data_6O0P
#
_model_server_result.job_id            SXrSgjnjMMdZpvFCsfrVmQ 
_model_server_result.datetime_utc      '2024-12-27 16:16:38' 
_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          6o0p 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":301}' 
#
_entry.id    6O0P 
#
_exptl.entry_id    6O0P 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              868.439 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "4-{4-[(4'-chloro-5,5-dimethyl[3,4,5,6-tetrahydro[1,1'-biphenyl]]-2-yl)methyl]piperazin-1-yl}-N-[(3-nitro-4-{[(oxan-4-yl )methyl]amino}phenyl)sulfonyl]-2-[(1H-pyrrolo[2,3-b]pyridin-5-yl)oxy]benzamide" 
_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            6O0P 
_cell.length_a            33.398 
_cell.length_b            48.945 
_cell.length_c            86.474 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6O0P 
_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    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C45 H50 Cl N7 O7 S' 
_chem_comp.formula_weight    868.439 
_chem_comp.id                LBM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "4-{4-[(4'-chloro-5,5-dimethyl[3,4,5,6-tetrahydro[1,1'-biphenyl]]-2-yl)methyl]piperazin-1-yl}-N-[(3-nitro-4-{[(oxan-4-yl )methyl]amino}phenyl)sulfonyl]-2-[(1H-pyrrolo[2,3-b]pyridin-5-yl)oxy]benzamide" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "Venetoclax, 2-((1H-pyrrolo[2,3-b]pyridin-5-yl)oxy)-4-(4-((4'-chloro-5,5-dimethyl-3,4,5,6-tetrahydro-[1,1'-biphenyl]-2-yl)methyl)pipe razin-1-yl)-N-((3-nitro-4-(((tetrahydro-2H-pyran-4-yl)methyl)amino)phenyl)sulfonyl)benzamide" 
#
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
C C1 LBM sing 173 n n 
C2 C1 LBM sing 174 n n 
C2 C3 LBM sing 175 n n 
C1 C6 LBM sing 176 n n 
C1 C44 LBM sing 177 n n 
C6 C5 LBM sing 178 n n 
C12 C11 LBM doub 179 n y 
C12 C7 LBM sing 180 n y 
C3 C4 LBM sing 181 n n 
C5 C4 LBM doub 182 n n 
C5 C7 LBM sing 183 n n 
C11 C10 LBM sing 184 n y 
C4 C13 LBM sing 185 n n 
C7 C8 LBM doub 186 n y 
C13 N LBM sing 187 n n 
C10 CL LBM sing 188 n n 
C10 C9 LBM doub 189 n y 
C8 C9 LBM sing 190 n y 
N C17 LBM sing 191 n n 
N C14 LBM sing 192 n n 
C17 C16 LBM sing 193 n n 
C14 C15 LBM sing 194 n n 
C16 N1 LBM sing 195 n n 
C15 N1 LBM sing 196 n n 
N1 C18 LBM sing 197 n n 
C18 C23 LBM doub 198 n y 
C18 C19 LBM sing 199 n y 
C23 C22 LBM sing 200 n y 
C19 C20 LBM doub 201 n y 
C22 C21 LBM doub 202 n y 
C20 O6 LBM sing 203 n n 
C20 C21 LBM sing 204 n y 
O6 C37 LBM sing 205 n n 
C21 C24 LBM sing 206 n n 
C37 C41 LBM doub 207 n y 
C37 C38 LBM sing 208 n y 
C41 C40 LBM sing 209 n y 
C38 N5 LBM doub 210 n y 
C24 O LBM doub 211 n n 
C24 N2 LBM sing 212 n n 
C40 C39 LBM doub 213 n y 
C40 C42 LBM sing 214 n y 
N5 C39 LBM sing 215 n y 
C39 N6 LBM sing 216 n y 
C42 C43 LBM doub 217 n y 
N2 S LBM sing 218 n n 
N6 C43 LBM sing 219 n y 
S O1 LBM doub 220 n n 
S O2 LBM doub 221 n n 
S C25 LBM sing 222 n n 
C25 C30 LBM doub 223 n y 
C25 C26 LBM sing 224 n y 
C30 C29 LBM sing 225 n y 
C26 C27 LBM doub 226 n y 
C29 C28 LBM doub 227 n y 
C27 C28 LBM sing 228 n y 
C27 N4 LBM sing 229 n n 
O5 N4 LBM doub 230 n n 
C28 N3 LBM sing 231 n n 
N4 O4 LBM sing 232 n n 
N3 C31 LBM sing 233 n n 
C31 C32 LBM sing 234 n n 
C36 C32 LBM sing 235 n n 
C36 C35 LBM sing 236 n n 
C32 C33 LBM sing 237 n n 
C33 C34 LBM sing 238 n n 
C35 O3 LBM sing 239 n n 
O3 C34 LBM sing 240 n n 
C11 H1 LBM sing 241 n n 
C12 H2 LBM sing 242 n n 
C13 H3 LBM sing 243 n n 
C13 H4 LBM sing 244 n n 
C14 H5 LBM sing 245 n n 
C14 H6 LBM sing 246 n n 
C15 H7 LBM sing 247 n n 
C15 H8 LBM sing 248 n n 
C16 H9 LBM sing 249 n n 
C16 H10 LBM sing 250 n n 
C17 H11 LBM sing 251 n n 
C17 H12 LBM sing 252 n n 
C19 H13 LBM sing 253 n n 
C22 H14 LBM sing 254 n n 
C23 H15 LBM sing 255 n n 
C26 H16 LBM sing 256 n n 
C29 H17 LBM sing 257 n n 
C31 H18 LBM sing 258 n n 
C31 H19 LBM sing 259 n n 
C H21 LBM sing 260 n n 
C H22 LBM sing 261 n n 
C H23 LBM sing 262 n n 
C2 H24 LBM sing 263 n n 
C2 H25 LBM sing 264 n n 
C3 H26 LBM sing 265 n n 
C3 H27 LBM sing 266 n n 
C30 H28 LBM sing 267 n n 
C32 H29 LBM sing 268 n n 
C33 H30 LBM sing 269 n n 
C33 H31 LBM sing 270 n n 
C34 H32 LBM sing 271 n n 
C34 H33 LBM sing 272 n n 
C35 H34 LBM sing 273 n n 
C35 H35 LBM sing 274 n n 
C36 H36 LBM sing 275 n n 
C36 H37 LBM sing 276 n n 
C38 H38 LBM sing 277 n n 
C41 H39 LBM sing 278 n n 
C42 H40 LBM sing 279 n n 
C43 H41 LBM sing 280 n n 
C44 H42 LBM sing 281 n n 
C44 H43 LBM sing 282 n n 
C44 H44 LBM sing 283 n n 
C6 H45 LBM sing 284 n n 
C6 H46 LBM sing 285 n n 
C8 H47 LBM sing 286 n n 
C9 H48 LBM sing 287 n n 
N2 H49 LBM sing 288 n n 
N3 H50 LBM sing 289 n n 
N6 H51 LBM sing 290 n n 
#
_atom_sites.entry_id                     6O0P 
_atom_sites.fract_transf_matrix[1][1]    0.029942 
_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]    0.020431 
_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]    0.011564 
_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 LBM A 1 301 1 LBM 199 . 
C 3 PEG A 1 302 1 PEG PEG . 
D 3 PEG A 1 303 2 PEG PEG . 
E 3 PEG A 1 304 3 PEG PEG . 
F 4 HOH A 1 401 31 HOH HOH . 
F 4 HOH A 2 402 25 HOH HOH . 
F 4 HOH A 3 403 30 HOH HOH . 
F 4 HOH A 4 404 8 HOH HOH . 
F 4 HOH A 5 405 28 HOH HOH . 
F 4 HOH A 6 406 32 HOH HOH . 
F 4 HOH A 7 407 9 HOH HOH . 
F 4 HOH A 8 408 21 HOH HOH . 
F 4 HOH A 9 409 18 HOH HOH . 
F 4 HOH A 10 410 7 HOH HOH . 
F 4 HOH A 11 411 12 HOH HOH . 
F 4 HOH A 12 412 24 HOH HOH . 
F 4 HOH A 13 413 29 HOH HOH . 
F 4 HOH A 14 414 14 HOH HOH . 
F 4 HOH A 15 415 1 HOH HOH . 
F 4 HOH A 16 416 13 HOH HOH . 
F 4 HOH A 17 417 5 HOH HOH . 
F 4 HOH A 18 418 22 HOH HOH . 
F 4 HOH A 19 419 10 HOH HOH . 
F 4 HOH A 20 420 2 HOH HOH . 
F 4 HOH A 21 421 33 HOH HOH . 
F 4 HOH A 22 422 4 HOH HOH . 
F 4 HOH A 23 423 34 HOH HOH . 
F 4 HOH A 24 424 11 HOH HOH . 
F 4 HOH A 25 425 15 HOH HOH . 
F 4 HOH A 26 426 26 HOH HOH . 
F 4 HOH A 27 427 17 HOH HOH . 
F 4 HOH A 28 428 3 HOH HOH . 
F 4 HOH A 29 429 38 HOH HOH . 
F 4 HOH A 30 430 19 HOH HOH . 
F 4 HOH A 31 431 36 HOH HOH . 
F 4 HOH A 32 432 27 HOH HOH . 
F 4 HOH A 33 433 16 HOH HOH . 
F 4 HOH A 34 434 20 HOH HOH . 
F 4 HOH A 35 435 39 HOH HOH . 
F 4 HOH A 36 436 37 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 C11 LBM . A . B 2 -11.76 0.605 -17.592 0.92 34.49 ? C11 LBM 301 A 1 
HETATM 2 C C12 LBM . A . B 2 -12.524 1.691 -17.98 0.92 33.19 ? C12 LBM 301 A 1 
HETATM 3 C C13 LBM . A . B 2 -15.3 3.065 -16.455 0.92 35.8 ? C13 LBM 301 A 1 
HETATM 4 C C14 LBM . A . B 2 -15.098 4.325 -14.396 0.92 30.84 ? C14 LBM 301 A 1 
HETATM 5 C C15 LBM . A . B 2 -15.858 4.926 -13.224 0.92 30.8 ? C15 LBM 301 A 1 
HETATM 6 C C16 LBM . A . B 2 -17.49 3.149 -13.407 0.92 25.42 ? C16 LBM 301 A 1 
HETATM 7 C C17 LBM . A . B 2 -16.707 2.567 -14.564 0.92 28.72 ? C17 LBM 301 A 1 
HETATM 8 C C19 LBM . A . B 2 -17.731 3.088 -10.527 0.92 22.39 ? C19 LBM 301 A 1 
HETATM 9 C C20 LBM . A . B 2 -18.142 3.279 -9.225 0.92 21.97 ? C20 LBM 301 A 1 
HETATM 10 C C22 LBM . A . B 2 -17.198 5.468 -9.228 0.92 22.32 ? C22 LBM 301 A 1 
HETATM 11 C C23 LBM . A . B 2 -16.776 5.282 -10.535 0.92 27.73 ? C23 LBM 301 A 1 
HETATM 12 C C24 LBM . A . B 2 -18.312 4.712 -7.13 0.92 33.84 ? C24 LBM 301 A 1 
HETATM 13 C C25 LBM . A . B 2 -17.198 3.9 -4.137 0.92 29.09 ? C25 LBM 301 A 1 
HETATM 14 C C26 LBM . A . B 2 -15.875 3.589 -3.871 0.92 23.87 ? C26 LBM 301 A 1 
HETATM 15 C C28 LBM . A . B 2 -16.544 1.299 -3.321 0.92 26.4 ? C28 LBM 301 A 1 
HETATM 16 C C29 LBM . A . B 2 -17.861 1.668 -3.597 0.92 26.93 ? C29 LBM 301 A 1 
HETATM 17 C C31 LBM . A . B 2 -17.219 -1.036 -2.751 0.92 32.46 ? C31 LBM 301 A 1 
HETATM 18 N N LBM . A . B 2 -16.015 3.626 -15.308 0.92 33.73 ? N LBM 301 A 1 
HETATM 19 C C LBM . A . B 2 -12.864 6.781 -20.208 0.92 36.48 ? C LBM 301 A 1 
HETATM 20 O O LBM . A . B 2 -19.33 4.208 -6.665 0.92 37.28 ? O LBM 301 A 1 
HETATM 21 C C1 LBM . A . B 2 -13.408 6.251 -18.881 0.92 39.47 ? C1 LBM 301 A 1 
HETATM 22 C C10 LBM . A . B 2 -11.021 0.656 -16.427 0.92 32.88 ? C10 LBM 301 A 1 
HETATM 23 C C18 LBM . A . B 2 -17.034 4.087 -11.204 0.92 26.27 ? C18 LBM 301 A 1 
HETATM 24 C C2 LBM . A . B 2 -14.881 5.86 -19.037 0.92 42.69 ? C2 LBM 301 A 1 
HETATM 25 C C21 LBM . A . B 2 -17.889 4.468 -8.544 0.92 22.07 ? C21 LBM 301 A 1 
HETATM 26 C C27 LBM . A . B 2 -15.555 2.31 -3.475 0.92 21.46 ? C27 LBM 301 A 1 
HETATM 27 C C3 LBM . A . B 2 -15.495 5.296 -17.758 0.92 38.18 ? C3 LBM 301 A 1 
HETATM 28 C C30 LBM . A . B 2 -18.194 2.949 -3.998 0.92 31.69 ? C30 LBM 301 A 1 
HETATM 29 C C32 LBM . A . B 2 -16.657 -2.083 -1.806 0.92 34.73 ? C32 LBM 301 A 1 
HETATM 30 C C33 LBM . A . B 2 -17.633 -3.232 -1.588 0.92 41.95 ? C33 LBM 301 A 1 
HETATM 31 C C34 LBM . A . B 2 -16.997 -4.282 -0.712 0.92 45.71 ? C34 LBM 301 A 1 
HETATM 32 C C35 LBM . A . B 2 -14.842 -3.722 -1.411 0.92 40.83 ? C35 LBM 301 A 1 
HETATM 33 C C36 LBM . A . B 2 -15.343 -2.641 -2.333 0.92 37.5 ? C36 LBM 301 A 1 
HETATM 34 C C37 LBM . A . B 2 -18.094 1.317 -7.843 0.92 28.46 ? C37 LBM 301 A 1 
HETATM 35 C C38 LBM . A . B 2 -18.712 0.146 -7.434 0.92 26.89 ? C38 LBM 301 A 1 
HETATM 36 C C39 LBM . A . B 2 -16.768 -0.635 -6.514 0.92 28.94 ? C39 LBM 301 A 1 
HETATM 37 C C4 LBM . A . B 2 -14.656 4.142 -17.281 0.92 36.06 ? C4 LBM 301 A 1 
HETATM 38 C C40 LBM . A . B 2 -16.046 0.533 -6.879 0.92 24.39 ? C40 LBM 301 A 1 
HETATM 39 C C41 LBM . A . B 2 -16.752 1.524 -7.564 0.92 21.65 ? C41 LBM 301 A 1 
HETATM 40 C C42 LBM . A . B 2 -14.704 0.329 -6.43 0.92 27.38 ? C42 LBM 301 A 1 
HETATM 41 C C43 LBM . A . B 2 -14.664 -0.896 -5.841 0.92 25.3 ? C43 LBM 301 A 1 
HETATM 42 C C44 LBM . A . B 2 -13.266 7.335 -17.813 0.92 39.99 ? C44 LBM 301 A 1 
HETATM 43 C C5 LBM . A . B 2 -13.352 4.013 -17.614 0.92 36.15 ? C5 LBM 301 A 1 
HETATM 44 C C6 LBM . A . B 2 -12.622 5.005 -18.462 0.92 32.11 ? C6 LBM 301 A 1 
HETATM 45 C C7 LBM . A . B 2 -12.549 2.834 -17.195 0.92 30.44 ? C7 LBM 301 A 1 
HETATM 46 C C8 LBM . A . B 2 -11.808 2.882 -16.022 0.92 30.17 ? C8 LBM 301 A 1 
HETATM 47 C C9 LBM . A . B 2 -11.047 1.792 -15.643 0.92 27.82 ? C9 LBM 301 A 1 
HETATM 48 N N1 LBM . A . B 2 -16.596 3.883 -12.509 0.92 31.5 ? N1 LBM 301 A 1 
HETATM 49 N N2 LBM . A . B 2 -17.464 5.463 -6.336 0.92 32.83 ? N2 LBM 301 A 1 
HETATM 50 N N3 LBM . A . B 2 -16.239 0.024 -2.919 0.92 28.29 ? N3 LBM 301 A 1 
HETATM 51 N N4 LBM . A . B 2 -14.137 2.054 -3.238 0.92 28.92 ? N4 LBM 301 A 1 
HETATM 52 N N5 LBM . A . B 2 -18.071 -0.83 -6.777 0.92 26.4 ? N5 LBM 301 A 1 
HETATM 53 N N6 LBM . A . B 2 -15.907 -1.486 -5.885 0.92 28.6 ? N6 LBM 301 A 1 
HETATM 54 O O1 LBM . A . B 2 -18.968 5.781 -4.394 0.92 33.08 ? O1 LBM 301 A 1 
HETATM 55 O O2 LBM . A . B 2 -16.583 6.42 -4.236 0.92 31.12 ? O2 LBM 301 A 1 
HETATM 56 O O3 LBM . A . B 2 -15.793 -4.774 -1.29 0.92 48.92 ? O3 LBM 301 A 1 
HETATM 57 O O4 LBM . A . B 2 -13.804 0.948 -2.842 0.92 26.15 ? O4 LBM 301 A 1 
HETATM 58 O O5 LBM . A . B 2 -13.344 2.961 -3.447 0.92 29.31 ? O5 LBM 301 A 1 
HETATM 59 O O6 LBM . A . B 2 -18.823 2.274 -8.549 0.92 26.59 ? O6 LBM 301 A 1 
HETATM 60 S S LBM . A . B 2 -17.594 5.521 -4.702 0.92 29.8 ? S LBM 301 A 1 
HETATM 61 CL CL LBM . A . B 2 -10.054 -0.711 -15.949 0.92 43.24 ? CL LBM 301 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           240 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           61 
#