data_6O0L
#
_model_server_result.job_id            QYRJ4iQelr4PnK8R8AfBXQ 
_model_server_result.datetime_utc      '2024-12-27 15:57:07' 
_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          6o0l 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":301}' 
#
_entry.id    6O0L 
#
_exptl.entry_id    6O0L 
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90.08 
_cell.angle_gamma         90 
_cell.entry_id            6O0L 
_cell.length_a            33.147 
_cell.length_b            82.005 
_cell.length_c            47.508 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6O0L 
_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,D,E,F,K 1 1 
B,G,H,I,J,L 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 
#
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 G N 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                     6O0L 
_atom_sites.fract_transf_matrix[1][1]    0.030169 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000043 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012194 
_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]    0.021049 
_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 LBM A 1 301 1 LBM 199 . 
D 3 PEG A 1 302 3 PEG PEG . 
E 3 PEG A 1 303 4 PEG PEG . 
F 4 CL A 1 304 2 CL CL . 
G 2 LBM C 1 301 1 LBM 199 . 
H 3 PEG C 1 302 1 PEG PEG . 
I 3 PEG C 1 303 2 PEG PEG . 
J 4 CL C 1 304 1 CL CL . 
K 5 HOH A 1 401 13 HOH HOH . 
K 5 HOH A 2 402 4 HOH HOH . 
K 5 HOH A 3 403 34 HOH HOH . 
K 5 HOH A 4 404 16 HOH HOH . 
K 5 HOH A 5 405 11 HOH HOH . 
K 5 HOH A 6 406 6 HOH HOH . 
K 5 HOH A 7 407 10 HOH HOH . 
K 5 HOH A 8 408 7 HOH HOH . 
K 5 HOH A 9 409 19 HOH HOH . 
K 5 HOH A 10 410 25 HOH HOH . 
L 5 HOH C 1 401 5 HOH HOH . 
L 5 HOH C 2 402 15 HOH HOH . 
L 5 HOH C 3 403 2 HOH HOH . 
L 5 HOH C 4 404 24 HOH HOH . 
L 5 HOH C 5 405 3 HOH HOH . 
L 5 HOH C 6 406 9 HOH HOH . 
L 5 HOH C 7 407 22 HOH HOH . 
L 5 HOH C 8 408 14 HOH HOH . 
L 5 HOH C 9 409 23 HOH HOH . 
L 5 HOH C 10 410 1 HOH HOH . 
L 5 HOH C 11 411 26 HOH HOH . 
L 5 HOH C 12 412 21 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 . . . C 2 -5.065 17.922 -1.326 1 36.09 ? C11 LBM 301 A 1 
HETATM 2 C C12 LBM . . . C 2 -5.795 18.427 -0.267 1 38.45 ? C12 LBM 301 A 1 
HETATM 3 C C13 LBM . . . C 2 -8.424 16.944 1.572 1 46.5 ? C13 LBM 301 A 1 
HETATM 4 C C14 LBM . . . C 2 -8.052 14.91 2.832 1 41.71 ? C14 LBM 301 A 1 
HETATM 5 C C15 LBM . . . C 2 -8.719 13.787 3.608 1 43.43 ? C15 LBM 301 A 1 
HETATM 6 C C16 LBM . . . C 2 -10.668 14.003 2.195 1 45.12 ? C16 LBM 301 A 1 
HETATM 7 C C17 LBM . . . C 2 -9.979 15.112 1.432 1 43.83 ? C17 LBM 301 A 1 
HETATM 8 C C19 LBM . . . C 2 -10.824 11.042 2.147 1 40.09 ? C19 LBM 301 A 1 
HETATM 9 C C20 LBM . . . C 2 -11.26 9.773 2.47 1 41.32 ? C20 LBM 301 A 1 
HETATM 10 C C22 LBM . . . C 2 -10.268 9.965 4.63 1 41.08 ? C22 LBM 301 A 1 
HETATM 11 C C23 LBM . . . C 2 -9.829 11.24 4.315 1 50.83 ? C23 LBM 301 A 1 
HETATM 12 C C24 LBM . . . C 2 -11.428 7.831 4.132 1 46.23 ? C24 LBM 301 A 1 
HETATM 13 C C25 LBM . . . C 2 -10.33 4.706 3.566 1 36.21 ? C25 LBM 301 A 1 
HETATM 14 C C26 LBM . . . C 2 -9.015 4.417 3.245 1 34.83 ? C26 LBM 301 A 1 
HETATM 15 C C28 LBM . . . C 2 -9.754 3.626 1.047 1 34.87 ? C28 LBM 301 A 1 
HETATM 16 C C29 LBM . . . C 2 -11.061 3.921 1.432 1 37.04 ? C29 LBM 301 A 1 
HETATM 17 C C31 LBM . . . C 2 -10.496 2.838 -1.209 1 46.03 ? C31 LBM 301 A 1 
HETATM 18 N N LBM . . . C 2 -9.055 15.845 2.303 1 46.79 ? N LBM 301 A 1 
HETATM 19 C C LBM . . . C 2 -5.958 21.221 4.637 1 44.26 ? C LBM 301 A 1 
HETATM 20 O O LBM . . . C 2 -12.515 7.368 3.802 1 43.54 ? O LBM 301 A 1 
HETATM 21 C C1 LBM . . . C 2 -6.346 19.801 4.225 1 46.46 ? C1 LBM 301 A 1 
HETATM 22 C C10 LBM . . . C 2 -4.286 16.795 -1.158 1 35.21 ? C10 LBM 301 A 1 
HETATM 23 C C18 LBM . . . C 2 -10.101 11.799 3.069 1 42.36 ? C18 LBM 301 A 1 
HETATM 24 C C2 LBM . . . C 2 -7.871 19.646 4.245 1 50.26 ? C2 LBM 301 A 1 
HETATM 25 C C21 LBM . . . C 2 -10.993 9.203 3.715 1 46.53 ? C21 LBM 301 A 1 
HETATM 26 C C27 LBM . . . C 2 -8.734 3.889 2.002 1 36.77 ? C27 LBM 301 A 1 
HETATM 27 C C3 LBM . . . C 2 -8.348 18.264 3.805 1 41.51 ? C3 LBM 301 A 1 
HETATM 28 C C30 LBM . . . C 2 -11.357 4.454 2.675 1 41.77 ? C30 LBM 301 A 1 
HETATM 29 C C32 LBM . . . C 2 -10.033 1.711 -2.115 1 50.42 ? C32 LBM 301 A 1 
HETATM 30 C C33 LBM . . . C 2 -11.075 1.395 -3.182 1 51.96 ? C33 LBM 301 A 1 
HETATM 31 C C34 LBM . . . C 2 -10.547 0.344 -4.124 1 53.45 ? C34 LBM 301 A 1 
HETATM 32 C C35 LBM . . . C 2 -8.328 0.968 -3.762 1 55.14 ? C35 LBM 301 A 1 
HETATM 33 C C36 LBM . . . C 2 -8.714 2.059 -2.795 1 49.58 ? C36 LBM 301 A 1 
HETATM 34 C C37 LBM . . . C 2 -11.32 8.264 0.613 1 33.42 ? C37 LBM 301 A 1 
HETATM 35 C C38 LBM . . . C 2 -11.992 7.754 -0.487 1 32.71 ? C38 LBM 301 A 1 
HETATM 36 C C39 LBM . . . C 2 -10.095 6.718 -1.243 1 26.2 ? C39 LBM 301 A 1 
HETATM 37 C C4 LBM . . . C 2 -7.7 17.871 2.506 1 39.87 ? C4 LBM 301 A 1 
HETATM 38 C C40 LBM . . . C 2 -9.318 7.198 -0.152 1 27.88 ? C40 LBM 301 A 1 
HETATM 39 C C41 LBM . . . C 2 -9.973 7.991 0.789 1 28.02 ? C41 LBM 301 A 1 
HETATM 40 C C42 LBM . . . C 2 -8.002 6.673 -0.345 1 38.56 ? C42 LBM 301 A 1 
HETATM 41 C C43 LBM . . . C 2 -8.03 5.934 -1.484 1 38.57 ? C43 LBM 301 A 1 
HETATM 42 C C44 LBM . . . C 2 -5.707 18.805 5.192 1 44.83 ? C44 LBM 301 A 1 
HETATM 43 C C5 LBM . . . C 2 -6.499 18.356 2.122 1 39.48 ? C5 LBM 301 A 1 
HETATM 44 C C6 LBM . . . C 2 -5.856 19.525 2.801 1 43.89 ? C6 LBM 301 A 1 
HETATM 45 C C7 LBM . . . C 2 -5.744 17.801 0.968 1 36.59 ? C7 LBM 301 A 1 
HETATM 46 C C8 LBM . . . C 2 -4.968 16.662 1.135 1 28.55 ? C8 LBM 301 A 1 
HETATM 47 C C9 LBM . . . C 2 -4.242 16.164 0.068 1 30.38 ? C9 LBM 301 A 1 
HETATM 48 N N1 LBM . . . C 2 -9.677 13.083 2.754 1 45.43 ? N1 LBM 301 A 1 
HETATM 49 N N2 LBM . . . C 2 -10.525 7.082 4.871 1 37.78 ? N2 LBM 301 A 1 
HETATM 50 N N3 LBM . . . C 2 -9.486 3.12 -0.203 1 44.98 ? N3 LBM 301 A 1 
HETATM 51 N N4 LBM . . . C 2 -7.323 3.628 1.722 1 44.83 ? N4 LBM 301 A 1 
HETATM 52 N N5 LBM . . . C 2 -11.402 6.987 -1.414 1 40.25 ? N5 LBM 301 A 1 
HETATM 53 N N6 LBM . . . C 2 -9.291 5.955 -2.035 1 30.22 ? N6 LBM 301 A 1 
HETATM 54 O O1 LBM . . . C 2 -12.05 5.204 5.446 1 37.4 ? O1 LBM 301 A 1 
HETATM 55 O O2 LBM . . . C 2 -9.652 5.088 6.041 1 38.78 ? O2 LBM 301 A 1 
HETATM 56 O O3 LBM . . . C 2 -9.339 0.77 -4.745 1 55.18 ? O3 LBM 301 A 1 
HETATM 57 O O4 LBM . . . C 2 -7.001 3.341 0.579 1 42.4 ? O4 LBM 301 A 1 
HETATM 58 O O5 LBM . . . C 2 -6.525 3.707 2.645 1 45.49 ? O5 LBM 301 A 1 
HETATM 59 O O6 LBM . . . C 2 -12.001 9.04 1.551 1 44.86 ? O6 LBM 301 A 1 
HETATM 60 S S LBM . . . C 2 -10.68 5.463 5.121 1 40.44 ? S LBM 301 A 1 
HETATM 61 CL CL LBM . . . C 2 -3.349 16.178 -2.489 1 51.14 ? CL LBM 301 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           296 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           61 
#