data_6YM4 # _model_server_result.job_id xWRR8ObyqxxUW_3f2dJPtA _model_server_result.datetime_utc '2024-10-19 22:27:35' _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 6ym4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 6YM4 # _exptl.entry_id 6YM4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 459.903 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2~{R})-2-[[2-[4-(3-chloranyl-2-fluoranyl-phenyl)phenyl]-3-cyano-1,7-naphthyridin-4-yl]amino]butanamide _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 93.37 _cell.angle_gamma 90 _cell.entry_id 6YM4 _cell.length_a 43.984 _cell.length_b 99.26 _cell.length_c 104.191 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YM4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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,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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 F N 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 covale ? covale1 A C ILE 347 A ILE 358 1_555 A N PHD 348 A PHD 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C PHD 348 A PHD 359 1_555 A N ILE 349 A ILE 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale3 B C ILE 347 B ILE 358 1_555 B N PHD 348 B PHD 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale4 B C PHD 348 B PHD 359 1_555 B N ILE 349 B ILE 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? # _chem_comp.formula 'C25 H19 Cl F N5 O' _chem_comp.formula_weight 459.903 _chem_comp.id P4Z _chem_comp.mon_nstd_flag . _chem_comp.name (2~{R})-2-[[2-[4-(3-chloranyl-2-fluoranyl-phenyl)phenyl]-3-cyano-1,7-naphthyridin-4-yl]amino]butanamide _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 C30 C29 P4Z sing 250 n n N33 C31 P4Z sing 251 n n C29 C28 P4Z sing 252 n n C31 O32 P4Z doub 253 n n C31 C28 P4Z sing 254 n n C28 N27 P4Z sing 255 n n N27 C23 P4Z sing 256 n n N26 C25 P4Z trip 257 n n C23 C24 P4Z doub 258 n y C23 C22 P4Z sing 259 n y C25 C24 P4Z sing 260 n n C1 C6 P4Z doub 261 n y C1 C2 P4Z sing 262 n y C21 C22 P4Z doub 263 n y C21 C20 P4Z sing 264 n y C24 C15 P4Z sing 265 n y C6 C5 P4Z sing 266 n y C22 C17 P4Z sing 267 n y C20 N19 P4Z doub 268 n y C15 C2 P4Z sing 269 n n C15 N16 P4Z doub 270 n y C17 N16 P4Z sing 271 n y C17 C18 P4Z doub 272 n y C2 C3 P4Z doub 273 n y C12 C11 P4Z doub 274 n y C12 C7 P4Z sing 275 n y N19 C18 P4Z sing 276 n y C11 C10 P4Z sing 277 n y C5 C7 P4Z sing 278 n n C5 C4 P4Z doub 279 n y C7 C8 P4Z doub 280 n y C10 C9 P4Z doub 281 n y C3 C4 P4Z sing 282 n y C8 C9 P4Z sing 283 n y C8 F14 P4Z sing 284 n n C9 CL1 P4Z sing 285 n n C4 H1 P4Z sing 286 n n C6 H2 P4Z sing 287 n n C10 H3 P4Z sing 288 n n C20 H4 P4Z sing 289 n n C21 H5 P4Z sing 290 n n C28 H6 P4Z sing 291 n n C1 H7 P4Z sing 292 n n C3 H8 P4Z sing 293 n n C11 H9 P4Z sing 294 n n C12 H10 P4Z sing 295 n n C18 H11 P4Z sing 296 n n N27 H12 P4Z sing 297 n n C29 H13 P4Z sing 298 n n C29 H14 P4Z sing 299 n n C30 H15 P4Z sing 300 n n C30 H16 P4Z sing 301 n n C30 H17 P4Z sing 302 n n N33 H18 P4Z sing 303 n n N33 H19 P4Z sing 304 n n # _atom_sites.entry_id 6YM4 _atom_sites.fract_transf_matrix[1][1] 0.022736 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001338 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010075 _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] 0.009614 _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 P4Z A 1 501 501 P4Z LIG . D 3 GOL A 1 502 601 GOL GOL . E 3 GOL A 1 503 701 GOL GOL . F 2 P4Z B 1 501 501 P4Z LIG . G 3 GOL B 1 502 601 GOL GOL . H 4 HOH A 1 601 112 HOH HOH . H 4 HOH A 2 602 158 HOH HOH . H 4 HOH A 3 603 168 HOH HOH . H 4 HOH A 4 604 35 HOH HOH . H 4 HOH A 5 605 74 HOH HOH . H 4 HOH A 6 606 163 HOH HOH . H 4 HOH A 7 607 80 HOH HOH . H 4 HOH A 8 608 27 HOH HOH . H 4 HOH A 9 609 11 HOH HOH . H 4 HOH A 10 610 136 HOH HOH . H 4 HOH A 11 611 130 HOH HOH . H 4 HOH A 12 612 87 HOH HOH . H 4 HOH A 13 613 64 HOH HOH . H 4 HOH A 14 614 83 HOH HOH . H 4 HOH A 15 615 12 HOH HOH . H 4 HOH A 16 616 63 HOH HOH . H 4 HOH A 17 617 161 HOH HOH . H 4 HOH A 18 618 20 HOH HOH . H 4 HOH A 19 619 21 HOH HOH . H 4 HOH A 20 620 8 HOH HOH . H 4 HOH A 21 621 9 HOH HOH . H 4 HOH A 22 622 99 HOH HOH . H 4 HOH A 23 623 9 HOH HOH . H 4 HOH A 24 624 79 HOH HOH . H 4 HOH A 25 625 82 HOH HOH . H 4 HOH A 26 626 109 HOH HOH . H 4 HOH A 27 627 59 HOH HOH . H 4 HOH A 28 628 89 HOH HOH . H 4 HOH A 29 629 97 HOH HOH . H 4 HOH A 30 630 122 HOH HOH . H 4 HOH A 31 631 144 HOH HOH . H 4 HOH A 32 632 58 HOH HOH . H 4 HOH A 33 633 152 HOH HOH . H 4 HOH A 34 634 100 HOH HOH . H 4 HOH A 35 635 166 HOH HOH . H 4 HOH A 36 636 167 HOH HOH . H 4 HOH A 37 637 76 HOH HOH . H 4 HOH A 38 638 162 HOH HOH . H 4 HOH A 39 639 90 HOH HOH . H 4 HOH A 40 640 16 HOH HOH . H 4 HOH A 41 641 127 HOH HOH . H 4 HOH A 42 642 73 HOH HOH . H 4 HOH A 43 643 110 HOH HOH . H 4 HOH A 44 644 140 HOH HOH . H 4 HOH A 45 645 17 HOH HOH . H 4 HOH A 46 646 104 HOH HOH . H 4 HOH A 47 647 13 HOH HOH . H 4 HOH A 48 648 95 HOH HOH . H 4 HOH A 49 649 78 HOH HOH . H 4 HOH A 50 650 16 HOH HOH . H 4 HOH A 51 651 19 HOH HOH . H 4 HOH A 52 652 24 HOH HOH . H 4 HOH A 53 653 70 HOH HOH . H 4 HOH A 54 654 6 HOH HOH . H 4 HOH A 55 655 77 HOH HOH . H 4 HOH A 56 656 157 HOH HOH . H 4 HOH A 57 657 94 HOH HOH . H 4 HOH A 58 658 23 HOH HOH . H 4 HOH A 59 659 126 HOH HOH . H 4 HOH A 60 660 147 HOH HOH . H 4 HOH A 61 661 26 HOH HOH . H 4 HOH A 62 662 150 HOH HOH . H 4 HOH A 63 663 156 HOH HOH . H 4 HOH A 64 664 160 HOH HOH . H 4 HOH A 65 665 18 HOH HOH . H 4 HOH A 66 666 65 HOH HOH . H 4 HOH A 67 667 124 HOH HOH . H 4 HOH A 68 668 7 HOH HOH . H 4 HOH A 69 669 116 HOH HOH . H 4 HOH A 70 670 15 HOH HOH . H 4 HOH A 71 671 81 HOH HOH . H 4 HOH A 72 672 10 HOH HOH . H 4 HOH A 73 673 135 HOH HOH . H 4 HOH A 74 674 1 HOH HOH . H 4 HOH A 75 675 32 HOH HOH . H 4 HOH A 76 676 31 HOH HOH . H 4 HOH A 77 677 85 HOH HOH . H 4 HOH A 78 678 25 HOH HOH . H 4 HOH A 79 679 7 HOH HOH . H 4 HOH A 80 680 155 HOH HOH . H 4 HOH A 81 681 125 HOH HOH . H 4 HOH A 82 682 29 HOH HOH . H 4 HOH A 83 683 119 HOH HOH . H 4 HOH A 84 684 17 HOH HOH . H 4 HOH A 85 685 165 HOH HOH . H 4 HOH A 86 686 164 HOH HOH . H 4 HOH A 87 687 117 HOH HOH . H 4 HOH A 88 688 6 HOH HOH . H 4 HOH A 89 689 159 HOH HOH . H 4 HOH A 90 690 142 HOH HOH . H 4 HOH A 91 691 118 HOH HOH . H 4 HOH A 92 692 18 HOH HOH . H 4 HOH A 93 693 115 HOH HOH . H 4 HOH A 94 694 120 HOH HOH . I 4 HOH B 1 601 15 HOH HOH . I 4 HOH B 2 602 88 HOH HOH . I 4 HOH B 3 603 102 HOH HOH . I 4 HOH B 4 604 111 HOH HOH . I 4 HOH B 5 605 21 HOH HOH . I 4 HOH B 6 606 12 HOH HOH . I 4 HOH B 7 607 51 HOH HOH . I 4 HOH B 8 608 72 HOH HOH . I 4 HOH B 9 609 61 HOH HOH . I 4 HOH B 10 610 131 HOH HOH . I 4 HOH B 11 611 5 HOH HOH . I 4 HOH B 12 612 56 HOH HOH . I 4 HOH B 13 613 114 HOH HOH . I 4 HOH B 14 614 103 HOH HOH . I 4 HOH B 15 615 123 HOH HOH . I 4 HOH B 16 616 86 HOH HOH . I 4 HOH B 17 617 69 HOH HOH . I 4 HOH B 18 618 60 HOH HOH . I 4 HOH B 19 619 3 HOH HOH . I 4 HOH B 20 620 4 HOH HOH . I 4 HOH B 21 621 67 HOH HOH . I 4 HOH B 22 622 96 HOH HOH . I 4 HOH B 23 623 84 HOH HOH . I 4 HOH B 24 624 55 HOH HOH . I 4 HOH B 25 625 129 HOH HOH . I 4 HOH B 26 626 75 HOH HOH . I 4 HOH B 27 627 2 HOH HOH . I 4 HOH B 28 628 5 HOH HOH . I 4 HOH B 29 629 132 HOH HOH . I 4 HOH B 30 630 134 HOH HOH . I 4 HOH B 31 631 101 HOH HOH . I 4 HOH B 32 632 151 HOH HOH . I 4 HOH B 33 633 66 HOH HOH . I 4 HOH B 34 634 13 HOH HOH . I 4 HOH B 35 635 171 HOH HOH . I 4 HOH B 36 636 8 HOH HOH . I 4 HOH B 37 637 146 HOH HOH . I 4 HOH B 38 638 44 HOH HOH . I 4 HOH B 39 639 24 HOH HOH . I 4 HOH B 40 640 68 HOH HOH . I 4 HOH B 41 641 52 HOH HOH . I 4 HOH B 42 642 47 HOH HOH . I 4 HOH B 43 643 143 HOH HOH . I 4 HOH B 44 644 49 HOH HOH . I 4 HOH B 45 645 71 HOH HOH . I 4 HOH B 46 646 92 HOH HOH . I 4 HOH B 47 647 107 HOH HOH . I 4 HOH B 48 648 91 HOH HOH . I 4 HOH B 49 649 11 HOH HOH . I 4 HOH B 50 650 170 HOH HOH . I 4 HOH B 51 651 128 HOH HOH . I 4 HOH B 52 652 45 HOH HOH . I 4 HOH B 53 653 20 HOH HOH . I 4 HOH B 54 654 98 HOH HOH . I 4 HOH B 55 655 138 HOH HOH . I 4 HOH B 56 656 57 HOH HOH . I 4 HOH B 57 657 62 HOH HOH . I 4 HOH B 58 658 149 HOH HOH . I 4 HOH B 59 659 22 HOH HOH . I 4 HOH B 60 660 106 HOH HOH . I 4 HOH B 61 661 139 HOH HOH . I 4 HOH B 62 662 14 HOH HOH . I 4 HOH B 63 663 113 HOH HOH . I 4 HOH B 64 664 154 HOH HOH . I 4 HOH B 65 665 10 HOH HOH . I 4 HOH B 66 666 48 HOH HOH . I 4 HOH B 67 667 141 HOH HOH . I 4 HOH B 68 668 133 HOH HOH . I 4 HOH B 69 669 46 HOH HOH . I 4 HOH B 70 670 145 HOH HOH . I 4 HOH B 71 671 4 HOH HOH . I 4 HOH B 72 672 105 HOH HOH . I 4 HOH B 73 673 14 HOH HOH . I 4 HOH B 74 674 3 HOH HOH . I 4 HOH B 75 675 1 HOH HOH . I 4 HOH B 76 676 153 HOH HOH . I 4 HOH B 77 677 93 HOH HOH . I 4 HOH B 78 678 22 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 P4Z . . . C 2 9.654 -0.276 -7.687 1 28.97 ? C4 P4Z 501 A 1 HETATM 2 C C5 P4Z . . . C 2 9.857 -1.151 -8.754 1 28.02 ? C5 P4Z 501 A 1 HETATM 3 C C6 P4Z . . . C 2 9.411 -0.827 -10.058 1 29.33 ? C6 P4Z 501 A 1 HETATM 4 C C7 P4Z . . . C 2 10.541 -2.432 -8.479 1 27.19 ? C7 P4Z 501 A 1 HETATM 5 C C8 P4Z . . . C 2 11.616 -2.499 -7.622 1 28.11 ? C8 P4Z 501 A 1 HETATM 6 C C10 P4Z . . . C 2 11.865 -4.784 -7.98 1 28.11 ? C10 P4Z 501 A 1 HETATM 7 C C15 P4Z . . . C 2 7.903 2.547 -9.522 1 29.49 ? C15 P4Z 501 A 1 HETATM 8 C C17 P4Z . . . C 2 7.915 4.875 -9.364 1 29.68 ? C17 P4Z 501 A 1 HETATM 9 C C20 P4Z . . . C 2 6.682 7.297 -9.656 1 30.48 ? C20 P4Z 501 A 1 HETATM 10 C C21 P4Z . . . C 2 6.045 6.24 -10.205 1 30.53 ? C21 P4Z 501 A 1 HETATM 11 C C22 P4Z . . . C 2 6.649 4.975 -10.023 1 31.45 ? C22 P4Z 501 A 1 HETATM 12 C C24 P4Z . . . C 2 6.651 2.529 -10.198 1 30.99 ? C24 P4Z 501 A 1 HETATM 13 C C28 P4Z . . . C 2 4.417 3.062 -12.332 1 35.64 ? C28 P4Z 501 A 1 HETATM 14 C C1 P4Z . . . C 2 8.792 0.361 -10.328 1 29.51 ? C1 P4Z 501 A 1 HETATM 15 C C2 P4Z . . . C 2 8.562 1.249 -9.237 1 30.68 ? C2 P4Z 501 A 1 HETATM 16 C C3 P4Z . . . C 2 9.026 0.931 -7.921 1 29.53 ? C3 P4Z 501 A 1 HETATM 17 C C9 P4Z . . . C 2 12.263 -3.654 -7.349 1 29.47 ? C9 P4Z 501 A 1 HETATM 18 C C11 P4Z . . . C 2 10.774 -4.734 -8.821 1 29.31 ? C11 P4Z 501 A 1 HETATM 19 C C12 P4Z . . . C 2 10.108 -3.565 -9.097 1 27.32 ? C12 P4Z 501 A 1 HETATM 20 CL CL1 P4Z . . . C 2 13.673 -3.63 -6.242 1 35.33 ? CL1 P4Z 501 A 1 HETATM 21 F F14 P4Z . . . C 2 12.106 -1.406 -6.996 1 28.88 ? F14 P4Z 501 A 1 HETATM 22 N N16 P4Z . . . C 2 8.511 3.674 -9.157 1 28.8 ? N16 P4Z 501 A 1 HETATM 23 C C18 P4Z . . . C 2 8.522 6.072 -8.957 1 29.71 ? C18 P4Z 501 A 1 HETATM 24 N N19 P4Z . . . C 2 7.871 7.218 -9.056 1 29.78 ? N19 P4Z 501 A 1 HETATM 25 C C23 P4Z . . . C 2 6.015 3.784 -10.491 1 31.98 ? C23 P4Z 501 A 1 HETATM 26 C C25 P4Z . . . C 2 5.981 1.284 -10.453 1 31.01 ? C25 P4Z 501 A 1 HETATM 27 N N26 P4Z . . . C 2 5.391 0.353 -10.7 1 29.93 ? N26 P4Z 501 A 1 HETATM 28 N N27 P4Z . . . C 2 4.797 3.941 -11.166 1 35.94 ? N27 P4Z 501 A 1 HETATM 29 C C29 P4Z . . . C 2 5.602 2.818 -13.273 1 39.54 ? C29 P4Z 501 A 1 HETATM 30 C C30 P4Z . . . C 2 5.446 3.045 -14.728 1 41.23 ? C30 P4Z 501 A 1 HETATM 31 C C31 P4Z . . . C 2 3.343 3.698 -13.127 1 36.58 ? C31 P4Z 501 A 1 HETATM 32 O O32 P4Z . . . C 2 3.212 4.862 -13.113 1 37.54 ? O32 P4Z 501 A 1 HETATM 33 N N33 P4Z . . . C 2 2.486 2.977 -13.825 1 35.26 ? N33 P4Z 501 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 33 #