41 HOH HOH . H 7 HOH R 9 209 43 HOH HOH . H 7 HOH R 10 210 47 HOH HOH . H 7 HOH R 11 211 49 HOH HOH . H 7 HOH R 12 212 52 HOH HOH . H 7 HOH R 13 213 54 HOH HOH . H 7 HOH R 14 214 59 HOH HOH . H 7 HOH R 15 215 68 HOH HOH . H 7 HOH R 16 216 70 HOH HOH . H 7 HOH R 17 217 71 HOH HOH . H 7 HOH R 18 218 72 HOH HOH . H 7 HOH R 19 219 92 HOH HOH . H 7 HOH R 20 220 93 HOH HOH . H 7 HOH R 21 221 95 HOH HOH . H 7 HOH R 22 222 114 HOH HOH . H 7 HOH R 23 223 115 HOH HOH . H 7 HOH R 24 224 125 HOH HOH . H 7 HOH R 25 225 132 HOH HOH . H 7 HOH R 26 226 140 HOH HOH . H 7 HOH R 27 227 143 HOH HOH . H 7 HOH R 28 228 147 HOH HOH . H 7 HOH R 29 229 155 HOH HOH . I 7 HOH S 1 1201 2 HOH HOH . I 7 HOH S 2 1202 4 HOH HOH . I 7 HOH S 3 1203 5 HOH HOH . I 7 HOH S 4 1204 8 HOH HOH . I 7 HOH S 5 1205 9 HOH HOH . I 7 HOH S 6 1206 11 HOH HOH . I 7 HOH S 7 1207 12 HOH HOH . I 7 HOH S 8 1208 14 HOH HOH . I 7 HOH S 9 1209 18 HOH HOH . I 7 HOH S 10 1210 19 HOH HOH . I 7 HOH S 11 1211 20 HOH HOH . I 7 HOH S 12 1212 22 HOH HOH . I 7 HOH S 13 1213 24 HOH HOH . I 7 HOH S 14 1214 25 HOH HOH . I 7 HOH S 15 1215 26 HOH HOH . I 7 HOH S 16 1216 27 HOH HOH . I 7 HOH S 17 1217 29 HOH HOH . I 7 HOH S 18 1218 30 HOH HOH . I 7 HOH S 19 1219 34 HOH HOH . I 7 HOH S 20 1220 35 HOH HOH . I 7 HOH S 21 1221 37 HOH HOH . I 7 HOH S 22 1222 44 HOH HOH . I 7 HOH S 23 1223 45 HOH HOH . I 7 HOH S 24 1224 46 HOH HOH . I 7 HOH S 25 1225 48 HOH HOH . I 7 HOH S 26 1226 51 HOH HOH . I 7 HOH S 27 1227 53 HOH HOH . I 7 HOH S 28 1228 55 HOH HOH . I 7 HOH S 29 1229 57 HOH HOH . I 7 HOH S 30 1230 61 HOH HOH . I 7 HOH S 31 1231 62 HOH HOH . I 7 HOH S 32 1232 65 HOH HOH . I 7 HOH S 33 1233 67 HOH HOH . I 7 HOH S 34 1234 69 HOH HOH . I 7 HOH S 35 1235 75 HOH HOH . I 7 HOH S 36 1236 76 HOH HOH . I 7 HOH S 37 1237 77 HOH HOH . I 7 HOH S 38 1238 78 HOH HOH . I 7 HOH S 39 1239 79 HOH HOH . I 7 HOH S 40 1240 80 HOH HOH . I 7 HOH S 41 1241 81 HOH HOH . I 7 HOH S 42 1242 82 HOH HOH . I 7 HOH S 43 1243 83 HOH HOH . I 7 HOH S 44 1244 84 HOH HOH . I 7 HOH S 45 1245 85 HOH HOH . I 7 HOH S 46 1246 86 HOH HOH . I 7 HOH S 47 1247 87 HOH HOH . I 7 HOH S 48 1248 88 HOH HOH . I 7 HOH S 49 1249 89 HOH HOH . I 7 HOH S 50 1250 90 HOH HOH . I 7 HOH S 51 1251 91 HOH HOH . I 7 HOH S 52 1252 96 HOH HOH . I 7 HOH S 53 1253 97 HOH HOH . I 7 HOH S 54 1254 98 HOH HOH . I 7 HOH S 55 1255 99 HOH HOH . I 7 HOH S 56 1256 100 HOH HOH . I 7 HOH S 57 1257 101 HOH HOH . I 7 HOH S 58 1258 102 HOH HOH . I 7 HOH S 59 1259 103 HOH HOH . I 7 HOH S 60 1260 104 HOH HOH . I 7 HOH S 61 1261 105 HOH HOH . I 7 HOH S 62 1262 106 HOH HOH . I 7 HOH S 63 1263 107 HOH HOH . I 7 HOH S 64 1264 108 HOH HOH . I 7 HOH S 65 1265 109 HOH HOH . I 7 HOH S 66 1266 110 HOH HOH . I 7 HOH S 67 1267 112 HOH HOH . I 7 HOH S 68 1268 113 HOH HOH . I 7 HOH S 69 1269 116 HOH HOH . I 7 HOH S 70 1270 117 HOH HOH . I 7 HOH S 71 1271 119 HOH HOH . I 7 HOH S 72 1272 121 HOH HOH . I 7 HOH S 73 1273 124 HOH HOH . I 7 HOH S 74 1274 126 HOH HOH . I 7 HOH S 75 1275 128 HOH HOH . I 7 HOH S 76 1276 130 HOH HOH . I 7 HOH S 77 1277 131 HOH HOH . I 7 HOH S 78 1278 133 HOH HOH . I 7 HOH S 79 1279 135 HOH HOH . I 7 HOH S 80 1280 138 HOH HOH . I 7 HOH S 81 1281 139 HOH HOH . I 7 HOH S 82 1282 141 HOH HOH . I 7 HOH S 83 1283 142 HOH HOH . I 7 HOH S 84 1284 144 HOH HOH . I 7 HOH S 85 1285 145 HOH HOH . I 7 HOH S 86 1286 146 HOH HOH . I 7 HOH S 87 1287 148 HOH HOH . I 7 HOH S 88 1288 150 HOH HOH . I 7 HOH S 89 1289 152 HOH HOH . I 7 HOH S 90 1290 153 HOH HOH . I 7 HOH S 91 1291 154 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 O O01 2PX . . . F 6 40.873 28.472 19.112 1 56.75 ? O01 2PX 1101 S 1 HETATM 2 C C02 2PX . . . F 6 40.484 28.782 20.24 1 49.09 ? C02 2PX 1101 S 1 HETATM 3 C C03 2PX . . . F 6 41.367 29.56 21.178 1 44.86 ? C03 2PX 1101 S 1 HETATM 4 C C04 2PX . . . F 6 41.361 30.993 20.77 1 46.63 ? C04 2PX 1101 S 1 HETATM 5 C C05 2PX . . . F 6 40.224 31.67 21.502 1 53.42 ? C05 2PX 1101 S 1 HETATM 6 C C06 2PX . . . F 6 40.026 31.676 22.869 1 61.21 ? C06 2PX 1101 S 1 HETATM 7 N N07 2PX . . . F 6 38.902 32.378 23.136 1 52.15 ? N07 2PX 1101 S 1 HETATM 8 C C08 2PX . . . F 6 38.349 32.833 21.969 1 40.15 ? C08 2PX 1101 S 1 HETATM 9 C C09 2PX . . . F 6 39.176 32.392 20.92 1 43.04 ? C09 2PX 1101 S 1 HETATM 10 C C10 2PX . . . F 6 38.852 32.717 19.611 1 34.06 ? C10 2PX 1101 S 1 HETATM 11 C C11 2PX . . . F 6 37.689 33.47 19.415 1 44.6 ? C11 2PX 1101 S 1 HETATM 12 C C12 2PX . . . F 6 36.887 33.894 20.469 1 42.47 ? C12 2PX 1101 S 1 HETATM 13 C C13 2PX . . . F 6 37.192 33.588 21.786 1 30.31 ? C13 2PX 1101 S 1 HETATM 14 N N14 2PX . . . F 6 42.696 29.025 21.169 1 55.2 ? N14 2PX 1101 S 1 HETATM 15 N N15 2PX . . . F 6 39.159 28.423 20.736 1 39.69 ? N15 2PX 1101 S 1 HETATM 16 C C16 2PX . . . F 6 38.185 27.672 19.94 1 35.27 ? C16 2PX 1101 S 1 HETATM 17 C C17 2PX . . . F 6 37.67 28.562 18.893 1 33.76 ? C17 2PX 1101 S 1 HETATM 18 C C18 2PX . . . F 6 37.057 29.786 19.471 1 30.63 ? C18 2PX 1101 S 1 HETATM 19 C C19 2PX . . . F 6 37.128 27.26 20.88 1 31.32 ? C19 2PX 1101 S 1 HETATM 20 C C20 2PX . . . F 6 36.374 28.41 21.461 1 26.57 ? C20 2PX 1101 S 1 HETATM 21 N N21 2PX . . . F 6 36.063 29.467 20.504 1 29.46 ? N21 2PX 1101 S 1 HETATM 22 C C22 2PX . . . F 6 35.082 30.524 20.744 1 32.33 ? C22 2PX 1101 S 1 HETATM 23 C C23 2PX . . . F 6 34.002 30.209 21.766 1 24.28 ? C23 2PX 1101 S 1 HETATM 24 C C24 2PX . . . F 6 32.721 29.798 21.497 1 26.2 ? C24 2PX 1101 S 1 HETATM 25 N N25 2PX . . . F 6 32.061 29.641 22.681 1 23.88 ? N25 2PX 1101 S 1 HETATM 26 C C26 2PX . . . F 6 32.888 29.96 23.735 1 27.02 ? C26 2PX 1101 S 1 HETATM 27 C C27 2PX . . . F 6 34.114 30.326 23.163 1 28.37 ? C27 2PX 1101 S 1 HETATM 28 C C28 2PX . . . F 6 35.161 30.702 24.015 1 27.3 ? C28 2PX 1101 S 1 HETATM 29 C C29 2PX . . . F 6 34.959 30.702 25.404 1 20.44 ? C29 2PX 1101 S 1 HETATM 30 C C30 2PX . . . F 6 36.083 31.11 26.259 1 25.21 ? C30 2PX 1101 S 1 HETATM 31 C C31 2PX . . . F 6 33.717 30.324 25.942 1 21.35 ? C31 2PX 1101 S 1 HETATM 32 C C32 2PX . . . F 6 32.654 29.948 25.129 1 19.02 ? C32 2PX 1101 S 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 106 _model_server_stats.create_model_time_ms 44 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #