data_7VC3 # _model_server_result.job_id 3gKQ4T8nEOKLA34pZzzxPw _model_server_result.datetime_utc '2024-11-21 23:20:23' _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 7vc3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1001}' # _entry.id 7VC3 # _exptl.entry_id 7VC3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 477.531 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-[(3S)-3-cyclopropyl-3-(hydroxymethyl)-2-oxidanylidene-pyrrolidin-1-yl]-N-[[3-fluoranyl-5-(1-methylpyrazol-4-yl)phenyl]methyl]-6-methyl-pyridine-2-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 111.38 _cell.angle_gamma 90 _cell.entry_id 7VC3 _cell.length_a 114.733 _cell.length_b 73.644 _cell.length_c 74.906 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7VC3 _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,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U _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 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 O GLU 479 A GLU 809 1_555 R NA NA . A NA 1017 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.717 ? metalc ? metalc2 A O THR 481 A THR 811 1_555 R NA NA . A NA 1017 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.192 ? # _chem_comp.formula 'C26 H28 F N5 O3' _chem_comp.formula_weight 477.531 _chem_comp.id 1XK _chem_comp.mon_nstd_flag . _chem_comp.name 4-[(3S)-3-cyclopropyl-3-(hydroxymethyl)-2-oxidanylidene-pyrrolidin-1-yl]-N-[[3-fluoranyl-5-(1-methylpyrazol-4-yl)phenyl]methyl]-6-methyl-pyridine-2-carboxamide _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 C24 C23 1XK sing 1 n n C24 C22 1XK sing 2 n n C23 C22 1XK sing 3 n n C22 C20 1XK sing 4 n n O1 C21 1XK sing 5 n n O2 C25 1XK doub 6 n n C20 C25 1XK sing 7 n n C20 C21 1XK sing 8 n n C20 C19 1XK sing 9 n n C25 N4 1XK sing 10 n n C C1 1XK sing 11 n n C2 C1 1XK doub 12 n y C2 C3 1XK sing 13 n y C19 C18 1XK sing 14 n n N4 C3 1XK sing 15 n n N4 C18 1XK sing 16 n n C1 N 1XK sing 17 n y C3 C4 1XK doub 18 n y N C5 1XK doub 19 n y C4 C5 1XK sing 20 n y C5 C6 1XK sing 21 n n C6 N1 1XK sing 22 n n C6 O 1XK doub 23 n n N1 C7 1XK sing 24 n n C7 C8 1XK sing 25 n n C8 C9 1XK doub 26 n y C8 C13 1XK sing 27 n y C9 C10 1XK sing 28 n y C13 C12 1XK doub 29 n y C10 F 1XK sing 30 n n C10 C11 1XK doub 31 n y C12 C11 1XK sing 32 n y C12 C14 1XK sing 33 n n C14 C15 1XK sing 34 n y C14 C17 1XK doub 35 n y C15 N2 1XK doub 36 n y C17 N3 1XK sing 37 n y N2 N3 1XK sing 38 n y N3 C16 1XK sing 39 n n C4 H1 1XK sing 40 n n C H2 1XK sing 41 n n C H3 1XK sing 42 n n C H4 1XK sing 43 n n N1 H5 1XK sing 44 n n C2 H6 1XK sing 45 n n C11 H7 1XK sing 46 n n C13 H8 1XK sing 47 n n C15 H9 1XK sing 48 n n C16 H10 1XK sing 49 n n C16 H11 1XK sing 50 n n C16 H12 1XK sing 51 n n C17 H13 1XK sing 52 n n C18 H14 1XK sing 53 n n C18 H15 1XK sing 54 n n C19 H16 1XK sing 55 n n C19 H17 1XK sing 56 n n C21 H18 1XK sing 57 n n C21 H19 1XK sing 58 n n C22 H20 1XK sing 59 n n C23 H21 1XK sing 60 n n C23 H22 1XK sing 61 n n C24 H23 1XK sing 62 n n C24 H24 1XK sing 63 n n C7 H25 1XK sing 64 n n C7 H26 1XK sing 65 n n C9 H27 1XK sing 66 n n O1 H28 1XK sing 67 n n # _atom_sites.entry_id 7VC3 _atom_sites.fract_transf_matrix[1][1] 0.008716 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003412 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013579 _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] 0.014336 _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 1XK A 1 1001 1001 1XK 1XK . C 3 PRO A 1 1002 1002 PRO PRO . D 4 GOL A 1 1003 1102 GOL GOL . E 4 GOL A 1 1004 1103 GOL GOL . F 4 GOL A 1 1005 1104 GOL GOL . G 5 CL A 1 1006 1201 CL CL . H 5 CL A 1 1007 1202 CL CL . I 5 CL A 1 1008 1203 CL CL . J 5 CL A 1 1009 1204 CL CL . K 5 CL A 1 1010 1205 CL CL . L 5 CL A 1 1011 1206 CL CL . M 5 CL A 1 1012 1207 CL CL . N 5 CL A 1 1013 1209 CL CL . O 5 CL A 1 1014 1210 CL CL . P 5 CL A 1 1015 1211 CL CL . Q 5 CL A 1 1016 1212 CL CL . R 6 NA A 1 1017 1213 NA NA . S 7 SO3 A 1 1018 1214 SO3 SO3 . T 8 ETA A 1 1019 1215 ETA ETA . U 9 HOH A 1 1101 111 HOH HOH . U 9 HOH A 2 1102 46 HOH HOH . U 9 HOH A 3 1103 31 HOH HOH . U 9 HOH A 4 1104 94 HOH HOH . U 9 HOH A 5 1105 128 HOH HOH . U 9 HOH A 6 1106 83 HOH HOH . U 9 HOH A 7 1107 57 HOH HOH . U 9 HOH A 8 1108 30 HOH HOH . U 9 HOH A 9 1109 52 HOH HOH . U 9 HOH A 10 1110 51 HOH HOH . U 9 HOH A 11 1111 23 HOH HOH . U 9 HOH A 12 1112 74 HOH HOH . U 9 HOH A 13 1113 1 HOH HOH . U 9 HOH A 14 1114 112 HOH HOH . U 9 HOH A 15 1115 105 HOH HOH . U 9 HOH A 16 1116 95 HOH HOH . U 9 HOH A 17 1117 8 HOH HOH . U 9 HOH A 18 1118 6 HOH HOH . U 9 HOH A 19 1119 120 HOH HOH . U 9 HOH A 20 1120 7 HOH HOH . U 9 HOH A 21 1121 32 HOH HOH . U 9 HOH A 22 1122 79 HOH HOH . U 9 HOH A 23 1123 65 HOH HOH . U 9 HOH A 24 1124 92 HOH HOH . U 9 HOH A 25 1125 116 HOH HOH . U 9 HOH A 26 1126 45 HOH HOH . U 9 HOH A 27 1127 88 HOH HOH . U 9 HOH A 28 1128 108 HOH HOH . U 9 HOH A 29 1129 28 HOH HOH . U 9 HOH A 30 1130 80 HOH HOH . U 9 HOH A 31 1131 24 HOH HOH . U 9 HOH A 32 1132 35 HOH HOH . U 9 HOH A 33 1133 15 HOH HOH . U 9 HOH A 34 1134 4 HOH HOH . U 9 HOH A 35 1135 84 HOH HOH . U 9 HOH A 36 1136 2 HOH HOH . U 9 HOH A 37 1137 41 HOH HOH . U 9 HOH A 38 1138 129 HOH HOH . U 9 HOH A 39 1139 39 HOH HOH . U 9 HOH A 40 1140 117 HOH HOH . U 9 HOH A 41 1141 38 HOH HOH . U 9 HOH A 42 1142 42 HOH HOH . U 9 HOH A 43 1143 97 HOH HOH . U 9 HOH A 44 1144 25 HOH HOH . U 9 HOH A 45 1145 98 HOH HOH . U 9 HOH A 46 1146 3 HOH HOH . U 9 HOH A 47 1147 18 HOH HOH . U 9 HOH A 48 1148 17 HOH HOH . U 9 HOH A 49 1149 48 HOH HOH . U 9 HOH A 50 1150 93 HOH HOH . U 9 HOH A 51 1151 75 HOH HOH . U 9 HOH A 52 1152 53 HOH HOH . U 9 HOH A 53 1153 34 HOH HOH . U 9 HOH A 54 1154 81 HOH HOH . U 9 HOH A 55 1155 36 HOH HOH . U 9 HOH A 56 1156 90 HOH HOH . U 9 HOH A 57 1157 13 HOH HOH . U 9 HOH A 58 1158 123 HOH HOH . U 9 HOH A 59 1159 21 HOH HOH . U 9 HOH A 60 1160 96 HOH HOH . U 9 HOH A 61 1161 106 HOH HOH . U 9 HOH A 62 1162 9 HOH HOH . U 9 HOH A 63 1163 59 HOH HOH . U 9 HOH A 64 1164 70 HOH HOH . U 9 HOH A 65 1165 99 HOH HOH . U 9 HOH A 66 1167 118 HOH HOH . U 9 HOH A 67 1168 113 HOH HOH . U 9 HOH A 68 1169 127 HOH HOH . U 9 HOH A 69 1170 82 HOH HOH . U 9 HOH A 70 1171 11 HOH HOH . U 9 HOH A 71 1172 22 HOH HOH . U 9 HOH A 72 1173 63 HOH HOH . U 9 HOH A 73 1174 101 HOH HOH . U 9 HOH A 74 1175 19 HOH HOH . U 9 HOH A 75 1176 10 HOH HOH . U 9 HOH A 76 1177 14 HOH HOH . U 9 HOH A 77 1178 49 HOH HOH . U 9 HOH A 78 1179 64 HOH HOH . U 9 HOH A 79 1180 69 HOH HOH . U 9 HOH A 80 1181 86 HOH HOH . U 9 HOH A 81 1182 58 HOH HOH . U 9 HOH A 82 1183 125 HOH HOH . U 9 HOH A 83 1184 27 HOH HOH . U 9 HOH A 84 1185 55 HOH HOH . U 9 HOH A 85 1186 44 HOH HOH . U 9 HOH A 86 1187 40 HOH HOH . U 9 HOH A 87 1188 37 HOH HOH . U 9 HOH A 88 1189 91 HOH HOH . U 9 HOH A 89 1190 43 HOH HOH . U 9 HOH A 90 1191 73 HOH HOH . U 9 HOH A 91 1192 16 HOH HOH . U 9 HOH A 92 1193 62 HOH HOH . U 9 HOH A 93 1194 66 HOH HOH . U 9 HOH A 94 1195 85 HOH HOH . U 9 HOH A 95 1196 12 HOH HOH . U 9 HOH A 96 1197 47 HOH HOH . U 9 HOH A 97 1198 5 HOH HOH . U 9 HOH A 98 1199 103 HOH HOH . U 9 HOH A 99 1200 107 HOH HOH . U 9 HOH A 100 1201 56 HOH HOH . U 9 HOH A 101 1202 26 HOH HOH . U 9 HOH A 102 1203 110 HOH HOH . U 9 HOH A 103 1204 61 HOH HOH . U 9 HOH A 104 1205 67 HOH HOH . U 9 HOH A 105 1206 29 HOH HOH . U 9 HOH A 106 1207 121 HOH HOH . U 9 HOH A 107 1208 104 HOH HOH . U 9 HOH A 108 1209 89 HOH HOH . U 9 HOH A 109 1210 77 HOH HOH . U 9 HOH A 110 1211 33 HOH HOH . U 9 HOH A 111 1212 72 HOH HOH . U 9 HOH A 112 1213 131 HOH HOH . U 9 HOH A 113 1214 102 HOH HOH . U 9 HOH A 114 1215 60 HOH HOH . U 9 HOH A 115 1216 68 HOH HOH . U 9 HOH A 116 1217 126 HOH HOH . U 9 HOH A 117 1218 54 HOH HOH . U 9 HOH A 118 1219 87 HOH HOH . U 9 HOH A 119 1220 130 HOH HOH . U 9 HOH A 120 1221 115 HOH HOH . U 9 HOH A 121 1222 109 HOH HOH . U 9 HOH A 122 1223 76 HOH HOH . U 9 HOH A 123 1224 71 HOH HOH . U 9 HOH A 124 1225 119 HOH HOH . U 9 HOH A 125 1226 122 HOH HOH . U 9 HOH A 126 1227 50 HOH HOH . U 9 HOH A 127 1228 78 HOH HOH . U 9 HOH A 128 1229 124 HOH HOH . U 9 HOH A 129 1230 114 HOH HOH . U 9 HOH A 130 1231 100 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 C4 1XK . . . B 2 14.828 -10.659 5.719 0.94 43.31 ? C4 1XK 1001 A 1 HETATM 2 C C 1XK . . . B 2 12.036 -8.494 7.985 0.94 36.1 ? C 1XK 1001 A 1 HETATM 3 N N 1XK . . . B 2 13.044 -10.556 7.281 0.94 42.55 ? N 1XK 1001 A 1 HETATM 4 N N1 1XK . . . B 2 12.898 -13.303 7.216 0.94 40.45 ? N1 1XK 1001 A 1 HETATM 5 C C3 1XK . . . B 2 14.819 -9.294 5.596 0.94 42.94 ? C3 1XK 1001 A 1 HETATM 6 C C2 1XK . . . B 2 13.918 -8.558 6.338 0.94 42.04 ? C2 1XK 1001 A 1 HETATM 7 C C1 1XK . . . B 2 13.041 -9.224 7.169 0.94 41.91 ? C1 1XK 1001 A 1 HETATM 8 O O 1XK . . . B 2 14.991 -13.346 6.426 0.94 41.68 ? O 1XK 1001 A 1 HETATM 9 C C10 1XK . . . B 2 12.306 -15.993 10.816 0.94 48.96 ? C10 1XK 1001 A 1 HETATM 10 C C11 1XK . . . B 2 13.568 -16.139 11.279 0.94 46.53 ? C11 1XK 1001 A 1 HETATM 11 C C12 1XK . . . B 2 14.614 -15.859 10.425 0.94 43 ? C12 1XK 1001 A 1 HETATM 12 C C13 1XK . . . B 2 14.352 -15.426 9.137 0.94 44.68 ? C13 1XK 1001 A 1 HETATM 13 C C14 1XK . . . B 2 15.99 -16.091 10.869 0.94 44.78 ? C14 1XK 1001 A 1 HETATM 14 C C15 1XK . . . B 2 16.438 -16.443 12.133 0.94 50.67 ? C15 1XK 1001 A 1 HETATM 15 C C16 1XK . . . B 2 19.557 -16.287 10.591 0.94 56.99 ? C16 1XK 1001 A 1 HETATM 16 C C17 1XK . . . B 2 17.123 -15.995 10.118 0.94 48.72 ? C17 1XK 1001 A 1 HETATM 17 C C18 1XK . . . B 2 16.411 -9.574 3.748 0.94 47.75 ? C18 1XK 1001 A 1 HETATM 18 C C19 1XK . . . B 2 16.537 -8.72 2.519 0.94 57.23 ? C19 1XK 1001 A 1 HETATM 19 C C20 1XK . . . B 2 16.62 -7.302 3.086 0.94 52.72 ? C20 1XK 1001 A 1 HETATM 20 C C21 1XK . . . B 2 18.053 -6.992 3.424 0.94 48.28 ? C21 1XK 1001 A 1 HETATM 21 C C22 1XK . . . B 2 15.989 -6.356 2.231 0.94 48.1 ? C22 1XK 1001 A 1 HETATM 22 C C23 1XK . . . B 2 14.859 -6.828 1.371 0.94 53.42 ? C23 1XK 1001 A 1 HETATM 23 C C24 1XK . . . B 2 16.187 -6.542 0.759 0.94 54.43 ? C24 1XK 1001 A 1 HETATM 24 C C25 1XK . . . B 2 15.772 -7.398 4.301 0.94 40.96 ? C25 1XK 1001 A 1 HETATM 25 C C5 1XK . . . B 2 13.936 -11.243 6.565 0.94 39.89 ? C5 1XK 1001 A 1 HETATM 26 C C6 1XK . . . B 2 13.995 -12.729 6.737 0.94 41.91 ? C6 1XK 1001 A 1 HETATM 27 C C7 1XK . . . B 2 12.766 -14.746 7.314 0.94 44.24 ? C7 1XK 1001 A 1 HETATM 28 C C8 1XK . . . B 2 13.05 -15.274 8.695 0.94 47.02 ? C8 1XK 1001 A 1 HETATM 29 C C9 1XK . . . B 2 12.01 -15.568 9.557 0.94 43.76 ? C9 1XK 1001 A 1 HETATM 30 F F 1XK . . . B 2 11.309 -16.302 11.631 0.94 45.47 ? F 1XK 1001 A 1 HETATM 31 N N2 1XK . . . B 2 17.746 -16.57 12.173 0.94 56.84 ? N2 1XK 1001 A 1 HETATM 32 N N3 1XK . . . B 2 18.147 -16.283 10.921 0.94 54.41 ? N3 1XK 1001 A 1 HETATM 33 N N4 1XK . . . B 2 15.695 -8.699 4.669 0.94 44.31 ? N4 1XK 1001 A 1 HETATM 34 O O1 1XK . . . B 2 18.245 -5.611 3.362 0.94 58.45 ? O1 1XK 1001 A 1 HETATM 35 O O2 1XK . . . B 2 15.246 -6.484 4.871 0.94 41.36 ? O2 1XK 1001 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 348 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 35 #