data_9HB7
#
_model_server_result.job_id            BWsK-3oMZiaDjm1AOgxc7g 
_model_server_result.datetime_utc      '2025-07-20 21:01:24' 
_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          9hb7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":502}' 
#
_entry.id    9HB7 
#
_exptl.entry_id    9HB7 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              400.433 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            8-(1~{H}-benzimidazol-2-ylmethyl)-3-ethyl-7-(phenylmethyl)purine-2,6-dione 
_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            9HB7 
_cell.length_a            101.144 
_cell.length_b            94.646 
_cell.length_c            88.74 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9HB7 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    'P 2 2ab' 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,G,H 
_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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 F 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
metalc ? metalc1 A NE2 HIS 200 A HIS 318 1_555 C FE FE . A FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? 
metalc ? metalc2 A NE2 HIS 205 A HIS 323 1_555 C FE FE . A FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? 
metalc ? metalc3 A OE1 GLU 245 A GLU 363 1_555 C FE FE . A FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? 
metalc ? metalc4 A OE2 GLU 245 A GLU 363 1_555 C FE FE . A FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? 
metalc ? metalc5 C FE FE . A FE 501 1_555 D NAP JCR . A JCR 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? 
metalc ? metalc6 C FE FE . A FE 501 1_555 G O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? 
metalc ? metalc7 B NE2 HIS 200 B HIS 318 1_555 E FE FE . B FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? 
metalc ? metalc8 B NE2 HIS 205 B HIS 323 1_555 E FE FE . B FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? 
metalc ? metalc9 B OE1 GLU 245 B GLU 363 1_555 E FE FE . B FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? 
metalc ? metalc10 B OE2 GLU 245 B GLU 363 1_555 E FE FE . B FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? 
metalc ? metalc11 E FE FE . B FE 501 1_555 F NAP JCR . B JCR 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? 
#
_chem_comp.formula           'C22 H20 N6 O2' 
_chem_comp.formula_weight    400.433 
_chem_comp.id                JCR 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              8-(1~{H}-benzimidazol-2-ylmethyl)-3-ethyl-7-(phenylmethyl)purine-2,6-dione 
_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
CAH CAL JCR doub 173 n y 
CAH CAG JCR sing 174 n y 
CAL CAZ JCR sing 175 n y 
CAG CAK JCR doub 176 n y 
O2 C2 JCR doub 177 n n 
CAE CAD JCR doub 178 n y 
CAE CAI JCR sing 179 n y 
CAZ NAS JCR sing 180 n y 
CAZ CAY JCR doub 181 n y 
CAM N3 JCR sing 182 n n 
CAM CAA JCR sing 183 n n 
CAD CAF JCR sing 184 n y 
C2 N3 JCR sing 185 n n 
C2 N1 JCR sing 186 n n 
NAS CAU JCR doub 187 n y 
N3 C4 JCR sing 188 n n 
CAI CAT JCR doub 189 n y 
N1 C6 JCR sing 190 n n 
CAK CAY JCR sing 191 n y 
CAY NAP JCR sing 192 n y 
C4 N9 JCR sing 193 n y 
C4 C5 JCR doub 194 n y 
C6 C5 JCR sing 195 n n 
C6 O6 JCR doub 196 n n 
CAF CAJ JCR doub 197 n y 
N9 C8 JCR doub 198 n y 
C5 N7 JCR sing 199 n y 
CAU NAP JCR sing 200 n y 
CAU CAN JCR sing 201 n n 
CAT CAJ JCR sing 202 n y 
CAT CAO JCR sing 203 n n 
C8 N7 JCR sing 204 n y 
C8 CAN JCR sing 205 n n 
N7 CAO JCR sing 206 n n 
N1 H1 JCR sing 207 n n 
CAI H2 JCR sing 208 n n 
CAE H3 JCR sing 209 n n 
CAD H4 JCR sing 210 n n 
CAF H5 JCR sing 211 n n 
CAJ H6 JCR sing 212 n n 
CAO H7 JCR sing 213 n n 
CAO H8 JCR sing 214 n n 
CAM H9 JCR sing 215 n n 
CAM H10 JCR sing 216 n n 
CAA H11 JCR sing 217 n n 
CAA H12 JCR sing 218 n n 
CAA H13 JCR sing 219 n n 
CAN H14 JCR sing 220 n n 
CAN H15 JCR sing 221 n n 
NAP H16 JCR sing 222 n n 
CAK H17 JCR sing 223 n n 
CAG H18 JCR sing 224 n n 
CAH H19 JCR sing 225 n n 
CAL H20 JCR sing 226 n n 
#
_atom_sites.entry_id                     9HB7 
_atom_sites.fract_transf_matrix[1][1]    0.009887 
_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]    0.010566 
_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]    0.011269 
_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 FE A 1 501 1 FE FE . 
D 3 JCR A 1 502 1 JCR DRG . 
E 2 FE B 1 501 2 FE FE . 
F 3 JCR B 1 502 2 JCR DRG . 
G 4 HOH A 1 601 1 HOH HOH . 
H 4 HOH B 1 601 2 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 C4 JCR . . . F 3 27.784 1.097 -39.797 1 129.31 ? C4 JCR 502 B 1 
HETATM 2 C C5 JCR . . . F 3 28.929 1.246 -39.109 1 129.61 ? C5 JCR 502 B 1 
HETATM 3 C C6 JCR . . . F 3 29.558 0.181 -38.604 1 122.87 ? C6 JCR 502 B 1 
HETATM 4 C C8 JCR . . . F 3 28.255 3.174 -39.737 1 137.9 ? C8 JCR 502 B 1 
HETATM 5 N N1 JCR . . . F 3 29.019 -1.093 -38.791 1 122.79 ? N1 JCR 502 B 1 
HETATM 6 N N3 JCR . . . F 3 27.241 -0.117 -39.994 1 125.84 ? N3 JCR 502 B 1 
HETATM 7 C CAI JCR . . . F 3 31.338 2.923 -40.649 1 136.85 ? CAI JCR 502 B 1 
HETATM 8 C CAE JCR . . . F 3 32.446 2.924 -41.487 1 135.36 ? CAE JCR 502 B 1 
HETATM 9 C CAD JCR . . . F 3 33.69 3.295 -40.989 1 136.07 ? CAD JCR 502 B 1 
HETATM 10 C CAF JCR . . . F 3 33.821 3.663 -39.654 1 137.75 ? CAF JCR 502 B 1 
HETATM 11 C CAJ JCR . . . F 3 32.711 3.661 -38.816 1 140 ? CAJ JCR 502 B 1 
HETATM 12 C CAT JCR . . . F 3 31.465 3.29 -39.311 1 139.36 ? CAT JCR 502 B 1 
HETATM 13 C CAO JCR . . . F 3 30.357 3.291 -38.461 1 137.42 ? CAO JCR 502 B 1 
HETATM 14 N N7 JCR . . . F 3 29.22 2.551 -39.079 1 135.53 ? N7 JCR 502 B 1 
HETATM 15 O O6 JCR . . . F 3 30.608 0.295 -37.971 1 114.41 ? O6 JCR 502 B 1 
HETATM 16 C C2 JCR . . . F 3 27.832 -1.215 -39.509 1 121.51 ? C2 JCR 502 B 1 
HETATM 17 O O2 JCR . . . F 3 27.332 -2.322 -39.696 1 116.69 ? O2 JCR 502 B 1 
HETATM 18 C CAM JCR . . . F 3 25.977 -0.25 -40.758 1 120.28 ? CAM JCR 502 B 1 
HETATM 19 C CAA JCR . . . F 3 24.767 -0.317 -39.824 1 112.29 ? CAA JCR 502 B 1 
HETATM 20 N N9 JCR . . . F 3 27.367 2.301 -40.188 1 131.63 ? N9 JCR 502 B 1 
HETATM 21 C CAN JCR . . . F 3 28.21 4.688 -39.937 1 144.3 ? CAN JCR 502 B 1 
HETATM 22 C CAU JCR . . . F 3 27.814 5.039 -41.372 1 150.22 ? CAU JCR 502 B 1 
HETATM 23 N NAP JCR . . . F 3 27.397 6.237 -41.753 1 153.26 ? NAP JCR 502 B 1 
HETATM 24 C CAY JCR . . . F 3 27.149 6.162 -43.058 1 155.88 ? CAY JCR 502 B 1 
HETATM 25 C CAK JCR . . . F 3 26.71 7.086 -43.91 1 156.7 ? CAK JCR 502 B 1 
HETATM 26 C CAG JCR . . . F 3 26.525 6.775 -45.25 1 156.83 ? CAG JCR 502 B 1 
HETATM 27 C CAH JCR . . . F 3 26.806 5.484 -45.674 1 157.18 ? CAH JCR 502 B 1 
HETATM 28 C CAL JCR . . . F 3 27.261 4.562 -44.74 1 156.84 ? CAL JCR 502 B 1 
HETATM 29 C CAZ JCR . . . F 3 27.422 4.914 -43.465 1 155.68 ? CAZ JCR 502 B 1 
HETATM 30 N NAS JCR . . . F 3 27.839 4.213 -42.41 1 152.85 ? NAS JCR 502 B 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           301 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           30 
#