data_4NYJ # _model_server_result.job_id UsdEz-tSNtUHIROkJBpDVA _model_server_result.datetime_utc '2024-10-15 16:23:01' _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 4nyj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1101}' # _entry.id 4NYJ # _exptl.entry_id 4NYJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 286.372 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-[1-(1H-indol-3-ylmethyl)piperidin-4-yl]glycinamide _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 4NYJ _cell.length_a 185.338 _cell.length_b 185.338 _cell.length_c 179.535 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NYJ _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 author_and_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 17 Q SER 17 1_555 D MG MG . Q MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc2 A OG1 THR 35 Q THR 35 1_555 D MG MG . Q MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc3 D MG MG . Q MG 201 1_555 E O1G GNP . Q GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? metalc ? metalc4 D MG MG . Q MG 201 1_555 E O1B GNP . Q GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc5 D MG MG . Q MG 201 1_555 G O HOH . Q HOH 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? metalc ? metalc6 D MG MG . Q MG 201 1_555 G O HOH . Q HOH 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? # _chem_comp.formula 'C16 H22 N4 O' _chem_comp.formula_weight 286.372 _chem_comp.id 2PZ _chem_comp.mon_nstd_flag . _chem_comp.name N-[1-(1H-indol-3-ylmethyl)piperidin-4-yl]glycinamide _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 O C 2PZ doub 1 n n CA C 2PZ sing 2 n n CA N 2PZ sing 3 n n C NAQ 2PZ sing 4 n n CAO CAP 2PZ sing 5 n n CAO CAN 2PZ sing 6 n n CAP NAK 2PZ sing 7 n n NAQ CAN 2PZ sing 8 n n CAN CAM 2PZ sing 9 n n NAK CAJ 2PZ sing 10 n n NAK CAL 2PZ sing 11 n n CAJ CAH 2PZ sing 12 n n CAM CAL 2PZ sing 13 n n CAI CAH 2PZ doub 14 n y CAI NAG 2PZ sing 15 n y CAH CAF 2PZ sing 16 n y NAG CAE 2PZ sing 17 n y CAF CAE 2PZ doub 18 n y CAF CAA 2PZ sing 19 n y CAE CAD 2PZ sing 20 n y CAA CAB 2PZ doub 21 n y CAD CAC 2PZ doub 22 n y CAB CAC 2PZ sing 23 n y CAD H1 2PZ sing 24 n n CAC H2 2PZ sing 25 n n CAB H3 2PZ sing 26 n n CAA H4 2PZ sing 27 n n NAG H5 2PZ sing 28 n n CAI H6 2PZ sing 29 n n CAJ H7 2PZ sing 30 n n CAJ H8 2PZ sing 31 n n CAP H10 2PZ sing 32 n n CAP H11 2PZ sing 33 n n CAO H12 2PZ sing 34 n n CAO H13 2PZ sing 35 n n CAL H14 2PZ sing 36 n n CAL H15 2PZ sing 37 n n CAM H16 2PZ sing 38 n n CAM H17 2PZ sing 39 n n CAN H18 2PZ sing 40 n n NAQ H19 2PZ sing 41 n n CA H20 2PZ sing 42 n n CA H21 2PZ sing 43 n n N H22 2PZ sing 44 n n N H23 2PZ sing 45 n n # _atom_sites.entry_id 4NYJ _atom_sites.fract_transf_matrix[1][1] 0.005396 _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] 0.005396 _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] 0.00557 _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 1 201 201 MG MG . E 5 GNP Q 1 202 202 GNP GNP . F 6 2PZ S 1 1101 1101 2PZ 2PZ . G 7 HOH Q 1 301 1 HOH HOH . G 7 HOH Q 2 302 2 HOH HOH . G 7 HOH Q 3 303 3 HOH HOH . G 7 HOH Q 4 304 4 HOH HOH . G 7 HOH Q 5 305 5 HOH HOH . G 7 HOH Q 6 306 6 HOH HOH . G 7 HOH Q 7 307 8 HOH HOH . G 7 HOH Q 8 308 9 HOH HOH . G 7 HOH Q 9 309 90 HOH HOH . G 7 HOH Q 10 310 93 HOH HOH . G 7 HOH Q 11 311 100 HOH HOH . G 7 HOH Q 12 312 110 HOH HOH . G 7 HOH Q 13 313 115 HOH HOH . G 7 HOH Q 14 314 119 HOH HOH . H 7 HOH R 1 201 11 HOH HOH . H 7 HOH R 2 202 12 HOH HOH . H 7 HOH R 3 203 13 HOH HOH . H 7 HOH R 4 204 14 HOH HOH . H 7 HOH R 5 205 15 HOH HOH . H 7 HOH R 6 206 16 HOH HOH . H 7 HOH R 7 207 17 HOH HOH . H 7 HOH R 8 208 18 HOH HOH . H 7 HOH R 9 209 19 HOH HOH . H 7 HOH R 10 210 20 HOH HOH . H 7 HOH R 11 211 21 HOH HOH . H 7 HOH R 12 212 22 HOH HOH . H 7 HOH R 13 213 23 HOH HOH . H 7 HOH R 14 214 24 HOH HOH . H 7 HOH R 15 215 26 HOH HOH . H 7 HOH R 16 216 96 HOH HOH . H 7 HOH R 17 217 114 HOH HOH . H 7 HOH R 18 218 117 HOH HOH . H 7 HOH R 19 219 121 HOH HOH . H 7 HOH R 20 220 123 HOH HOH . H 7 HOH R 21 221 127 HOH HOH . H 7 HOH R 22 222 134 HOH HOH . H 7 HOH R 23 223 137 HOH HOH . I 7 HOH S 1 1201 7 HOH HOH . I 7 HOH S 2 1202 27 HOH HOH . I 7 HOH S 3 1203 28 HOH HOH . I 7 HOH S 4 1204 29 HOH HOH . I 7 HOH S 5 1205 30 HOH HOH . I 7 HOH S 6 1206 31 HOH HOH . I 7 HOH S 7 1207 32 HOH HOH . I 7 HOH S 8 1208 33 HOH HOH . I 7 HOH S 9 1209 34 HOH HOH . I 7 HOH S 10 1210 35 HOH HOH . I 7 HOH S 11 1211 38 HOH HOH . I 7 HOH S 12 1212 39 HOH HOH . I 7 HOH S 13 1213 40 HOH HOH . I 7 HOH S 14 1214 41 HOH HOH . I 7 HOH S 15 1215 42 HOH HOH . I 7 HOH S 16 1216 43 HOH HOH . I 7 HOH S 17 1217 45 HOH HOH . I 7 HOH S 18 1218 46 HOH HOH . I 7 HOH S 19 1219 48 HOH HOH . I 7 HOH S 20 1220 49 HOH HOH . I 7 HOH S 21 1221 50 HOH HOH . I 7 HOH S 22 1222 51 HOH HOH . I 7 HOH S 23 1223 52 HOH HOH . I 7 HOH S 24 1224 53 HOH HOH . I 7 HOH S 25 1225 55 HOH HOH . I 7 HOH S 26 1226 56 HOH HOH . I 7 HOH S 27 1227 58 HOH HOH . I 7 HOH S 28 1228 59 HOH HOH . I 7 HOH S 29 1229 60 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 63 HOH HOH . I 7 HOH S 33 1233 64 HOH HOH . I 7 HOH S 34 1234 65 HOH HOH . I 7 HOH S 35 1235 66 HOH HOH . I 7 HOH S 36 1236 67 HOH HOH . I 7 HOH S 37 1237 68 HOH HOH . I 7 HOH S 38 1238 69 HOH HOH . I 7 HOH S 39 1239 70 HOH HOH . I 7 HOH S 40 1240 71 HOH HOH . I 7 HOH S 41 1241 72 HOH HOH . I 7 HOH S 42 1242 73 HOH HOH . I 7 HOH S 43 1243 74 HOH HOH . I 7 HOH S 44 1244 75 HOH HOH . I 7 HOH S 45 1245 76 HOH HOH . I 7 HOH S 46 1246 77 HOH HOH . I 7 HOH S 47 1247 78 HOH HOH . I 7 HOH S 48 1248 79 HOH HOH . I 7 HOH S 49 1249 80 HOH HOH . I 7 HOH S 50 1250 81 HOH HOH . I 7 HOH S 51 1251 82 HOH HOH . I 7 HOH S 52 1252 84 HOH HOH . I 7 HOH S 53 1253 85 HOH HOH . I 7 HOH S 54 1254 86 HOH HOH . I 7 HOH S 55 1255 87 HOH HOH . I 7 HOH S 56 1256 88 HOH HOH . I 7 HOH S 57 1257 89 HOH HOH . I 7 HOH S 58 1258 91 HOH HOH . I 7 HOH S 59 1259 92 HOH HOH . I 7 HOH S 60 1260 94 HOH HOH . I 7 HOH S 61 1261 95 HOH HOH . I 7 HOH S 62 1262 97 HOH HOH . I 7 HOH S 63 1263 98 HOH HOH . I 7 HOH S 64 1264 99 HOH HOH . I 7 HOH S 65 1265 102 HOH HOH . I 7 HOH S 66 1266 103 HOH HOH . I 7 HOH S 67 1267 104 HOH HOH . I 7 HOH S 68 1268 105 HOH HOH . I 7 HOH S 69 1269 106 HOH HOH . I 7 HOH S 70 1270 107 HOH HOH . I 7 HOH S 71 1271 108 HOH HOH . I 7 HOH S 72 1272 109 HOH HOH . I 7 HOH S 73 1273 112 HOH HOH . I 7 HOH S 74 1274 116 HOH HOH . I 7 HOH S 75 1275 118 HOH HOH . I 7 HOH S 76 1276 122 HOH HOH . I 7 HOH S 77 1277 124 HOH HOH . I 7 HOH S 78 1278 125 HOH HOH . I 7 HOH S 79 1279 126 HOH HOH . I 7 HOH S 80 1280 128 HOH HOH . I 7 HOH S 81 1281 129 HOH HOH . I 7 HOH S 82 1282 131 HOH HOH . I 7 HOH S 83 1283 132 HOH HOH . I 7 HOH S 84 1284 133 HOH HOH . I 7 HOH S 85 1285 135 HOH HOH . I 7 HOH S 86 1286 136 HOH HOH . I 7 HOH S 87 1287 138 HOH HOH . I 7 HOH S 88 1288 139 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 CAD 2PZ . . . F 6 -29.733 33.138 -64.18 1 51.6 ? CAD 2PZ 1101 S 1 HETATM 2 C CAC 2PZ . . . F 6 -30.016 34.035 -63.21 1 57.71 ? CAC 2PZ 1101 S 1 HETATM 3 C CAB 2PZ . . . F 6 -30.25 35.415 -63.536 1 52.18 ? CAB 2PZ 1101 S 1 HETATM 4 C CAA 2PZ . . . F 6 -30.194 35.818 -64.836 1 51.01 ? CAA 2PZ 1101 S 1 HETATM 5 C CAF 2PZ . . . F 6 -29.902 34.892 -65.861 1 53.6 ? CAF 2PZ 1101 S 1 HETATM 6 C CAE 2PZ . . . F 6 -29.667 33.564 -65.553 1 52.35 ? CAE 2PZ 1101 S 1 HETATM 7 N NAG 2PZ . . . F 6 -29.411 32.889 -66.718 1 41.03 ? NAG 2PZ 1101 S 1 HETATM 8 C CAI 2PZ . . . F 6 -29.468 33.726 -67.76 1 46.28 ? CAI 2PZ 1101 S 1 HETATM 9 C CAH 2PZ . . . F 6 -29.77 35.019 -67.31 1 51.15 ? CAH 2PZ 1101 S 1 HETATM 10 C CAJ 2PZ . . . F 6 -29.914 36.293 -68.161 1 56.86 ? CAJ 2PZ 1101 S 1 HETATM 11 N NAK 2PZ . . . F 6 -28.869 36.436 -68.745 1 73.53 1 NAK 2PZ 1101 S 1 HETATM 12 C CAP 2PZ . . . F 6 -27.661 36.528 -67.935 1 57.38 ? CAP 2PZ 1101 S 1 HETATM 13 C CAO 2PZ . . . F 6 -26.667 37.612 -68.367 1 67.65 ? CAO 2PZ 1101 S 1 HETATM 14 C CAL 2PZ . . . F 6 -28.911 36.997 -70.067 1 71.34 ? CAL 2PZ 1101 S 1 HETATM 15 C CAM 2PZ . . . F 6 -28.023 38.215 -70.285 1 75.68 ? CAM 2PZ 1101 S 1 HETATM 16 C CAN 2PZ . . . F 6 -27.273 38.664 -69.098 1 81.42 ? CAN 2PZ 1101 S 1 HETATM 17 N NAQ 2PZ . . . F 6 -26.207 39.68 -69.493 1 95.55 ? NAQ 2PZ 1101 S 1 HETATM 18 C C 2PZ . . . F 6 -25.126 39.416 -70.363 1 105.67 ? C 2PZ 1101 S 1 HETATM 19 O O 2PZ . . . F 6 -24.969 38.345 -70.862 1 103.39 ? O 2PZ 1101 S 1 HETATM 20 C CA 2PZ . . . F 6 -24.105 40.559 -70.681 1 100.36 ? CA 2PZ 1101 S 1 HETATM 21 N N 2PZ . . . F 6 -24.56 41.824 -70.122 1 100.5 1 N 2PZ 1101 S 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 21 #