data_8GCZ # _model_server_result.job_id bc3HqwdvMHcwhqtWpoZqtA _model_server_result.datetime_utc '2025-01-25 14:29:41' _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 8gcz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":513}' # _entry.id 8GCZ # _exptl.entry_id 8GCZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 411.901 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (3S,5S)-5-(aminomethyl)-N-(4-chloro-3-fluorophenyl)-1-(4-methylpiperazine-1-carbonyl)piperidine-3-carboxamide _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 8GCZ _cell.length_a 61.781 _cell.length_b 65.931 _cell.length_c 91.178 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GCZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,J,K,L,M,N,O,P _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 3 _struct_asym.id N _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 disulf ? disulf1 A SG CYS 13 A CYS 54 1_555 A SG CYS 33 A CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.981 ? disulf ? disulf2 A SG CYS 78 A CYS 119 1_555 A SG CYS 91 A CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? disulf ? disulf3 A SG CYS 104 A CYS 218 1_555 A SG CYS 133 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? disulf ? disulf4 A SG CYS 114 A CYS 228 1_555 A SG CYS 125 A CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf5 A SG CYS 182 A CYS 296 1_555 A SG CYS 201 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? disulf ? disulf6 A SG CYS 247 A CYS 378 1_555 A SG CYS 308 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? disulf ? disulf7 A SG CYS 254 A CYS 385 1_555 A SG CYS 281 A CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? disulf ? disulf8 A SG CYS 264 A CYS 395 1_555 A SG CYS 273 A CYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? covale ? covale1 A ND2 ASN 120 A ASN 234 1_555 B C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.48 ? covale ? covale2 A ND2 ASN 127 A ASN 241 1_555 C C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale3 A ND2 ASN 148 A ASN 262 1_555 D C1 NAG . A NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale4 A ND2 ASN 162 A ASN 276 1_555 E C1 NAG . A NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale5 A ND2 ASN 175 A ASN 289 1_555 F C1 NAG . A NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale6 A ND2 ASN 181 A ASN 295 1_555 G C1 NAG . A NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale7 A ND2 ASN 204 A ASN 334 1_555 H C1 NAG . A NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale8 A ND2 ASN 225 A ASN 355 1_555 J C1 NAG . A NAG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.398 ? covale ? covale9 A ND2 ASN 255 A ASN 386 1_555 I C1 NAG . A NAG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? covale ? covale10 A ND2 ASN 261 A ASN 392 1_555 L C1 NAG . A NAG 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale11 A ND2 ASN 311 A ASN 448 1_555 K C1 NAG . A NAG 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale12 A ND2 ASN 324 A ASN 461 1_555 M C1 NAG . A NAG 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? # _chem_comp.formula 'C19 H27 Cl F N5 O2' _chem_comp.formula_weight 411.901 _chem_comp.id YZI _chem_comp.mon_nstd_flag . _chem_comp.name (3S,5S)-5-(aminomethyl)-N-(4-chloro-3-fluorophenyl)-1-(4-methylpiperazine-1-carbonyl)piperidine-3-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 CL1 C17 YZI sing 439 n n C19 C17 YZI doub 440 n y C19 C20 YZI sing 441 n y C17 C15 YZI sing 442 n y C20 C13 YZI doub 443 n y F16 C15 YZI sing 444 n n C15 C14 YZI doub 445 n y C13 C14 YZI sing 446 n y C13 N12 YZI sing 447 n n N12 C10 YZI sing 448 n n C10 O11 YZI doub 449 n n C10 C09 YZI sing 450 n n C09 C21 YZI sing 451 n n C09 C08 YZI sing 452 n n C21 C22 YZI sing 453 n n C22 C23 YZI sing 454 n n C22 C25 YZI sing 455 n n C23 N24 YZI sing 456 n n C08 N07 YZI sing 457 n n C25 N07 YZI sing 458 n n N07 C06 YZI sing 459 n n C27 N05 YZI sing 460 n n C27 C28 YZI sing 461 n n C06 N05 YZI sing 462 n n C06 O26 YZI doub 463 n n N05 C04 YZI sing 464 n n C04 C03 YZI sing 465 n n C28 N02 YZI sing 466 n n C03 N02 YZI sing 467 n n N02 C01 YZI sing 468 n n C01 H1 YZI sing 469 n n C01 H2 YZI sing 470 n n C01 H3 YZI sing 471 n n C03 H4 YZI sing 472 n n C03 H5 YZI sing 473 n n C04 H6 YZI sing 474 n n C04 H7 YZI sing 475 n n C08 H8 YZI sing 476 n n C08 H9 YZI sing 477 n n C09 H10 YZI sing 478 n n C14 H11 YZI sing 479 n n C19 H12 YZI sing 480 n n C20 H13 YZI sing 481 n n C21 H14 YZI sing 482 n n C21 H15 YZI sing 483 n n C22 H16 YZI sing 484 n n C23 H17 YZI sing 485 n n C23 H18 YZI sing 486 n n C25 H19 YZI sing 487 n n C25 H20 YZI sing 488 n n C27 H21 YZI sing 489 n n C27 H22 YZI sing 490 n n C28 H23 YZI sing 491 n n C28 H24 YZI sing 492 n n N12 H26 YZI sing 493 n n N24 H27 YZI sing 494 n n N24 H28 YZI sing 495 n n # _atom_sites.entry_id 8GCZ _atom_sites.fract_transf_matrix[1][1] 0.016186 _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] 0.015167 _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] 0.010968 _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 B 2 NAG A 1 501 502 NAG NAG . C 2 NAG A 1 502 503 NAG NAG . D 2 NAG A 1 503 504 NAG NAG . E 2 NAG A 1 504 505 NAG NAG . F 2 NAG A 1 505 506 NAG NAG . G 2 NAG A 1 506 507 NAG NAG . H 2 NAG A 1 507 508 NAG NAG . I 2 NAG A 1 508 509 NAG NAG . J 2 NAG A 1 509 510 NAG NAG . K 2 NAG A 1 510 511 NAG NAG . L 2 NAG A 1 511 512 NAG NAG . M 2 NAG A 1 512 513 NAG NAG . N 3 YZI A 1 513 1 YZI Z90 . O 4 EPE A 1 514 1 EPE EPE . P 5 HOH A 1 601 11 HOH HOH . P 5 HOH A 2 602 12 HOH HOH . P 5 HOH A 3 603 22 HOH HOH . P 5 HOH A 4 604 4 HOH HOH . P 5 HOH A 5 605 13 HOH HOH . P 5 HOH A 6 606 20 HOH HOH . P 5 HOH A 7 607 5 HOH HOH . P 5 HOH A 8 608 3 HOH HOH . P 5 HOH A 9 609 21 HOH HOH . P 5 HOH A 10 610 6 HOH HOH . P 5 HOH A 11 611 19 HOH HOH . P 5 HOH A 12 612 18 HOH HOH . P 5 HOH A 13 613 2 HOH HOH . P 5 HOH A 14 614 15 HOH HOH . P 5 HOH A 15 615 8 HOH HOH . P 5 HOH A 16 616 23 HOH HOH . P 5 HOH A 17 617 1 HOH HOH . P 5 HOH A 18 618 17 HOH HOH . P 5 HOH A 19 619 24 HOH HOH . P 5 HOH A 20 620 16 HOH HOH . P 5 HOH A 21 621 10 HOH HOH . P 5 HOH A 22 622 7 HOH HOH . P 5 HOH A 23 623 9 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 C01 YZI . . . N 3 -1.402 13.675 -8.098 1 71.38 ? C01 YZI 513 A 1 HETATM 2 C C03 YZI . . . N 3 -0.093 12.776 -9.571 1 67.53 ? C03 YZI 513 A 1 HETATM 3 C C04 YZI . . . N 3 0.607 13.699 -10.549 1 63.5 ? C04 YZI 513 A 1 HETATM 4 C C06 YZI . . . N 3 0.009 16.121 -11.181 1 65.16 ? C06 YZI 513 A 1 HETATM 5 C C08 YZI . . . N 3 -2.267 16.985 -12.362 1 62.61 ? C08 YZI 513 A 1 HETATM 6 C C09 YZI . . . N 3 -2.047 17.57 -13.769 1 56.07 ? C09 YZI 513 A 1 HETATM 7 C C10 YZI . . . N 3 -3.077 17.28 -14.881 1 53.14 ? C10 YZI 513 A 1 HETATM 8 C C13 YZI . . . N 3 -3.469 16.817 -17.356 1 47.54 ? C13 YZI 513 A 1 HETATM 9 C C14 YZI . . . N 3 -4.831 16.961 -17.32 1 46.56 ? C14 YZI 513 A 1 HETATM 10 C C15 YZI . . . N 3 -5.554 16.718 -18.469 1 46.5 ? C15 YZI 513 A 1 HETATM 11 C C17 YZI . . . N 3 -4.949 16.345 -19.633 1 49.55 ? C17 YZI 513 A 1 HETATM 12 C C19 YZI . . . N 3 -3.596 16.209 -19.662 1 49.73 ? C19 YZI 513 A 1 HETATM 13 C C20 YZI . . . N 3 -2.866 16.45 -18.521 1 50.8 ? C20 YZI 513 A 1 HETATM 14 C C21 YZI . . . N 3 -1.855 19.002 -13.708 1 56.35 ? C21 YZI 513 A 1 HETATM 15 C C22 YZI . . . N 3 -0.514 19.175 -13.164 1 58.3 ? C22 YZI 513 A 1 HETATM 16 C C23 YZI . . . N 3 -0.191 20.675 -13.043 1 58.85 ? C23 YZI 513 A 1 HETATM 17 C C25 YZI . . . N 3 -0.517 18.568 -11.765 1 62.22 ? C25 YZI 513 A 1 HETATM 18 C C27 YZI . . . N 3 -1.405 14.028 -11.489 1 64.73 ? C27 YZI 513 A 1 HETATM 19 C C28 YZI . . . N 3 -2.103 13.907 -10.142 1 67.06 ? C28 YZI 513 A 1 HETATM 20 F F16 YZI . . . N 3 -6.872 16.837 -18.476 1 46.71 ? F16 YZI 513 A 1 HETATM 21 N N02 YZI . . . N 3 -1.376 13.153 -9.225 1 69.84 ? N02 YZI 513 A 1 HETATM 22 N N05 YZI . . . N 3 -0.257 14.658 -11.103 1 66.66 ? N05 YZI 513 A 1 HETATM 23 N N07 YZI . . . N 3 -0.923 17.144 -11.734 1 64.5 ? N07 YZI 513 A 1 HETATM 24 N N12 YZI . . . N 3 -2.599 17.069 -16.224 1 47.93 ? N12 YZI 513 A 1 HETATM 25 N N24 YZI . . . N 3 0.71 20.894 -11.904 1 63.7 ? N24 YZI 513 A 1 HETATM 26 O O11 YZI . . . N 3 -4.198 17.252 -14.656 1 53.75 ? O11 YZI 513 A 1 HETATM 27 O O26 YZI . . . N 3 1.036 16.51 -10.774 1 69.09 ? O26 YZI 513 A 1 HETATM 28 CL CL1 YZI . . . N 3 -5.867 16.032 -21.107 1 52.16 ? CL1 YZI 513 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #