data_6L6E # _model_server_result.job_id xfVYhhBB6BXkP8itUwSMaw _model_server_result.datetime_utc '2025-02-05 09:46:06' _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 6l6e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":901}' # _entry.id 6L6E # _exptl.entry_id 6L6E _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 483.951 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '4-[(3-chloranyl-4-methoxy-phenyl)methylamino]-2-[(2S)-2-(hydroxymethyl)pyrrolidin-1-yl]-N-(pyrimidin-2-ylmethyl)pyrimid ine-5-carboxamide' _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 6L6E _cell.length_a 75.837 _cell.length_b 75.837 _cell.length_c 160.61 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6L6E _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall 'P 4nw 2abw' _symmetry.space_group_name_H-M 'P 43 21 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,F _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 metalc ? metalc1 A NE2 HIS 83 A HIS 617 1_555 C ZN ZN . A ZN 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc2 A NE2 HIS 119 A HIS 653 1_555 C ZN ZN . A ZN 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc3 A OD2 ASP 120 A ASP 654 1_555 C ZN ZN . A ZN 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc4 A OD1 ASP 120 A ASP 654 1_555 D MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc5 A OD1 ASP 230 A ASP 764 1_555 C ZN ZN . A ZN 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc6 C ZN ZN . A ZN 902 1_555 E O2 SO4 . A SO4 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc7 C ZN ZN . A ZN 902 1_555 F O HOH . A HOH 1032 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? metalc ? metalc8 D MG MG . A MG 903 1_555 F O HOH . A HOH 1020 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc9 D MG MG . A MG 903 1_555 F O HOH . A HOH 1021 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc10 D MG MG . A MG 903 1_555 F O HOH . A HOH 1029 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc11 D MG MG . A MG 903 1_555 F O HOH . A HOH 1032 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc12 D MG MG . A MG 903 1_555 F O HOH . A HOH 1052 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? # _chem_comp.formula 'C23 H26 Cl N7 O3' _chem_comp.formula_weight 483.951 _chem_comp.id E6L _chem_comp.mon_nstd_flag . _chem_comp.name '4-[(3-chloranyl-4-methoxy-phenyl)methylamino]-2-[(2S)-2-(hydroxymethyl)pyrrolidin-1-yl]-N-(pyrimidin-2-ylmethyl)pyrimid ine-5-carboxamide' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Avanafil # 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 C1 O2 E6L sing 83 n n O2 C3 E6L sing 84 n n C3 C8 E6L doub 85 n y C3 C4 E6L sing 86 n y C8 C7 E6L sing 87 n y CL1 C4 E6L sing 88 n n C4 C5 E6L doub 89 n y C7 C6 E6L doub 90 n y C5 C6 E6L sing 91 n y C6 C9 E6L sing 92 n n C20 N19 E6L sing 93 n n C20 C21 E6L sing 94 n n N19 C17 E6L sing 95 n n O18 C17 E6L doub 96 n n C17 C16 E6L sing 97 n n N26 C21 E6L doub 98 n y N26 C25 E6L sing 99 n y C21 N22 E6L sing 100 n y C9 N10 E6L sing 101 n n N10 C11 E6L sing 102 n n C16 C15 E6L doub 103 n y C16 C11 E6L sing 104 n y C15 N14 E6L sing 105 n y C11 N12 E6L doub 106 n y C25 C24 E6L doub 107 n y N22 C23 E6L doub 108 n y N14 C13 E6L doub 109 n y N12 C13 E6L sing 110 n y C13 N27 E6L sing 111 n n C24 C23 E6L sing 112 n y C32 O33 E6L sing 113 n n C32 C31 E6L sing 114 n n N27 C28 E6L sing 115 n n N27 C31 E6L sing 116 n n C28 C29 E6L sing 117 n n C31 C30 E6L sing 118 n n C29 C30 E6L sing 119 n n C1 H1 E6L sing 120 n n C1 H2 E6L sing 121 n n C1 H3 E6L sing 122 n n C5 H4 E6L sing 123 n n C7 H5 E6L sing 124 n n C8 H6 E6L sing 125 n n C9 H7 E6L sing 126 n n C9 H8 E6L sing 127 n n C15 H9 E6L sing 128 n n C20 H10 E6L sing 129 n n C20 H11 E6L sing 130 n n C23 H12 E6L sing 131 n n C24 H13 E6L sing 132 n n C25 H14 E6L sing 133 n n C28 H15 E6L sing 134 n n C28 H16 E6L sing 135 n n C29 H17 E6L sing 136 n n C29 H18 E6L sing 137 n n C30 H19 E6L sing 138 n n C30 H20 E6L sing 139 n n C31 H21 E6L sing 140 n n C32 H22 E6L sing 141 n n C32 H23 E6L sing 142 n n N10 H24 E6L sing 143 n n N19 H25 E6L sing 144 n n O33 H26 E6L sing 145 n n # _atom_sites.entry_id 6L6E _atom_sites.fract_transf_matrix[1][1] 0.013186 _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] 0.013186 _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] 0.006226 _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 E6L A 1 901 1 E6L AVA . C 3 ZN A 1 902 1 ZN ZN . D 4 MG A 1 903 1 MG MG . E 5 SO4 A 1 904 1 SO4 SO4 . F 6 HOH A 1 1001 38 HOH HOH . F 6 HOH A 2 1002 100 HOH HOH . F 6 HOH A 3 1003 50 HOH HOH . F 6 HOH A 4 1004 39 HOH HOH . F 6 HOH A 5 1005 33 HOH HOH . F 6 HOH A 6 1006 51 HOH HOH . F 6 HOH A 7 1007 65 HOH HOH . F 6 HOH A 8 1008 26 HOH HOH . F 6 HOH A 9 1009 96 HOH HOH . F 6 HOH A 10 1010 56 HOH HOH . F 6 HOH A 11 1011 16 HOH HOH . F 6 HOH A 12 1012 75 HOH HOH . F 6 HOH A 13 1013 29 HOH HOH . F 6 HOH A 14 1014 43 HOH HOH . F 6 HOH A 15 1015 54 HOH HOH . F 6 HOH A 16 1016 24 HOH HOH . F 6 HOH A 17 1017 30 HOH HOH . F 6 HOH A 18 1018 59 HOH HOH . F 6 HOH A 19 1019 46 HOH HOH . F 6 HOH A 20 1020 4 HOH HOH . F 6 HOH A 21 1021 5 HOH HOH . F 6 HOH A 22 1022 57 HOH HOH . F 6 HOH A 23 1023 70 HOH HOH . F 6 HOH A 24 1024 92 HOH HOH . F 6 HOH A 25 1025 42 HOH HOH . F 6 HOH A 26 1026 62 HOH HOH . F 6 HOH A 27 1027 28 HOH HOH . F 6 HOH A 28 1028 45 HOH HOH . F 6 HOH A 29 1029 1 HOH HOH . F 6 HOH A 30 1030 77 HOH HOH . F 6 HOH A 31 1031 13 HOH HOH . F 6 HOH A 32 1032 3 HOH HOH . F 6 HOH A 33 1033 97 HOH HOH . F 6 HOH A 34 1034 95 HOH HOH . F 6 HOH A 35 1035 53 HOH HOH . F 6 HOH A 36 1036 98 HOH HOH . F 6 HOH A 37 1037 55 HOH HOH . F 6 HOH A 38 1038 36 HOH HOH . F 6 HOH A 39 1039 23 HOH HOH . F 6 HOH A 40 1040 11 HOH HOH . F 6 HOH A 41 1041 41 HOH HOH . F 6 HOH A 42 1042 20 HOH HOH . F 6 HOH A 43 1043 34 HOH HOH . F 6 HOH A 44 1044 15 HOH HOH . F 6 HOH A 45 1045 31 HOH HOH . F 6 HOH A 46 1046 49 HOH HOH . F 6 HOH A 47 1047 21 HOH HOH . F 6 HOH A 48 1048 88 HOH HOH . F 6 HOH A 49 1049 58 HOH HOH . F 6 HOH A 50 1050 14 HOH HOH . F 6 HOH A 51 1051 67 HOH HOH . F 6 HOH A 52 1052 2 HOH HOH . F 6 HOH A 53 1053 47 HOH HOH . F 6 HOH A 54 1054 10 HOH HOH . F 6 HOH A 55 1055 83 HOH HOH . F 6 HOH A 56 1056 60 HOH HOH . F 6 HOH A 57 1057 86 HOH HOH . F 6 HOH A 58 1058 84 HOH HOH . F 6 HOH A 59 1059 12 HOH HOH . F 6 HOH A 60 1060 66 HOH HOH . F 6 HOH A 61 1061 52 HOH HOH . F 6 HOH A 62 1062 25 HOH HOH . F 6 HOH A 63 1063 72 HOH HOH . F 6 HOH A 64 1064 44 HOH HOH . F 6 HOH A 65 1065 22 HOH HOH . F 6 HOH A 66 1066 63 HOH HOH . F 6 HOH A 67 1067 8 HOH HOH . F 6 HOH A 68 1068 99 HOH HOH . F 6 HOH A 69 1069 69 HOH HOH . F 6 HOH A 70 1070 79 HOH HOH . F 6 HOH A 71 1071 64 HOH HOH . F 6 HOH A 72 1072 71 HOH HOH . F 6 HOH A 73 1073 37 HOH HOH . F 6 HOH A 74 1074 40 HOH HOH . F 6 HOH A 75 1075 68 HOH HOH . F 6 HOH A 76 1076 89 HOH HOH . F 6 HOH A 77 1077 101 HOH HOH . F 6 HOH A 78 1078 27 HOH HOH . F 6 HOH A 79 1079 32 HOH HOH . F 6 HOH A 80 1080 19 HOH HOH . F 6 HOH A 81 1081 61 HOH HOH . F 6 HOH A 82 1082 48 HOH HOH . F 6 HOH A 83 1083 18 HOH HOH . F 6 HOH A 84 1084 76 HOH HOH . F 6 HOH A 85 1085 9 HOH HOH . F 6 HOH A 86 1086 35 HOH HOH . F 6 HOH A 87 1087 82 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 C11 E6L . . . B 2 0.11 -28.871 -26.226 1 31.22 ? C11 E6L 901 A 1 HETATM 2 C C1 E6L . . . B 2 0.306 -32.477 -32.805 1 33.04 ? C1 E6L 901 A 1 HETATM 3 C C3 E6L . . . B 2 0.147 -32.396 -30.449 1 26.6 ? C3 E6L 901 A 1 HETATM 4 C C4 E6L . . . B 2 -0.44 -32.781 -29.273 1 24.46 ? C4 E6L 901 A 1 HETATM 5 C C5 E6L . . . B 2 0.063 -32.271 -28.007 1 28.62 ? C5 E6L 901 A 1 HETATM 6 C C6 E6L . . . B 2 1.112 -31.426 -27.994 1 28.72 ? C6 E6L 901 A 1 HETATM 7 C C7 E6L . . . B 2 1.717 -31.034 -29.181 1 29.86 ? C7 E6L 901 A 1 HETATM 8 C C8 E6L . . . B 2 1.227 -31.532 -30.436 1 28.83 ? C8 E6L 901 A 1 HETATM 9 C C9 E6L . . . B 2 1.657 -30.867 -26.595 1 30.11 ? C9 E6L 901 A 1 HETATM 10 C C13 E6L . . . B 2 -2.042 -29.088 -25.445 1 28.53 ? C13 E6L 901 A 1 HETATM 11 C C15 E6L . . . B 2 -1.434 -26.956 -26.23 1 30.93 ? C15 E6L 901 A 1 HETATM 12 C C16 E6L . . . B 2 -0.171 -27.473 -26.509 1 27.49 ? C16 E6L 901 A 1 HETATM 13 C C17 E6L . . . B 2 0.86 -26.608 -27.09 1 31.8 ? C17 E6L 901 A 1 HETATM 14 C C20 E6L . . . B 2 1.599 -24.332 -27.948 1 41.78 ? C20 E6L 901 A 1 HETATM 15 C C21 E6L . . . B 2 2.461 -23.496 -26.858 1 51.11 ? C21 E6L 901 A 1 HETATM 16 C C23 E6L . . . B 2 3.882 -23.47 -25.032 1 57.63 ? C23 E6L 901 A 1 HETATM 17 C C24 E6L . . . B 2 3.909 -22.07 -25.07 1 58.65 ? C24 E6L 901 A 1 HETATM 18 C C25 E6L . . . B 2 3.177 -21.418 -26.048 1 58.63 ? C25 E6L 901 A 1 HETATM 19 C C28 E6L . . . B 2 -4.425 -29.385 -24.272 1 29.27 ? C28 E6L 901 A 1 HETATM 20 C C29 E6L . . . B 2 -4.931 -30.438 -23.607 1 30.16 ? C29 E6L 901 A 1 HETATM 21 C C30 E6L . . . B 2 -3.617 -31.224 -23.048 1 28.23 ? C30 E6L 901 A 1 HETATM 22 C C31 E6L . . . B 2 -2.711 -31.172 -24.053 1 28.22 ? C31 E6L 901 A 1 HETATM 23 C C32 E6L . . . B 2 -2.836 -32.368 -25.055 1 27.17 ? C32 E6L 901 A 1 HETATM 24 N N10 E6L . . . B 2 1.458 -29.44 -26.528 1 33.76 ? N10 E6L 901 A 1 HETATM 25 N N12 E6L . . . B 2 -0.857 -29.632 -25.692 1 32.52 ? N12 E6L 901 A 1 HETATM 26 N N14 E6L . . . B 2 -2.344 -27.764 -25.702 1 26.79 ? N14 E6L 901 A 1 HETATM 27 N N19 E6L . . . B 2 0.563 -25.15 -27.351 1 35.3 ? N19 E6L 901 A 1 HETATM 28 N N22 E6L . . . B 2 3.134 -24.129 -25.961 1 53.94 ? N22 E6L 901 A 1 HETATM 29 N N26 E6L . . . B 2 2.471 -22.137 -26.922 1 60 ? N26 E6L 901 A 1 HETATM 30 N N27 E6L . . . B 2 -3.067 -29.91 -24.862 1 27.77 ? N27 E6L 901 A 1 HETATM 31 O O2 E6L . . . B 2 -0.365 -32.92 -31.702 1 31.96 ? O2 E6L 901 A 1 HETATM 32 O O18 E6L . . . B 2 1.927 -27.048 -27.345 1 33.26 ? O18 E6L 901 A 1 HETATM 33 O O33 E6L . . . B 2 -2.338 -33.572 -24.429 1 29.74 ? O33 E6L 901 A 1 HETATM 34 CL CL1 E6L . . . B 2 -1.809 -33.882 -29.303 1 30.41 ? CL1 E6L 901 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 34 #