data_4X8C # _model_server_result.job_id sPIyY4Q6UG3VqKYLeebs6g _model_server_result.datetime_utc '2024-10-18 04:19:50' _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 4x8c # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":703}' # _entry.id 4X8C # _exptl.entry_id 4X8C _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 474.555 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(3S,4R)-3-amino-4-hydroxypiperidin-1-yl]{2-[1-(cyclopropylmethyl)-1H-pyrrolo[2,3-b]pyridin-2-yl]-7-methoxy-1-methyl-1H-benzimidazol-5-yl}methanone' _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 123.13 _cell.angle_gamma 90 _cell.entry_id 4X8C _cell.length_a 145.5 _cell.length_b 60.42 _cell.length_c 113.31 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4X8C _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _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 metalc ? metalc1 A OD1 ASP 184 A ASP 176 1_555 C CA CA . A CA 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.596 ? metalc ? metalc2 A OE1 GLU 361 A GLU 353 1_555 B CA CA . A CA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.887 ? metalc ? metalc3 A O PHE 415 A PHE 407 1_555 B CA CA . A CA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.872 ? metalc ? metalc4 A O LEU 418 A LEU 410 1_555 B CA CA . A CA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.085 ? metalc ? metalc5 A OE1 GLU 419 A GLU 411 1_555 B CA CA . A CA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.11 ? # _chem_comp.formula 'C26 H30 N6 O3' _chem_comp.formula_weight 474.555 _chem_comp.id 3YZ _chem_comp.mon_nstd_flag . _chem_comp.name '[(3S,4R)-3-amino-4-hydroxypiperidin-1-yl]{2-[1-(cyclopropylmethyl)-1H-pyrrolo[2,3-b]pyridin-2-yl]-7-methoxy-1-methyl-1H-benzimidazol-5-yl}methanone' _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 N34 C33 3YZ sing 1 n n O32 C31 3YZ sing 2 n n C31 C33 3YZ sing 3 n n C31 C30 3YZ sing 4 n n C33 C35 3YZ sing 5 n n C35 N28 3YZ sing 6 n n C30 C29 3YZ sing 7 n n N28 C29 3YZ sing 8 n n N28 C26 3YZ sing 9 n n C26 O27 3YZ doub 10 n n C26 C5 3YZ sing 11 n n C5 C4 3YZ doub 12 n y C5 C6 3YZ sing 13 n y C4 C3 3YZ sing 14 n y C6 C7 3YZ doub 15 n y C1 O2 3YZ sing 16 n n C3 O2 3YZ sing 17 n n C3 C25 3YZ doub 18 n y C7 C25 3YZ sing 19 n y C7 N8 3YZ sing 20 n y C21 C20 3YZ sing 21 n n C21 C22 3YZ sing 22 n n C25 N23 3YZ sing 23 n y N8 C9 3YZ doub 24 n y C20 C19 3YZ sing 25 n n C20 C22 3YZ sing 26 n n C19 N18 3YZ sing 27 n n N23 C9 3YZ sing 28 n y N23 C24 3YZ sing 29 n n C9 C10 3YZ sing 30 n n N18 C10 3YZ sing 31 n y N18 C17 3YZ sing 32 n y C10 C11 3YZ doub 33 n y C17 N16 3YZ doub 34 n y C17 C12 3YZ sing 35 n y N16 C15 3YZ sing 36 n y C11 C12 3YZ sing 37 n y C12 C13 3YZ doub 38 n y C15 C14 3YZ doub 39 n y C13 C14 3YZ sing 40 n y C14 H1 3YZ sing 41 n n C13 H2 3YZ sing 42 n n C11 H3 3YZ sing 43 n n C6 H4 3YZ sing 44 n n C4 H5 3YZ sing 45 n n C15 H6 3YZ sing 46 n n C21 H7 3YZ sing 47 n n C21 H8 3YZ sing 48 n n C22 H9 3YZ sing 49 n n C22 H10 3YZ sing 50 n n C30 H11 3YZ sing 51 n n C30 H12 3YZ sing 52 n n C29 H13 3YZ sing 53 n n C29 H14 3YZ sing 54 n n C35 H15 3YZ sing 55 n n C35 H16 3YZ sing 56 n n C20 H17 3YZ sing 57 n n C33 H18 3YZ sing 58 n n C31 H19 3YZ sing 59 n n C24 H20 3YZ sing 60 n n C24 H21 3YZ sing 61 n n C24 H22 3YZ sing 62 n n C1 H23 3YZ sing 63 n n C1 H24 3YZ sing 64 n n C1 H25 3YZ sing 65 n n C19 H26 3YZ sing 66 n n C19 H27 3YZ sing 67 n n N34 H28 3YZ sing 68 n n N34 H29 3YZ sing 69 n n O32 H31 3YZ sing 70 n n # _atom_sites.entry_id 4X8C _atom_sites.fract_transf_matrix[1][1] 0.006873 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004485 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016551 _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] 0.010539 _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 CA A 1 701 900 CA CA . C 2 CA A 1 702 901 CA CA . D 3 3YZ A 1 703 664 3YZ UNL . E 4 HOH A 1 801 14 HOH HOH . E 4 HOH A 2 802 21 HOH HOH . E 4 HOH A 3 803 3 HOH HOH . E 4 HOH A 4 804 1 HOH HOH . E 4 HOH A 5 805 2 HOH HOH . E 4 HOH A 6 806 4 HOH HOH . E 4 HOH A 7 807 5 HOH HOH . E 4 HOH A 8 808 6 HOH HOH . E 4 HOH A 9 809 7 HOH HOH . E 4 HOH A 10 810 8 HOH HOH . E 4 HOH A 11 811 9 HOH HOH . E 4 HOH A 12 812 10 HOH HOH . E 4 HOH A 13 813 11 HOH HOH . E 4 HOH A 14 814 12 HOH HOH . E 4 HOH A 15 815 13 HOH HOH . E 4 HOH A 16 816 15 HOH HOH . E 4 HOH A 17 817 16 HOH HOH . E 4 HOH A 18 818 17 HOH HOH . E 4 HOH A 19 819 18 HOH HOH . E 4 HOH A 20 820 19 HOH HOH . E 4 HOH A 21 821 20 HOH HOH . E 4 HOH A 22 822 22 HOH HOH . E 4 HOH A 23 823 23 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 C14 3YZ . . . D 3 31.914 45.14 31.672 1 156.08 ? C14 3YZ 703 A 1 HETATM 2 C C13 3YZ . . . D 3 30.605 44.811 31.432 1 158.27 ? C13 3YZ 703 A 1 HETATM 3 C C11 3YZ . . . D 3 28.999 44.197 29.496 1 180.18 ? C11 3YZ 703 A 1 HETATM 4 C C6 3YZ . . . D 3 27.344 42.166 24.18 1 125.1 ? C6 3YZ 703 A 1 HETATM 5 C C4 3YZ . . . D 3 25.195 43.294 24.001 1 141.96 ? C4 3YZ 703 A 1 HETATM 6 C C15 3YZ . . . D 3 32.771 45.199 30.6 1 162.34 ? C15 3YZ 703 A 1 HETATM 7 C C12 3YZ . . . D 3 30.209 44.555 30.138 1 172.04 ? C12 3YZ 703 A 1 HETATM 8 C C5 3YZ . . . D 3 26.139 42.398 23.56 1 123.57 ? C5 3YZ 703 A 1 HETATM 9 C C7 3YZ . . . D 3 27.591 42.899 25.324 1 130.25 ? C7 3YZ 703 A 1 HETATM 10 C C25 3YZ . . . D 3 26.652 43.801 25.775 1 137.64 ? C25 3YZ 703 A 1 HETATM 11 C C3 3YZ . . . D 3 25.457 44.015 25.139 1 138.41 ? C3 3YZ 703 A 1 HETATM 12 C C10 3YZ . . . D 3 29.277 44.09 28.152 1 169.93 ? C10 3YZ 703 A 1 HETATM 13 C C17 3YZ . . . D 3 31.175 44.652 29.162 1 171.81 ? C17 3YZ 703 A 1 HETATM 14 C C9 3YZ . . . D 3 28.423 43.761 27.079 1 146.33 ? C9 3YZ 703 A 1 HETATM 15 C C26 3YZ . . . D 3 25.85 41.638 22.35 1 111.25 ? C26 3YZ 703 A 1 HETATM 16 C C21 3YZ . . . D 3 31.161 46.645 25.533 1 149.24 ? C21 3YZ 703 A 1 HETATM 17 C C22 3YZ . . . D 3 31.179 46.893 27.011 1 150.9 ? C22 3YZ 703 A 1 HETATM 18 C C30 3YZ . . . D 3 24.316 44.373 20.644 1 116.33 ? C30 3YZ 703 A 1 HETATM 19 C C29 3YZ . . . D 3 25.572 43.788 21.24 1 108.9 ? C29 3YZ 703 A 1 HETATM 20 C C35 3YZ . . . D 3 25.162 41.683 20.011 1 129.32 ? C35 3YZ 703 A 1 HETATM 21 C C20 3YZ . . . D 3 31.877 45.694 26.444 1 153.84 ? C20 3YZ 703 A 1 HETATM 22 C C33 3YZ . . . D 3 23.905 42.275 19.422 1 127.85 ? C33 3YZ 703 A 1 HETATM 23 C C31 3YZ . . . D 3 24.065 43.769 19.286 1 119.39 ? C31 3YZ 703 A 1 HETATM 24 C C24 3YZ . . . D 3 26.604 45.344 27.743 1 139.24 ? C24 3YZ 703 A 1 HETATM 25 C C1 3YZ . . . D 3 24.393 46.153 24.981 1 110.9 ? C1 3YZ 703 A 1 HETATM 26 C C19 3YZ . . . D 3 31.279 44.359 26.681 1 161.31 ? C19 3YZ 703 A 1 HETATM 27 N N16 3YZ . . . D 3 32.46 44.966 29.324 1 170.28 ? N16 3YZ 703 A 1 HETATM 28 N N8 3YZ . . . D 3 28.692 42.88 26.142 1 136.3 ? N8 3YZ 703 A 1 HETATM 29 N N23 3YZ . . . D 3 27.204 44.338 26.897 1 139.27 ? N23 3YZ 703 A 1 HETATM 30 N N18 3YZ . . . D 3 30.6 44.367 27.957 1 169.91 ? N18 3YZ 703 A 1 HETATM 31 N N28 3YZ . . . D 3 25.495 42.354 21.237 1 116.56 ? N28 3YZ 703 A 1 HETATM 32 N N34 3YZ . . . D 3 23.774 41.725 18.053 1 123.21 ? N34 3YZ 703 A 1 HETATM 33 O O27 3YZ . . . D 3 25.948 40.42 22.405 1 98.67 ? O27 3YZ 703 A 1 HETATM 34 O O32 3YZ . . . D 3 25.198 44.026 18.474 1 123.59 ? O32 3YZ 703 A 1 HETATM 35 O O2 3YZ . . . D 3 24.604 44.943 25.692 1 115.64 ? O2 3YZ 703 A 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 35 #