data_8Z46 # _model_server_result.job_id c5Ojb5oL00DKscxduTrYpQ _model_server_result.datetime_utc '2025-07-07 19:52:46' _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 8z46 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8Z46 # _exptl.entry_id 8Z46 _exptl.method 'X-RAY DIFFRACTION' # _entity.details 'According to the author, the ligand used in the experiments was in its racemic form.' _entity.formula_weight 534.011 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2~{S})-~{N}-(3-azanyl-3-oxidanylidene-propyl)-4-[4-[[(1~{S})-1-(2-chlorophenyl)-3-oxidanyl-propyl]amino]-6-(methylamino)-1,3,5-triazin-2-yl]-1-ethanoyl-piperazine-2-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 114.92 _cell.angle_gamma 90 _cell.entry_id 8Z46 _cell.length_a 97.886 _cell.length_b 81.99 _cell.length_c 51.77 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8Z46 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 145 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 145 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id C25 _struct_conn.ptnr2_label_comp_id A1D70 _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id A1D70 _struct_conn.ptnr2_auth_seq_id 401 _struct_conn.ptnr2_symmetry 1_555 _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 1.609 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C23 H32 Cl N9 O4' _chem_comp.formula_weight 534.011 _chem_comp.id A1D70 _chem_comp.mon_nstd_flag . _chem_comp.name (2~{S})-~{N}-(3-azanyl-3-oxidanylidene-propyl)-4-[4-[[(1~{S})-1-(2-chlorophenyl)-3-oxidanyl-propyl]amino]-6-(methylamino)-1,3,5-triazin-2-yl]-1-ethanoyl-piperazine-2-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 O26 C24 A1D70 doub 1 n n O29 C28 A1D70 doub 2 n n C25 C24 A1D70 sing 3 n n C24 N23 A1D70 sing 4 n n C28 C27 A1D70 sing 5 n n C28 N30 A1D70 sing 6 n n N23 C27 A1D70 sing 7 n n N23 C22 A1D70 sing 8 n n C27 C36 A1D70 sing 9 n n C31 N30 A1D70 sing 10 n n C31 C32 A1D70 sing 11 n n C22 C21 A1D70 sing 12 n n O35 C33 A1D70 doub 13 n n C32 C33 A1D70 sing 14 n n C36 N20 A1D70 sing 15 n n C33 N34 A1D70 sing 16 n n C21 N20 A1D70 sing 17 n n N20 C19 A1D70 sing 18 n n C19 N37 A1D70 doub 19 n y C19 N18 A1D70 sing 20 n y N37 C03 A1D70 sing 21 n y N18 C05 A1D70 doub 22 n y C03 N02 A1D70 sing 23 n n C03 N04 A1D70 doub 24 n y N02 C01 A1D70 sing 25 n n CL17 C16 A1D70 sing 26 n n C05 N04 A1D70 sing 27 n y C05 N06 A1D70 sing 28 n n C07 N06 A1D70 sing 29 n n C07 C08 A1D70 sing 30 n n C07 C11 A1D70 sing 31 n n C09 C08 A1D70 sing 32 n n C09 O10 A1D70 sing 33 n n C16 C11 A1D70 doub 34 n y C16 C15 A1D70 sing 35 n y C11 C12 A1D70 sing 36 n y C15 C14 A1D70 doub 37 n y C12 C13 A1D70 doub 38 n y C14 C13 A1D70 sing 39 n y C01 H1 A1D70 sing 40 n n C01 H2 A1D70 sing 41 n n C01 H3 A1D70 sing 42 n n C07 H4 A1D70 sing 43 n n C08 H5 A1D70 sing 44 n n C08 H6 A1D70 sing 45 n n C09 H7 A1D70 sing 46 n n C09 H8 A1D70 sing 47 n n C12 H9 A1D70 sing 48 n n C13 H10 A1D70 sing 49 n n C14 H11 A1D70 sing 50 n n C15 H12 A1D70 sing 51 n n C21 H13 A1D70 sing 52 n n C21 H14 A1D70 sing 53 n n C22 H15 A1D70 sing 54 n n C22 H16 A1D70 sing 55 n n C25 H17 A1D70 sing 56 n n C25 H18 A1D70 sing 57 n n C25 H19 A1D70 sing 58 n n C27 H20 A1D70 sing 59 n n C31 H21 A1D70 sing 60 n n C31 H22 A1D70 sing 61 n n C32 H23 A1D70 sing 62 n n C32 H24 A1D70 sing 63 n n C36 H25 A1D70 sing 64 n n C36 H26 A1D70 sing 65 n n N02 H27 A1D70 sing 66 n n N06 H28 A1D70 sing 67 n n N30 H29 A1D70 sing 68 n n N34 H30 A1D70 sing 69 n n N34 H31 A1D70 sing 70 n n O10 H32 A1D70 sing 71 n n # _atom_sites.entry_id 8Z46 _atom_sites.fract_transf_matrix[1][1] 0.010216 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004746 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012197 _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] 0.021299 _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 A1D70 A 1 401 401 A1D70 702 . C 3 HOH A 1 501 41 HOH HOH . C 3 HOH A 2 502 22 HOH HOH . C 3 HOH A 3 503 112 HOH HOH . C 3 HOH A 4 504 52 HOH HOH . C 3 HOH A 5 505 60 HOH HOH . C 3 HOH A 6 506 62 HOH HOH . C 3 HOH A 7 507 46 HOH HOH . C 3 HOH A 8 508 28 HOH HOH . C 3 HOH A 9 509 69 HOH HOH . C 3 HOH A 10 510 71 HOH HOH . C 3 HOH A 11 511 100 HOH HOH . C 3 HOH A 12 512 105 HOH HOH . C 3 HOH A 13 513 77 HOH HOH . C 3 HOH A 14 514 107 HOH HOH . C 3 HOH A 15 515 43 HOH HOH . C 3 HOH A 16 516 129 HOH HOH . C 3 HOH A 17 517 36 HOH HOH . C 3 HOH A 18 518 140 HOH HOH . C 3 HOH A 19 519 44 HOH HOH . C 3 HOH A 20 520 90 HOH HOH . C 3 HOH A 21 521 19 HOH HOH . C 3 HOH A 22 522 122 HOH HOH . C 3 HOH A 23 523 16 HOH HOH . C 3 HOH A 24 524 65 HOH HOH . C 3 HOH A 25 525 55 HOH HOH . C 3 HOH A 26 526 30 HOH HOH . C 3 HOH A 27 527 56 HOH HOH . C 3 HOH A 28 528 59 HOH HOH . C 3 HOH A 29 529 106 HOH HOH . C 3 HOH A 30 530 57 HOH HOH . C 3 HOH A 31 531 42 HOH HOH . C 3 HOH A 32 532 32 HOH HOH . C 3 HOH A 33 533 9 HOH HOH . C 3 HOH A 34 534 68 HOH HOH . C 3 HOH A 35 535 143 HOH HOH . C 3 HOH A 36 536 66 HOH HOH . C 3 HOH A 37 537 126 HOH HOH . C 3 HOH A 38 538 79 HOH HOH . C 3 HOH A 39 539 61 HOH HOH . C 3 HOH A 40 540 67 HOH HOH . C 3 HOH A 41 541 12 HOH HOH . C 3 HOH A 42 542 118 HOH HOH . C 3 HOH A 43 543 89 HOH HOH . C 3 HOH A 44 544 137 HOH HOH . C 3 HOH A 45 545 2 HOH HOH . C 3 HOH A 46 546 25 HOH HOH . C 3 HOH A 47 547 72 HOH HOH . C 3 HOH A 48 548 101 HOH HOH . C 3 HOH A 49 549 27 HOH HOH . C 3 HOH A 50 550 110 HOH HOH . C 3 HOH A 51 551 74 HOH HOH . C 3 HOH A 52 552 53 HOH HOH . C 3 HOH A 53 553 39 HOH HOH . C 3 HOH A 54 554 4 HOH HOH . C 3 HOH A 55 555 29 HOH HOH . C 3 HOH A 56 556 104 HOH HOH . C 3 HOH A 57 557 21 HOH HOH . C 3 HOH A 58 558 45 HOH HOH . C 3 HOH A 59 559 6 HOH HOH . C 3 HOH A 60 560 97 HOH HOH . C 3 HOH A 61 561 7 HOH HOH . C 3 HOH A 62 562 1 HOH HOH . C 3 HOH A 63 563 121 HOH HOH . C 3 HOH A 64 564 54 HOH HOH . C 3 HOH A 65 565 11 HOH HOH . C 3 HOH A 66 566 10 HOH HOH . C 3 HOH A 67 567 82 HOH HOH . C 3 HOH A 68 568 5 HOH HOH . C 3 HOH A 69 569 26 HOH HOH . C 3 HOH A 70 570 73 HOH HOH . C 3 HOH A 71 571 80 HOH HOH . C 3 HOH A 72 572 85 HOH HOH . C 3 HOH A 73 573 58 HOH HOH . C 3 HOH A 74 574 50 HOH HOH . C 3 HOH A 75 575 40 HOH HOH . C 3 HOH A 76 576 127 HOH HOH . C 3 HOH A 77 577 135 HOH HOH . C 3 HOH A 78 578 47 HOH HOH . C 3 HOH A 79 579 88 HOH HOH . C 3 HOH A 80 580 113 HOH HOH . C 3 HOH A 81 581 3 HOH HOH . C 3 HOH A 82 582 139 HOH HOH . C 3 HOH A 83 583 23 HOH HOH . C 3 HOH A 84 584 102 HOH HOH . C 3 HOH A 85 585 20 HOH HOH . C 3 HOH A 86 586 34 HOH HOH . C 3 HOH A 87 587 37 HOH HOH . C 3 HOH A 88 588 31 HOH HOH . C 3 HOH A 89 589 75 HOH HOH . C 3 HOH A 90 590 17 HOH HOH . C 3 HOH A 91 591 78 HOH HOH . C 3 HOH A 92 592 115 HOH HOH . C 3 HOH A 93 593 142 HOH HOH . C 3 HOH A 94 594 24 HOH HOH . C 3 HOH A 95 595 15 HOH HOH . C 3 HOH A 96 596 96 HOH HOH . C 3 HOH A 97 597 49 HOH HOH . C 3 HOH A 98 598 109 HOH HOH . C 3 HOH A 99 599 111 HOH HOH . C 3 HOH A 100 600 18 HOH HOH . C 3 HOH A 101 601 130 HOH HOH . C 3 HOH A 102 602 87 HOH HOH . C 3 HOH A 103 603 141 HOH HOH . C 3 HOH A 104 604 99 HOH HOH . C 3 HOH A 105 605 33 HOH HOH . C 3 HOH A 106 606 98 HOH HOH . C 3 HOH A 107 607 81 HOH HOH . C 3 HOH A 108 608 13 HOH HOH . C 3 HOH A 109 609 133 HOH HOH . C 3 HOH A 110 610 124 HOH HOH . C 3 HOH A 111 611 70 HOH HOH . C 3 HOH A 112 612 86 HOH HOH . C 3 HOH A 113 613 48 HOH HOH . C 3 HOH A 114 614 91 HOH HOH . C 3 HOH A 115 615 8 HOH HOH . C 3 HOH A 116 616 83 HOH HOH . C 3 HOH A 117 617 14 HOH HOH . C 3 HOH A 118 618 117 HOH HOH . C 3 HOH A 119 619 38 HOH HOH . C 3 HOH A 120 620 95 HOH HOH . C 3 HOH A 121 621 123 HOH HOH . C 3 HOH A 122 622 125 HOH HOH . C 3 HOH A 123 623 144 HOH HOH . C 3 HOH A 124 624 103 HOH HOH . C 3 HOH A 125 625 128 HOH HOH . C 3 HOH A 126 626 64 HOH HOH . C 3 HOH A 127 627 134 HOH HOH . C 3 HOH A 128 628 35 HOH HOH . C 3 HOH A 129 629 114 HOH HOH . C 3 HOH A 130 630 138 HOH HOH . C 3 HOH A 131 631 116 HOH HOH . C 3 HOH A 132 632 94 HOH HOH . C 3 HOH A 133 633 119 HOH HOH . C 3 HOH A 134 634 136 HOH HOH . C 3 HOH A 135 635 51 HOH HOH . C 3 HOH A 136 636 92 HOH HOH . C 3 HOH A 137 637 131 HOH HOH . C 3 HOH A 138 638 76 HOH HOH . C 3 HOH A 139 639 84 HOH HOH . C 3 HOH A 140 640 63 HOH HOH . C 3 HOH A 141 641 108 HOH HOH . C 3 HOH A 142 642 93 HOH HOH . C 3 HOH A 143 643 132 HOH HOH . C 3 HOH A 144 644 120 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 A1D70 . . . B 2 15.315 11.906 25.766 1 53.71 ? C01 A1D70 401 A 1 HETATM 2 C C03 A1D70 . . . B 2 13.642 13.157 24.44 1 50.82 ? C03 A1D70 401 A 1 HETATM 3 C C05 A1D70 . . . B 2 11.506 12.903 25.164 1 42.94 ? C05 A1D70 401 A 1 HETATM 4 C C07 A1D70 . . . B 2 9.195 12.378 25.966 1 38.44 ? C07 A1D70 401 A 1 HETATM 5 C C08 A1D70 . . . B 2 8.417 11.237 26.633 1 35.77 ? C08 A1D70 401 A 1 HETATM 6 C C09 A1D70 . . . B 2 8.439 9.857 26.006 1 41.64 ? C09 A1D70 401 A 1 HETATM 7 C C11 A1D70 . . . B 2 9.022 13.615 26.799 1 33.54 ? C11 A1D70 401 A 1 HETATM 8 C C12 A1D70 . . . B 2 9.681 13.778 28.022 1 35.77 ? C12 A1D70 401 A 1 HETATM 9 C C13 A1D70 . . . B 2 9.414 14.95 28.74 1 32.93 ? C13 A1D70 401 A 1 HETATM 10 C C14 A1D70 . . . B 2 8.542 15.927 28.297 1 28.39 ? C14 A1D70 401 A 1 HETATM 11 C C15 A1D70 . . . B 2 7.899 15.739 27.087 1 31.48 ? C15 A1D70 401 A 1 HETATM 12 C C16 A1D70 . . . B 2 8.162 14.585 26.409 1 30.61 ? C16 A1D70 401 A 1 HETATM 13 C C19 A1D70 . . . B 2 11.98 14.375 23.426 1 45.31 ? C19 A1D70 401 A 1 HETATM 14 C C21 A1D70 . . . B 2 10.023 15.35 22.156 1 38.57 ? C21 A1D70 401 A 1 HETATM 15 C C22 A1D70 . . . B 2 9.611 14.844 20.762 1 37.51 ? C22 A1D70 401 A 1 HETATM 16 C C24 A1D70 . . . B 2 9.751 16.255 18.665 1 35.38 ? C24 A1D70 401 A 1 HETATM 17 C C25 A1D70 . . . B 2 8.258 16.274 18.582 1 29.58 ? C25 A1D70 401 A 1 HETATM 18 C C27 A1D70 . . . B 2 11.701 15.248 19.854 1 45.55 ? C27 A1D70 401 A 1 HETATM 19 C C28 A1D70 . . . B 2 11.592 13.736 19.407 1 45.59 ? C28 A1D70 401 A 1 HETATM 20 C C31 A1D70 . . . B 2 11.977 11.225 19.899 1 45.62 ? C31 A1D70 401 A 1 HETATM 21 C C32 A1D70 . . . B 2 11.353 10.467 21.062 1 42.88 ? C32 A1D70 401 A 1 HETATM 22 C C33 A1D70 . . . B 2 10.013 10.979 21.621 1 40.08 ? C33 A1D70 401 A 1 HETATM 23 C C36 A1D70 . . . B 2 12.337 15.523 21.215 1 45.22 ? C36 A1D70 401 A 1 HETATM 24 N N02 A1D70 . . . B 2 15.019 12.731 24.603 1 54.69 ? N02 A1D70 401 A 1 HETATM 25 N N04 A1D70 . . . B 2 12.767 12.587 25.252 1 46.94 ? N04 A1D70 401 A 1 HETATM 26 N N06 A1D70 . . . B 2 10.598 12.225 26.057 1 39.07 ? N06 A1D70 401 A 1 HETATM 27 N N18 A1D70 . . . B 2 11.124 13.801 24.25 1 41.29 ? N18 A1D70 401 A 1 HETATM 28 N N20 A1D70 . . . B 2 11.501 15.335 22.447 1 42.77 ? N20 A1D70 401 A 1 HETATM 29 N N23 A1D70 . . . B 2 10.339 15.511 19.767 1 38.4 ? N23 A1D70 401 A 1 HETATM 30 N N30 A1D70 . . . B 2 12.088 12.637 20.245 1 51.02 ? N30 A1D70 401 A 1 HETATM 31 N N34 A1D70 . . . B 2 9.495 10.362 22.843 1 41.26 ? N34 A1D70 401 A 1 HETATM 32 N N37 A1D70 . . . B 2 13.265 14.044 23.501 1 52.75 ? N37 A1D70 401 A 1 HETATM 33 O O10 A1D70 . . . B 2 8.077 9.091 27.113 1 36.89 ? O10 A1D70 401 A 1 HETATM 34 O O26 A1D70 . . . B 2 10.358 16.844 17.823 1 37.89 ? O26 A1D70 401 A 1 HETATM 35 O O29 A1D70 . . . B 2 11.016 13.416 18.372 1 50.53 ? O29 A1D70 401 A 1 HETATM 36 O O35 A1D70 . . . B 2 9.41 11.843 21.049 1 40.03 ? O35 A1D70 401 A 1 HETATM 37 CL CL17 A1D70 . . . B 2 7.388 14.275 24.85 1 32.44 ? CL17 A1D70 401 A 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 245 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 37 #