data_236D # _model_server_result.job_id YF9v7yZu5Gl3mdPSoEvL2Q _model_server_result.datetime_utc '2024-10-18 13:24:01' _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 236d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":7}' # _entry.id 236D # _exptl.entry_id 236D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 638.619 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "3'-DESAMINO-3'-(3-CYANO-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 236D _cell.length_a 28.186 _cell.length_b 28.186 _cell.length_c 53.352 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 236D _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 28.186 28.186 26.676 # _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 H34 N2 O12' _chem_comp.formula_weight 638.619 _chem_comp.id CMD _chem_comp.mon_nstd_flag . _chem_comp.name "3'-DESAMINO-3'-(3-CYANO-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 CMD doub 1 n y C1 C20 CMD sing 2 n y C1 H1 CMD sing 3 n n C2 C3 CMD sing 4 n y C2 H2 CMD sing 5 n n C3 C4 CMD doub 6 n y C3 H3 CMD sing 7 n n C4 O4 CMD sing 8 n n C4 C5 CMD sing 9 n y O4 C21 CMD sing 10 n n C5 C6 CMD sing 11 n n C5 C20 CMD doub 12 n y C6 O6 CMD doub 13 n n C6 C7 CMD sing 14 n n C7 C8 CMD doub 15 n y C7 C18 CMD sing 16 n y C8 O8 CMD sing 17 n n C8 C9 CMD sing 18 n y O8 HO8 CMD sing 19 n n C9 C10 CMD sing 20 n n C9 C16 CMD doub 21 n y C10 O10 CMD sing 22 n n C10 C11 CMD sing 23 n n C10 H10 CMD sing 24 n n O10 C1' CMD sing 25 n n C11 C12 CMD sing 26 n n C11 H111 CMD sing 27 n n C11 H112 CMD sing 28 n n C12 O12 CMD sing 29 n n C12 C13 CMD sing 30 n n C12 C15 CMD sing 31 n n O12 HO12 CMD sing 32 n n C13 O13 CMD doub 33 n n C13 C14 CMD sing 34 n n C14 O14 CMD sing 35 n n C14 H141 CMD sing 36 n n C14 H142 CMD sing 37 n n O14 HO14 CMD sing 38 n n C15 C16 CMD sing 39 n n C15 H151 CMD sing 40 n n C15 H152 CMD sing 41 n n C16 C17 CMD sing 42 n y C17 O17 CMD sing 43 n n C17 C18 CMD doub 44 n y O17 HO17 CMD sing 45 n n C18 C19 CMD sing 46 n n C19 O19 CMD doub 47 n n C19 C20 CMD sing 48 n n C21 H211 CMD sing 49 n n C21 H212 CMD sing 50 n n C21 H213 CMD sing 51 n n C1' C2' CMD sing 52 n n C1' O5' CMD sing 53 n n C1' H1' CMD sing 54 n n C2' C3' CMD sing 55 n n C2' "H2'1" CMD sing 56 n n C2' "H2'2" CMD sing 57 n n C3' C4' CMD sing 58 n n C3' N3' CMD sing 59 n n C3' H3' CMD sing 60 n n C4' O4' CMD sing 61 n n C4' C5' CMD sing 62 n n C4' H4' CMD sing 63 n n O4' HO4' CMD sing 64 n n C5' O5' CMD sing 65 n n C5' C6' CMD sing 66 n n C5' H5' CMD sing 67 n n C6' "H6'1" CMD sing 68 n n C6' "H6'2" CMD sing 69 n n C6' "H6'3" CMD sing 70 n n N3' C33 CMD sing 71 n n N3' C53 CMD sing 72 n n C33 C23 CMD sing 73 n n C33 C73 CMD sing 74 n n C33 H33 CMD sing 75 n n C23 O16 CMD sing 76 n n C23 H231 CMD sing 77 n n C23 H232 CMD sing 78 n n O16 C63 CMD sing 79 n n C63 C53 CMD sing 80 n n C63 H631 CMD sing 81 n n C63 H632 CMD sing 82 n n C53 H531 CMD sing 83 n n C53 H532 CMD sing 84 n n C73 N73 CMD trip 85 n n # _atom_sites.entry_id 236D _atom_sites.fract_transf_matrix[1][1] 0.035479 _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] 0.035479 _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] 0.018743 _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 CMD A 1 7 7 CMD CMD . 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 . C 3 HOH A 50 57 57 HOH HOH . C 3 HOH A 51 58 58 HOH HOH . C 3 HOH A 52 59 59 HOH HOH . C 3 HOH A 53 60 60 HOH HOH . C 3 HOH A 54 61 61 HOH HOH . C 3 HOH A 55 62 62 HOH HOH . C 3 HOH A 56 63 63 HOH HOH . C 3 HOH A 57 64 64 HOH HOH . C 3 HOH A 58 65 65 HOH HOH . C 3 HOH A 59 66 66 HOH HOH . C 3 HOH A 60 67 67 HOH HOH . C 3 HOH A 61 68 68 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 CMD . . . B 2 15.466 18.321 5.079 1 12.28 ? C1 CMD 7 A 1 HETATM 2 C C2 CMD . . . B 2 16.658 19.042 5.036 1 12.14 ? C2 CMD 7 A 1 HETATM 3 C C3 CMD . . . B 2 17.952 18.377 4.956 1 12.4 ? C3 CMD 7 A 1 HETATM 4 C C4 CMD . . . B 2 17.974 16.909 4.866 1 11.96 ? C4 CMD 7 A 1 HETATM 5 O O4 CMD . . . B 2 19.099 16.196 4.775 1 12 ? O4 CMD 7 A 1 HETATM 6 C C5 CMD . . . B 2 16.711 16.272 4.892 1 12.03 ? C5 CMD 7 A 1 HETATM 7 C C6 CMD . . . B 2 16.655 14.781 4.839 1 12.1 ? C6 CMD 7 A 1 HETATM 8 O O6 CMD . . . B 2 17.642 14.051 4.743 1 12.03 ? O6 CMD 7 A 1 HETATM 9 C C7 CMD . . . B 2 15.33 14.104 4.882 1 12.18 ? C7 CMD 7 A 1 HETATM 10 C C8 CMD . . . B 2 15.288 12.703 4.818 1 12.42 ? C8 CMD 7 A 1 HETATM 11 O O8 CMD . . . B 2 16.354 11.962 4.738 1 12.68 ? O8 CMD 7 A 1 HETATM 12 C C9 CMD . . . B 2 14.023 12.081 4.828 1 13 ? C9 CMD 7 A 1 HETATM 13 C C10 CMD . . . B 2 14.034 10.499 4.738 1 13.62 ? C10 CMD 7 A 1 HETATM 14 O O10 CMD . . . B 2 14.817 10.127 5.901 1 14.54 ? O10 CMD 7 A 1 HETATM 15 C C11 CMD . . . B 2 12.67 9.885 4.674 1 13.54 ? C11 CMD 7 A 1 HETATM 16 C C12 CMD . . . B 2 11.621 10.632 5.442 1 13.43 ? C12 CMD 7 A 1 HETATM 17 O O12 CMD . . . B 2 11.79 10.488 6.866 1 13.78 ? O12 CMD 7 A 1 HETATM 18 C C13 CMD . . . B 2 10.229 10.009 5.159 1 13.69 ? C13 CMD 7 A 1 HETATM 19 O O13 CMD . . . B 2 9.874 10.409 4.049 1 13.89 ? O13 CMD 7 A 1 HETATM 20 C C14 CMD . . . B 2 9.854 8.577 5.554 1 14.02 ? C14 CMD 7 A 1 HETATM 21 O O14 CMD . . . B 2 8.414 8.29 5.655 1 14.12 ? O14 CMD 7 A 1 HETATM 22 C C15 CMD . . . B 2 11.503 12.134 4.983 1 13.17 ? C15 CMD 7 A 1 HETATM 23 C C16 CMD . . . B 2 12.802 12.746 4.935 1 12.74 ? C16 CMD 7 A 1 HETATM 24 C C17 CMD . . . B 2 12.884 14.152 4.994 1 12.3 ? C17 CMD 7 A 1 HETATM 25 O O17 CMD . . . B 2 11.731 14.919 5.095 1 12.27 ? O17 CMD 7 A 1 HETATM 26 C C18 CMD . . . B 2 14.073 14.888 4.999 1 12.22 ? C18 CMD 7 A 1 HETATM 27 C C19 CMD . . . B 2 14.18 16.325 5.047 1 12.14 ? C19 CMD 7 A 1 HETATM 28 O O19 CMD . . . B 2 13.197 17.047 5.154 1 12.22 ? O19 CMD 7 A 1 HETATM 29 C C20 CMD . . . B 2 15.516 16.92 5.01 1 12.09 ? C20 CMD 7 A 1 HETATM 30 C C21 CMD . . . B 2 20.398 17.007 4.77 1 11.95 ? C21 CMD 7 A 1 HETATM 31 C C1' CMD . . . B 2 15.553 8.966 5.975 1 15.49 ? C1' CMD 7 A 1 HETATM 32 C C2' CMD . . . B 2 16.585 9.014 7.064 1 16.04 ? C2' CMD 7 A 1 HETATM 33 C C3' CMD . . . B 2 15.86 9.166 8.424 1 16.71 ? C3' CMD 7 A 1 HETATM 34 C C4' CMD . . . B 2 14.896 7.96 8.59 1 16.56 ? C4' CMD 7 A 1 HETATM 35 O O4' CMD . . . B 2 15.739 6.77 8.723 1 16.79 ? O4' CMD 7 A 1 HETATM 36 C C5' CMD . . . B 2 13.882 7.94 7.475 1 16.18 ? C5' CMD 7 A 1 HETATM 37 O O5' CMD . . . B 2 14.6 7.85 6.141 1 15.93 ? O5' CMD 7 A 1 HETATM 38 C C6' CMD . . . B 2 13.011 6.655 7.459 1 16.19 ? C6' CMD 7 A 1 HETATM 39 N N3' CMD . . . B 2 16.869 9.163 9.534 1 17.32 ? N3' CMD 7 A 1 HETATM 40 C C33 CMD . . . B 2 16.156 9.076 10.761 1 17.83 ? C33 CMD 7 A 1 HETATM 41 C C23 CMD . . . B 2 16.669 10.113 11.839 1 17.85 ? C23 CMD 7 A 1 HETATM 42 O O16 CMD . . . B 2 18.129 10.017 11.753 1 18.03 ? O16 CMD 7 A 1 HETATM 43 C C63 CMD . . . B 2 18.631 10.626 10.542 1 17.82 ? C63 CMD 7 A 1 HETATM 44 C C53 CMD . . . B 2 17.763 10.263 9.337 1 17.54 ? C53 CMD 7 A 1 HETATM 45 C C73 CMD . . . B 2 16.432 7.672 11.305 1 18.36 ? C73 CMD 7 A 1 HETATM 46 N N73 CMD . . . B 2 17.286 7.055 11.839 1 18.72 ? N73 CMD 7 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 46 #