data_3OCB # _model_server_result.job_id ODOKB3zEO9obcl2EPfoy7w _model_server_result.datetime_utc '2025-04-30 17:30:52' _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 3ocb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1}' # _entry.id 3OCB # _exptl.entry_id 3OCB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 398.889 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2S)-2-(4-chlorobenzyl)-3-oxo-3-[4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperazin-1-yl]propan-1-amine _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 104.27 _cell.angle_gamma 90 _cell.entry_id 3OCB _cell.length_a 86.265 _cell.length_b 56.013 _cell.length_c 91.65 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3OCB _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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,E,G,I 1 1 B,D,F,H,J 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 ? 3 E N N ? 3 F N 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 covale ? covale1 A C LYS 168 A LYS 307 1_555 A N TPO 169 A TPO 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 A C TPO 169 A TPO 308 1_555 A N PHE 170 A PHE 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 B C LYS 168 B LYS 307 1_555 B N TPO 169 B TPO 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 B C TPO 169 B TPO 308 1_555 B N PHE 170 B PHE 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? # _chem_comp.formula 'C20 H23 Cl N6 O' _chem_comp.formula_weight 398.889 _chem_comp.id XM1 _chem_comp.mon_nstd_flag . _chem_comp.name (2S)-2-(4-chlorobenzyl)-3-oxo-3-[4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperazin-1-yl]propan-1-amine _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 C2 C1 XM1 doub 397 n y N8 C1 XM1 sing 398 n y C1 N11 XM1 sing 399 n n CL1 C25 XM1 sing 400 n n C7 C2 XM1 sing 401 n y C3 C2 XM1 sing 402 n y C4 C3 XM1 doub 403 n y C3 H3 XM1 sing 404 n n N6 C4 XM1 sing 405 n y C4 H4 XM1 sing 406 n n N5 C21 XM1 sing 407 n n N5 HN5 XM1 sing 408 n n N5 HN5A XM1 sing 409 n n N6 C7 XM1 sing 410 n y N10 C7 XM1 doub 411 n y C9 N8 XM1 doub 412 n y N10 C9 XM1 sing 413 n y C9 H9 XM1 sing 414 n n N11 C12 XM1 sing 415 n n N11 C16 XM1 sing 416 n n C12 C13 XM1 sing 417 n n C12 H12 XM1 sing 418 n n C12 H12A XM1 sing 419 n n C13 N14 XM1 sing 420 n n C13 H13 XM1 sing 421 n n C13 H13A XM1 sing 422 n n C15 N14 XM1 sing 423 n n N14 C17 XM1 sing 424 n n C16 C15 XM1 sing 425 n n C15 H15 XM1 sing 426 n n C15 H15A XM1 sing 427 n n C16 H16 XM1 sing 428 n n C16 H16A XM1 sing 429 n n C17 O18 XM1 doub 430 n n C17 C19 XM1 sing 431 n n C19 C20 XM1 sing 432 n n C19 C21 XM1 sing 433 n n C19 H19 XM1 sing 434 n n C22 C20 XM1 sing 435 n n C20 H20 XM1 sing 436 n n C20 H20A XM1 sing 437 n n C21 H21 XM1 sing 438 n n C21 H21A XM1 sing 439 n n C23 C22 XM1 doub 440 n y C27 C22 XM1 sing 441 n y C24 C23 XM1 sing 442 n y C23 H23 XM1 sing 443 n n C25 C24 XM1 doub 444 n y C24 H24 XM1 sing 445 n n C25 C26 XM1 sing 446 n y C26 C27 XM1 doub 447 n y C26 H26 XM1 sing 448 n n C27 H27 XM1 sing 449 n n N6 HN6 XM1 sing 450 n n # _atom_sites.entry_id 3OCB _atom_sites.fract_transf_matrix[1][1] 0.011592 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002949 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017853 _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] 0.011259 _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 E 3 XM1 A 1 1 1 XM1 XM1 . F 3 XM1 B 1 2 2 XM1 XM1 . G 4 HOH A 1 2 2 HOH HOH . G 4 HOH A 2 3 3 HOH HOH . G 4 HOH A 3 5 5 HOH HOH . G 4 HOH A 4 7 7 HOH HOH . G 4 HOH A 5 8 8 HOH HOH . G 4 HOH A 6 10 10 HOH HOH . G 4 HOH A 7 12 12 HOH HOH . G 4 HOH A 8 13 13 HOH HOH . G 4 HOH A 9 14 14 HOH HOH . G 4 HOH A 10 15 15 HOH HOH . G 4 HOH A 11 16 16 HOH HOH . G 4 HOH A 12 17 17 HOH HOH . G 4 HOH A 13 19 19 HOH HOH . G 4 HOH A 14 20 20 HOH HOH . G 4 HOH A 15 21 21 HOH HOH . G 4 HOH A 16 22 22 HOH HOH . G 4 HOH A 17 26 26 HOH HOH . G 4 HOH A 18 27 27 HOH HOH . G 4 HOH A 19 28 28 HOH HOH . G 4 HOH A 20 29 29 HOH HOH . G 4 HOH A 21 30 30 HOH HOH . G 4 HOH A 22 35 35 HOH HOH . G 4 HOH A 23 38 38 HOH HOH . G 4 HOH A 24 39 39 HOH HOH . G 4 HOH A 25 40 40 HOH HOH . G 4 HOH A 26 41 41 HOH HOH . G 4 HOH A 27 44 44 HOH HOH . G 4 HOH A 28 45 45 HOH HOH . G 4 HOH A 29 46 46 HOH HOH . G 4 HOH A 30 49 49 HOH HOH . G 4 HOH A 31 50 50 HOH HOH . G 4 HOH A 32 51 51 HOH HOH . G 4 HOH A 33 54 54 HOH HOH . G 4 HOH A 34 55 55 HOH HOH . G 4 HOH A 35 57 57 HOH HOH . G 4 HOH A 36 58 58 HOH HOH . G 4 HOH A 37 60 60 HOH HOH . G 4 HOH A 38 63 63 HOH HOH . G 4 HOH A 39 64 64 HOH HOH . G 4 HOH A 40 65 65 HOH HOH . G 4 HOH A 41 66 66 HOH HOH . G 4 HOH A 42 67 67 HOH HOH . G 4 HOH A 43 68 68 HOH HOH . G 4 HOH A 44 72 72 HOH HOH . G 4 HOH A 45 75 75 HOH HOH . G 4 HOH A 46 76 76 HOH HOH . G 4 HOH A 47 77 77 HOH HOH . G 4 HOH A 48 78 78 HOH HOH . G 4 HOH A 49 79 79 HOH HOH . G 4 HOH A 50 82 82 HOH HOH . G 4 HOH A 51 83 83 HOH HOH . G 4 HOH A 52 85 85 HOH HOH . G 4 HOH A 53 93 93 HOH HOH . G 4 HOH A 54 95 95 HOH HOH . G 4 HOH A 55 96 96 HOH HOH . G 4 HOH A 56 97 97 HOH HOH . G 4 HOH A 57 98 98 HOH HOH . H 4 HOH B 1 1 1 HOH HOH . H 4 HOH B 2 4 4 HOH HOH . H 4 HOH B 3 6 6 HOH HOH . H 4 HOH B 4 9 9 HOH HOH . H 4 HOH B 5 11 11 HOH HOH . H 4 HOH B 6 18 18 HOH HOH . H 4 HOH B 7 23 23 HOH HOH . H 4 HOH B 8 24 24 HOH HOH . H 4 HOH B 9 25 25 HOH HOH . H 4 HOH B 10 31 31 HOH HOH . H 4 HOH B 11 32 32 HOH HOH . H 4 HOH B 12 33 33 HOH HOH . H 4 HOH B 13 36 36 HOH HOH . H 4 HOH B 14 37 37 HOH HOH . H 4 HOH B 15 42 42 HOH HOH . H 4 HOH B 16 43 43 HOH HOH . H 4 HOH B 17 47 47 HOH HOH . H 4 HOH B 18 52 52 HOH HOH . H 4 HOH B 19 53 53 HOH HOH . H 4 HOH B 20 56 56 HOH HOH . H 4 HOH B 21 61 61 HOH HOH . H 4 HOH B 22 62 62 HOH HOH . H 4 HOH B 23 69 69 HOH HOH . H 4 HOH B 24 70 70 HOH HOH . H 4 HOH B 25 71 71 HOH HOH . H 4 HOH B 26 73 73 HOH HOH . H 4 HOH B 27 74 74 HOH HOH . H 4 HOH B 28 80 80 HOH HOH . H 4 HOH B 29 81 81 HOH HOH . H 4 HOH B 30 84 84 HOH HOH . H 4 HOH B 31 86 86 HOH HOH . H 4 HOH B 32 87 87 HOH HOH . H 4 HOH B 33 88 88 HOH HOH . H 4 HOH B 34 89 89 HOH HOH . H 4 HOH B 35 90 90 HOH HOH . H 4 HOH B 36 91 91 HOH HOH . H 4 HOH B 37 94 94 HOH HOH . H 4 HOH B 38 99 99 HOH HOH . I 4 HOH C 1 48 48 HOH HOH . J 4 HOH D 1 34 34 HOH HOH . J 4 HOH D 2 59 59 HOH HOH . J 4 HOH D 3 92 92 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 XM1 . . . E 3 14.535 -1.991 15.882 1 46.61 ? C1 XM1 1 A 1 HETATM 2 CL CL1 XM1 . . . E 3 8.406 4.074 14.396 1 64.23 ? CL1 XM1 1 A 1 HETATM 3 C C2 XM1 . . . E 3 15.667 -1.218 15.529 1 45.92 ? C2 XM1 1 A 1 HETATM 4 C C3 XM1 . . . E 3 15.866 0.201 15.512 1 45.45 ? C3 XM1 1 A 1 HETATM 5 C C4 XM1 . . . E 3 17.171 0.305 15.077 1 45.03 ? C4 XM1 1 A 1 HETATM 6 N N5 XM1 . . . E 3 12.234 -0.408 21.274 1 57.13 ? N5 XM1 1 A 1 HETATM 7 N N6 XM1 . . . E 3 17.746 -0.953 14.84 1 45.27 ? N6 XM1 1 A 1 HETATM 8 C C7 XM1 . . . E 3 16.818 -1.894 15.119 1 45.25 ? C7 XM1 1 A 1 HETATM 9 N N8 XM1 . . . E 3 14.637 -3.335 15.805 1 46.37 ? N8 XM1 1 A 1 HETATM 10 C C9 XM1 . . . E 3 15.809 -3.858 15.391 1 45.47 ? C9 XM1 1 A 1 HETATM 11 N N10 XM1 . . . E 3 16.938 -3.224 15.032 1 45.22 ? N10 XM1 1 A 1 HETATM 12 N N11 XM1 . . . E 3 13.37 -1.376 16.311 1 47.4 ? N11 XM1 1 A 1 HETATM 13 C C12 XM1 . . . E 3 12.278 -2.266 16.766 1 48.3 ? C12 XM1 1 A 1 HETATM 14 C C13 XM1 . . . E 3 10.92 -1.591 17.079 1 49.33 ? C13 XM1 1 A 1 HETATM 15 N N14 XM1 . . . E 3 11.058 -0.367 17.897 1 50.84 ? N14 XM1 1 A 1 HETATM 16 C C15 XM1 . . . E 3 12.091 0.569 17.401 1 49.66 ? C15 XM1 1 A 1 HETATM 17 C C16 XM1 . . . E 3 13.442 -0.143 17.129 1 48.8 ? C16 XM1 1 A 1 HETATM 18 C C17 XM1 . . . E 3 10.412 -0.2 19.082 1 52.52 ? C17 XM1 1 A 1 HETATM 19 O O18 XM1 . . . E 3 9.546 -0.995 19.462 1 52.32 ? O18 XM1 1 A 1 HETATM 20 C C19 XM1 . . . E 3 10.656 1.061 19.954 1 54.69 ? C19 XM1 1 A 1 HETATM 21 C C20 XM1 . . . E 3 9.413 1.984 19.987 1 56.27 ? C20 XM1 1 A 1 HETATM 22 C C21 XM1 . . . E 3 11.265 0.711 21.329 1 55.3 ? C21 XM1 1 A 1 HETATM 23 C C22 XM1 . . . E 3 9.145 2.514 18.591 1 57.89 ? C22 XM1 1 A 1 HETATM 24 C C23 XM1 . . . E 3 8.318 1.779 17.709 1 58.87 ? C23 XM1 1 A 1 HETATM 25 C C24 XM1 . . . E 3 8.087 2.269 16.405 1 60.4 ? C24 XM1 1 A 1 HETATM 26 C C25 XM1 . . . E 3 8.69 3.484 15.995 1 61.33 ? C25 XM1 1 A 1 HETATM 27 C C26 XM1 . . . E 3 9.524 4.216 16.874 1 59.51 ? C26 XM1 1 A 1 HETATM 28 C C27 XM1 . . . E 3 9.752 3.722 18.176 1 58.18 ? C27 XM1 1 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 366 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 28 #