data_7ACD # _model_server_result.job_id r7Mum2Rn0E7-y3b9M01Yqw _model_server_result.datetime_utc '2024-11-13 20:48:41' _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 7acd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 7ACD # _exptl.entry_id 7ACD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 558.714 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-[(4,4-dimethylpiperidin-1-yl)methyl]-2-oxidanyl-~{N}-[[(3~{R})-3-oxidanyl-1-[6-[(phenylmethyl)amino]pyrimidin-4-yl]piperidin-3-yl]methyl]benzamide _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 120 _cell.entry_id 7ACD _cell.length_a 63.8 _cell.length_b 63.8 _cell.length_c 224.92 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7ACD _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall 'P 32 2"' _symmetry.space_group_name_H-M 'P 32 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 PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,F 1 1 B,D,E,G 2 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 C _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 B SG CYS 233 B CYS 338 1_555 B SG CYS 283 B CYS 388 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc1 B OD2 ASP 52 B ASP 157 1_555 D MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.978 ? # _chem_comp.formula 'C32 H42 N6 O3' _chem_comp.formula_weight 558.714 _chem_comp.id R72 _chem_comp.mon_nstd_flag . _chem_comp.name 4-[(4,4-dimethylpiperidin-1-yl)methyl]-2-oxidanyl-~{N}-[[(3~{R})-3-oxidanyl-1-[6-[(phenylmethyl)amino]pyrimidin-4-yl]piperidin-3-yl]methyl]benzamide _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 C35 C36 R72 doub 283 n y C35 C34 R72 sing 284 n y C05 C04 R72 sing 285 n n C05 N06 R72 sing 286 n n C07 N06 R72 sing 287 n n C07 C08 R72 sing 288 n n C36 C31 R72 sing 289 n y C34 C33 R72 doub 290 n y C04 C02 R72 sing 291 n n C01 C02 R72 sing 292 n n N06 C40 R72 sing 293 n n C08 C09 R72 doub 294 n y C08 C11 R72 sing 295 n y C02 C03 R72 sing 296 n n C02 C41 R72 sing 297 n n C09 C10 R72 sing 298 n y C40 C41 R72 sing 299 n n C11 C12 R72 doub 300 n y C31 C30 R72 sing 301 n n C31 C32 R72 doub 302 n y C33 C32 R72 sing 303 n y C10 C14 R72 doub 304 n y N29 C30 R72 sing 305 n n N29 C28 R72 sing 306 n n C12 C14 R72 sing 307 n y C12 O13 R72 sing 308 n n C21 C20 R72 sing 309 n n C21 N23 R72 sing 310 n n C14 C15 R72 sing 311 n n C20 C19 R72 sing 312 n n C37 C28 R72 doub 313 n y C37 C24 R72 sing 314 n y C28 N27 R72 sing 315 n y C15 O39 R72 doub 316 n n C15 N16 R72 sing 317 n n C19 C18 R72 sing 318 n n N23 C24 R72 sing 319 n n N23 C22 R72 sing 320 n n C24 N25 R72 doub 321 n y N16 C17 R72 sing 322 n n C22 C18 R72 sing 323 n n N27 C26 R72 doub 324 n y C18 C17 R72 sing 325 n n C18 O38 R72 sing 326 n n N25 C26 R72 sing 327 n y C11 H1 R72 sing 328 n n C17 H2 R72 sing 329 n n C17 H3 R72 sing 330 n n C10 H4 R72 sing 331 n n C19 H5 R72 sing 332 n n C19 H6 R72 sing 333 n n C22 H7 R72 sing 334 n n C22 H8 R72 sing 335 n n C20 H9 R72 sing 336 n n C20 H10 R72 sing 337 n n C26 H11 R72 sing 338 n n C01 H12 R72 sing 339 n n C01 H13 R72 sing 340 n n C01 H14 R72 sing 341 n n C03 H15 R72 sing 342 n n C03 H16 R72 sing 343 n n C03 H17 R72 sing 344 n n C04 H18 R72 sing 345 n n C04 H19 R72 sing 346 n n C05 H20 R72 sing 347 n n C05 H21 R72 sing 348 n n C07 H22 R72 sing 349 n n C07 H23 R72 sing 350 n n C09 H24 R72 sing 351 n n C21 H25 R72 sing 352 n n C21 H26 R72 sing 353 n n C30 H27 R72 sing 354 n n C30 H28 R72 sing 355 n n C32 H29 R72 sing 356 n n C33 H30 R72 sing 357 n n C34 H31 R72 sing 358 n n C35 H32 R72 sing 359 n n C36 H33 R72 sing 360 n n C37 H34 R72 sing 361 n n C40 H35 R72 sing 362 n n C40 H36 R72 sing 363 n n C41 H37 R72 sing 364 n n C41 H38 R72 sing 365 n n N16 H40 R72 sing 366 n n N29 H41 R72 sing 367 n n O13 H42 R72 sing 368 n n O38 H43 R72 sing 369 n n # _atom_sites.entry_id 7ACD _atom_sites.fract_transf_matrix[1][1] 0.015674 _atom_sites.fract_transf_matrix[1][2] 0.009049 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018099 _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] 0.004446 _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 3 R72 A 1 601 1 R72 T30 . D 4 MG B 1 401 1 MG MG . E 5 ACT B 1 402 2 ACT ACT . F 6 HOH A 1 701 55 HOH HOH . F 6 HOH A 2 702 65 HOH HOH . F 6 HOH A 3 703 72 HOH HOH . F 6 HOH A 4 704 34 HOH HOH . F 6 HOH A 5 705 54 HOH HOH . F 6 HOH A 6 706 5 HOH HOH . F 6 HOH A 7 707 15 HOH HOH . F 6 HOH A 8 708 24 HOH HOH . F 6 HOH A 9 709 26 HOH HOH . F 6 HOH A 10 710 40 HOH HOH . F 6 HOH A 11 711 9 HOH HOH . F 6 HOH A 12 712 48 HOH HOH . F 6 HOH A 13 713 19 HOH HOH . F 6 HOH A 14 714 27 HOH HOH . F 6 HOH A 15 715 53 HOH HOH . F 6 HOH A 16 716 41 HOH HOH . F 6 HOH A 17 717 10 HOH HOH . F 6 HOH A 18 718 56 HOH HOH . F 6 HOH A 19 719 103 HOH HOH . F 6 HOH A 20 720 61 HOH HOH . F 6 HOH A 21 721 113 HOH HOH . F 6 HOH A 22 722 52 HOH HOH . F 6 HOH A 23 723 94 HOH HOH . F 6 HOH A 24 724 21 HOH HOH . F 6 HOH A 25 725 71 HOH HOH . F 6 HOH A 26 726 22 HOH HOH . F 6 HOH A 27 727 105 HOH HOH . F 6 HOH A 28 728 37 HOH HOH . F 6 HOH A 29 729 42 HOH HOH . F 6 HOH A 30 730 107 HOH HOH . F 6 HOH A 31 731 67 HOH HOH . F 6 HOH A 32 732 90 HOH HOH . F 6 HOH A 33 733 127 HOH HOH . F 6 HOH A 34 734 75 HOH HOH . F 6 HOH A 35 735 104 HOH HOH . F 6 HOH A 36 736 125 HOH HOH . F 6 HOH A 37 737 108 HOH HOH . F 6 HOH A 38 738 98 HOH HOH . F 6 HOH A 39 739 116 HOH HOH . F 6 HOH A 40 740 84 HOH HOH . F 6 HOH A 41 741 87 HOH HOH . F 6 HOH A 42 742 106 HOH HOH . F 6 HOH A 43 743 91 HOH HOH . F 6 HOH A 44 744 122 HOH HOH . G 6 HOH B 1 501 79 HOH HOH . G 6 HOH B 2 502 99 HOH HOH . G 6 HOH B 3 503 45 HOH HOH . G 6 HOH B 4 504 2 HOH HOH . G 6 HOH B 5 505 25 HOH HOH . G 6 HOH B 6 506 68 HOH HOH . G 6 HOH B 7 507 51 HOH HOH . G 6 HOH B 8 508 8 HOH HOH . G 6 HOH B 9 509 60 HOH HOH . G 6 HOH B 10 510 11 HOH HOH . G 6 HOH B 11 511 7 HOH HOH . G 6 HOH B 12 512 6 HOH HOH . G 6 HOH B 13 513 14 HOH HOH . G 6 HOH B 14 514 66 HOH HOH . G 6 HOH B 15 515 77 HOH HOH . G 6 HOH B 16 516 3 HOH HOH . G 6 HOH B 17 517 4 HOH HOH . G 6 HOH B 18 518 70 HOH HOH . G 6 HOH B 19 519 50 HOH HOH . G 6 HOH B 20 520 96 HOH HOH . G 6 HOH B 21 521 36 HOH HOH . G 6 HOH B 22 522 35 HOH HOH . G 6 HOH B 23 523 29 HOH HOH . G 6 HOH B 24 524 38 HOH HOH . G 6 HOH B 25 525 63 HOH HOH . G 6 HOH B 26 526 18 HOH HOH . G 6 HOH B 27 527 12 HOH HOH . G 6 HOH B 28 528 23 HOH HOH . G 6 HOH B 29 529 64 HOH HOH . G 6 HOH B 30 530 80 HOH HOH . G 6 HOH B 31 531 16 HOH HOH . G 6 HOH B 32 532 46 HOH HOH . G 6 HOH B 33 533 20 HOH HOH . G 6 HOH B 34 534 39 HOH HOH . G 6 HOH B 35 535 120 HOH HOH . G 6 HOH B 36 536 62 HOH HOH . G 6 HOH B 37 537 49 HOH HOH . G 6 HOH B 38 538 17 HOH HOH . G 6 HOH B 39 539 31 HOH HOH . G 6 HOH B 40 540 57 HOH HOH . G 6 HOH B 41 541 47 HOH HOH . G 6 HOH B 42 542 30 HOH HOH . G 6 HOH B 43 543 32 HOH HOH . G 6 HOH B 44 544 33 HOH HOH . G 6 HOH B 45 545 74 HOH HOH . G 6 HOH B 46 546 43 HOH HOH . G 6 HOH B 47 547 58 HOH HOH . G 6 HOH B 48 548 86 HOH HOH . G 6 HOH B 49 549 88 HOH HOH . G 6 HOH B 50 550 73 HOH HOH . G 6 HOH B 51 551 85 HOH HOH . G 6 HOH B 52 552 28 HOH HOH . G 6 HOH B 53 553 93 HOH HOH . G 6 HOH B 54 554 100 HOH HOH . G 6 HOH B 55 555 97 HOH HOH . G 6 HOH B 56 556 89 HOH HOH . G 6 HOH B 57 557 121 HOH HOH . G 6 HOH B 58 558 102 HOH HOH . G 6 HOH B 59 559 101 HOH HOH . G 6 HOH B 60 560 59 HOH HOH . G 6 HOH B 61 561 69 HOH HOH . G 6 HOH B 62 562 78 HOH HOH . G 6 HOH B 63 563 112 HOH HOH . G 6 HOH B 64 564 119 HOH HOH . G 6 HOH B 65 565 81 HOH HOH . G 6 HOH B 66 566 117 HOH HOH . G 6 HOH B 67 567 118 HOH HOH . G 6 HOH B 68 568 95 HOH HOH . G 6 HOH B 69 569 124 HOH HOH . G 6 HOH B 70 570 82 HOH HOH . G 6 HOH B 71 571 111 HOH HOH . G 6 HOH B 72 572 126 HOH HOH . G 6 HOH B 73 573 123 HOH HOH . G 6 HOH B 74 574 92 HOH HOH . G 6 HOH B 75 575 109 HOH HOH . G 6 HOH B 76 576 114 HOH HOH . G 6 HOH B 77 577 76 HOH HOH . G 6 HOH B 78 578 115 HOH HOH . G 6 HOH B 79 579 83 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 C18 R72 . . . C 3 -44.271 35.827 26.496 1 42.72 ? C18 R72 601 A 1 HETATM 2 C C14 R72 . . . C 3 -44.546 31.66 24.374 1 41.2 ? C14 R72 601 A 1 HETATM 3 C C11 R72 . . . C 3 -42.878 30.38 23.093 1 42.59 ? C11 R72 601 A 1 HETATM 4 C C17 R72 . . . C 3 -44.437 34.433 27.093 1 36.5 ? C17 R72 601 A 1 HETATM 5 C C10 R72 . . . C 3 -45.628 30.894 23.644 1 48.7 ? C10 R72 601 A 1 HETATM 6 C C15 R72 . . . C 3 -45.011 32.698 25.386 1 50.76 ? C15 R72 601 A 1 HETATM 7 C C19 R72 . . . C 3 -45.169 35.995 25.26 1 42.53 ? C19 R72 601 A 1 HETATM 8 C C22 R72 . . . C 3 -42.819 36.071 26.107 1 35.13 ? C22 R72 601 A 1 HETATM 9 C C20 R72 . . . C 3 -44.903 37.326 24.487 1 37.88 ? C20 R72 601 A 1 HETATM 10 C C24 R72 . . . C 3 -41.581 38.251 25.893 1 40.86 ? C24 R72 601 A 1 HETATM 11 C C26 R72 . . . C 3 -40.134 39.156 27.55 1 39.18 ? C26 R72 601 A 1 HETATM 12 C C01 R72 . . . C 3 -44.304 24.043 21.975 1 48.23 ? C01 R72 601 A 1 HETATM 13 C C02 R72 . . . C 3 -43.159 24.722 22.731 1 53.95 ? C02 R72 601 A 1 HETATM 14 C C03 R72 . . . C 3 -42.444 23.738 23.648 1 40.65 ? C03 R72 601 A 1 HETATM 15 C C04 R72 . . . C 3 -42.174 25.292 21.715 1 46.51 ? C04 R72 601 A 1 HETATM 16 C C05 R72 . . . C 3 -42.572 26.667 21.167 1 47.46 ? C05 R72 601 A 1 HETATM 17 C C07 R72 . . . C 3 -43.467 28.629 21.418 1 34.82 ? C07 R72 601 A 1 HETATM 18 C C08 R72 . . . C 3 -43.819 29.704 22.451 1 45.19 ? C08 R72 601 A 1 HETATM 19 C C09 R72 . . . C 3 -45.288 29.999 22.752 1 55.26 ? C09 R72 601 A 1 HETATM 20 C C12 R72 . . . C 3 -43.268 31.437 24.126 1 36.97 ? C12 R72 601 A 1 HETATM 21 C C21 R72 . . . C 3 -43.411 37.674 24.305 1 40.39 ? C21 R72 601 A 1 HETATM 22 C C28 R72 . . . C 3 -40.114 40.105 25.38 1 43.65 ? C28 R72 601 A 1 HETATM 23 C C30 R72 . . . C 3 -39.893 41.239 23.104 1 44.19 ? C30 R72 601 A 1 HETATM 24 C C31 R72 . . . C 3 -41.105 42.144 22.843 1 44.85 ? C31 R72 601 A 1 HETATM 25 C C32 R72 . . . C 3 -41.859 42.599 23.829 1 43.09 ? C32 R72 601 A 1 HETATM 26 C C33 R72 . . . C 3 -43.052 43.496 23.531 1 45.37 ? C33 R72 601 A 1 HETATM 27 C C34 R72 . . . C 3 -43.324 43.818 22.286 1 52.63 ? C34 R72 601 A 1 HETATM 28 C C35 R72 . . . C 3 -42.456 43.299 21.144 1 51.19 ? C35 R72 601 A 1 HETATM 29 C C36 R72 . . . C 3 -41.424 42.526 21.4 1 42.92 ? C36 R72 601 A 1 HETATM 30 C C37 R72 . . . C 3 -41.024 39.279 24.961 1 40.41 ? C37 R72 601 A 1 HETATM 31 C C40 R72 . . . C 3 -44.125 27.006 22.696 1 50.48 ? C40 R72 601 A 1 HETATM 32 C C41 R72 . . . C 3 -43.805 25.802 23.581 1 47.05 ? C41 R72 601 A 1 HETATM 33 N N06 R72 . . . C 3 -43.1 27.516 22.032 1 44.16 ? N06 R72 601 A 1 HETATM 34 N N16 R72 . . . C 3 -44.006 33.442 26.134 1 36.36 ? N16 R72 601 A 1 HETATM 35 N N23 R72 . . . C 3 -42.603 37.313 25.432 1 37.95 ? N23 R72 601 A 1 HETATM 36 N N25 R72 . . . C 3 -41.167 38.204 27.073 1 37.26 ? N25 R72 601 A 1 HETATM 37 N N27 R72 . . . C 3 -39.651 40.045 26.754 1 35.51 ? N27 R72 601 A 1 HETATM 38 N N29 R72 . . . C 3 -39.545 41.134 24.513 1 46 ? N29 R72 601 A 1 HETATM 39 O O13 R72 . . . C 3 -42.271 32.148 24.811 1 40.03 ? O13 R72 601 A 1 HETATM 40 O O38 R72 . . . C 3 -44.681 36.733 27.478 1 44.58 ? O38 R72 601 A 1 HETATM 41 O O39 R72 . . . C 3 -46.185 32.877 25.542 1 45.36 ? O39 R72 601 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 41 #