data_234D # _model_server_result.job_id 7g5z0YdJNLOOK-rvWNY6og _model_server_result.datetime_utc '2024-10-18 15:29:47' _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 234d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":7}' # _entry.id 234D # _exptl.entry_id 234D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 643.635 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "3'-DESAMINO-3'-(2-METHOXY-4-MORPHOLINYL)-DOXORUBICIN" _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 234D _cell.length_a 28.206 _cell.length_b 28.206 _cell.length_c 53.646 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 234D _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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 # 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' 8_665 -y+1,-x+1,-z+1/2 0 -1 0 -1 0 0 0 0 -1 28.206 28.206 26.823 # _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 hydrog WATSON-CRICK hydrog1 A N3 DC 1 A DC 1 1_555 A N1 DG 6 A DG 6 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N4 DC 1 A DC 1 1_555 A O6 DG 6 A DG 6 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O2 DC 1 A DC 1 1_555 A N2 DG 6 A DG 6 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 DG 2 A DG 2 1_555 A N3 DC 5 A DC 5 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N2 DG 2 A DG 2 1_555 A O2 DC 5 A DC 5 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O6 DG 2 A DG 2 1_555 A N4 DC 5 A DC 5 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N1 DA 3 A DA 3 1_555 A N3 DT 4 A DT 4 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N6 DA 3 A DA 3 1_555 A O4 DT 4 A DT 4 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N3 DT 4 A DT 4 1_555 A N1 DA 3 A DA 3 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A O4 DT 4 A DT 4 1_555 A N6 DA 3 A DA 3 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N3 DC 5 A DC 5 1_555 A N1 DG 2 A DG 2 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N4 DC 5 A DC 5 1_555 A O6 DG 2 A DG 2 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A O2 DC 5 A DC 5 1_555 A N2 DG 2 A DG 2 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N1 DG 6 A DG 6 1_555 A N3 DC 1 A DC 1 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N2 DG 6 A DG 6 1_555 A O2 DC 1 A DC 1 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A O6 DG 6 A DG 6 1_555 A N4 DC 1 A DC 1 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C32 H37 N O13' _chem_comp.formula_weight 643.635 _chem_comp.id DMM _chem_comp.mon_nstd_flag . _chem_comp.name "3'-DESAMINO-3'-(2-METHOXY-4-MORPHOLINYL)-DOXORUBICIN" _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 C1 C2 DMM doub 113 n y C1 C20 DMM sing 114 n y C1 H1 DMM sing 115 n n C2 C3 DMM sing 116 n y C2 H2 DMM sing 117 n n C3 C4 DMM doub 118 n y C3 H3 DMM sing 119 n n C4 O4 DMM sing 120 n n C4 C5 DMM sing 121 n y O4 C21 DMM sing 122 n n C5 C6 DMM sing 123 n n C5 C20 DMM doub 124 n y C6 O6 DMM doub 125 n n C6 C7 DMM sing 126 n n C7 C8 DMM doub 127 n y C7 C18 DMM sing 128 n y C8 O8 DMM sing 129 n n C8 C9 DMM sing 130 n y O8 HO8 DMM sing 131 n n C9 C10 DMM sing 132 n n C9 C16 DMM doub 133 n y C10 O10 DMM sing 134 n n C10 C11 DMM sing 135 n n C10 H10 DMM sing 136 n n O10 C1' DMM sing 137 n n C11 C12 DMM sing 138 n n C11 H111 DMM sing 139 n n C11 H112 DMM sing 140 n n C12 O12 DMM sing 141 n n C12 C13 DMM sing 142 n n C12 C15 DMM sing 143 n n O12 HO12 DMM sing 144 n n C13 O13 DMM doub 145 n n C13 C14 DMM sing 146 n n C14 O14 DMM sing 147 n n C14 H141 DMM sing 148 n n C14 H142 DMM sing 149 n n O14 HO14 DMM sing 150 n n C15 C16 DMM sing 151 n n C15 H151 DMM sing 152 n n C15 H152 DMM sing 153 n n C16 C17 DMM sing 154 n y C17 O17 DMM sing 155 n n C17 C18 DMM doub 156 n y O17 HO17 DMM sing 157 n n C18 C19 DMM sing 158 n n C19 O19 DMM doub 159 n n C19 C20 DMM sing 160 n n C21 H211 DMM sing 161 n n C21 H212 DMM sing 162 n n C21 H213 DMM sing 163 n n C1' C2' DMM sing 164 n n C1' O5' DMM sing 165 n n C1' H1' DMM sing 166 n n C2' C3' DMM sing 167 n n C2' "H2'1" DMM sing 168 n n C2' "H2'2" DMM sing 169 n n C3' C4' DMM sing 170 n n C3' N3' DMM sing 171 n n C3' H3' DMM sing 172 n n C4' O4' DMM sing 173 n n C4' C5' DMM sing 174 n n C4' H4' DMM sing 175 n n O4' HO4' DMM sing 176 n n C5' O5' DMM sing 177 n n C5' C6' DMM sing 178 n n C5' H5' DMM sing 179 n n C6' "H6'1" DMM sing 180 n n C6' "H6'2" DMM sing 181 n n C6' "H6'3" DMM sing 182 n n N3' C33 DMM sing 183 n n N3' C53 DMM sing 184 n n C33 C23 DMM sing 185 n n C33 H331 DMM sing 186 n n C33 H332 DMM sing 187 n n C23 O16 DMM sing 188 n n C23 O23 DMM sing 189 n n C23 H23 DMM sing 190 n n O16 C63 DMM sing 191 n n C63 C53 DMM sing 192 n n C63 H631 DMM sing 193 n n C63 H632 DMM sing 194 n n C53 H531 DMM sing 195 n n C53 H532 DMM sing 196 n n O23 C73 DMM sing 197 n n C73 H731 DMM sing 198 n n C73 H732 DMM sing 199 n n C73 H733 DMM sing 200 n n # _atom_sites.entry_id 234D _atom_sites.fract_transf_matrix[1][1] 0.035453 _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] 0.035453 _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] 0.018641 _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 DMM A 1 7 7 DMM DMM . C 3 HOH A 1 8 8 HOH HOH . C 3 HOH A 2 9 9 HOH HOH . C 3 HOH A 3 10 10 HOH HOH . C 3 HOH A 4 11 11 HOH HOH . C 3 HOH A 5 12 12 HOH HOH . C 3 HOH A 6 13 13 HOH HOH . C 3 HOH A 7 14 14 HOH HOH . C 3 HOH A 8 15 15 HOH HOH . C 3 HOH A 9 16 16 HOH HOH . C 3 HOH A 10 17 17 HOH HOH . C 3 HOH A 11 18 18 HOH HOH . C 3 HOH A 12 19 19 HOH HOH . C 3 HOH A 13 20 20 HOH HOH . C 3 HOH A 14 21 21 HOH HOH . C 3 HOH A 15 22 22 HOH HOH . C 3 HOH A 16 23 23 HOH HOH . C 3 HOH A 17 24 24 HOH HOH . C 3 HOH A 18 25 25 HOH HOH . C 3 HOH A 19 26 26 HOH HOH . C 3 HOH A 20 27 27 HOH HOH . C 3 HOH A 21 28 28 HOH HOH . C 3 HOH A 22 29 29 HOH HOH . C 3 HOH A 23 30 30 HOH HOH . C 3 HOH A 24 31 31 HOH HOH . C 3 HOH A 25 32 32 HOH HOH . C 3 HOH A 26 33 33 HOH HOH . C 3 HOH A 27 34 34 HOH HOH . C 3 HOH A 28 35 35 HOH HOH . C 3 HOH A 29 36 36 HOH HOH . C 3 HOH A 30 37 37 HOH HOH . C 3 HOH A 31 38 38 HOH HOH . C 3 HOH A 32 39 39 HOH HOH . C 3 HOH A 33 40 40 HOH HOH . C 3 HOH A 34 41 41 HOH HOH . C 3 HOH A 35 42 42 HOH HOH . C 3 HOH A 36 43 43 HOH HOH . C 3 HOH A 37 44 44 HOH HOH . C 3 HOH A 38 45 45 HOH HOH . C 3 HOH A 39 46 46 HOH HOH . C 3 HOH A 40 47 47 HOH HOH . C 3 HOH A 41 48 48 HOH HOH . C 3 HOH A 42 49 49 HOH HOH . C 3 HOH A 43 50 50 HOH HOH . C 3 HOH A 44 51 51 HOH HOH . C 3 HOH A 45 52 52 HOH HOH . C 3 HOH A 46 53 53 HOH HOH . C 3 HOH A 47 54 54 HOH HOH . C 3 HOH A 48 55 55 HOH HOH . C 3 HOH A 49 56 56 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 DMM . . . B 2 15.398 18.311 5.263 1 13.9 ? C1 DMM 7 A 1 HETATM 2 C C2 DMM . . . B 2 16.582 19.064 5.22 1 14 ? C2 DMM 7 A 1 HETATM 3 C C3 DMM . . . B 2 17.88 18.39 5.091 1 14.37 ? C3 DMM 7 A 1 HETATM 4 C C4 DMM . . . B 2 17.888 16.918 5.037 1 14.26 ? C4 DMM 7 A 1 HETATM 5 O O4 DMM . . . B 2 18.96 16.151 4.914 1 15.1 ? O4 DMM 7 A 1 HETATM 6 C C5 DMM . . . B 2 16.633 16.247 5.016 1 14.09 ? C5 DMM 7 A 1 HETATM 7 C C6 DMM . . . B 2 16.619 14.746 4.909 1 13.81 ? C6 DMM 7 A 1 HETATM 8 O O6 DMM . . . B 2 17.601 13.934 4.839 1 14.3 ? O6 DMM 7 A 1 HETATM 9 C C7 DMM . . . B 2 15.305 14.041 4.941 1 13.65 ? C7 DMM 7 A 1 HETATM 10 C C8 DMM . . . B 2 15.268 12.65 4.833 1 14.01 ? C8 DMM 7 A 1 HETATM 11 O O8 DMM . . . B 2 16.331 11.835 4.689 1 13.78 ? O8 DMM 7 A 1 HETATM 12 C C9 DMM . . . B 2 13.979 12.044 4.828 1 14.2 ? C9 DMM 7 A 1 HETATM 13 C C10 DMM . . . B 2 13.968 10.456 4.753 1 14.89 ? C10 DMM 7 A 1 HETATM 14 O O10 DMM . . . B 2 14.755 10.14 5.933 1 15.3 ? O10 DMM 7 A 1 HETATM 15 C C11 DMM . . . B 2 12.614 9.875 4.833 1 15.03 ? C11 DMM 7 A 1 HETATM 16 C C12 DMM . . . B 2 11.531 10.668 5.542 1 15.03 ? C12 DMM 7 A 1 HETATM 17 O O12 DMM . . . B 2 11.638 10.71 6.958 1 15.81 ? O12 DMM 7 A 1 HETATM 18 C C13 DMM . . . B 2 10.188 9.945 5.225 1 15.58 ? C13 DMM 7 A 1 HETATM 19 O O13 DMM . . . B 2 9.971 10.174 4.002 1 15.78 ? O13 DMM 7 A 1 HETATM 20 C C14 DMM . . . B 2 9.923 8.422 5.542 1 15.78 ? C14 DMM 7 A 1 HETATM 21 O O14 DMM . . . B 2 8.541 8.121 5.896 1 16.13 ? O14 DMM 7 A 1 HETATM 22 C C15 DMM . . . B 2 11.418 12.154 4.962 1 14.55 ? C15 DMM 7 A 1 HETATM 23 C C16 DMM . . . B 2 12.772 12.707 4.935 1 13.85 ? C16 DMM 7 A 1 HETATM 24 C C17 DMM . . . B 2 12.862 14.12 5 1 13.44 ? C17 DMM 7 A 1 HETATM 25 O O17 DMM . . . B 2 11.68 14.805 5.123 1 12.71 ? O17 DMM 7 A 1 HETATM 26 C C18 DMM . . . B 2 14.032 14.85 5.027 1 13.22 ? C18 DMM 7 A 1 HETATM 27 C C19 DMM . . . B 2 14.106 16.295 5.139 1 13.57 ? C19 DMM 7 A 1 HETATM 28 O O19 DMM . . . B 2 13.138 17.005 5.22 1 12.89 ? O19 DMM 7 A 1 HETATM 29 C C20 DMM . . . B 2 15.446 16.915 5.112 1 13.71 ? C20 DMM 7 A 1 HETATM 30 C C21 DMM . . . B 2 20.322 16.825 4.935 1 15.1 ? C21 DMM 7 A 1 HETATM 31 C C1' DMM . . . B 2 15.536 9.006 6.051 1 16.11 ? C1' DMM 7 A 1 HETATM 32 C C2' DMM . . . B 2 16.419 9.071 7.258 1 16.5 ? C2' DMM 7 A 1 HETATM 33 C C3' DMM . . . B 2 15.508 9.096 8.535 1 16.72 ? C3' DMM 7 A 1 HETATM 34 C C4' DMM . . . B 2 14.726 7.757 8.53 1 16.76 ? C4' DMM 7 A 1 HETATM 35 O O4' DMM . . . B 2 15.75 6.702 8.594 1 17 ? O4' DMM 7 A 1 HETATM 36 C C5' DMM . . . B 2 13.804 7.728 7.333 1 16.46 ? C5' DMM 7 A 1 HETATM 37 O O5' DMM . . . B 2 14.664 7.822 6.041 1 16.44 ? O5' DMM 7 A 1 HETATM 38 C C6' DMM . . . B 2 13.017 6.417 7.065 1 16.76 ? C6' DMM 7 A 1 HETATM 39 N N3' DMM . . . B 2 16.343 9.325 9.764 1 17.01 ? N3' DMM 7 A 1 HETATM 40 C C33 DMM . . . B 2 15.832 8.538 10.863 1 16.92 ? C33 DMM 7 A 1 HETATM 41 C C23 DMM . . . B 2 16.833 8.436 12.017 1 17 ? C23 DMM 7 A 1 HETATM 42 O O16 DMM . . . B 2 17.705 9.596 12.017 1 16.86 ? O16 DMM 7 A 1 HETATM 43 C C63 DMM . . . B 2 18.54 9.748 10.863 1 17.2 ? C63 DMM 7 A 1 HETATM 44 C C53 DMM . . . B 2 17.744 9.283 9.581 1 16.84 ? C53 DMM 7 A 1 HETATM 45 O O23 DMM . . . B 2 17.502 7.13 12.022 1 17.03 ? O23 DMM 7 A 1 HETATM 46 C C73 DMM . . . B 2 18.483 6.485 12.87 1 17.02 ? C73 DMM 7 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 46 #