data_3LCD # _model_server_result.job_id diWc8AbpCZnp1lLeX1I8xw _model_server_result.datetime_utc '2025-08-31 14:25:31' _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 3lcd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":923}' # _entry.id 3LCD # _exptl.entry_id 3LCD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 525.473 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N~3~-(2,6-dichlorobenzyl)-5-(4-{[(2R)-2-(pyrrolidin-1-ylmethyl)pyrrolidin-1-yl]carbonyl}phenyl)pyrazine-2,3-diamine _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 90 _cell.entry_id 3LCD _cell.length_a 57.649 _cell.length_b 74.125 _cell.length_c 91.024 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LCD _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id C _struct_conn.ptnr1_label_comp_id ALA _struct_conn.ptnr1_label_seq_id 147 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id ALA _struct_conn.ptnr1_auth_seq_id 681 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id N _struct_conn.ptnr2_label_comp_id ASP _struct_conn.ptnr2_label_seq_id 148 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id ASP _struct_conn.ptnr2_auth_seq_id 741 _struct_conn.ptnr2_symmetry 1_555 _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 1.33 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C27 H30 Cl2 N6 O' _chem_comp.formula_weight 525.473 _chem_comp.id BDY _chem_comp.mon_nstd_flag . _chem_comp.name N~3~-(2,6-dichlorobenzyl)-5-(4-{[(2R)-2-(pyrrolidin-1-ylmethyl)pyrrolidin-1-yl]carbonyl}phenyl)pyrazine-2,3-diamine _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 N1 C2 BDY sing 70 n n N3 C4 BDY doub 71 n y N3 C2 BDY sing 72 n y C4 C5 BDY sing 73 n y C5 N6 BDY doub 74 n y C5 C18 BDY sing 75 n y C7 C2 BDY doub 76 n y C7 N6 BDY sing 77 n y C7 N8 BDY sing 78 n n C10 C9 BDY sing 79 n n C10 C11 BDY doub 80 n y C10 C16 BDY sing 81 n y C13 C11 BDY sing 82 n y C13 C14 BDY doub 83 n y C15 C14 BDY sing 84 n y C15 C16 BDY doub 85 n y C20 C21 BDY doub 86 n y C20 C19 BDY sing 87 n y C21 C22 BDY sing 88 n y C21 C24 BDY sing 89 n n C22 C23 BDY doub 90 n y C24 O25 BDY doub 91 n n C24 N26 BDY sing 92 n n C28 C27 BDY sing 93 n n C28 C29 BDY sing 94 n n N8 C9 BDY sing 95 n n C11 CL12 BDY sing 96 n n C16 CL17 BDY sing 97 n n C18 C19 BDY doub 98 n y C18 C23 BDY sing 99 n y N26 C27 BDY sing 100 n n N26 C30 BDY sing 101 n n C29 C30 BDY sing 102 n n C30 C31 BDY sing 103 n n C31 N32 BDY sing 104 n n N32 C33 BDY sing 105 n n N32 C36 BDY sing 106 n n C33 C34 BDY sing 107 n n C34 C35 BDY sing 108 n n C35 C36 BDY sing 109 n n N1 HN1 BDY sing 110 n n N1 HN1A BDY sing 111 n n C4 H4 BDY sing 112 n n C13 H13 BDY sing 113 n n C15 H15 BDY sing 114 n n C20 H20 BDY sing 115 n n C22 H22 BDY sing 116 n n C28 H28 BDY sing 117 n n C28 H28A BDY sing 118 n n N8 HN8 BDY sing 119 n n C9 H9 BDY sing 120 n n C9 H9A BDY sing 121 n n C14 H14 BDY sing 122 n n C19 H19 BDY sing 123 n n C23 H23 BDY sing 124 n n C27 H27 BDY sing 125 n n C27 H27A BDY sing 126 n n C29 H29 BDY sing 127 n n C29 H29A BDY sing 128 n n C30 H30 BDY sing 129 n n C31 H31 BDY sing 130 n n C31 H31A BDY sing 131 n n C33 H33 BDY sing 132 n n C33 H33A BDY sing 133 n n C34 H34 BDY sing 134 n n C34 H34A BDY sing 135 n n C35 H35 BDY sing 136 n n C35 H35A BDY sing 137 n n C36 H36 BDY sing 138 n n C36 H36A BDY sing 139 n n # _atom_sites.entry_id 3LCD _atom_sites.fract_transf_matrix[1][1] 0.017346 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013491 _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] 0.010986 _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 SO4 A 1 1 1 SO4 SO4 . C 2 SO4 A 1 2 2 SO4 SO4 . D 3 BDY A 1 923 1 BDY BDY . E 4 HOH A 1 3 3 HOH HOH . E 4 HOH A 2 5 5 HOH HOH . E 4 HOH A 3 7 7 HOH HOH . E 4 HOH A 4 8 8 HOH HOH . E 4 HOH A 5 9 9 HOH HOH . E 4 HOH A 6 11 11 HOH HOH . E 4 HOH A 7 13 13 HOH HOH . E 4 HOH A 8 14 14 HOH HOH . E 4 HOH A 9 15 15 HOH HOH . E 4 HOH A 10 16 16 HOH HOH . E 4 HOH A 11 20 20 HOH HOH . E 4 HOH A 12 21 21 HOH HOH . E 4 HOH A 13 22 22 HOH HOH . E 4 HOH A 14 23 23 HOH HOH . E 4 HOH A 15 24 24 HOH HOH . E 4 HOH A 16 27 27 HOH HOH . E 4 HOH A 17 29 29 HOH HOH . E 4 HOH A 18 30 30 HOH HOH . E 4 HOH A 19 31 31 HOH HOH . E 4 HOH A 20 34 34 HOH HOH . E 4 HOH A 21 37 37 HOH HOH . E 4 HOH A 22 38 38 HOH HOH . E 4 HOH A 23 39 39 HOH HOH . E 4 HOH A 24 40 40 HOH HOH . E 4 HOH A 25 41 41 HOH HOH . E 4 HOH A 26 45 45 HOH HOH . E 4 HOH A 27 46 46 HOH HOH . E 4 HOH A 28 47 47 HOH HOH . E 4 HOH A 29 48 48 HOH HOH . E 4 HOH A 30 50 50 HOH HOH . E 4 HOH A 31 51 51 HOH HOH . E 4 HOH A 32 58 58 HOH HOH . E 4 HOH A 33 59 59 HOH HOH . E 4 HOH A 34 60 60 HOH HOH . E 4 HOH A 35 62 62 HOH HOH . E 4 HOH A 36 65 65 HOH HOH . E 4 HOH A 37 67 67 HOH HOH . E 4 HOH A 38 70 70 HOH HOH . E 4 HOH A 39 72 72 HOH HOH . E 4 HOH A 40 73 73 HOH HOH . E 4 HOH A 41 75 75 HOH HOH . E 4 HOH A 42 76 76 HOH HOH . E 4 HOH A 43 77 77 HOH HOH . E 4 HOH A 44 924 2 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 N N1 BDY . . . D 3 -19.948 4.831 -17.47 1 28.79 ? N1 BDY 923 A 1 HETATM 2 N N3 BDY . . . D 3 -20.139 2.706 -18.445 1 27.97 ? N3 BDY 923 A 1 HETATM 3 C C4 BDY . . . D 3 -20.956 1.72 -18.819 1 28.45 ? C4 BDY 923 A 1 HETATM 4 C C5 BDY . . . D 3 -22.316 1.773 -18.651 1 30.31 ? C5 BDY 923 A 1 HETATM 5 C C7 BDY . . . D 3 -22.123 3.853 -17.724 1 28.6 ? C7 BDY 923 A 1 HETATM 6 C C10 BDY . . . D 3 -24.687 4.461 -15.814 1 31.2 ? C10 BDY 923 A 1 HETATM 7 C C13 BDY . . . D 3 -26.339 2.964 -14.859 1 32.31 ? C13 BDY 923 A 1 HETATM 8 C C15 BDY . . . D 3 -24.776 4.042 -13.447 1 31.51 ? C15 BDY 923 A 1 HETATM 9 C C20 BDY . . . D 3 -25.186 -0.597 -18.717 1 34.7 ? C20 BDY 923 A 1 HETATM 10 C C21 BDY . . . D 3 -24.841 -1.423 -19.763 1 35.29 ? C21 BDY 923 A 1 HETATM 11 C C22 BDY . . . D 3 -23.67 -1.199 -20.455 1 35.35 ? C22 BDY 923 A 1 HETATM 12 C C24 BDY . . . D 3 -25.773 -2.516 -20.108 1 36.88 ? C24 BDY 923 A 1 HETATM 13 C C28 BDY . . . D 3 -24.024 -5.696 -20.083 1 37.84 ? C28 BDY 923 A 1 HETATM 14 C C2 BDY . . . D 3 -20.749 3.766 -17.893 1 29.21 ? C2 BDY 923 A 1 HETATM 15 N N6 BDY . . . D 3 -22.914 2.842 -18.108 1 29.9 ? N6 BDY 923 A 1 HETATM 16 N N8 BDY . . . D 3 -22.648 5.026 -17.127 1 28.35 ? N8 BDY 923 A 1 HETATM 17 C C9 BDY . . . D 3 -24.107 5.131 -17.036 1 29.12 ? C9 BDY 923 A 1 HETATM 18 C C11 BDY . . . D 3 -25.762 3.595 -15.94 1 32.72 ? C11 BDY 923 A 1 HETATM 19 CL CL12 BDY . . . D 3 -26.456 3.272 -17.478 1 35.12 ? CL12 BDY 923 A 1 HETATM 20 C C14 BDY . . . D 3 -25.84 3.183 -13.597 1 32.06 ? C14 BDY 923 A 1 HETATM 21 C C16 BDY . . . D 3 -24.21 4.675 -14.533 1 31.15 ? C16 BDY 923 A 1 HETATM 22 CL CL17 BDY . . . D 3 -22.893 5.739 -14.204 1 33.49 ? CL17 BDY 923 A 1 HETATM 23 C C18 BDY . . . D 3 -23.175 0.677 -19.042 1 32.6 ? C18 BDY 923 A 1 HETATM 24 C C19 BDY . . . D 3 -24.356 0.445 -18.363 1 33.51 ? C19 BDY 923 A 1 HETATM 25 C C23 BDY . . . D 3 -22.842 -0.157 -20.091 1 33.39 ? C23 BDY 923 A 1 HETATM 26 O O25 BDY . . . D 3 -26.958 -2.271 -19.923 1 36.13 ? O25 BDY 923 A 1 HETATM 27 N N26 BDY . . . D 3 -25.287 -3.73 -20.608 1 38.81 ? N26 BDY 923 A 1 HETATM 28 C C27 BDY . . . D 3 -23.95 -4.204 -20.327 1 38.49 ? C27 BDY 923 A 1 HETATM 29 C C29 BDY . . . D 3 -25.469 -6.087 -20.23 1 38.92 ? C29 BDY 923 A 1 HETATM 30 C C30 BDY . . . D 3 -26.208 -4.849 -20.689 1 40.36 ? C30 BDY 923 A 1 HETATM 31 C C31 BDY . . . D 3 -26.774 -5.104 -22.077 1 42.69 ? C31 BDY 923 A 1 HETATM 32 N N32 BDY . . . D 3 -27.285 -3.89 -22.706 1 45.6 ? N32 BDY 923 A 1 HETATM 33 C C33 BDY . . . D 3 -27.239 -4.117 -24.151 1 46.31 ? C33 BDY 923 A 1 HETATM 34 C C34 BDY . . . D 3 -28.555 -3.66 -24.739 1 46.74 ? C34 BDY 923 A 1 HETATM 35 C C35 BDY . . . D 3 -29.485 -3.422 -23.576 1 47.13 ? C35 BDY 923 A 1 HETATM 36 C C36 BDY . . . D 3 -28.686 -3.704 -22.326 1 46.27 ? C36 BDY 923 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 78 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 631 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #