data_2DRD
#
_model_server_result.job_id            StHAMKPzDe7wQrs8Zgfssw 
_model_server_result.datetime_utc      '2025-03-06 08:11:00' 
_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          2drd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":2001}' 
#
_entry.id    2DRD 
#
_exptl.entry_id    2DRD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              457.476 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE' 
_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          98.17 
_cell.angle_gamma         90 
_cell.entry_id            2DRD 
_cell.length_a            225.801 
_cell.length_b            134.466 
_cell.length_c            162.115 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2DRD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C23 H27 N3 O7' 
_chem_comp.formula_weight    457.476 
_chem_comp.id                MIY 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     MINOCYCLINE 
#
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
O8 C21 MIY doub 235 n n 
C21 N2 MIY sing 236 n n 
C21 C2 MIY sing 237 n n 
N2 HN21 MIY sing 238 n n 
N2 HN22 MIY sing 239 n n 
C2 C1 MIY sing 240 n n 
C2 C3 MIY doub 241 n n 
C1 O1 MIY doub 242 n n 
C1 C18 MIY sing 243 n n 
C3 O2 MIY sing 244 n n 
C3 C4 MIY sing 245 n n 
O2 HO2 MIY sing 246 n n 
C4 N1 MIY sing 247 n n 
C4 C5 MIY sing 248 n n 
C4 H4 MIY sing 249 n n 
N1 C20 MIY sing 250 n n 
N1 C19 MIY sing 251 n n 
C20 H201 MIY sing 252 n n 
C20 H202 MIY sing 253 n n 
C20 H203 MIY sing 254 n n 
C19 H191 MIY sing 255 n n 
C19 H192 MIY sing 256 n n 
C19 H193 MIY sing 257 n n 
C5 C18 MIY sing 258 n n 
C5 C6 MIY sing 259 n n 
C5 H5 MIY sing 260 n n 
C18 O7 MIY sing 261 n n 
C18 C17 MIY sing 262 n n 
O7 HO7 MIY sing 263 n n 
C17 O6 MIY sing 264 n n 
C17 C16 MIY doub 265 n n 
O6 HO6 MIY sing 266 n n 
C16 C7 MIY sing 267 n n 
C16 C15 MIY sing 268 n n 
C7 C6 MIY sing 269 n n 
C7 C8 MIY sing 270 n n 
C7 H7 MIY sing 271 n n 
C6 H61 MIY sing 272 n n 
C6 H62 MIY sing 273 n n 
C15 O5 MIY doub 274 n n 
C15 C14 MIY sing 275 n n 
C14 C9 MIY doub 276 n y 
C14 C13 MIY sing 277 n y 
C9 C8 MIY sing 278 n n 
C9 C10 MIY sing 279 n y 
C8 H81 MIY sing 280 n n 
C8 H82 MIY sing 281 n n 
C13 O4 MIY sing 282 n n 
C13 C12 MIY doub 283 n y 
O4 HO4 MIY sing 284 n n 
C12 C11 MIY sing 285 n y 
C12 H12 MIY sing 286 n n 
C11 C10 MIY doub 287 n y 
C11 H11 MIY sing 288 n n 
C10 N7 MIY sing 289 n n 
N7 CN7 MIY sing 290 n n 
N7 C71 MIY sing 291 n n 
CN7 HN71 MIY sing 292 n n 
CN7 HN72 MIY sing 293 n n 
CN7 HN73 MIY sing 294 n n 
C71 H711 MIY sing 295 n n 
C71 H712 MIY sing 296 n n 
C71 H713 MIY sing 297 n n 
#
_atom_sites.entry_id                     2DRD 
_atom_sites.fract_transf_matrix[1][1]    0.004429 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000636 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007437 
_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]    0.006232 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
_pdbx_nonpoly_scheme.asym_id          D 
_pdbx_nonpoly_scheme.entity_id        2 
_pdbx_nonpoly_scheme.mon_id           MIY 
_pdbx_nonpoly_scheme.pdb_strand_id    A 
_pdbx_nonpoly_scheme.ndb_seq_num      1 
_pdbx_nonpoly_scheme.pdb_seq_num      2001 
_pdbx_nonpoly_scheme.auth_seq_num     2001 
_pdbx_nonpoly_scheme.pdb_mon_id       MIY 
_pdbx_nonpoly_scheme.auth_mon_id      MIY 
_pdbx_nonpoly_scheme.pdb_ins_code     . 
#
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 O O8 MIY . . . D 2 171.708 124.579 24.838 1 131.75 ? O8 MIY 2001 A 1 
HETATM 2 C C21 MIY . . . D 2 170.663 125.094 25.267 1 130.17 ? C21 MIY 2001 A 1 
HETATM 3 N N2 MIY . . . D 2 169.746 125.681 24.465 1 129.72 ? N2 MIY 2001 A 1 
HETATM 4 C C2 MIY . . . D 2 170.338 125.127 26.726 1 128.58 ? C2 MIY 2001 A 1 
HETATM 5 C C1 MIY . . . D 2 170.544 126.378 27.493 1 127.49 ? C1 MIY 2001 A 1 
HETATM 6 O O1 MIY . . . D 2 170.891 127.381 26.901 1 127.55 ? O1 MIY 2001 A 1 
HETATM 7 C C3 MIY . . . D 2 169.844 124.034 27.383 1 128.1 ? C3 MIY 2001 A 1 
HETATM 8 O O2 MIY . . . D 2 169.789 122.869 26.713 1 128.16 ? O2 MIY 2001 A 1 
HETATM 9 C C4 MIY . . . D 2 169.318 124.045 28.853 1 127.09 ? C4 MIY 2001 A 1 
HETATM 10 N N1 MIY . . . D 2 169.891 122.894 29.734 1 126.9 ? N1 MIY 2001 A 1 
HETATM 11 C C20 MIY . . . D 2 169.276 122.676 31.086 1 125.72 ? C20 MIY 2001 A 1 
HETATM 12 C C19 MIY . . . D 2 171.365 122.749 29.861 1 123.29 ? C19 MIY 2001 A 1 
HETATM 13 C C5 MIY . . . D 2 169.254 125.46 29.521 1 125.5 ? C5 MIY 2001 A 1 
HETATM 14 C C18 MIY . . . D 2 170.383 126.385 29.034 1 126.51 ? C18 MIY 2001 A 1 
HETATM 15 O O7 MIY . . . D 2 171.62 125.879 29.557 1 127.44 ? O7 MIY 2001 A 1 
HETATM 16 C C17 MIY . . . D 2 170.215 127.725 29.781 1 125.34 ? C17 MIY 2001 A 1 
HETATM 17 O O6 MIY . . . D 2 171.307 128.499 29.889 1 129.28 ? O6 MIY 2001 A 1 
HETATM 18 C C16 MIY . . . D 2 169.11 128.173 30.423 1 120.38 ? C16 MIY 2001 A 1 
HETATM 19 C C7 MIY . . . D 2 167.844 127.366 30.522 1 119.97 ? C7 MIY 2001 A 1 
HETATM 20 C C6 MIY . . . D 2 167.88 126.169 29.542 1 122.36 ? C6 MIY 2001 A 1 
HETATM 21 C C15 MIY . . . D 2 169.165 129.523 31.025 1 117.6 ? C15 MIY 2001 A 1 
HETATM 22 O O5 MIY . . . D 2 170.195 130.203 31.141 1 115.13 ? O5 MIY 2001 A 1 
HETATM 23 C C14 MIY . . . D 2 167.901 130.185 31.419 1 117.69 ? C14 MIY 2001 A 1 
HETATM 24 C C9 MIY . . . D 2 166.686 129.637 31.016 1 118.5 ? C9 MIY 2001 A 1 
HETATM 25 C C8 MIY . . . D 2 166.671 128.325 30.208 1 119.75 ? C8 MIY 2001 A 1 
HETATM 26 C C13 MIY . . . D 2 168.006 131.368 32.143 1 117.76 ? C13 MIY 2001 A 1 
HETATM 27 O O4 MIY . . . D 2 169.256 131.832 32.499 1 117.37 ? O4 MIY 2001 A 1 
HETATM 28 C C12 MIY . . . D 2 166.845 132.049 32.504 1 118.39 ? C12 MIY 2001 A 1 
HETATM 29 C C11 MIY . . . D 2 165.615 131.524 32.11 1 118.68 ? C11 MIY 2001 A 1 
HETATM 30 C C10 MIY . . . D 2 165.523 130.331 31.375 1 117.22 ? C10 MIY 2001 A 1 
HETATM 31 N N7 MIY . . . D 2 164.266 129.895 30.97 1 115.75 ? N7 MIY 2001 A 1 
HETATM 32 C CN7 MIY . . . D 2 163.833 130.95 30.045 1 112.32 ? CN7 MIY 2001 A 1 
HETATM 33 C C71 MIY . . . D 2 163.304 129.906 32.093 1 115.81 ? C71 MIY 2001 A 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           292 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           33 
#