data_6BD7
#
_model_server_result.job_id            3HYG7gvpoVzGhDnlnRxjjg 
_model_server_result.datetime_utc      '2025-04-25 18:01:41' 
_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          6bd7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":602}' 
#
_entry.id    6BD7 
#
_exptl.entry_id    6BD7 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              486.67 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'tert-butyl [(2S)-1-{[(2R)-3-oxo-2-[(propan-2-yl)amino]-3-{[(pyridin-3-yl)methyl]amino}propyl]sulfanyl}-3-phenylpropan-2-yl]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            6BD7 
_cell.length_a            77.559 
_cell.length_b            102.8 
_cell.length_c            128.57 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6BD7 
_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        ? 
_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' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? 
metalc ? metalc2 B FE HEM . A HEM 601 1_555 C N33 D7J . A D7J 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? 
#
_chem_comp.formula           'C26 H38 N4 O3 S' 
_chem_comp.formula_weight    486.67 
_chem_comp.id                D7J 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'tert-butyl [(2S)-1-{[(2R)-3-oxo-2-[(propan-2-yl)amino]-3-{[(pyridin-3-yl)methyl]amino}propyl]sulfanyl}-3-phenylpropan-2-yl]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
C24 C21 D7J sing 83 n n 
O19 C18 D7J doub 84 n n 
C14 C13 D7J doub 85 n y 
C14 C15 D7J sing 86 n y 
C23 C21 D7J sing 87 n n 
C13 C12 D7J sing 88 n y 
C21 C22 D7J sing 89 n n 
C21 O20 D7J sing 90 n n 
C18 O20 D7J sing 91 n n 
C18 N17 D7J sing 92 n n 
C15 C16 D7J doub 93 n y 
C12 C11 D7J doub 94 n y 
C16 C11 D7J sing 95 n y 
C11 C10 D7J sing 96 n n 
N17 C09 D7J sing 97 n n 
C10 C09 D7J sing 98 n n 
C09 C08 D7J sing 99 n n 
C32 C31 D7J doub 100 n y 
C32 N33 D7J sing 101 n y 
C31 C30 D7J sing 102 n y 
C08 S07 D7J sing 103 n n 
N33 C34 D7J doub 104 n y 
C30 C29 D7J doub 105 n y 
S07 C06 D7J sing 106 n n 
C34 C29 D7J sing 107 n y 
C29 C28 D7J sing 108 n n 
C05 C06 D7J sing 109 n n 
C05 N04 D7J sing 110 n n 
C05 C25 D7J sing 111 n n 
N27 C28 D7J sing 112 n n 
N27 C25 D7J sing 113 n n 
N04 C02 D7J sing 114 n n 
C25 O26 D7J doub 115 n n 
C01 C02 D7J sing 116 n n 
C02 C03 D7J sing 117 n n 
C01 H1 D7J sing 118 n n 
C01 H2 D7J sing 119 n n 
C01 H3 D7J sing 120 n n 
C02 H4 D7J sing 121 n n 
C03 H5 D7J sing 122 n n 
C03 H6 D7J sing 123 n n 
C03 H7 D7J sing 124 n n 
C05 H8 D7J sing 125 n n 
C06 H9 D7J sing 126 n n 
C06 H10 D7J sing 127 n n 
C08 H11 D7J sing 128 n n 
C08 H12 D7J sing 129 n n 
C09 H13 D7J sing 130 n n 
C10 H14 D7J sing 131 n n 
C10 H15 D7J sing 132 n n 
C12 H16 D7J sing 133 n n 
C13 H17 D7J sing 134 n n 
C14 H18 D7J sing 135 n n 
C15 H19 D7J sing 136 n n 
C16 H20 D7J sing 137 n n 
C22 H21 D7J sing 138 n n 
C22 H22 D7J sing 139 n n 
C22 H23 D7J sing 140 n n 
C23 H24 D7J sing 141 n n 
C23 H25 D7J sing 142 n n 
C23 H26 D7J sing 143 n n 
C24 H27 D7J sing 144 n n 
C24 H28 D7J sing 145 n n 
C24 H29 D7J sing 146 n n 
C28 H30 D7J sing 147 n n 
C28 H31 D7J sing 148 n n 
C30 H32 D7J sing 149 n n 
C31 H33 D7J sing 150 n n 
C32 H34 D7J sing 151 n n 
C34 H35 D7J sing 152 n n 
N04 H36 D7J sing 153 n n 
N17 H38 D7J sing 154 n n 
N27 H39 D7J sing 155 n n 
#
_atom_sites.entry_id                     6BD7 
_atom_sites.fract_transf_matrix[1][1]    0.012893 
_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]    0.009728 
_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]    0.007778 
_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 D7J A 1 602 700 D7J 43C . 
#
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 C01 D7J . . . C 3 -14.272 -33.772 -6.396 1 124.48 ? C01 D7J 602 A 1 
HETATM 2 C C02 D7J . . . C 3 -15.736 -33.825 -6.35 1 126.95 ? C02 D7J 602 A 1 
HETATM 3 C C03 D7J . . . C 3 -16.141 -34.555 -5.179 1 128.3 ? C03 D7J 602 A 1 
HETATM 4 C C05 D7J . . . C 3 -17.461 -34.028 -7.931 1 128.54 ? C05 D7J 602 A 1 
HETATM 5 C C06 D7J . . . C 3 -18.634 -34.955 -7.721 1 119.92 ? C06 D7J 602 A 1 
HETATM 6 C C08 D7J . . . C 3 -19.646 -34.623 -10.482 1 108.87 ? C08 D7J 602 A 1 
HETATM 7 C C09 D7J . . . C 3 -18.535 -33.733 -11.031 1 115.04 ? C09 D7J 602 A 1 
HETATM 8 C C10 D7J . . . C 3 -19.136 -32.355 -11.527 1 104.3 ? C10 D7J 602 A 1 
HETATM 9 C C11 D7J . . . C 3 -18.24 -31.422 -12.25 1 103.69 ? C11 D7J 602 A 1 
HETATM 10 C C12 D7J . . . C 3 -18.767 -30.302 -12.896 1 102.94 ? C12 D7J 602 A 1 
HETATM 11 C C13 D7J . . . C 3 -17.976 -29.408 -13.58 1 105.39 ? C13 D7J 602 A 1 
HETATM 12 C C14 D7J . . . C 3 -16.605 -29.604 -13.663 1 110.11 ? C14 D7J 602 A 1 
HETATM 13 C C15 D7J . . . C 3 -16.045 -30.711 -13.037 1 107.98 ? C15 D7J 602 A 1 
HETATM 14 C C16 D7J . . . C 3 -16.852 -31.603 -12.333 1 107.42 ? C16 D7J 602 A 1 
HETATM 15 C C18 D7J . . . C 3 -17.733 -35.413 -13.047 1 147.43 ? C18 D7J 602 A 1 
HETATM 16 C C21 D7J . . . C 3 -16.254 -37.399 -13.53 1 144.83 ? C21 D7J 602 A 1 
HETATM 17 C C22 D7J . . . C 3 -15.858 -38.719 -12.785 1 143.79 ? C22 D7J 602 A 1 
HETATM 18 C C23 D7J . . . C 3 -14.982 -36.548 -13.623 1 147.84 ? C23 D7J 602 A 1 
HETATM 19 C C24 D7J . . . C 3 -16.784 -37.777 -14.929 1 144.27 ? C24 D7J 602 A 1 
HETATM 20 C C25 D7J . . . C 3 -17.917 -32.644 -7.265 1 128.83 ? C25 D7J 602 A 1 
HETATM 21 C C28 D7J . . . C 3 -18.06 -30.185 -7.343 1 97.78 ? C28 D7J 602 A 1 
HETATM 22 C C29 D7J . . . C 3 -18.725 -29.467 -8.475 1 70.06 ? C29 D7J 602 A 1 
HETATM 23 C C30 D7J . . . C 3 -18.003 -28.908 -9.471 1 64.73 ? C30 D7J 602 A 1 
HETATM 24 C C31 D7J . . . C 3 -18.549 -28.268 -10.524 1 66.8 ? C31 D7J 602 A 1 
HETATM 25 C C32 D7J . . . C 3 -19.979 -28.205 -10.62 1 64.62 ? C32 D7J 602 A 1 
HETATM 26 C C34 D7J . . . C 3 -20.074 -29.363 -8.639 1 78.98 ? C34 D7J 602 A 1 
HETATM 27 N N04 D7J . . . C 3 -16.223 -34.569 -7.414 1 131.08 ? N04 D7J 602 A 1 
HETATM 28 N N17 D7J . . . C 3 -17.52 -34.502 -11.947 1 131.28 ? N17 D7J 602 A 1 
HETATM 29 N N27 D7J . . . C 3 -17.605 -31.448 -7.866 1 115.57 ? N27 D7J 602 A 1 
HETATM 30 N N33 D7J . . . C 3 -20.714 -28.703 -9.678 1 71.72 ? N33 D7J 602 A 1 
HETATM 31 O O19 D7J . . . C 3 -17.692 -35.008 -14.182 1 163.19 ? O19 D7J 602 A 1 
HETATM 32 O O20 D7J . . . C 3 -17.346 -36.752 -12.774 1 145.62 ? O20 D7J 602 A 1 
HETATM 33 O O26 D7J . . . C 3 -18.576 -32.651 -6.257 1 130.25 ? O26 D7J 602 A 1 
HETATM 34 S S07 D7J . . . C 3 -19.996 -34.223 -8.732 1 111.49 ? S07 D7J 602 A 1 
#
_model_server_stats.io_time_ms              81 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           372 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           34 
#