data_4JVB # _model_server_result.job_id QZrtYEdZ1noVI8Q5J1UiVA _model_server_result.datetime_utc '2025-09-10 02:59:44' _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 4jvb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4JVB # _exptl.entry_id 4JVB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 560.687 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-benzyl-2-(4-{[(2R)-2-(2-phenyl-1H-benzimidazol-1-yl)pent-4-en-1-yl]oxy}phenyl)-1H-benzimidazole _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 120 _cell.entry_id 4JVB _cell.length_a 55.68 _cell.length_b 55.68 _cell.length_c 116.55 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4JVB _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _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 _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 'C38 H32 N4 O' _chem_comp.formula_weight 560.687 _chem_comp.id 1M0 _chem_comp.mon_nstd_flag . _chem_comp.name 1-benzyl-2-(4-{[(2R)-2-(2-phenyl-1H-benzimidazol-1-yl)pent-4-en-1-yl]oxy}phenyl)-1H-benzimidazole _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 CAC CAB 1M0 doub 1 n y CAC CAD 1M0 sing 2 n y CAB CAA 1M0 sing 3 n y NAG CAD 1M0 sing 4 n y NAG CAH 1M0 doub 5 n y CAD CAE 1M0 doub 6 n y CAP CAO 1M0 doub 7 n y CAP CAK 1M0 sing 8 n y CAO CAN 1M0 sing 9 n y CAH CAK 1M0 sing 10 n n CAH NAI 1M0 sing 11 n y CBL CBK 1M0 doub 12 n y CBL CBM 1M0 sing 13 n y CAK CAL 1M0 doub 14 n y CAA CAF 1M0 doub 15 n y CAE CAF 1M0 sing 16 n y CAE NAI 1M0 sing 17 n y CAN CAM 1M0 doub 18 n y CBK CBI 1M0 sing 19 n y CAL CAM 1M0 sing 20 n y CBM CBN 1M0 doub 21 n y NAI CAJ 1M0 sing 22 n n CBI CBH 1M0 sing 23 n n CBI CBO 1M0 doub 24 n y CBN CBO 1M0 sing 25 n y CAJ CBJ 1M0 sing 26 n n CAJ CAQ 1M0 sing 27 n n CBJ CBP 1M0 sing 28 n n CBH NBC 1M0 sing 29 n n CBP CBQ 1M0 doub 30 n n CAQ OAR 1M0 sing 31 n n OAR CAS 1M0 sing 32 n n NBC CBB 1M0 sing 33 n y NBC CAY 1M0 sing 34 n y CAS CAT 1M0 doub 35 n y CAS CAX 1M0 sing 36 n y CAT CAU 1M0 sing 37 n y CBG CBB 1M0 doub 38 n y CBG CBF 1M0 sing 39 n y CAX CAW 1M0 doub 40 n y CAU CAV 1M0 doub 41 n y CBB CBA 1M0 sing 42 n y CAW CAV 1M0 sing 43 n y CAV CAY 1M0 sing 44 n n CBF CBE 1M0 doub 45 n y CAY NAZ 1M0 doub 46 n y CBA NAZ 1M0 sing 47 n y CBA CBD 1M0 doub 48 n y CBE CBD 1M0 sing 49 n y CBK H1 1M0 sing 50 n n CBL H2 1M0 sing 51 n n CBM H3 1M0 sing 52 n n CBN H4 1M0 sing 53 n n CBO H5 1M0 sing 54 n n CBH H6 1M0 sing 55 n n CBH H7 1M0 sing 56 n n CBG H8 1M0 sing 57 n n CBF H9 1M0 sing 58 n n CBE H10 1M0 sing 59 n n CBD H11 1M0 sing 60 n n CAU H12 1M0 sing 61 n n CAT H13 1M0 sing 62 n n CAW H14 1M0 sing 63 n n CAX H15 1M0 sing 64 n n CAQ H16 1M0 sing 65 n n CAQ H17 1M0 sing 66 n n CAJ H18 1M0 sing 67 n n CBJ H19 1M0 sing 68 n n CBJ H20 1M0 sing 69 n n CBP H21 1M0 sing 70 n n CBQ H23 1M0 sing 71 n n CBQ H24 1M0 sing 72 n n CAF H26 1M0 sing 73 n n CAA H27 1M0 sing 74 n n CAB H28 1M0 sing 75 n n CAC H29 1M0 sing 76 n n CAL H30 1M0 sing 77 n n CAM H31 1M0 sing 78 n n CAN H32 1M0 sing 79 n n CAO H33 1M0 sing 80 n n CAP H34 1M0 sing 81 n n # _atom_sites.entry_id 4JVB _atom_sites.fract_transf_matrix[1][1] 0.01796 _atom_sites.fract_transf_matrix[1][2] 0.010369 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020738 _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] 0.00858 _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 1M0 B 1 201 1 1M0 1M0 . C 3 HOH B 1 301 301 HOH HOH . C 3 HOH B 2 302 302 HOH HOH . C 3 HOH B 3 303 303 HOH HOH . C 3 HOH B 4 304 304 HOH HOH . C 3 HOH B 5 305 305 HOH HOH . C 3 HOH B 6 306 306 HOH HOH . C 3 HOH B 7 307 307 HOH HOH . C 3 HOH B 8 308 308 HOH HOH . C 3 HOH B 9 309 309 HOH HOH . C 3 HOH B 10 310 310 HOH HOH . C 3 HOH B 11 311 311 HOH HOH . C 3 HOH B 12 312 312 HOH HOH . C 3 HOH B 13 313 313 HOH HOH . C 3 HOH B 14 314 314 HOH HOH . C 3 HOH B 15 315 315 HOH HOH . C 3 HOH B 16 316 316 HOH HOH . C 3 HOH B 17 317 317 HOH HOH . C 3 HOH B 18 318 318 HOH HOH . C 3 HOH B 19 319 319 HOH HOH . C 3 HOH B 20 320 320 HOH HOH . C 3 HOH B 21 321 321 HOH HOH . C 3 HOH B 22 322 322 HOH HOH . C 3 HOH B 23 323 323 HOH HOH . C 3 HOH B 24 324 324 HOH HOH . C 3 HOH B 25 325 325 HOH HOH . C 3 HOH B 26 326 327 HOH HOH . C 3 HOH B 27 327 328 HOH HOH . C 3 HOH B 28 328 329 HOH HOH . C 3 HOH B 29 329 331 HOH HOH . C 3 HOH B 30 330 332 HOH HOH . C 3 HOH B 31 331 333 HOH HOH . C 3 HOH B 32 332 334 HOH HOH . C 3 HOH B 33 333 335 HOH HOH . C 3 HOH B 34 334 336 HOH HOH . C 3 HOH B 35 335 337 HOH HOH . C 3 HOH B 36 336 338 HOH HOH . C 3 HOH B 37 337 339 HOH HOH . C 3 HOH B 38 338 340 HOH HOH . C 3 HOH B 39 339 341 HOH HOH . C 3 HOH B 40 340 342 HOH HOH . C 3 HOH B 41 341 343 HOH HOH . C 3 HOH B 42 342 344 HOH HOH . C 3 HOH B 43 343 345 HOH HOH . C 3 HOH B 44 344 346 HOH HOH . C 3 HOH B 45 345 347 HOH HOH . C 3 HOH B 46 346 348 HOH HOH . C 3 HOH B 47 347 349 HOH HOH . C 3 HOH B 48 348 350 HOH HOH . C 3 HOH B 49 349 351 HOH HOH . C 3 HOH B 50 350 352 HOH HOH . C 3 HOH B 51 351 353 HOH HOH . C 3 HOH B 52 352 354 HOH HOH . C 3 HOH B 53 353 355 HOH HOH . C 3 HOH B 54 354 356 HOH HOH . C 3 HOH B 55 355 357 HOH HOH . C 3 HOH B 56 356 358 HOH HOH . C 3 HOH B 57 357 359 HOH HOH . C 3 HOH B 58 358 360 HOH HOH . C 3 HOH B 59 359 361 HOH HOH . C 3 HOH B 60 360 362 HOH HOH . C 3 HOH B 61 361 363 HOH HOH . C 3 HOH B 62 362 364 HOH HOH . C 3 HOH B 63 363 365 HOH HOH . C 3 HOH B 64 364 366 HOH HOH . C 3 HOH B 65 365 367 HOH HOH . C 3 HOH B 66 366 368 HOH HOH . C 3 HOH B 67 367 369 HOH HOH . C 3 HOH B 68 368 370 HOH HOH . C 3 HOH B 69 369 372 HOH HOH . C 3 HOH B 70 370 373 HOH HOH . C 3 HOH B 71 371 374 HOH HOH . C 3 HOH B 72 372 375 HOH HOH . C 3 HOH B 73 373 376 HOH HOH . C 3 HOH B 74 374 377 HOH HOH . C 3 HOH B 75 375 378 HOH HOH . C 3 HOH B 76 376 379 HOH HOH . C 3 HOH B 77 377 380 HOH HOH . C 3 HOH B 78 378 381 HOH HOH . C 3 HOH B 79 379 382 HOH HOH . C 3 HOH B 80 380 383 HOH HOH . C 3 HOH B 81 381 385 HOH HOH . C 3 HOH B 82 382 386 HOH HOH . C 3 HOH B 83 383 387 HOH HOH . C 3 HOH B 84 384 388 HOH HOH . C 3 HOH B 85 385 389 HOH HOH . C 3 HOH B 86 386 390 HOH HOH . C 3 HOH B 87 387 391 HOH HOH . C 3 HOH B 88 388 392 HOH HOH . C 3 HOH B 89 389 393 HOH HOH . C 3 HOH B 90 390 394 HOH HOH . C 3 HOH B 91 391 395 HOH HOH . C 3 HOH B 92 392 396 HOH HOH . C 3 HOH B 93 393 398 HOH HOH . C 3 HOH B 94 394 399 HOH HOH . C 3 HOH B 95 395 400 HOH HOH . C 3 HOH B 96 396 401 HOH HOH . C 3 HOH B 97 397 403 HOH HOH . C 3 HOH B 98 398 404 HOH HOH . C 3 HOH B 99 399 405 HOH HOH . C 3 HOH B 100 400 406 HOH HOH . C 3 HOH B 101 401 408 HOH HOH . C 3 HOH B 102 402 409 HOH HOH . C 3 HOH B 103 403 410 HOH HOH . C 3 HOH B 104 404 411 HOH HOH . C 3 HOH B 105 405 412 HOH HOH . C 3 HOH B 106 406 413 HOH HOH . C 3 HOH B 107 407 414 HOH HOH . C 3 HOH B 108 408 415 HOH HOH . C 3 HOH B 109 409 416 HOH HOH . C 3 HOH B 110 410 417 HOH HOH . C 3 HOH B 111 411 418 HOH HOH . C 3 HOH B 112 412 419 HOH HOH . C 3 HOH B 113 413 420 HOH HOH . C 3 HOH B 114 414 421 HOH HOH . C 3 HOH B 115 415 422 HOH HOH . C 3 HOH B 116 416 423 HOH HOH . C 3 HOH B 117 417 424 HOH HOH . C 3 HOH B 118 418 425 HOH HOH . C 3 HOH B 119 419 426 HOH HOH . C 3 HOH B 120 420 428 HOH HOH . C 3 HOH B 121 421 430 HOH HOH . C 3 HOH B 122 422 431 HOH HOH . C 3 HOH B 123 423 432 HOH HOH . C 3 HOH B 124 424 433 HOH HOH . C 3 HOH B 125 425 434 HOH HOH . C 3 HOH B 126 426 435 HOH HOH . C 3 HOH B 127 427 436 HOH HOH . C 3 HOH B 128 428 437 HOH HOH . C 3 HOH B 129 429 438 HOH HOH . C 3 HOH B 130 430 439 HOH HOH . C 3 HOH B 131 431 440 HOH HOH . C 3 HOH B 132 432 441 HOH HOH . C 3 HOH B 133 433 442 HOH HOH . C 3 HOH B 134 434 443 HOH HOH . C 3 HOH B 135 435 444 HOH HOH . C 3 HOH B 136 436 445 HOH HOH . C 3 HOH B 137 437 446 HOH HOH . C 3 HOH B 138 438 447 HOH HOH . C 3 HOH B 139 439 448 HOH HOH . C 3 HOH B 140 440 449 HOH HOH . C 3 HOH B 141 441 450 HOH HOH . C 3 HOH B 142 442 451 HOH HOH . C 3 HOH B 143 443 452 HOH HOH . C 3 HOH B 144 444 453 HOH HOH . C 3 HOH B 145 445 454 HOH HOH . C 3 HOH B 146 446 455 HOH HOH . C 3 HOH B 147 447 456 HOH HOH . C 3 HOH B 148 448 457 HOH HOH . C 3 HOH B 149 449 458 HOH HOH . C 3 HOH B 150 450 459 HOH HOH . C 3 HOH B 151 451 462 HOH HOH . C 3 HOH B 152 452 463 HOH HOH . C 3 HOH B 153 453 468 HOH HOH . C 3 HOH B 154 454 469 HOH HOH . C 3 HOH B 155 455 471 HOH HOH . C 3 HOH B 156 456 472 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 CBK 1M0 . . . B 2 24.604 -8.672 -16.376 1 30 ? CBK 1M0 201 B 1 HETATM 2 C CBL 1M0 . . . B 2 23.903 -9.719 -16.984 1 31.57 ? CBL 1M0 201 B 1 HETATM 3 C CBM 1M0 . . . B 2 23.359 -10.825 -16.31 1 22.8 ? CBM 1M0 201 B 1 HETATM 4 C CBN 1M0 . . . B 2 23.591 -10.823 -14.91 1 26.62 ? CBN 1M0 201 B 1 HETATM 5 C CBO 1M0 . . . B 2 24.246 -9.72 -14.319 1 25.97 ? CBO 1M0 201 B 1 HETATM 6 C CBI 1M0 . . . B 2 24.763 -8.655 -14.991 1 21.8 ? CBI 1M0 201 B 1 HETATM 7 C CBH 1M0 . . . B 2 25.508 -7.551 -14.368 1 26.03 ? CBH 1M0 201 B 1 HETATM 8 N NBC 1M0 . . . B 2 25.582 -7.832 -12.89 1 27.28 ? NBC 1M0 201 B 1 HETATM 9 C CBB 1M0 . . . B 2 26.606 -8.547 -12.302 1 24.91 ? CBB 1M0 201 B 1 HETATM 10 C CBG 1M0 . . . B 2 27.765 -9.069 -12.788 1 25.21 ? CBG 1M0 201 B 1 HETATM 11 C CBF 1M0 . . . B 2 28.687 -9.738 -11.93 1 27.49 ? CBF 1M0 201 B 1 HETATM 12 C CBE 1M0 . . . B 2 28.305 -9.834 -10.568 1 31 ? CBE 1M0 201 B 1 HETATM 13 C CBD 1M0 . . . B 2 27.101 -9.258 -10.087 1 28.49 ? CBD 1M0 201 B 1 HETATM 14 C CBA 1M0 . . . B 2 26.276 -8.635 -10.959 1 29.06 ? CBA 1M0 201 B 1 HETATM 15 N NAZ 1M0 . . . B 2 25.078 -7.992 -10.742 1 30.95 ? NAZ 1M0 201 B 1 HETATM 16 C CAY 1M0 . . . B 2 24.64 -7.53 -11.921 1 33.91 ? CAY 1M0 201 B 1 HETATM 17 C CAV 1M0 . . . B 2 23.497 -6.838 -12.198 1 28.82 ? CAV 1M0 201 B 1 HETATM 18 C CAU 1M0 . . . B 2 22.226 -7.353 -12.484 1 42.86 ? CAU 1M0 201 B 1 HETATM 19 C CAT 1M0 . . . B 2 21.174 -6.422 -12.833 1 49.61 ? CAT 1M0 201 B 1 HETATM 20 C CAW 1M0 . . . B 2 23.635 -5.466 -12.262 1 30.88 ? CAW 1M0 201 B 1 HETATM 21 C CAX 1M0 . . . B 2 22.638 -4.561 -12.558 1 35.78 ? CAX 1M0 201 B 1 HETATM 22 C CAS 1M0 . . . B 2 21.391 -5.024 -12.87 1 45.91 ? CAS 1M0 201 B 1 HETATM 23 O OAR 1M0 . . . B 2 20.591 -3.929 -13.221 1 55.28 ? OAR 1M0 201 B 1 HETATM 24 C CAQ 1M0 . . . B 2 19.233 -3.668 -13.304 1 56.11 ? CAQ 1M0 201 B 1 HETATM 25 C CAJ 1M0 . . . B 2 18.553 -3.857 -14.674 1 46.67 ? CAJ 1M0 201 B 1 HETATM 26 C CBJ 1M0 . . . B 2 17.057 -3.526 -14.444 1 54.84 ? CBJ 1M0 201 B 1 HETATM 27 C CBP 1M0 . . . B 2 16.84 -2.441 -13.366 1 71.22 ? CBP 1M0 201 B 1 HETATM 28 C CBQ 1M0 . . . B 2 15.927 -2.994 -12.248 1 69.09 ? CBQ 1M0 201 B 1 HETATM 29 N NAI 1M0 . . . B 2 19.016 -3.184 -16.024 1 38.34 ? NAI 1M0 201 B 1 HETATM 30 C CAE 1M0 . . . B 2 19.053 -1.921 -16.55 1 38.31 ? CAE 1M0 201 B 1 HETATM 31 C CAF 1M0 . . . B 2 18.804 -0.697 -16.053 1 36.51 ? CAF 1M0 201 B 1 HETATM 32 C CAA 1M0 . . . B 2 18.933 0.473 -16.815 1 38.2 ? CAA 1M0 201 B 1 HETATM 33 C CAB 1M0 . . . B 2 19.387 0.421 -18.149 1 36.11 ? CAB 1M0 201 B 1 HETATM 34 C CAC 1M0 . . . B 2 19.679 -0.884 -18.601 1 38.19 ? CAC 1M0 201 B 1 HETATM 35 C CAD 1M0 . . . B 2 19.507 -1.998 -17.839 1 39.6 ? CAD 1M0 201 B 1 HETATM 36 N NAG 1M0 . . . B 2 19.733 -3.3 -18.102 1 32.17 ? NAG 1M0 201 B 1 HETATM 37 C CAH 1M0 . . . B 2 19.385 -3.997 -17.03 1 38.23 ? CAH 1M0 201 B 1 HETATM 38 C CAK 1M0 . . . B 2 19.542 -5.316 -16.907 1 46.71 ? CAK 1M0 201 B 1 HETATM 39 C CAL 1M0 . . . B 2 20.748 -5.728 -16.358 1 58.57 ? CAL 1M0 201 B 1 HETATM 40 C CAM 1M0 . . . B 2 21.059 -7.068 -16.156 1 64.71 ? CAM 1M0 201 B 1 HETATM 41 C CAN 1M0 . . . B 2 20.124 -8.008 -16.514 1 62.97 ? CAN 1M0 201 B 1 HETATM 42 C CAO 1M0 . . . B 2 18.915 -7.602 -17.06 1 61.59 ? CAO 1M0 201 B 1 HETATM 43 C CAP 1M0 . . . B 2 18.613 -6.258 -17.258 1 61.33 ? CAP 1M0 201 B 1 # _model_server_stats.io_time_ms 66 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 43 #