data_6FDU # _model_server_result.job_id 0YbL7QznWqa-Ge-3MsiS2w _model_server_result.datetime_utc '2024-11-24 00:45:20' _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 6fdu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 6FDU # _exptl.entry_id 6FDU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 479.403 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2~{S},3~{S})-2-[[(2~{S})-2-[3,5-bis(chloranyl)phenyl]-2-(dimethylamino)ethanoyl]amino]-~{N}-[[2-(iminomethyl)pyrimidin-4-yl]methyl]-3-methyl-pentanamide _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 96 _cell.angle_gamma 90 _cell.entry_id 6FDU _cell.length_a 44.08 _cell.length_b 57.093 _cell.length_c 116.381 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6FDU _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 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 D _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 B _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 210 _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 345 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id D _struct_conn.ptnr2_label_atom_id CBE _struct_conn.ptnr2_label_comp_id D5W _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id D5W _struct_conn.ptnr2_auth_seq_id 501 _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 1.676 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C22 H28 Cl2 N6 O2' _chem_comp.formula_weight 479.403 _chem_comp.id D5W _chem_comp.mon_nstd_flag . _chem_comp.name (2~{S},3~{S})-2-[[(2~{S})-2-[3,5-bis(chloranyl)phenyl]-2-(dimethylamino)ethanoyl]amino]-~{N}-[[2-(iminomethyl)pyrimidin-4-yl]methyl]-3-methyl-pentanamide _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 NBF CBE D5W doub 83 n n N1 C6 D5W doub 84 n y N1 C2 D5W sing 85 n y CBE C2 D5W sing 86 n n C6 C5 D5W sing 87 n y C2 N3 D5W doub 88 n y C5 C4 D5W doub 89 n y N3 C4 D5W sing 90 n y C4 CAX D5W sing 91 n n CAX NAF D5W sing 92 n n NAF C D5W sing 93 n n O C D5W doub 94 n n CG1 CD1 D5W sing 95 n n CG1 CB D5W sing 96 n n CG2 CB D5W sing 97 n n C CA D5W sing 98 n n CB CA D5W sing 99 n n CA N D5W sing 100 n n N CAG D5W sing 101 n n CAG OAQ D5W doub 102 n n CAG CAH D5W sing 103 n n CAW NAU D5W sing 104 n n NAU CAH D5W sing 105 n n NAU CAV D5W sing 106 n n CLA CAK D5W sing 107 n n CAJ CAK D5W doub 108 n y CAJ CAI D5W sing 109 n y CAH CAI D5W sing 110 n n CAK CAL D5W sing 111 n y CAI CAN D5W doub 112 n y CAL CAM D5W doub 113 n y CAN CAM D5W sing 114 n y CAM CLB D5W sing 115 n n C5 H1 D5W sing 116 n n C6 H2 D5W sing 117 n n CAJ H3 D5W sing 118 n n CAL H4 D5W sing 119 n n CAN H5 D5W sing 120 n n CAH H6 D5W sing 121 n n CAW H8 D5W sing 122 n n CAW H9 D5W sing 123 n n CAW H10 D5W sing 124 n n CAV H11 D5W sing 125 n n CAV H12 D5W sing 126 n n CAV H13 D5W sing 127 n n N H14 D5W sing 128 n n CA H15 D5W sing 129 n n CB H16 D5W sing 130 n n CG2 H17 D5W sing 131 n n CG2 H18 D5W sing 132 n n CG2 H19 D5W sing 133 n n CG1 H20 D5W sing 134 n n CG1 H21 D5W sing 135 n n CD1 H22 D5W sing 136 n n CD1 H23 D5W sing 137 n n CD1 H24 D5W sing 138 n n NAF H25 D5W sing 139 n n CAX H26 D5W sing 140 n n CAX H27 D5W sing 141 n n CBE H28 D5W sing 142 n n NBF H29 D5W sing 143 n n # _atom_sites.entry_id 6FDU _atom_sites.fract_transf_matrix[1][1] 0.022686 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002386 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017515 _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] 0.00864 _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 2 CL A 1 501 1 CL CL . D 3 D5W B 1 501 1 D5W DRG . E 2 CL B 1 502 2 CL CL . F 4 HOH A 1 601 202 HOH HOH . F 4 HOH A 2 602 56 HOH HOH . F 4 HOH A 3 603 24 HOH HOH . F 4 HOH A 4 604 2 HOH HOH . F 4 HOH A 5 605 42 HOH HOH . F 4 HOH A 6 606 52 HOH HOH . F 4 HOH A 7 607 2 HOH HOH . F 4 HOH A 8 608 34 HOH HOH . F 4 HOH A 9 609 195 HOH HOH . F 4 HOH A 10 610 74 HOH HOH . F 4 HOH A 11 611 3 HOH HOH . F 4 HOH A 12 612 111 HOH HOH . F 4 HOH A 13 613 23 HOH HOH . F 4 HOH A 14 614 27 HOH HOH . F 4 HOH A 15 615 1 HOH HOH . F 4 HOH A 16 616 4 HOH HOH . F 4 HOH A 17 617 26 HOH HOH . F 4 HOH A 18 618 201 HOH HOH . F 4 HOH A 19 619 39 HOH HOH . F 4 HOH A 20 620 46 HOH HOH . F 4 HOH A 21 621 171 HOH HOH . F 4 HOH A 22 622 180 HOH HOH . F 4 HOH A 23 623 126 HOH HOH . F 4 HOH A 24 624 13 HOH HOH . F 4 HOH A 25 625 34 HOH HOH . F 4 HOH A 26 626 73 HOH HOH . F 4 HOH A 27 627 17 HOH HOH . F 4 HOH A 28 628 203 HOH HOH . F 4 HOH A 29 629 58 HOH HOH . F 4 HOH A 30 630 194 HOH HOH . F 4 HOH A 31 631 170 HOH HOH . F 4 HOH A 32 632 53 HOH HOH . F 4 HOH A 33 633 181 HOH HOH . F 4 HOH A 34 634 2 HOH HOH . F 4 HOH A 35 635 10 HOH HOH . F 4 HOH A 36 636 204 HOH HOH . F 4 HOH A 37 637 7 HOH HOH . F 4 HOH A 38 638 172 HOH HOH . F 4 HOH A 39 639 198 HOH HOH . F 4 HOH A 40 640 12 HOH HOH . F 4 HOH A 41 641 57 HOH HOH . F 4 HOH A 42 642 47 HOH HOH . F 4 HOH A 43 643 63 HOH HOH . F 4 HOH A 44 644 28 HOH HOH . F 4 HOH A 45 645 14 HOH HOH . F 4 HOH A 46 646 17 HOH HOH . F 4 HOH A 47 647 40 HOH HOH . F 4 HOH A 48 648 169 HOH HOH . F 4 HOH A 49 649 129 HOH HOH . F 4 HOH A 50 650 199 HOH HOH . F 4 HOH A 51 651 155 HOH HOH . F 4 HOH A 52 652 196 HOH HOH . G 4 HOH B 1 601 38 HOH HOH . G 4 HOH B 2 602 187 HOH HOH . G 4 HOH B 3 603 30 HOH HOH . G 4 HOH B 4 604 20 HOH HOH . G 4 HOH B 5 605 115 HOH HOH . G 4 HOH B 6 606 182 HOH HOH . G 4 HOH B 7 607 192 HOH HOH . G 4 HOH B 8 608 185 HOH HOH . G 4 HOH B 9 609 183 HOH HOH . G 4 HOH B 10 610 28 HOH HOH . G 4 HOH B 11 611 79 HOH HOH . G 4 HOH B 12 612 48 HOH HOH . G 4 HOH B 13 613 109 HOH HOH . G 4 HOH B 14 614 167 HOH HOH . G 4 HOH B 15 615 176 HOH HOH . G 4 HOH B 16 616 178 HOH HOH . G 4 HOH B 17 617 165 HOH HOH . G 4 HOH B 18 618 173 HOH HOH . G 4 HOH B 19 619 193 HOH HOH . G 4 HOH B 20 620 1 HOH HOH . G 4 HOH B 21 621 43 HOH HOH . G 4 HOH B 22 622 14 HOH HOH . G 4 HOH B 23 623 44 HOH HOH . G 4 HOH B 24 624 11 HOH HOH . G 4 HOH B 25 625 10 HOH HOH . G 4 HOH B 26 626 2 HOH HOH . G 4 HOH B 27 627 38 HOH HOH . G 4 HOH B 28 628 205 HOH HOH . G 4 HOH B 29 629 30 HOH HOH . G 4 HOH B 30 630 189 HOH HOH . G 4 HOH B 31 631 9 HOH HOH . G 4 HOH B 32 632 158 HOH HOH . G 4 HOH B 33 633 36 HOH HOH . G 4 HOH B 34 634 188 HOH HOH . G 4 HOH B 35 635 35 HOH HOH . G 4 HOH B 36 636 162 HOH HOH . G 4 HOH B 37 637 51 HOH HOH . G 4 HOH B 38 638 190 HOH HOH . G 4 HOH B 39 639 93 HOH HOH . G 4 HOH B 40 640 200 HOH HOH . G 4 HOH B 41 641 9 HOH HOH . G 4 HOH B 42 642 67 HOH HOH . G 4 HOH B 43 643 134 HOH HOH . G 4 HOH B 44 644 60 HOH HOH . G 4 HOH B 45 645 21 HOH HOH . G 4 HOH B 46 646 18 HOH HOH . G 4 HOH B 47 647 35 HOH HOH . G 4 HOH B 48 648 177 HOH HOH . G 4 HOH B 49 649 6 HOH HOH . G 4 HOH B 50 650 2 HOH HOH . G 4 HOH B 51 651 71 HOH HOH . G 4 HOH B 52 652 157 HOH HOH . G 4 HOH B 53 653 186 HOH HOH . G 4 HOH B 54 654 64 HOH HOH . G 4 HOH B 55 655 55 HOH HOH . G 4 HOH B 56 656 45 HOH HOH . G 4 HOH B 57 657 23 HOH HOH . G 4 HOH B 58 658 8 HOH HOH . G 4 HOH B 59 659 9 HOH HOH . G 4 HOH B 60 660 191 HOH HOH . G 4 HOH B 61 661 33 HOH HOH . G 4 HOH B 62 662 197 HOH HOH . G 4 HOH B 63 663 41 HOH HOH . G 4 HOH B 64 664 11 HOH HOH . G 4 HOH B 65 665 22 HOH HOH . G 4 HOH B 66 666 42 HOH HOH . G 4 HOH B 67 667 33 HOH HOH . G 4 HOH B 68 668 13 HOH HOH . G 4 HOH B 69 669 19 HOH HOH . G 4 HOH B 70 670 88 HOH HOH . G 4 HOH B 71 671 61 HOH HOH . G 4 HOH B 72 672 38 HOH HOH . G 4 HOH B 73 673 46 HOH HOH . G 4 HOH B 74 674 99 HOH HOH . G 4 HOH B 75 675 166 HOH HOH . G 4 HOH B 76 676 168 HOH HOH . G 4 HOH B 77 677 25 HOH HOH . G 4 HOH B 78 678 97 HOH HOH . G 4 HOH B 79 679 110 HOH HOH . G 4 HOH B 80 680 2 HOH HOH . G 4 HOH B 81 681 104 HOH HOH . G 4 HOH B 82 682 135 HOH HOH . G 4 HOH B 83 683 160 HOH HOH . G 4 HOH B 84 684 174 HOH HOH . G 4 HOH B 85 685 125 HOH HOH . G 4 HOH B 86 686 184 HOH HOH . G 4 HOH B 87 687 75 HOH HOH . G 4 HOH B 88 688 159 HOH HOH . G 4 HOH B 89 689 136 HOH HOH . G 4 HOH B 90 690 56 HOH HOH . G 4 HOH B 91 691 122 HOH HOH . G 4 HOH B 92 692 179 HOH HOH . G 4 HOH B 93 693 163 HOH HOH . G 4 HOH B 94 694 175 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 C4 D5W . . . D 3 -40.347 -2.288 155.669 1 54.13 ? C4 D5W 501 B 1 HETATM 2 C C5 D5W . . . D 3 -41.368 -3.008 155.023 1 55.9 ? C5 D5W 501 B 1 HETATM 3 C C6 D5W . . . D 3 -41.121 -3.688 153.829 1 55.17 ? C6 D5W 501 B 1 HETATM 4 N N1 D5W . . . D 3 -39.898 -3.653 153.286 1 51.95 ? N1 D5W 501 B 1 HETATM 5 N N3 D5W . . . D 3 -39.132 -2.271 155.097 1 50.58 ? N3 D5W 501 B 1 HETATM 6 C CAJ D5W . . . D 3 -44.906 -4.192 163.3 1 119.14 ? CAJ D5W 501 B 1 HETATM 7 C CAK D5W . . . D 3 -45.884 -5.051 163.858 1 123.22 ? CAK D5W 501 B 1 HETATM 8 CL CLA D5W . . . D 3 -46.422 -6.596 163.109 1 126.45 ? CLA D5W 501 B 1 HETATM 9 C CAL D5W . . . D 3 -46.516 -4.745 165.051 1 119.81 ? CAL D5W 501 B 1 HETATM 10 C CAM D5W . . . D 3 -46.196 -3.586 165.719 1 114 ? CAM D5W 501 B 1 HETATM 11 CL CLB D5W . . . D 3 -47.083 -3.289 167.259 1 103.52 ? CLB D5W 501 B 1 HETATM 12 C CAN D5W . . . D 3 -45.223 -2.726 165.177 1 116.57 ? CAN D5W 501 B 1 HETATM 13 C CAI D5W . . . D 3 -44.55 -2.98 163.941 1 115.8 ? CAI D5W 501 B 1 HETATM 14 C CAH D5W . . . D 3 -43.49 -1.988 163.408 1 108.25 ? CAH D5W 501 B 1 HETATM 15 N NAU D5W . . . D 3 -43.995 -0.595 163.108 1 114.21 ? NAU D5W 501 B 1 HETATM 16 C CAW D5W . . . D 3 -42.851 0.353 163.019 1 115.95 ? CAW D5W 501 B 1 HETATM 17 C CAV D5W . . . D 3 -44.973 -0.012 164.067 1 114.66 ? CAV D5W 501 B 1 HETATM 18 C CAG D5W . . . D 3 -42.662 -2.362 162.154 1 95.69 ? CAG D5W 501 B 1 HETATM 19 O OAQ D5W . . . D 3 -41.429 -2.374 162.215 1 77.08 ? OAQ D5W 501 B 1 HETATM 20 N N D5W . . . D 3 -43.287 -2.651 160.993 1 89.97 ? N D5W 501 B 1 HETATM 21 C CA D5W . . . D 3 -42.621 -3.196 159.787 1 83.25 ? CA D5W 501 B 1 HETATM 22 C CB D5W . . . D 3 -43.458 -4.439 159.352 1 89.92 ? CB D5W 501 B 1 HETATM 23 C CG2 D5W . . . D 3 -44.783 -4.075 158.656 1 90.82 ? CG2 D5W 501 B 1 HETATM 24 C CG1 D5W . . . D 3 -42.674 -5.462 158.498 1 92.58 ? CG1 D5W 501 B 1 HETATM 25 C CD1 D5W . . . D 3 -41.692 -6.336 159.266 1 91.82 ? CD1 D5W 501 B 1 HETATM 26 C C D5W . . . D 3 -42.299 -2.218 158.627 1 68.12 ? C D5W 501 B 1 HETATM 27 O O D5W . . . D 3 -43.079 -1.346 158.222 1 46.96 ? O D5W 501 B 1 HETATM 28 N NAF D5W . . . D 3 -41.083 -2.374 158.053 1 60.17 ? NAF D5W 501 B 1 HETATM 29 C CAX D5W . . . D 3 -40.579 -1.531 156.967 1 53.72 ? CAX D5W 501 B 1 HETATM 30 C C2 D5W . . . D 3 -38.931 -2.942 153.933 1 47.03 ? C2 D5W 501 B 1 HETATM 31 C CBE D5W . . . D 3 -37.559 -2.883 153.367 1 37.18 ? CBE D5W 501 B 1 HETATM 32 N NBF D5W . . . D 3 -37.338 -3.422 152.214 1 35.17 ? NBF D5W 501 B 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 32 #