data_6YM3 # _model_server_result.job_id 2S20tOsxPqm9nR2YPOaE9A _model_server_result.datetime_utc '2024-10-19 13:45:25' _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 6ym3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 6YM3 # _exptl.entry_id 6YM3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 440.494 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2~{R})-2-[[3-cyano-2-[4-(2-ethoxyphenyl)phenyl]-5,8-dihydro-1,7-naphthyridin-4-yl]amino]propanoic acid' _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 92.96 _cell.angle_gamma 90 _cell.entry_id 6YM3 _cell.length_a 43.934 _cell.length_b 98.132 _cell.length_c 104.256 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YM3 _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 _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 E 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.35 ? covale ? covale2 A C PHD 348 A PHD 359 1_555 A N ILE 349 A ILE 360 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.329 ? covale ? covale3 A C PHD 348 A PHD 359 1_555 A N ILE 349 A ILE 360 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.34 ? covale ? covale4 B C ILE 347 B ILE 358 1_555 B N PHD 348 B PHD 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.343 ? covale ? covale5 B C PHD 348 B PHD 359 1_555 B N ILE 349 B ILE 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.35 ? # _chem_comp.formula 'C26 H24 N4 O3' _chem_comp.formula_weight 440.494 _chem_comp.id OYZ _chem_comp.mon_nstd_flag . _chem_comp.name '(2~{R})-2-[[3-cyano-2-[4-(2-ethoxyphenyl)phenyl]-5,8-dihydro-1,7-naphthyridin-4-yl]amino]propanoic acid' _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 C27 C26 OYZ doub 237 n y C27 C28 OYZ sing 238 n y C26 C25 OYZ sing 239 n y C28 C23 OYZ doub 240 n y C25 C24 OYZ doub 241 n y C23 C24 OYZ sing 242 n y C23 C22 OYZ sing 243 n n C21 C22 OYZ doub 244 n y C21 C20 OYZ sing 245 n y C24 O29 OYZ sing 246 n n C22 C32 OYZ sing 247 n y C20 C19 OYZ doub 248 n y O29 C30 OYZ sing 249 n n C30 C31 OYZ sing 250 n n C32 C33 OYZ doub 251 n y C19 C33 OYZ sing 252 n y C19 C1 OYZ sing 253 n n N10 C1 OYZ doub 254 n y N10 C9 OYZ sing 255 n y C1 C2 OYZ sing 256 n y C8 C9 OYZ sing 257 n n C8 N7 OYZ sing 258 n n C9 C4 OYZ doub 259 n y N18 C17 OYZ trip 260 n n C17 C2 OYZ sing 261 n n C2 C3 OYZ doub 262 n y N7 C6 OYZ doub 263 n n C4 C3 OYZ sing 264 n y C4 C5 OYZ sing 265 n n C3 N11 OYZ sing 266 n n C6 C5 OYZ sing 267 n n N11 C12 OYZ sing 268 n n C12 C16 OYZ sing 269 n n C12 C13 OYZ sing 270 n n C13 O15 OYZ doub 271 n n C13 O14 OYZ sing 272 n n C5 H1 OYZ sing 273 n n C5 H2 OYZ sing 274 n n C6 H3 OYZ sing 275 n n C8 H4 OYZ sing 276 n n C8 H5 OYZ sing 277 n n C20 H6 OYZ sing 278 n n C21 H7 OYZ sing 279 n n C26 H8 OYZ sing 280 n n C28 H9 OYZ sing 281 n n C31 H10 OYZ sing 282 n n C31 H11 OYZ sing 283 n n C31 H12 OYZ sing 284 n n C30 H13 OYZ sing 285 n n C30 H14 OYZ sing 286 n n C25 H15 OYZ sing 287 n n C27 H16 OYZ sing 288 n n C32 H17 OYZ sing 289 n n C33 H18 OYZ sing 290 n n N11 H19 OYZ sing 291 n n C12 H20 OYZ sing 292 n n C16 H21 OYZ sing 293 n n C16 H22 OYZ sing 294 n n C16 H23 OYZ sing 295 n n O14 H24 OYZ sing 296 n n # _atom_sites.entry_id 6YM3 _atom_sites.fract_transf_matrix[1][1] 0.022761 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001177 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01019 _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] 0.009605 _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 OYZ A 1 501 2 OYZ LIG . D 3 PO4 A 1 502 2 PO4 PO4 . E 2 OYZ B 1 501 1 OYZ LIG . F 3 PO4 B 1 502 4 PO4 PO4 . G 4 HOH A 1 601 113 HOH HOH . G 4 HOH A 2 602 63 HOH HOH . G 4 HOH A 3 603 73 HOH HOH . G 4 HOH A 4 604 98 HOH HOH . G 4 HOH A 5 605 160 HOH HOH . G 4 HOH A 6 606 58 HOH HOH . G 4 HOH A 7 607 118 HOH HOH . G 4 HOH A 8 608 24 HOH HOH . G 4 HOH A 9 609 124 HOH HOH . G 4 HOH A 10 610 45 HOH HOH . G 4 HOH A 11 611 13 HOH HOH . G 4 HOH A 12 612 102 HOH HOH . G 4 HOH A 13 613 128 HOH HOH . G 4 HOH A 14 614 7 HOH HOH . G 4 HOH A 15 615 115 HOH HOH . G 4 HOH A 16 616 56 HOH HOH . G 4 HOH A 17 617 57 HOH HOH . G 4 HOH A 18 618 52 HOH HOH . G 4 HOH A 19 619 132 HOH HOH . G 4 HOH A 20 620 14 HOH HOH . G 4 HOH A 21 621 53 HOH HOH . G 4 HOH A 22 622 34 HOH HOH . G 4 HOH A 23 623 123 HOH HOH . G 4 HOH A 24 624 46 HOH HOH . G 4 HOH A 25 625 9 HOH HOH . G 4 HOH A 26 626 77 HOH HOH . G 4 HOH A 27 627 55 HOH HOH . G 4 HOH A 28 628 5 HOH HOH . G 4 HOH A 29 629 36 HOH HOH . G 4 HOH A 30 630 67 HOH HOH . G 4 HOH A 31 631 138 HOH HOH . G 4 HOH A 32 632 64 HOH HOH . G 4 HOH A 33 633 79 HOH HOH . G 4 HOH A 34 634 120 HOH HOH . G 4 HOH A 35 635 116 HOH HOH . G 4 HOH A 36 636 23 HOH HOH . G 4 HOH A 37 637 42 HOH HOH . G 4 HOH A 38 638 135 HOH HOH . G 4 HOH A 39 639 134 HOH HOH . G 4 HOH A 40 640 130 HOH HOH . G 4 HOH A 41 641 26 HOH HOH . G 4 HOH A 42 642 89 HOH HOH . G 4 HOH A 43 643 15 HOH HOH . G 4 HOH A 44 644 12 HOH HOH . G 4 HOH A 45 645 38 HOH HOH . G 4 HOH A 46 646 149 HOH HOH . G 4 HOH A 47 647 1 HOH HOH . G 4 HOH A 48 648 21 HOH HOH . G 4 HOH A 49 649 81 HOH HOH . G 4 HOH A 50 650 27 HOH HOH . G 4 HOH A 51 651 83 HOH HOH . G 4 HOH A 52 652 39 HOH HOH . G 4 HOH A 53 653 82 HOH HOH . G 4 HOH A 54 654 139 HOH HOH . G 4 HOH A 55 655 18 HOH HOH . G 4 HOH A 56 656 47 HOH HOH . G 4 HOH A 57 657 75 HOH HOH . G 4 HOH A 58 658 8 HOH HOH . G 4 HOH A 59 659 148 HOH HOH . G 4 HOH A 60 660 121 HOH HOH . G 4 HOH A 61 661 28 HOH HOH . G 4 HOH A 62 662 72 HOH HOH . G 4 HOH A 63 663 162 HOH HOH . G 4 HOH A 64 664 43 HOH HOH . G 4 HOH A 65 665 117 HOH HOH . G 4 HOH A 66 666 126 HOH HOH . G 4 HOH A 67 667 161 HOH HOH . G 4 HOH A 68 668 150 HOH HOH . G 4 HOH A 69 669 6 HOH HOH . G 4 HOH A 70 670 80 HOH HOH . G 4 HOH A 71 671 62 HOH HOH . G 4 HOH A 72 672 78 HOH HOH . G 4 HOH A 73 673 129 HOH HOH . G 4 HOH A 74 674 145 HOH HOH . G 4 HOH A 75 675 143 HOH HOH . G 4 HOH A 76 676 142 HOH HOH . G 4 HOH A 77 677 147 HOH HOH . G 4 HOH A 78 678 122 HOH HOH . G 4 HOH A 79 679 144 HOH HOH . G 4 HOH A 80 680 133 HOH HOH . G 4 HOH A 81 681 146 HOH HOH . H 4 HOH B 1 601 112 HOH HOH . H 4 HOH B 2 602 54 HOH HOH . H 4 HOH B 3 603 16 HOH HOH . H 4 HOH B 4 604 60 HOH HOH . H 4 HOH B 5 605 90 HOH HOH . H 4 HOH B 6 606 74 HOH HOH . H 4 HOH B 7 607 29 HOH HOH . H 4 HOH B 8 608 71 HOH HOH . H 4 HOH B 9 609 125 HOH HOH . H 4 HOH B 10 610 157 HOH HOH . H 4 HOH B 11 611 32 HOH HOH . H 4 HOH B 12 612 159 HOH HOH . H 4 HOH B 13 613 4 HOH HOH . H 4 HOH B 14 614 119 HOH HOH . H 4 HOH B 15 615 109 HOH HOH . H 4 HOH B 16 616 61 HOH HOH . H 4 HOH B 17 617 86 HOH HOH . H 4 HOH B 18 618 68 HOH HOH . H 4 HOH B 19 619 22 HOH HOH . H 4 HOH B 20 620 3 HOH HOH . H 4 HOH B 21 621 20 HOH HOH . H 4 HOH B 22 622 33 HOH HOH . H 4 HOH B 23 623 91 HOH HOH . H 4 HOH B 24 624 155 HOH HOH . H 4 HOH B 25 625 97 HOH HOH . H 4 HOH B 26 626 10 HOH HOH . H 4 HOH B 27 627 156 HOH HOH . H 4 HOH B 28 628 11 HOH HOH . H 4 HOH B 29 629 41 HOH HOH . H 4 HOH B 30 630 106 HOH HOH . H 4 HOH B 31 631 65 HOH HOH . H 4 HOH B 32 632 88 HOH HOH . H 4 HOH B 33 633 2 HOH HOH . H 4 HOH B 34 634 25 HOH HOH . H 4 HOH B 35 635 31 HOH HOH . H 4 HOH B 36 636 51 HOH HOH . H 4 HOH B 37 637 84 HOH HOH . H 4 HOH B 38 638 93 HOH HOH . H 4 HOH B 39 639 59 HOH HOH . H 4 HOH B 40 640 94 HOH HOH . H 4 HOH B 41 641 40 HOH HOH . H 4 HOH B 42 642 19 HOH HOH . H 4 HOH B 43 643 85 HOH HOH . H 4 HOH B 44 644 30 HOH HOH . H 4 HOH B 45 645 111 HOH HOH . H 4 HOH B 46 646 48 HOH HOH . H 4 HOH B 47 647 76 HOH HOH . H 4 HOH B 48 648 87 HOH HOH . H 4 HOH B 49 649 37 HOH HOH . H 4 HOH B 50 650 158 HOH HOH . H 4 HOH B 51 651 103 HOH HOH . H 4 HOH B 52 652 95 HOH HOH . H 4 HOH B 53 653 92 HOH HOH . H 4 HOH B 54 654 136 HOH HOH . H 4 HOH B 55 655 152 HOH HOH . H 4 HOH B 56 656 17 HOH HOH . H 4 HOH B 57 657 96 HOH HOH . H 4 HOH B 58 658 49 HOH HOH . H 4 HOH B 59 659 35 HOH HOH . H 4 HOH B 60 660 154 HOH HOH . H 4 HOH B 61 661 69 HOH HOH . H 4 HOH B 62 662 107 HOH HOH . H 4 HOH B 63 663 153 HOH HOH . H 4 HOH B 64 664 151 HOH HOH . H 4 HOH B 65 665 141 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 OYZ . . . E 2 8.227 -4.84 48.463 1 27.81 ? C4 OYZ 501 B 1 HETATM 2 C C5 OYZ . . . E 2 8.801 -3.74 49.031 1 24.87 ? C5 OYZ 501 B 1 HETATM 3 C C6 OYZ . . . E 2 8.171 -2.531 48.933 1 26.81 ? C6 OYZ 501 B 1 HETATM 4 C C8 OYZ . . . E 2 6.499 -3.483 47.728 1 27.69 ? C8 OYZ 501 B 1 HETATM 5 C C13 OYZ . . . E 2 11.419 -7.06 51.166 1 33.5 ? C13 OYZ 501 B 1 HETATM 6 C C17 OYZ . . . E 2 8.764 -8.379 47.882 1 28.69 ? C17 OYZ 501 B 1 HETATM 7 C C20 OYZ . . . E 2 5.846 -7.803 45.193 1 30.21 ? C20 OYZ 501 B 1 HETATM 8 C C21 OYZ . . . E 2 5.189 -8.854 44.536 1 27.95 ? C21 OYZ 501 B 1 HETATM 9 C C22 OYZ . . . E 2 4.971 -10.092 45.12 1 30.58 ? C22 OYZ 501 B 1 HETATM 10 C C24 OYZ . . . E 2 4.488 -12.413 44.549 1 28.83 ? C24 OYZ 501 B 1 HETATM 11 C C26 OYZ . . . E 2 2.674 -12.989 43.038 1 24.46 ? C26 OYZ 501 B 1 HETATM 12 C C28 OYZ . . . E 2 3.199 -10.697 43.627 1 30.27 ? C28 OYZ 501 B 1 HETATM 13 C C31 OYZ . . . E 2 6.693 -14.279 46.647 1 43.83 ? C31 OYZ 501 B 1 HETATM 14 C C30 OYZ . . . E 2 5.5 -14.199 45.675 1 41.44 ? C30 OYZ 501 B 1 HETATM 15 O O29 OYZ . . . E 2 5.488 -12.77 45.359 1 39.35 ? O29 OYZ 501 B 1 HETATM 16 C C25 OYZ . . . E 2 3.717 -13.376 43.887 1 29.45 ? C25 OYZ 501 B 1 HETATM 17 C C27 OYZ . . . E 2 2.428 -11.655 42.922 1 24.3 ? C27 OYZ 501 B 1 HETATM 18 C C23 OYZ . . . E 2 4.263 -11.084 44.433 1 27.01 ? C23 OYZ 501 B 1 HETATM 19 C C32 OYZ . . . E 2 5.41 -10.276 46.448 1 31.72 ? C32 OYZ 501 B 1 HETATM 20 C C33 OYZ . . . E 2 6.065 -9.221 47.099 1 27.99 ? C33 OYZ 501 B 1 HETATM 21 C C19 OYZ . . . E 2 6.303 -7.994 46.524 1 30.16 ? C19 OYZ 501 B 1 HETATM 22 C C1 OYZ . . . E 2 6.98 -6.961 47.211 1 28.62 ? C1 OYZ 501 B 1 HETATM 23 C C2 OYZ . . . E 2 8.197 -7.122 47.889 1 29.47 ? C2 OYZ 501 B 1 HETATM 24 N N18 OYZ . . . E 2 9.1 -9.461 47.811 1 37.04 ? N18 OYZ 501 B 1 HETATM 25 N N10 OYZ . . . E 2 6.456 -5.753 47.181 1 27.38 ? N10 OYZ 501 B 1 HETATM 26 C C9 OYZ . . . E 2 7.055 -4.713 47.77 1 27.76 ? C9 OYZ 501 B 1 HETATM 27 N N7 OYZ . . . E 2 7.054 -2.412 48.286 1 29.47 ? N7 OYZ 501 B 1 HETATM 28 C C3 OYZ . . . E 2 8.793 -6.08 48.562 1 30.67 ? C3 OYZ 501 B 1 HETATM 29 N N11 OYZ . . . E 2 9.919 -6.204 49.293 1 35.04 ? N11 OYZ 501 B 1 HETATM 30 C C12 OYZ . . . E 2 10.295 -7.408 50.137 1 34.63 ? C12 OYZ 501 B 1 HETATM 31 C C16 OYZ . . . E 2 9.217 -8.192 50.925 1 37.87 ? C16 OYZ 501 B 1 HETATM 32 O O15 OYZ . . . E 2 11.723 -5.88 51.362 1 34.3 ? O15 OYZ 501 B 1 HETATM 33 O O14 OYZ . . . E 2 11.944 -8.03 51.715 1 38.46 ? O14 OYZ 501 B 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 33 #