data_3NLD # _model_server_result.job_id P9HdTaOmGPpCR8sE500BGw _model_server_result.datetime_utc '2024-11-17 21:54:52' _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 3nld # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":800}' # _entry.id 3NLD # _exptl.entry_id 3NLD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 372.48 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 6-{[(3S,4S)-4-(2-{[2-(3-fluorophenyl)ethyl]amino}ethoxy)pyrrolidin-3-yl]methyl}-4-methylpyridin-2-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 90 _cell.angle_gamma 90 _cell.entry_id 3NLD _cell.length_a 57.397 _cell.length_b 106.885 _cell.length_c 157.369 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NLD _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 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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 G N N ? 6 N 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 metalc ? metalc1 A SG CYS 58 A CYS 96 1_555 I ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc2 A SG CYS 63 A CYS 101 1_555 I ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.512 ? metalc ? metalc3 A SG CYS 148 A CYS 186 1_555 C FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc4 I ZN ZN . A ZN 900 1_555 B SG CYS 58 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc5 I ZN ZN . A ZN 900 1_555 B SG CYS 63 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc6 B SG CYS 148 B CYS 186 1_555 J FE HEM . B HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? # _chem_comp.formula 'C21 H29 F N4 O' _chem_comp.formula_weight 372.48 _chem_comp.id JSS _chem_comp.mon_nstd_flag . _chem_comp.name 6-{[(3S,4S)-4-(2-{[2-(3-fluorophenyl)ethyl]amino}ethoxy)pyrrolidin-3-yl]methyl}-4-methylpyridin-2-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 O1 C1 JSS sing 318 n n C2 C1 JSS sing 319 n n C1 H1 JSS sing 320 n n C1 H1A JSS sing 321 n n O1 C3' JSS sing 322 n n N2 C2 JSS sing 323 n n C2 H2 JSS sing 324 n n C2 H2A JSS sing 325 n n C3 N2 JSS sing 326 n n N2 HN2 JSS sing 327 n n C4 C3 JSS sing 328 n n C3 H3 JSS sing 329 n n C3 H3A JSS sing 330 n n C11 C4 JSS sing 331 n n C4 H4 JSS sing 332 n n C4 H4A JSS sing 333 n n C2' N1' JSS sing 334 n n N1' C5' JSS sing 335 n n N1' HN1' JSS sing 336 n n C16 C11 JSS doub 337 n y C11 C12 JSS sing 338 n y C13 C12 JSS doub 339 n y C12 H12 JSS sing 340 n n C14 C13 JSS sing 341 n y C13 F13 JSS sing 342 n n C15 C14 JSS doub 343 n y C14 H14 JSS sing 344 n n C15 C16 JSS sing 345 n y C15 H15 JSS sing 346 n n C16 H16 JSS sing 347 n n N1A C2A JSS doub 348 n y N1A C6A JSS sing 349 n y C2' C3' JSS sing 350 n n C2' H2' JSS sing 351 n n C2' "H2'A" JSS sing 352 n n C7A C2A JSS sing 353 n n C2A C3A JSS sing 354 n y C3' C4' JSS sing 355 n n C3' H3' JSS sing 356 n n C3A C4A JSS doub 357 n y C3A H3AA JSS sing 358 n n C5' C4' JSS sing 359 n n C7A C4' JSS sing 360 n n C4' H4' JSS sing 361 n n C5A C4A JSS sing 362 n y C4A C8A JSS sing 363 n n C5' H5' JSS sing 364 n n C5' "H5'A" JSS sing 365 n n C6A C5A JSS doub 366 n y C5A H5A JSS sing 367 n n N6A C6A JSS sing 368 n n N6A HN6A JSS sing 369 n n N6A HN6B JSS sing 370 n n C7A H7A JSS sing 371 n n C7A H7AA JSS sing 372 n n C8A H8A JSS sing 373 n n C8A H8AA JSS sing 374 n n C8A H8AB JSS sing 375 n n # _atom_sites.entry_id 3NLD _atom_sites.fract_transf_matrix[1][1] 0.017423 _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] 0.009356 _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] 0.006354 _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 C 2 HEM A 1 500 500 HEM HEM . D 3 H4B A 1 600 600 H4B H4B . E 4 ACT A 1 850 850 ACT ACT . F 5 GOL A 1 880 880 GOL GOL . G 6 JSS A 1 800 800 JSS JSS . H 7 CAD A 1 950 950 CAD CAD . I 8 ZN A 1 900 900 ZN ZN . J 2 HEM B 1 500 500 HEM HEM . K 3 H4B B 1 600 600 H4B H4B . L 4 ACT B 1 850 850 ACT ACT . M 5 GOL B 1 880 880 GOL GOL . N 6 JSS B 1 800 800 JSS JSS . O 7 CAD B 1 950 950 CAD CAD . P 9 HOH A 1 1001 1001 HOH HOH . P 9 HOH A 2 1002 1002 HOH HOH . P 9 HOH A 3 1003 1003 HOH HOH . P 9 HOH A 4 1004 1004 HOH HOH . P 9 HOH A 5 1005 1005 HOH HOH . P 9 HOH A 6 1006 1006 HOH HOH . P 9 HOH A 7 1007 1007 HOH HOH . P 9 HOH A 8 1008 1008 HOH HOH . P 9 HOH A 9 1009 1009 HOH HOH . P 9 HOH A 10 1010 1010 HOH HOH . P 9 HOH A 11 1011 1011 HOH HOH . P 9 HOH A 12 1012 1012 HOH HOH . P 9 HOH A 13 1013 1013 HOH HOH . P 9 HOH A 14 1014 1014 HOH HOH . P 9 HOH A 15 1015 1015 HOH HOH . P 9 HOH A 16 1016 1016 HOH HOH . P 9 HOH A 17 1017 1017 HOH HOH . P 9 HOH A 18 1018 1018 HOH HOH . P 9 HOH A 19 1019 1019 HOH HOH . P 9 HOH A 20 1020 1020 HOH HOH . P 9 HOH A 21 1021 1021 HOH HOH . P 9 HOH A 22 1022 1022 HOH HOH . P 9 HOH A 23 1023 1023 HOH HOH . P 9 HOH A 24 1024 1024 HOH HOH . P 9 HOH A 25 1025 1025 HOH HOH . P 9 HOH A 26 1026 1026 HOH HOH . P 9 HOH A 27 1027 1027 HOH HOH . P 9 HOH A 28 1028 1028 HOH HOH . P 9 HOH A 29 1029 1029 HOH HOH . P 9 HOH A 30 1030 1030 HOH HOH . P 9 HOH A 31 1031 1031 HOH HOH . P 9 HOH A 32 1032 1032 HOH HOH . P 9 HOH A 33 1033 1033 HOH HOH . P 9 HOH A 34 1034 1034 HOH HOH . P 9 HOH A 35 1035 1035 HOH HOH . P 9 HOH A 36 1036 1036 HOH HOH . P 9 HOH A 37 1037 1037 HOH HOH . P 9 HOH A 38 1038 1038 HOH HOH . P 9 HOH A 39 1039 1039 HOH HOH . P 9 HOH A 40 1040 1040 HOH HOH . P 9 HOH A 41 1041 1041 HOH HOH . P 9 HOH A 42 1042 1042 HOH HOH . P 9 HOH A 43 1043 1043 HOH HOH . P 9 HOH A 44 1044 1044 HOH HOH . P 9 HOH A 45 1045 1045 HOH HOH . P 9 HOH A 46 1046 1046 HOH HOH . P 9 HOH A 47 1047 1047 HOH HOH . P 9 HOH A 48 1048 1048 HOH HOH . P 9 HOH A 49 1049 1049 HOH HOH . P 9 HOH A 50 1050 1050 HOH HOH . P 9 HOH A 51 1051 1051 HOH HOH . P 9 HOH A 52 1052 1052 HOH HOH . P 9 HOH A 53 1053 1053 HOH HOH . P 9 HOH A 54 1054 1054 HOH HOH . P 9 HOH A 55 1055 1055 HOH HOH . P 9 HOH A 56 1056 1056 HOH HOH . P 9 HOH A 57 1057 1057 HOH HOH . P 9 HOH A 58 1058 1058 HOH HOH . P 9 HOH A 59 1059 1059 HOH HOH . P 9 HOH A 60 1060 1060 HOH HOH . P 9 HOH A 61 1061 1061 HOH HOH . P 9 HOH A 62 1062 1062 HOH HOH . P 9 HOH A 63 1063 1063 HOH HOH . P 9 HOH A 64 1064 1064 HOH HOH . P 9 HOH A 65 1065 1065 HOH HOH . P 9 HOH A 66 1066 1066 HOH HOH . P 9 HOH A 67 1067 1067 HOH HOH . P 9 HOH A 68 1068 1068 HOH HOH . P 9 HOH A 69 1069 1069 HOH HOH . P 9 HOH A 70 1070 1070 HOH HOH . Q 9 HOH B 1 1001 1001 HOH HOH . Q 9 HOH B 2 1002 1002 HOH HOH . Q 9 HOH B 3 1003 1003 HOH HOH . Q 9 HOH B 4 1004 1004 HOH HOH . Q 9 HOH B 5 1005 1005 HOH HOH . Q 9 HOH B 6 1006 1006 HOH HOH . Q 9 HOH B 7 1007 1007 HOH HOH . Q 9 HOH B 8 1008 1008 HOH HOH . Q 9 HOH B 9 1009 1009 HOH HOH . Q 9 HOH B 10 1010 1010 HOH HOH . Q 9 HOH B 11 1011 1011 HOH HOH . Q 9 HOH B 12 1012 1012 HOH HOH . Q 9 HOH B 13 1013 1013 HOH HOH . Q 9 HOH B 14 1014 1014 HOH HOH . Q 9 HOH B 15 1015 1015 HOH HOH . Q 9 HOH B 16 1016 1016 HOH HOH . Q 9 HOH B 17 1017 1017 HOH HOH . Q 9 HOH B 18 1018 1018 HOH HOH . Q 9 HOH B 19 1019 1019 HOH HOH . Q 9 HOH B 20 1020 1020 HOH HOH . Q 9 HOH B 21 1021 1021 HOH HOH . Q 9 HOH B 22 1022 1022 HOH HOH . Q 9 HOH B 23 1023 1023 HOH HOH . Q 9 HOH B 24 1024 1024 HOH HOH . Q 9 HOH B 25 1025 1025 HOH HOH . Q 9 HOH B 26 1026 1026 HOH HOH . Q 9 HOH B 27 1027 1027 HOH HOH . Q 9 HOH B 28 1028 1028 HOH HOH . Q 9 HOH B 29 1029 1029 HOH HOH . Q 9 HOH B 30 1030 1030 HOH HOH . Q 9 HOH B 31 1031 1031 HOH HOH . Q 9 HOH B 32 1032 1032 HOH HOH . Q 9 HOH B 33 1033 1033 HOH HOH . Q 9 HOH B 34 1034 1034 HOH HOH . Q 9 HOH B 35 1035 1035 HOH HOH . Q 9 HOH B 36 1036 1036 HOH HOH . Q 9 HOH B 37 1037 1037 HOH HOH . Q 9 HOH B 38 1038 1038 HOH HOH . Q 9 HOH B 39 1039 1039 HOH HOH . Q 9 HOH B 40 1040 1040 HOH HOH . Q 9 HOH B 41 1041 1041 HOH HOH . Q 9 HOH B 42 1042 1042 HOH HOH . Q 9 HOH B 43 1043 1043 HOH HOH . Q 9 HOH B 44 1044 1044 HOH HOH . Q 9 HOH B 45 1045 1045 HOH HOH . Q 9 HOH B 46 1046 1046 HOH HOH . Q 9 HOH B 47 1047 1047 HOH HOH . Q 9 HOH B 48 1048 1048 HOH HOH . Q 9 HOH B 49 1049 1049 HOH HOH . Q 9 HOH B 50 1050 1050 HOH HOH . Q 9 HOH B 51 1051 1051 HOH HOH . Q 9 HOH B 52 1052 1052 HOH HOH . Q 9 HOH B 53 1053 1053 HOH HOH . Q 9 HOH B 54 1054 1054 HOH HOH . Q 9 HOH B 55 1055 1055 HOH HOH . Q 9 HOH B 56 1056 1056 HOH HOH . Q 9 HOH B 57 1057 1057 HOH HOH . Q 9 HOH B 58 1058 1058 HOH HOH . Q 9 HOH B 59 1059 1059 HOH HOH . Q 9 HOH B 60 1060 1060 HOH HOH . Q 9 HOH B 61 1061 1061 HOH HOH . Q 9 HOH B 62 1062 1062 HOH HOH . Q 9 HOH B 63 1063 1063 HOH HOH . Q 9 HOH B 64 1064 1064 HOH HOH . Q 9 HOH B 65 1065 1065 HOH HOH . Q 9 HOH B 66 1066 1066 HOH HOH . Q 9 HOH B 67 1067 1067 HOH HOH . Q 9 HOH B 68 1068 1068 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 JSS . . . N 6 -0.227 3.412 65.287 1 58.19 ? C1 JSS 800 B 1 HETATM 2 O O1 JSS . . . N 6 -0.343 4.665 64.599 1 55.35 ? O1 JSS 800 B 1 HETATM 3 C C2 JSS . . . N 6 1.065 2.727 64.858 1 62.37 ? C2 JSS 800 B 1 HETATM 4 N N2 JSS . . . N 6 1.055 2.372 63.458 1 63.61 ? N2 JSS 800 B 1 HETATM 5 C C3 JSS . . . N 6 0.668 1.024 63.126 1 67.09 ? C3 JSS 800 B 1 HETATM 6 C C4 JSS . . . N 6 0.675 0.792 61.629 1 72.6 ? C4 JSS 800 B 1 HETATM 7 N N1' JSS . . . N 6 -2.721 7.12 64.183 1 48.32 ? N1' JSS 800 B 1 HETATM 8 C C11 JSS . . . N 6 0.219 -0.62 61.411 1 77.95 ? C11 JSS 800 B 1 HETATM 9 C C12 JSS . . . N 6 1.124 -1.647 61.65 1 80.51 ? C12 JSS 800 B 1 HETATM 10 C C13 JSS . . . N 6 0.707 -2.966 61.457 1 83.64 ? C13 JSS 800 B 1 HETATM 11 F F13 JSS . . . N 6 1.591 -3.956 61.696 1 86.66 ? F13 JSS 800 B 1 HETATM 12 C C14 JSS . . . N 6 -0.608 -3.258 61.042 1 82.98 ? C14 JSS 800 B 1 HETATM 13 C C15 JSS . . . N 6 -1.52 -2.223 60.811 1 81.15 ? C15 JSS 800 B 1 HETATM 14 C C16 JSS . . . N 6 -1.1 -0.9 60.998 1 80.35 ? C16 JSS 800 B 1 HETATM 15 N N1A JSS . . . N 6 -0.196 9.648 66.357 1 42.65 ? N1A JSS 800 B 1 HETATM 16 C C2' JSS . . . N 6 -2.236 5.837 63.798 1 48.31 ? C2' JSS 800 B 1 HETATM 17 C C2A JSS . . . N 6 0.203 8.428 66.696 1 41.34 ? C2A JSS 800 B 1 HETATM 18 C C3' JSS . . . N 6 -1.519 5.346 65.04 1 49.15 ? C3' JSS 800 B 1 HETATM 19 C C3A JSS . . . N 6 0.749 8.222 67.936 1 40.48 ? C3A JSS 800 B 1 HETATM 20 C C4' JSS . . . N 6 -1.273 6.549 65.944 1 48.95 ? C4' JSS 800 B 1 HETATM 21 C C4A JSS . . . N 6 0.841 9.253 68.829 1 37.89 ? C4A JSS 800 B 1 HETATM 22 C C5' JSS . . . N 6 -2.469 7.405 65.593 1 48.42 ? C5' JSS 800 B 1 HETATM 23 C C5A JSS . . . N 6 0.377 10.52 68.464 1 35.59 ? C5A JSS 800 B 1 HETATM 24 C C6A JSS . . . N 6 -0.132 10.687 67.2 1 36.87 ? C6A JSS 800 B 1 HETATM 25 N N6A JSS . . . N 6 -0.571 11.891 66.717 1 36.72 ? N6A JSS 800 B 1 HETATM 26 C C7A JSS . . . N 6 0.06 7.325 65.682 1 46.51 ? C7A JSS 800 B 1 HETATM 27 C C8A JSS . . . N 6 1.414 8.939 70.199 1 35.44 ? C8A JSS 800 B 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #