data_6BD5 # _model_server_result.job_id UIt3oww0mSd1DOSNubT0Bw _model_server_result.datetime_utc '2025-01-21 04:18:02' _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 6bd5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":602}' # _entry.id 6BD5 # _exptl.entry_id 6BD5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 422.585 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'tert-butyl (2-{[(2R)-2-(cyclopentylamino)-3-oxo-3-{[(pyridin-3-yl)methyl]amino}propyl]sulfanyl}ethyl)carbamate' _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 6BD5 _cell.length_a 77.449 _cell.length_b 101.95 _cell.length_c 129.18 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6BD5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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_545 -x,-y-1,z -1 0 0 0 -1 0 0 0 1 0 -101.95 0 3 'crystal symmetry operation' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 4_545 x,-y-1,-z 1 0 0 0 -1 0 0 0 -1 0 -101.95 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 SG CYS 422 A CYS 442 1_555 B FE HEM . A HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? metalc ? metalc2 B FE HEM . A HEM 601 1_555 C N28 D7M . A D7M 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? # _chem_comp.formula 'C21 H34 N4 O3 S' _chem_comp.formula_weight 422.585 _chem_comp.id D7M _chem_comp.mon_nstd_flag . _chem_comp.name 'tert-butyl (2-{[(2R)-2-(cyclopentylamino)-3-oxo-3-{[(pyridin-3-yl)methyl]amino}propyl]sulfanyl}ethyl)carbamate' _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 C04 C02 D7M sing 83 n n O05 C02 D7M sing 84 n n O05 C06 D7M sing 85 n n C02 C01 D7M sing 86 n n C02 C03 D7M sing 87 n n N08 C06 D7M sing 88 n n N08 C09 D7M sing 89 n n C06 O07 D7M doub 90 n n C09 C10 D7M sing 91 n n C10 S11 D7M sing 92 n n C26 C27 D7M doub 93 n y C26 C25 D7M sing 94 n y C27 N28 D7M sing 95 n y S11 C12 D7M sing 96 n n N28 C29 D7M doub 97 n y C25 C24 D7M doub 98 n y C12 C13 D7M sing 99 n n C29 C24 D7M sing 100 n y C24 C23 D7M sing 101 n n C13 C20 D7M sing 102 n n C13 N14 D7M sing 103 n n O21 C20 D7M doub 104 n n C20 N22 D7M sing 105 n n N22 C23 D7M sing 106 n n N14 C15 D7M sing 107 n n C15 C16 D7M sing 108 n n C15 C19 D7M sing 109 n n C16 C17 D7M sing 110 n n C17 C18 D7M sing 111 n n C19 C18 D7M sing 112 n n C10 H1 D7M sing 113 n n C10 H2 D7M sing 114 n n C12 H3 D7M sing 115 n n C12 H4 D7M sing 116 n n C13 H5 D7M sing 117 n n C15 H6 D7M sing 118 n n C16 H7 D7M sing 119 n n C16 H8 D7M sing 120 n n C17 H9 D7M sing 121 n n C17 H10 D7M sing 122 n n C18 H11 D7M sing 123 n n C18 H12 D7M sing 124 n n C19 H13 D7M sing 125 n n C19 H14 D7M sing 126 n n C01 H15 D7M sing 127 n n C01 H16 D7M sing 128 n n C01 H17 D7M sing 129 n n C03 H18 D7M sing 130 n n C03 H19 D7M sing 131 n n C03 H20 D7M sing 132 n n C04 H21 D7M sing 133 n n C04 H22 D7M sing 134 n n C04 H23 D7M sing 135 n n N08 H24 D7M sing 136 n n C09 H25 D7M sing 137 n n C09 H26 D7M sing 138 n n N14 H27 D7M sing 139 n n N22 H29 D7M sing 140 n n C23 H30 D7M sing 141 n n C23 H31 D7M sing 142 n n C25 H32 D7M sing 143 n n C26 H33 D7M sing 144 n n C27 H34 D7M sing 145 n n C29 H35 D7M sing 146 n n # _atom_sites.entry_id 6BD5 _atom_sites.fract_transf_matrix[1][1] 0.012912 _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] 0.009809 _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] 0.007741 _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 HEM A 1 601 500 HEM HEM . C 3 D7M A 1 602 700 D7M 58C . # 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 C20 D7M . . . C 3 -18.264 -31.703 -8.525 1 143.19 ? C20 D7M 602 A 1 HETATM 2 C C10 D7M . . . C 3 -18.704 -32.114 -11.798 1 119.03 ? C10 D7M 602 A 1 HETATM 3 C C12 D7M . . . C 3 -18.985 -34.02 -9.289 1 109.65 ? C12 D7M 602 A 1 HETATM 4 C C13 D7M . . . C 3 -17.778 -33.096 -8.968 1 153.36 ? C13 D7M 602 A 1 HETATM 5 C C15 D7M . . . C 3 -17.501 -33.473 -6.629 1 148.7 ? C15 D7M 602 A 1 HETATM 6 C C16 D7M . . . C 3 -17.69 -34.866 -6.124 1 156.91 ? C16 D7M 602 A 1 HETATM 7 C C17 D7M . . . C 3 -16.255 -35.272 -5.991 1 155.49 ? C17 D7M 602 A 1 HETATM 8 C C18 D7M . . . C 3 -15.528 -34.043 -5.463 1 148.7 ? C18 D7M 602 A 1 HETATM 9 C C19 D7M . . . C 3 -16.429 -32.855 -5.762 1 148.33 ? C19 D7M 602 A 1 HETATM 10 C C01 D7M . . . C 3 -18.424 -37.584 -13.664 1 136.99 ? C01 D7M 602 A 1 HETATM 11 C C02 D7M . . . C 3 -16.903 -37.372 -13.82 1 148.14 ? C02 D7M 602 A 1 HETATM 12 C C03 D7M . . . C 3 -16.13 -38.049 -12.642 1 167.04 ? C03 D7M 602 A 1 HETATM 13 C C04 D7M . . . C 3 -16.442 -38.078 -15.144 1 116.23 ? C04 D7M 602 A 1 HETATM 14 O O05 D7M . . . C 3 -16.625 -35.916 -13.882 1 161.76 ? O05 D7M 602 A 1 HETATM 15 C C06 D7M . . . C 3 -17.134 -34.989 -12.994 1 168.44 ? C06 D7M 602 A 1 HETATM 16 O O07 D7M . . . C 3 -17.297 -35.326 -11.79 1 179.44 ? O07 D7M 602 A 1 HETATM 17 N N08 D7M . . . C 3 -17.185 -33.611 -13.29 1 154.62 ? N08 D7M 602 A 1 HETATM 18 C C09 D7M . . . C 3 -17.242 -32.51 -12.276 1 145.29 ? C09 D7M 602 A 1 HETATM 19 S S11 D7M . . . C 3 -19.71 -33.507 -10.916 1 148.89 ? S11 D7M 602 A 1 HETATM 20 N N14 D7M . . . C 3 -16.896 -33.598 -7.94 1 148.39 ? N14 D7M 602 A 1 HETATM 21 O O21 D7M . . . C 3 -19.524 -31.583 -8.527 1 142.31 ? O21 D7M 602 A 1 HETATM 22 N N22 D7M . . . C 3 -17.495 -30.607 -8.157 1 134.99 ? N22 D7M 602 A 1 HETATM 23 C C23 D7M . . . C 3 -18.102 -29.318 -7.825 1 118.28 ? C23 D7M 602 A 1 HETATM 24 C C24 D7M . . . C 3 -18.727 -28.862 -9.141 1 99.14 ? C24 D7M 602 A 1 HETATM 25 C C25 D7M . . . C 3 -18.052 -28.913 -10.353 1 104.06 ? C25 D7M 602 A 1 HETATM 26 C C26 D7M . . . C 3 -18.625 -28.564 -11.565 1 104.35 ? C26 D7M 602 A 1 HETATM 27 C C27 D7M . . . C 3 -19.967 -28.177 -11.546 1 105.43 ? C27 D7M 602 A 1 HETATM 28 N N28 D7M . . . C 3 -20.636 -28.144 -10.381 1 88.64 ? N28 D7M 602 A 1 HETATM 29 C C29 D7M . . . C 3 -20.06 -28.488 -9.216 1 92.89 ? C29 D7M 602 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 407 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 29 #