data_3S2O # _model_server_result.job_id YqzugCsU33B0JFDE8a02sA _model_server_result.datetime_utc '2024-11-25 09:05:40' _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 3s2o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":393}' # _entry.id 3S2O # _exptl.entry_id 3S2O _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 400.945 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (3S)-3-(2-amino-5-chloro-1H-benzimidazol-1-yl)-N-[(1R,3S,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-2-yl]pentanamide _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 3S2O _cell.length_a 101.88 _cell.length_b 101.88 _cell.length_c 170.181 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3S2O _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _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 _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 # 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 171 A CYS 155 1_555 A SG CYS 375 A CYS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? disulf ? disulf2 A SG CYS 233 A CYS 217 1_555 A SG CYS 398 A CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 A SG CYS 285 A CYS 269 1_555 A SG CYS 335 A CYS 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? # _chem_comp.formula 'C22 H29 Cl N4 O' _chem_comp.formula_weight 400.945 _chem_comp.id EV6 _chem_comp.mon_nstd_flag . _chem_comp.name (3S)-3-(2-amino-5-chloro-1H-benzimidazol-1-yl)-N-[(1R,3S,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-2-yl]pentanamide _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 N9 C1 EV6 sing 83 n y C6 C1 EV6 doub 84 n y C1 C2 EV6 sing 85 n y C2 C3 EV6 doub 86 n y C2 H2 EV6 sing 87 n n C4 C3 EV6 sing 88 n y C3 H3 EV6 sing 89 n n C5 C4 EV6 doub 90 n y C4 CL11 EV6 sing 91 n n C6 C5 EV6 sing 92 n y C5 H5 EV6 sing 93 n n N7 C6 EV6 sing 94 n y C8 N7 EV6 doub 95 n y N10 C8 EV6 sing 96 n n C8 N9 EV6 sing 97 n y N9 C12 EV6 sing 98 n n N10 HN10 EV6 sing 99 n n N10 HN1A EV6 sing 100 n n C15 C12 EV6 sing 101 n n C13 C12 EV6 sing 102 n n C12 H12 EV6 sing 103 n n C13 C14 EV6 sing 104 n n C13 H13 EV6 sing 105 n n C13 H13A EV6 sing 106 n n C14 H14 EV6 sing 107 n n C14 H14A EV6 sing 108 n n C14 H14B EV6 sing 109 n n C15 C16 EV6 sing 110 n n C15 H15 EV6 sing 111 n n C15 H15A EV6 sing 112 n n N17 C16 EV6 sing 113 n n C16 O18 EV6 doub 114 n n N17 C19 EV6 sing 115 n n N17 HN17 EV6 sing 116 n n C20 C19 EV6 sing 117 n n C19 C26 EV6 sing 118 n n C19 H19 EV6 sing 119 n n C25 C20 EV6 sing 120 n n C20 C21 EV6 sing 121 n n C20 H20 EV6 sing 122 n n C21 C22 EV6 sing 123 n n C21 H21 EV6 sing 124 n n C21 H21A EV6 sing 125 n n C23 C22 EV6 sing 126 n n C22 C28 EV6 sing 127 n n C22 H22 EV6 sing 128 n n C24 C23 EV6 sing 129 n n C23 H23 EV6 sing 130 n n C23 H23A EV6 sing 131 n n C25 C24 EV6 sing 132 n n C24 C27 EV6 sing 133 n n C24 H24 EV6 sing 134 n n C25 H25 EV6 sing 135 n n C25 H25A EV6 sing 136 n n C27 C26 EV6 sing 137 n n C26 C28 EV6 sing 138 n n C26 H26 EV6 sing 139 n n C27 H27 EV6 sing 140 n n C27 H27A EV6 sing 141 n n C28 H28 EV6 sing 142 n n C28 H28A EV6 sing 143 n n # _atom_sites.entry_id 3S2O _atom_sites.fract_transf_matrix[1][1] 0.009815 _atom_sites.fract_transf_matrix[1][2] 0.005667 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011334 _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] 0.005876 _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 EV6 A 1 393 393 EV6 EV6 . C 3 IOD A 1 394 394 IOD IOD . D 3 IOD A 1 395 395 IOD IOD . E 4 HOH A 1 396 396 HOH HOH . E 4 HOH A 2 397 397 HOH HOH . E 4 HOH A 3 398 398 HOH HOH . E 4 HOH A 4 399 399 HOH HOH . E 4 HOH A 5 400 400 HOH HOH . E 4 HOH A 6 401 401 HOH HOH . E 4 HOH A 7 402 402 HOH HOH . E 4 HOH A 8 403 403 HOH HOH . E 4 HOH A 9 404 404 HOH HOH . E 4 HOH A 10 405 405 HOH HOH . E 4 HOH A 11 406 406 HOH HOH . E 4 HOH A 12 407 407 HOH HOH . E 4 HOH A 13 408 408 HOH HOH . E 4 HOH A 14 409 409 HOH HOH . E 4 HOH A 15 410 410 HOH HOH . E 4 HOH A 16 411 411 HOH HOH . E 4 HOH A 17 412 412 HOH HOH . E 4 HOH A 18 413 413 HOH HOH . E 4 HOH A 19 414 414 HOH HOH . E 4 HOH A 20 415 415 HOH HOH . E 4 HOH A 21 416 416 HOH HOH . E 4 HOH A 22 417 417 HOH HOH . E 4 HOH A 23 418 418 HOH HOH . E 4 HOH A 24 419 419 HOH HOH . E 4 HOH A 25 420 420 HOH HOH . E 4 HOH A 26 421 421 HOH HOH . E 4 HOH A 27 422 422 HOH HOH . E 4 HOH A 28 423 423 HOH HOH . E 4 HOH A 29 424 424 HOH HOH . E 4 HOH A 30 425 425 HOH HOH . E 4 HOH A 31 426 426 HOH HOH . E 4 HOH A 32 427 427 HOH HOH . E 4 HOH A 33 428 428 HOH HOH . E 4 HOH A 34 429 429 HOH HOH . E 4 HOH A 35 430 430 HOH HOH . E 4 HOH A 36 431 431 HOH HOH . E 4 HOH A 37 432 432 HOH HOH . E 4 HOH A 38 433 433 HOH HOH . E 4 HOH A 39 434 434 HOH HOH . E 4 HOH A 40 435 435 HOH HOH . E 4 HOH A 41 436 436 HOH HOH . E 4 HOH A 42 437 437 HOH HOH . E 4 HOH A 43 438 438 HOH HOH . E 4 HOH A 44 439 439 HOH HOH . E 4 HOH A 45 440 440 HOH HOH . E 4 HOH A 46 441 441 HOH HOH . E 4 HOH A 47 442 442 HOH HOH . E 4 HOH A 48 443 443 HOH HOH . E 4 HOH A 49 444 444 HOH HOH . E 4 HOH A 50 445 445 HOH HOH . E 4 HOH A 51 446 446 HOH HOH . E 4 HOH A 52 447 447 HOH HOH . E 4 HOH A 53 448 448 HOH HOH . E 4 HOH A 54 449 449 HOH HOH . E 4 HOH A 55 450 450 HOH HOH . E 4 HOH A 56 451 451 HOH HOH . E 4 HOH A 57 452 452 HOH HOH . E 4 HOH A 58 453 453 HOH HOH . E 4 HOH A 59 454 454 HOH HOH . E 4 HOH A 60 455 455 HOH HOH . E 4 HOH A 61 456 456 HOH HOH . E 4 HOH A 62 457 457 HOH HOH . E 4 HOH A 63 458 458 HOH HOH . E 4 HOH A 64 459 459 HOH HOH . E 4 HOH A 65 460 460 HOH HOH . E 4 HOH A 66 461 461 HOH HOH . E 4 HOH A 67 462 462 HOH HOH . E 4 HOH A 68 463 463 HOH HOH . E 4 HOH A 69 464 464 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 EV6 . . . B 2 -15.965 39.738 9.574 1 34.6 ? C1 EV6 393 A 1 HETATM 2 C C2 EV6 . . . B 2 -16.209 40.072 10.915 1 35.79 ? C2 EV6 393 A 1 HETATM 3 C C3 EV6 . . . B 2 -16.663 39.102 11.815 1 34.97 ? C3 EV6 393 A 1 HETATM 4 C C4 EV6 . . . B 2 -16.867 37.806 11.346 1 36.58 ? C4 EV6 393 A 1 HETATM 5 C C5 EV6 . . . B 2 -16.64 37.404 10.004 1 36.34 ? C5 EV6 393 A 1 HETATM 6 C C6 EV6 . . . B 2 -16.191 38.344 9.092 1 34.27 ? C6 EV6 393 A 1 HETATM 7 N N7 EV6 . . . B 2 -15.887 38.3 7.784 1 33.47 ? N7 EV6 393 A 1 HETATM 8 C C8 EV6 . . . B 2 -15.51 39.57 7.509 1 33.07 ? C8 EV6 393 A 1 HETATM 9 N N9 EV6 . . . B 2 -15.52 40.456 8.538 1 33.38 ? N9 EV6 393 A 1 HETATM 10 N N10 EV6 . . . B 2 -15.135 39.872 6.254 1 32.15 ? N10 EV6 393 A 1 HETATM 11 CL CL11 EV6 . . . B 2 -17.466 36.587 12.481 1 38.33 ? CL11 EV6 393 A 1 HETATM 12 C C12 EV6 . . . B 2 -15.224 41.928 8.633 1 31.75 ? C12 EV6 393 A 1 HETATM 13 C C13 EV6 . . . B 2 -13.854 42.325 8.113 1 32.5 ? C13 EV6 393 A 1 HETATM 14 C C14 EV6 . . . B 2 -12.785 41.493 8.81 1 33.07 ? C14 EV6 393 A 1 HETATM 15 C C15 EV6 . . . B 2 -16.343 42.691 7.933 1 31.79 ? C15 EV6 393 A 1 HETATM 16 C C16 EV6 . . . B 2 -17.695 42.201 8.419 1 34.35 ? C16 EV6 393 A 1 HETATM 17 N N17 EV6 . . . B 2 -18.555 41.547 7.607 1 32.67 ? N17 EV6 393 A 1 HETATM 18 O O18 EV6 . . . B 2 -17.957 42.389 9.6 1 38.39 ? O18 EV6 393 A 1 HETATM 19 C C19 EV6 . . . B 2 -19.86 41.112 8.139 1 31.61 ? C19 EV6 393 A 1 HETATM 20 C C20 EV6 . . . B 2 -20.8 40.849 6.987 1 31.38 ? C20 EV6 393 A 1 HETATM 21 C C21 EV6 . . . B 2 -22.2 40.612 7.578 1 32.73 ? C21 EV6 393 A 1 HETATM 22 C C22 EV6 . . . B 2 -22.254 39.373 8.469 1 32.07 ? C22 EV6 393 A 1 HETATM 23 C C23 EV6 . . . B 2 -21.89 38.165 7.585 1 31.48 ? C23 EV6 393 A 1 HETATM 24 C C24 EV6 . . . B 2 -20.458 38.347 7.044 1 30.75 ? C24 EV6 393 A 1 HETATM 25 C C25 EV6 . . . B 2 -20.352 39.613 6.214 1 31.32 ? C25 EV6 393 A 1 HETATM 26 C C26 EV6 . . . B 2 -19.8 39.834 8.974 1 31.74 ? C26 EV6 393 A 1 HETATM 27 C C27 EV6 . . . B 2 -19.447 38.593 8.159 1 32.35 ? C27 EV6 393 A 1 HETATM 28 C C28 EV6 . . . B 2 -21.2 39.569 9.571 1 32.24 ? C28 EV6 393 A 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 357 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #