data_380D
#
_model_server_result.job_id            urRz7pmzFme_NSUc60mKdQ 
_model_server_result.datetime_utc      '2024-10-18 15:29:42' 
_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          380d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":7}' 
#
_entry.id    380D 
#
_exptl.entry_id    380D 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              606.416 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-BROMO-4'-EPIDAUNORUBICIN" 
_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            380D 
_cell.length_a            37.23 
_cell.length_b            37.23 
_cell.length_c            61.96 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 380D 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 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,D,E,F 
_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
? 2 C N N 
? 2 D 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
covale ? covale1 A O3' DG 2 A DG 2 1_555 A P G49 3 A G49 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.592 ? 
covale ? covale2 A O3' G49 3 A G49 3 1_555 A P CBR 4 A CBR 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.602 ? 
covale ? covale3 A CM2 G49 3 A G49 3 1_555 C N3' DM8 . A DM8 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? 
covale ? covale4 A O3' CBR 4 A CBR 4 1_555 A P DC 5 A DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.61 ? 
covale ? covale5 B O3' DG 2 B DG 8 1_555 B P G49 3 B G49 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.6 ? 
covale ? covale6 B O3' G49 3 B G49 9 1_555 B P CBR 4 B CBR 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.603 ? 
covale ? covale7 B CM2 G49 3 B G49 9 1_555 D N3' DM8 . B DM8 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? 
covale ? covale8 B O3' CBR 4 B CBR 10 1_555 B P DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.598 ? 
hydrog WATSON-CRICK hydrog1 A N3 DC 1 A DC 1 1_555 B N1 DG 6 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 A N4 DC 1 A DC 1 1_555 B O6 DG 6 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 A O2 DC 1 A DC 1 1_555 B N2 DG 6 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 A N1 DG 2 A DG 2 1_555 B N3 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 A N2 DG 2 A DG 2 1_555 B O2 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 A O6 DG 2 A DG 2 1_555 B N4 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 A N1 G49 3 A G49 3 1_555 B N3 CBR 4 B CBR 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 A N2 G49 3 A G49 3 1_555 B O2 CBR 4 B CBR 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 A O6 G49 3 A G49 3 1_555 B N4 CBR 4 B CBR 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog10 A N3 CBR 4 A CBR 4 1_555 B N1 G49 3 B G49 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog11 A N4 CBR 4 A CBR 4 1_555 B O6 G49 3 B G49 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog12 A O2 CBR 4 A CBR 4 1_555 B N2 G49 3 B G49 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog13 A N3 DC 5 A DC 5 1_555 B N1 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog14 A N4 DC 5 A DC 5 1_555 B O6 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog15 A O2 DC 5 A DC 5 1_555 B N2 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog16 A N1 DG 6 A DG 6 1_555 B N3 DC 1 B DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog17 A N2 DG 6 A DG 6 1_555 B O2 DC 1 B DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog18 A O6 DG 6 A DG 6 1_555 B N4 DC 1 B DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_chem_comp.formula           'C27 H28 Br N O10' 
_chem_comp.formula_weight    606.416 
_chem_comp.id                DM8 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-BROMO-4'-EPIDAUNORUBICIN" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'WP401;DAUNOMYCIN DERIVATIVE;DAUNORUBICIN DERIVATIVE' 
#
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 DM8 doub 110 n y 
C1 C15 DM8 sing 111 n y 
C1 H1 DM8 sing 112 n n 
C2 C3 DM8 sing 113 n y 
C2 H2 DM8 sing 114 n n 
C3 C4 DM8 doub 115 n y 
C3 H3 DM8 sing 116 n n 
C4 C16 DM8 sing 117 n y 
C4 O4 DM8 sing 118 n n 
C5 C16 DM8 sing 119 n n 
C5 C17 DM8 sing 120 n n 
C5 O5 DM8 doub 121 n n 
C6 C17 DM8 doub 122 n y 
C6 C20 DM8 sing 123 n y 
C6 O6 DM8 sing 124 n n 
C7 C8 DM8 sing 125 n n 
C7 C20 DM8 sing 126 n n 
C7 O7 DM8 sing 127 n n 
C7 H7 DM8 sing 128 n n 
C8 C9 DM8 sing 129 n n 
C8 H81 DM8 sing 130 n n 
C8 H82 DM8 sing 131 n n 
C9 C10 DM8 sing 132 n n 
C9 C13 DM8 sing 133 n n 
C9 O9 DM8 sing 134 n n 
C10 C19 DM8 sing 135 n n 
C10 H101 DM8 sing 136 n n 
C10 H102 DM8 sing 137 n n 
C11 C18 DM8 doub 138 n y 
C11 C19 DM8 sing 139 n y 
C11 O11 DM8 sing 140 n n 
C12 C15 DM8 sing 141 n n 
C12 C18 DM8 sing 142 n n 
C12 O12 DM8 doub 143 n n 
C13 C14 DM8 sing 144 n n 
C13 O13 DM8 doub 145 n n 
C14 H141 DM8 sing 146 n n 
C14 H142 DM8 sing 147 n n 
C14 H143 DM8 sing 148 n n 
C15 C16 DM8 doub 149 n y 
C17 C18 DM8 sing 150 n y 
C19 C20 DM8 doub 151 n y 
C21 O4 DM8 sing 152 n n 
C21 H211 DM8 sing 153 n n 
C21 H212 DM8 sing 154 n n 
C21 H213 DM8 sing 155 n n 
O6 H6 DM8 sing 156 n n 
O7 C1' DM8 sing 157 n n 
O9 H9 DM8 sing 158 n n 
O11 H11 DM8 sing 159 n n 
C1' C2' DM8 sing 160 n n 
C1' O5' DM8 sing 161 n n 
C1' H1' DM8 sing 162 n n 
C2' C3' DM8 sing 163 n n 
C2' BR DM8 sing 164 n n 
C2' H2' DM8 sing 165 n n 
C3' C4' DM8 sing 166 n n 
C3' N3' DM8 sing 167 n n 
C3' H3' DM8 sing 168 n n 
C4' C5' DM8 sing 169 n n 
C4' O4' DM8 sing 170 n n 
C4' H4' DM8 sing 171 n n 
C5' C6' DM8 sing 172 n n 
C5' O5' DM8 sing 173 n n 
C5' H5' DM8 sing 174 n n 
C6' "H6'1" DM8 sing 175 n n 
C6' "H6'2" DM8 sing 176 n n 
C6' "H6'3" DM8 sing 177 n n 
O4' HO4' DM8 sing 178 n n 
N3' "HN'1" DM8 sing 179 n n 
N3' "HN'2" DM8 sing 180 n n 
#
_atom_sites.entry_id                     380D 
_atom_sites.fract_transf_matrix[1][1]    0.02686 
_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]    0.02686 
_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]    0.016139 
_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 DM8 A 1 7 3 DM8 DM8 . 
D 2 DM8 B 1 13 9 DM8 DM8 . 
E 3 HOH A 1 18 18 HOH HOH . 
E 3 HOH A 2 19 19 HOH HOH . 
E 3 HOH A 3 22 22 HOH HOH . 
E 3 HOH A 4 24 24 HOH HOH . 
E 3 HOH A 5 26 26 HOH HOH . 
E 3 HOH A 6 30 30 HOH HOH . 
E 3 HOH A 7 31 31 HOH HOH . 
E 3 HOH A 8 33 33 HOH HOH . 
E 3 HOH A 9 35 35 HOH HOH . 
E 3 HOH A 10 40 40 HOH HOH . 
E 3 HOH A 11 41 41 HOH HOH . 
E 3 HOH A 12 44 44 HOH HOH . 
E 3 HOH A 13 45 45 HOH HOH . 
E 3 HOH A 14 47 47 HOH HOH . 
F 3 HOH B 1 15 15 HOH HOH . 
F 3 HOH B 2 16 16 HOH HOH . 
F 3 HOH B 3 17 17 HOH HOH . 
F 3 HOH B 4 20 20 HOH HOH . 
F 3 HOH B 5 21 21 HOH HOH . 
F 3 HOH B 6 23 23 HOH HOH . 
F 3 HOH B 7 25 25 HOH HOH . 
F 3 HOH B 8 27 27 HOH HOH . 
F 3 HOH B 9 28 28 HOH HOH . 
F 3 HOH B 10 29 29 HOH HOH . 
F 3 HOH B 11 32 32 HOH HOH . 
F 3 HOH B 12 34 34 HOH HOH . 
F 3 HOH B 13 36 36 HOH HOH . 
F 3 HOH B 14 37 37 HOH HOH . 
F 3 HOH B 15 38 38 HOH HOH . 
F 3 HOH B 16 39 39 HOH HOH . 
F 3 HOH B 17 42 42 HOH HOH . 
F 3 HOH B 18 43 43 HOH HOH . 
F 3 HOH B 19 46 46 HOH HOH . 
F 3 HOH B 20 48 48 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 DM8 . . . C 2 3.037 18.634 19.854 1 13.97 ? C1 DM8 7 A 1 
HETATM 2 C C2 DM8 . . . C 2 3.979 19.532 20.355 1 12.88 ? C2 DM8 7 A 1 
HETATM 3 C C3 DM8 . . . C 2 4.724 20.32 19.492 1 13.26 ? C3 DM8 7 A 1 
HETATM 4 C C4 DM8 . . . C 2 4.565 20.207 18.135 1 11.51 ? C4 DM8 7 A 1 
HETATM 5 C C5 DM8 . . . C 2 3.499 19.094 16.159 1 11.4 ? C5 DM8 7 A 1 
HETATM 6 C C6 DM8 . . . C 2 2.367 17.951 14.296 1 8.24 ? C6 DM8 7 A 1 
HETATM 7 C C7 DM8 . . . C 2 1.418 16.781 12.347 1 10.79 ? C7 DM8 7 A 1 
HETATM 8 C C8 DM8 . . . C 2 0.236 15.971 11.923 1 11.46 ? C8 DM8 7 A 1 
HETATM 9 C C9 DM8 . . . C 2 -0.026 14.767 12.773 1 13 ? C9 DM8 7 A 1 
HETATM 10 C C10 DM8 . . . C 2 -0.327 15.254 14.193 1 11.87 ? C10 DM8 7 A 1 
HETATM 11 C C11 DM8 . . . C 2 0.82 16.5 16.04 1 10.25 ? C11 DM8 7 A 1 
HETATM 12 C C12 DM8 . . . C 2 1.917 17.526 17.957 1 12.85 ? C12 DM8 7 A 1 
HETATM 13 C C13 DM8 . . . C 2 -1.235 13.923 12.239 1 16.34 ? C13 DM8 7 A 1 
HETATM 14 C C14 DM8 . . . C 2 -1.009 12.659 11.403 1 13.15 ? C14 DM8 7 A 1 
HETATM 15 C C15 DM8 . . . C 2 2.87 18.512 18.48 1 12.96 ? C15 DM8 7 A 1 
HETATM 16 C C16 DM8 . . . C 2 3.65 19.278 17.612 1 13.08 ? C16 DM8 7 A 1 
HETATM 17 C C17 DM8 . . . C 2 2.521 18.124 15.655 1 10.2 ? C17 DM8 7 A 1 
HETATM 18 C C18 DM8 . . . C 2 1.761 17.382 16.524 1 9.35 ? C18 DM8 7 A 1 
HETATM 19 C C19 DM8 . . . C 2 0.655 16.336 14.677 1 9.65 ? C19 DM8 7 A 1 
HETATM 20 C C20 DM8 . . . C 2 1.454 17.049 13.807 1 8.42 ? C20 DM8 7 A 1 
HETATM 21 C C21 DM8 . . . C 2 6.363 21.745 17.874 1 14.92 ? C21 DM8 7 A 1 
HETATM 22 O O4 DM8 . . . C 2 5.284 21.015 17.343 1 15.96 ? O4 DM8 7 A 1 
HETATM 23 O O5 DM8 . . . C 2 4.104 19.848 15.375 1 13.56 ? O5 DM8 7 A 1 
HETATM 24 O O6 DM8 . . . C 2 3.054 18.79 13.416 1 9.26 ? O6 DM8 7 A 1 
HETATM 25 O O7 DM8 . . . C 2 2.668 16.213 11.923 1 16.59 ? O7 DM8 7 A 1 
HETATM 26 O O9 DM8 . . . C 2 1.149 13.984 12.765 1 16.01 ? O9 DM8 7 A 1 
HETATM 27 O O11 DM8 . . . C 2 0.022 15.658 16.83 1 9.83 ? O11 DM8 7 A 1 
HETATM 28 O O12 DM8 . . . C 2 1.396 16.686 18.716 1 14.17 ? O12 DM8 7 A 1 
HETATM 29 O O13 DM8 . . . C 2 -2.395 14.212 12.6 1 16.45 ? O13 DM8 7 A 1 
HETATM 30 C C1' DM8 . . . C 2 3.206 16.547 10.634 1 14.31 ? C1' DM8 7 A 1 
HETATM 31 C C2' DM8 . . . C 2 4.704 16.211 10.635 1 14.95 ? C2' DM8 7 A 1 
HETATM 32 C C3' DM8 . . . C 2 4.925 14.647 10.53 1 14.61 ? C3' DM8 7 A 1 
HETATM 33 C C4' DM8 . . . C 2 4.09 13.942 9.429 1 12.44 ? C4' DM8 7 A 1 
HETATM 34 C C5' DM8 . . . C 2 2.634 14.327 9.557 1 12.84 ? C5' DM8 7 A 1 
HETATM 35 C C6' DM8 . . . C 2 1.851 13.787 8.389 1 12.32 ? C6' DM8 7 A 1 
HETATM 36 O O5' DM8 . . . C 2 2.561 15.784 9.553 1 14.87 ? O5' DM8 7 A 1 
HETATM 37 O O4' DM8 . . . C 2 4.169 12.535 9.478 1 12.28 ? O4' DM8 7 A 1 
HETATM 38 N N3' DM8 . . . C 2 6.328 14.289 10.363 1 11.6 ? N3' DM8 7 A 1 
HETATM 39 BR BR DM8 . . . C 2 5.487 17.202 9.272 1 20.05 ? BR DM8 7 A 1 
#
_model_server_stats.io_time_ms              58 
_model_server_stats.parse_time_ms           5 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           290 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           39 
#