data_7D5U
#
_model_server_result.job_id            Jn2s34_6822ltQVodI35FQ 
_model_server_result.datetime_utc      '2024-12-21 14:22:28' 
_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          7d5u 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    7D5U 
#
_exptl.entry_id    7D5U 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              453.417 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            N-[3-[(9S)-7-azanyl-2,2-bis(fluoranyl)-9-prop-1-ynyl-6-oxa-8-azaspiro[3.5]non-7-en-9-yl]-4-fluoranyl-phenyl]-5-cyano-pyridine-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          90 
_cell.angle_gamma         90 
_cell.entry_id            7D5U 
_cell.length_a            62.926 
_cell.length_b            74.339 
_cell.length_c            108.389 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7D5U 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_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 
_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 
#
_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 A SG CYS 159 A CYS 171 1_555 A SG CYS 359 A CYS 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? 
disulf ? disulf2 A SG CYS 218 A CYS 230 1_555 A SG CYS 383 A CYS 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? 
disulf ? disulf3 A SG CYS 270 A CYS 282 1_555 A SG CYS 319 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? 
#
_chem_comp.formula           'C23 H18 F3 N5 O2' 
_chem_comp.formula_weight    453.417 
_chem_comp.id                GX6 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              N-[3-[(9S)-7-azanyl-2,2-bis(fluoranyl)-9-prop-1-ynyl-6-oxa-8-azaspiro[3.5]non-7-en-9-yl]-4-fluoranyl-phenyl]-5-cyano-pyridine-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
F2 C20 GX6 sing 129 n n 
F3 C20 GX6 sing 130 n n 
C20 C19 GX6 sing 131 n n 
C20 C21 GX6 sing 132 n n 
C19 C18 GX6 sing 133 n n 
F1 C1 GX6 sing 134 n n 
C21 C18 GX6 sing 135 n n 
C17 C16 GX6 sing 136 n n 
C18 C22 GX6 sing 137 n n 
C18 C14 GX6 sing 138 n n 
C16 C15 GX6 trip 139 n n 
C1 C2 GX6 doub 140 n y 
C1 C13 GX6 sing 141 n y 
C22 O2 GX6 sing 142 n n 
C15 C14 GX6 sing 143 n n 
C2 C3 GX6 sing 144 n y 
C14 C13 GX6 sing 145 n n 
C14 N5 GX6 sing 146 n n 
C13 C12 GX6 doub 147 n y 
O2 C23 GX6 sing 148 n n 
C3 C4 GX6 doub 149 n y 
N5 C23 GX6 doub 150 n n 
C12 C4 GX6 sing 151 n y 
C23 N4 GX6 sing 152 n n 
C4 N1 GX6 sing 153 n n 
N1 C5 GX6 sing 154 n n 
O1 C5 GX6 doub 155 n n 
C5 C6 GX6 sing 156 n n 
C6 C11 GX6 doub 157 n y 
C6 N2 GX6 sing 158 n y 
C11 C10 GX6 sing 159 n y 
N2 C7 GX6 doub 160 n y 
C10 C8 GX6 doub 161 n y 
C7 C8 GX6 sing 162 n y 
C8 C9 GX6 sing 163 n n 
C9 N3 GX6 trip 164 n n 
C2 H1 GX6 sing 165 n n 
C3 H2 GX6 sing 166 n n 
N1 H3 GX6 sing 167 n n 
C7 H4 GX6 sing 168 n n 
C10 H5 GX6 sing 169 n n 
C11 H6 GX6 sing 170 n n 
C12 H7 GX6 sing 171 n n 
C17 H8 GX6 sing 172 n n 
C17 H9 GX6 sing 173 n n 
C17 H10 GX6 sing 174 n n 
C19 H11 GX6 sing 175 n n 
C19 H12 GX6 sing 176 n n 
C21 H13 GX6 sing 177 n n 
C21 H14 GX6 sing 178 n n 
C22 H15 GX6 sing 179 n n 
C22 H16 GX6 sing 180 n n 
N4 H17 GX6 sing 181 n n 
N4 H18 GX6 sing 182 n n 
#
_atom_sites.entry_id                     7D5U 
_atom_sites.fract_transf_matrix[1][1]    0.015892 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013452 
_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]    0.009226 
_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 GX6 A 1 401 1 GX6 INX . 
D 4 HOH A 1 501 70 HOH HOH . 
D 4 HOH A 2 502 37 HOH HOH . 
D 4 HOH A 3 503 29 HOH HOH . 
D 4 HOH A 4 504 101 HOH HOH . 
D 4 HOH A 5 505 203 HOH HOH . 
D 4 HOH A 6 506 32 HOH HOH . 
D 4 HOH A 7 507 81 HOH HOH . 
D 4 HOH A 8 508 61 HOH HOH . 
D 4 HOH A 9 509 12 HOH HOH . 
D 4 HOH A 10 510 75 HOH HOH . 
D 4 HOH A 11 511 15 HOH HOH . 
D 4 HOH A 12 512 123 HOH HOH . 
D 4 HOH A 13 513 84 HOH HOH . 
D 4 HOH A 14 514 65 HOH HOH . 
D 4 HOH A 15 515 195 HOH HOH . 
D 4 HOH A 16 516 78 HOH HOH . 
D 4 HOH A 17 517 35 HOH HOH . 
D 4 HOH A 18 518 9 HOH HOH . 
D 4 HOH A 19 519 100 HOH HOH . 
D 4 HOH A 20 520 6 HOH HOH . 
D 4 HOH A 21 521 23 HOH HOH . 
D 4 HOH A 22 522 62 HOH HOH . 
D 4 HOH A 23 523 134 HOH HOH . 
D 4 HOH A 24 524 57 HOH HOH . 
D 4 HOH A 25 525 55 HOH HOH . 
D 4 HOH A 26 526 14 HOH HOH . 
D 4 HOH A 27 527 63 HOH HOH . 
D 4 HOH A 28 528 89 HOH HOH . 
D 4 HOH A 29 529 41 HOH HOH . 
D 4 HOH A 30 530 31 HOH HOH . 
D 4 HOH A 31 531 64 HOH HOH . 
D 4 HOH A 32 532 185 HOH HOH . 
D 4 HOH A 33 533 21 HOH HOH . 
D 4 HOH A 34 534 90 HOH HOH . 
D 4 HOH A 35 535 71 HOH HOH . 
D 4 HOH A 36 536 16 HOH HOH . 
D 4 HOH A 37 537 36 HOH HOH . 
D 4 HOH A 38 538 2 HOH HOH . 
D 4 HOH A 39 539 111 HOH HOH . 
D 4 HOH A 40 540 13 HOH HOH . 
D 4 HOH A 41 541 40 HOH HOH . 
D 4 HOH A 42 542 74 HOH HOH . 
D 4 HOH A 43 543 33 HOH HOH . 
D 4 HOH A 44 544 5 HOH HOH . 
D 4 HOH A 45 545 49 HOH HOH . 
D 4 HOH A 46 546 1 HOH HOH . 
D 4 HOH A 47 547 66 HOH HOH . 
D 4 HOH A 48 548 34 HOH HOH . 
D 4 HOH A 49 549 85 HOH HOH . 
D 4 HOH A 50 550 68 HOH HOH . 
D 4 HOH A 51 551 107 HOH HOH . 
D 4 HOH A 52 552 82 HOH HOH . 
D 4 HOH A 53 553 22 HOH HOH . 
D 4 HOH A 54 554 52 HOH HOH . 
D 4 HOH A 55 555 50 HOH HOH . 
D 4 HOH A 56 556 114 HOH HOH . 
D 4 HOH A 57 557 25 HOH HOH . 
D 4 HOH A 58 558 199 HOH HOH . 
D 4 HOH A 59 559 45 HOH HOH . 
D 4 HOH A 60 560 122 HOH HOH . 
D 4 HOH A 61 561 179 HOH HOH . 
D 4 HOH A 62 562 28 HOH HOH . 
D 4 HOH A 63 563 83 HOH HOH . 
D 4 HOH A 64 564 48 HOH HOH . 
D 4 HOH A 65 565 30 HOH HOH . 
D 4 HOH A 66 566 155 HOH HOH . 
D 4 HOH A 67 567 184 HOH HOH . 
D 4 HOH A 68 568 76 HOH HOH . 
D 4 HOH A 69 569 102 HOH HOH . 
D 4 HOH A 70 570 109 HOH HOH . 
D 4 HOH A 71 571 169 HOH HOH . 
D 4 HOH A 72 572 143 HOH HOH . 
D 4 HOH A 73 573 59 HOH HOH . 
D 4 HOH A 74 574 178 HOH HOH . 
D 4 HOH A 75 575 181 HOH HOH . 
D 4 HOH A 76 576 103 HOH HOH . 
D 4 HOH A 77 577 120 HOH HOH . 
D 4 HOH A 78 578 204 HOH HOH . 
D 4 HOH A 79 579 182 HOH HOH . 
D 4 HOH A 80 580 69 HOH HOH . 
D 4 HOH A 81 581 126 HOH HOH . 
D 4 HOH A 82 582 177 HOH HOH . 
D 4 HOH A 83 583 127 HOH HOH . 
D 4 HOH A 84 584 67 HOH HOH . 
D 4 HOH A 85 585 91 HOH HOH . 
E 4 HOH D 1 301 43 HOH HOH . 
E 4 HOH D 2 302 4 HOH HOH . 
E 4 HOH D 3 303 112 HOH HOH . 
E 4 HOH D 4 304 77 HOH HOH . 
E 4 HOH D 5 305 46 HOH HOH . 
E 4 HOH D 6 306 187 HOH HOH . 
E 4 HOH D 7 307 58 HOH HOH . 
E 4 HOH D 8 308 20 HOH HOH . 
E 4 HOH D 9 309 17 HOH HOH . 
E 4 HOH D 10 310 38 HOH HOH . 
E 4 HOH D 11 311 197 HOH HOH . 
E 4 HOH D 12 312 19 HOH HOH . 
E 4 HOH D 13 313 186 HOH HOH . 
E 4 HOH D 14 314 106 HOH HOH . 
E 4 HOH D 15 315 147 HOH HOH . 
E 4 HOH D 16 316 88 HOH HOH . 
E 4 HOH D 17 317 119 HOH HOH . 
E 4 HOH D 18 318 108 HOH HOH . 
E 4 HOH D 19 319 98 HOH HOH . 
E 4 HOH D 20 320 7 HOH HOH . 
E 4 HOH D 21 321 10 HOH HOH . 
E 4 HOH D 22 322 105 HOH HOH . 
E 4 HOH D 23 323 8 HOH HOH . 
E 4 HOH D 24 324 117 HOH HOH . 
E 4 HOH D 25 325 113 HOH HOH . 
E 4 HOH D 26 326 18 HOH HOH . 
E 4 HOH D 27 327 44 HOH HOH . 
E 4 HOH D 28 328 60 HOH HOH . 
E 4 HOH D 29 329 86 HOH HOH . 
E 4 HOH D 30 330 27 HOH HOH . 
E 4 HOH D 31 331 47 HOH HOH . 
E 4 HOH D 32 332 137 HOH HOH . 
E 4 HOH D 33 333 94 HOH HOH . 
E 4 HOH D 34 334 202 HOH HOH . 
E 4 HOH D 35 335 53 HOH HOH . 
E 4 HOH D 36 336 80 HOH HOH . 
E 4 HOH D 37 337 115 HOH HOH . 
E 4 HOH D 38 338 201 HOH HOH . 
E 4 HOH D 39 339 200 HOH HOH . 
E 4 HOH D 40 340 189 HOH HOH . 
E 4 HOH D 41 341 190 HOH HOH . 
E 4 HOH D 42 342 191 HOH HOH . 
E 4 HOH D 43 343 56 HOH HOH . 
E 4 HOH D 44 344 183 HOH HOH . 
E 4 HOH D 45 345 125 HOH HOH . 
E 4 HOH D 46 346 194 HOH HOH . 
E 4 HOH D 47 347 198 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 C1 GX6 . . . C 3 19.119 -6.49 -18.45 1 64.5 ? C1 GX6 401 A 1 
HETATM 2 C C2 GX6 . . . C 3 18.532 -7.705 -18.314 1 60.48 ? C2 GX6 401 A 1 
HETATM 3 C C3 GX6 . . . C 3 19.226 -8.75 -17.705 1 57.21 ? C3 GX6 401 A 1 
HETATM 4 C C4 GX6 . . . C 3 20.58 -8.575 -17.34 1 49.29 ? C4 GX6 401 A 1 
HETATM 5 C C5 GX6 . . . C 3 20.952 -10.888 -16.331 1 72.92 ? C5 GX6 401 A 1 
HETATM 6 C C6 GX6 . . . C 3 21.934 -11.626 -15.607 1 66.03 ? C6 GX6 401 A 1 
HETATM 7 N N1 GX6 . . . C 3 21.273 -9.608 -16.738 1 49.03 ? N1 GX6 401 A 1 
HETATM 8 N N2 GX6 . . . C 3 23.079 -10.988 -15.166 1 52.01 ? N2 GX6 401 A 1 
HETATM 9 N N3 GX6 . . . C 3 25.743 -14.18 -13.018 1 73.31 ? N3 GX6 401 A 1 
HETATM 10 O O1 GX6 . . . C 3 19.915 -11.374 -16.572 1 63.89 ? O1 GX6 401 A 1 
HETATM 11 C C7 GX6 . . . C 3 24.001 -11.619 -14.504 1 47.27 ? C7 GX6 401 A 1 
HETATM 12 C C8 GX6 . . . C 3 23.927 -12.972 -14.321 1 63.06 ? C8 GX6 401 A 1 
HETATM 13 C C9 GX6 . . . C 3 24.911 -13.64 -13.605 1 59.16 ? C9 GX6 401 A 1 
HETATM 14 C C10 GX6 . . . C 3 22.743 -13.693 -14.81 1 58.51 ? C10 GX6 401 A 1 
HETATM 15 C C11 GX6 . . . C 3 21.753 -12.977 -15.4 1 59.25 ? C11 GX6 401 A 1 
HETATM 16 C C12 GX6 . . . C 3 21.193 -7.361 -17.541 1 55.52 ? C12 GX6 401 A 1 
HETATM 17 C C13 GX6 . . . C 3 20.484 -6.314 -18.087 1 64.35 ? C13 GX6 401 A 1 
HETATM 18 C C14 GX6 . . . C 3 21.152 -4.895 -18.209 1 55.09 ? C14 GX6 401 A 1 
HETATM 19 C C15 GX6 . . . C 3 20.265 -3.85 -17.621 1 53.43 ? C15 GX6 401 A 1 
HETATM 20 O O2 GX6 . . . C 3 23.763 -5.494 -19.09 1 64.28 ? O2 GX6 401 A 1 
HETATM 21 F F1 GX6 . . . C 3 18.453 -5.499 -18.986 1 63.03 ? F1 GX6 401 A 1 
HETATM 22 C C16 GX6 . . . C 3 19.535 -3.021 -17.155 1 63.14 ? C16 GX6 401 A 1 
HETATM 23 C C17 GX6 . . . C 3 18.626 -2.016 -16.564 1 52.95 ? C17 GX6 401 A 1 
HETATM 24 C C18 GX6 . . . C 3 21.555 -4.613 -19.607 1 67.44 ? C18 GX6 401 A 1 
HETATM 25 C C19 GX6 . . . C 3 22.09 -3.193 -19.865 1 69.2 ? C19 GX6 401 A 1 
HETATM 26 C C20 GX6 . . . C 3 21.214 -3.028 -21.15 1 72.16 ? C20 GX6 401 A 1 
HETATM 27 F F2 GX6 . . . C 3 22.085 -3.058 -22.247 1 82.12 ? F2 GX6 401 A 1 
HETATM 28 F F3 GX6 . . . C 3 20.374 -1.928 -21.194 1 86.75 ? F3 GX6 401 A 1 
HETATM 29 C C21 GX6 . . . C 3 20.424 -4.264 -20.733 1 61.38 ? C21 GX6 401 A 1 
HETATM 30 C C22 GX6 . . . C 3 22.565 -5.772 -19.926 1 55.35 ? C22 GX6 401 A 1 
HETATM 31 C C23 GX6 . . . C 3 23.599 -5.155 -17.801 1 52.32 ? C23 GX6 401 A 1 
HETATM 32 N N4 GX6 . . . C 3 24.737 -5.153 -17.131 1 53.12 ? N4 GX6 401 A 1 
HETATM 33 N N5 GX6 . . . C 3 22.386 -4.894 -17.262 1 45.59 ? N5 GX6 401 A 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           698 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           33 
#