data_8BUC
#
_model_server_result.job_id            7zQT_Cfh5l2GCTc0tXxx9Q 
_model_server_result.datetime_utc      '2024-11-29 15:28:09' 
_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          8buc 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"V","auth_seq_id":1101}' 
#
_entry.id    8BUC 
#
_exptl.entry_id    8BUC 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              318.781 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-(1~{H}-benzimidazol-2-ylsulfanyl)-~{N}-(5-chloranylpyridin-2-yl)ethanamide 
_entity.pdbx_number_of_molecules    3 
_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         120 
_cell.entry_id            8BUC 
_cell.length_a            249.773 
_cell.length_b            249.773 
_cell.length_c            218.027 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8BUC 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    'P 31 2"' 
_symmetry.space_group_name_H-M     'P 31 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? trimeric 3 author_defined_assembly 1 
? trimeric 3 author_defined_assembly 2 
? trimeric 3 author_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,J,K,L,M,N 1 1 
D,E,F,O,P,Q,R 2 1 
G,H,I,S,T,U,V,W 3 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
? 5 M N N 
? 5 Q N N 
? 5 V 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
disulf ? disulf1 A SG CYS 22 A CYS 18 1_555 A SG CYS 317 A CYS 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf2 G SG CYS 22 G CYS 18 1_555 G SG CYS 317 G CYS 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
covale ? covale1 B C TYR 184 B TYR 892 1_555 B N TPO 185 B TPO 893 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale2 B C TPO 185 B TPO 893 1_555 B N ASN 186 B ASN 894 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale3 E C TYR 184 E TYR 892 1_555 E N TPO 185 E TPO 893 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale4 E C TPO 185 E TPO 893 1_555 E N ASN 186 E ASN 894 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? 
covale ? covale5 H C TYR 184 H TYR 892 1_555 H N TPO 185 H TPO 893 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 
covale ? covale6 H C TPO 185 H TPO 893 1_555 H N ASN 186 H ASN 894 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 
#
_chem_comp.formula           'C14 H11 Cl N4 O S' 
_chem_comp.formula_weight    318.781 
_chem_comp.id                RKO 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-(1~{H}-benzimidazol-2-ylsulfanyl)-~{N}-(5-chloranylpyridin-2-yl)ethanamide 
_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
CL1 C4 RKO sing 295 n n 
C4 C3 RKO doub 296 n y 
C4 C5 RKO sing 297 n y 
C3 N2 RKO sing 298 n y 
C5 C6 RKO doub 299 n y 
N2 C2 RKO doub 300 n y 
C6 C2 RKO sing 301 n y 
C2 N1 RKO sing 302 n n 
N1 C1 RKO sing 303 n n 
C1 O1 RKO doub 304 n n 
C1 C7 RKO sing 305 n n 
C7 S1 RKO sing 306 n n 
S1 C8 RKO sing 307 n n 
C8 N3 RKO doub 308 n y 
C8 N4 RKO sing 309 n y 
N3 C9 RKO sing 310 n y 
N4 C10 RKO sing 311 n y 
C9 C10 RKO doub 312 n y 
C9 C14 RKO sing 313 n y 
C10 C11 RKO sing 314 n y 
C14 C13 RKO doub 315 n y 
C11 C12 RKO doub 316 n y 
C13 C12 RKO sing 317 n y 
C11 H7 RKO sing 318 n n 
C12 H8 RKO sing 319 n n 
C13 H9 RKO sing 320 n n 
C14 H10 RKO sing 321 n n 
C3 H2 RKO sing 322 n n 
C5 H3 RKO sing 323 n n 
C6 H4 RKO sing 324 n n 
C7 H5 RKO sing 325 n n 
C7 H6 RKO sing 326 n n 
N1 H1 RKO sing 327 n n 
N4 H11 RKO sing 328 n n 
#
_atom_sites.entry_id                     8BUC 
_atom_sites.fract_transf_matrix[1][1]    0.004004 
_atom_sites.fract_transf_matrix[1][2]    0.002311 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.004623 
_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]    0.004587 
_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
J 4 SO4 A 1 1201 2 SO4 SO4 . 
K 4 SO4 A 1 1202 5 SO4 SO4 . 
L 4 SO4 A 1 1203 8 SO4 SO4 . 
M 5 RKO B 1 1101 1101 RKO dC3 . 
N 4 SO4 C 1 301 7 SO4 SO4 . 
O 6 CIT D 1 1201 1201 CIT CIT . 
P 4 SO4 D 1 1202 1 SO4 SO4 . 
Q 5 RKO E 1 1101 1101 RKO dC3 . 
R 6 CIT F 1 301 301 CIT CIT . 
S 4 SO4 G 1 1201 3 SO4 SO4 . 
T 4 SO4 G 1 1202 6 SO4 SO4 . 
U 4 SO4 G 1 1203 9 SO4 SO4 . 
V 5 RKO H 1 1101 1101 RKO dC3 . 
W 4 SO4 I 1 301 4 SO4 SO4 . 
#
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 RKO . . . V 5 -132.634 13.793 8.825 1 149.2 ? C1 RKO 1101 H 1 
HETATM 2 C C10 RKO . . . V 5 -134.734 17.804 11.386 1 131.81 ? C10 RKO 1101 H 1 
HETATM 3 C C11 RKO . . . V 5 -135.122 18.288 12.632 1 136.91 ? C11 RKO 1101 H 1 
HETATM 4 C C12 RKO . . . V 5 -134.461 19.401 13.105 1 157.98 ? C12 RKO 1101 H 1 
HETATM 5 C C13 RKO . . . V 5 -133.449 20.011 12.363 1 164 ? C13 RKO 1101 H 1 
HETATM 6 C C14 RKO . . . V 5 -133.064 19.525 11.134 1 148.76 ? C14 RKO 1101 H 1 
HETATM 7 C C2 RKO . . . V 5 -130.757 12.144 8.998 1 130.04 ? C2 RKO 1101 H 1 
HETATM 8 C C3 RKO . . . V 5 -128.686 11.179 9.158 1 132.48 ? C3 RKO 1101 H 1 
HETATM 9 C C4 RKO . . . V 5 -129.202 10.093 9.816 1 114.55 ? C4 RKO 1101 H 1 
HETATM 10 C C5 RKO . . . V 5 -130.556 10.025 10.061 1 109.68 ? C5 RKO 1101 H 1 
HETATM 11 C C6 RKO . . . V 5 -131.351 11.058 9.636 1 123.82 ? C6 RKO 1101 H 1 
HETATM 12 C C7 RKO . . . V 5 -133.038 14.987 7.988 1 178.19 ? C7 RKO 1101 H 1 
HETATM 13 C C8 RKO . . . V 5 -134.448 16.731 9.494 1 157.77 ? C8 RKO 1101 H 1 
HETATM 14 C C9 RKO . . . V 5 -133.717 18.404 10.635 1 142.23 ? C9 RKO 1101 H 1 
HETATM 15 N N1 RKO . . . V 5 -131.436 13.259 8.477 1 138.14 ? N1 RKO 1101 H 1 
HETATM 16 N N2 RKO . . . V 5 -129.454 12.194 8.729 1 133.31 ? N2 RKO 1101 H 1 
HETATM 17 N N3 RKO . . . V 5 -133.543 17.718 9.433 1 145.82 ? N3 RKO 1101 H 1 
HETATM 18 N N4 RKO . . . V 5 -135.179 16.738 10.634 1 129.33 ? N4 RKO 1101 H 1 
HETATM 19 O O1 RKO . . . V 5 -133.343 13.357 9.719 1 133.42 ? O1 RKO 1101 H 1 
HETATM 20 S S1 RKO . . . V 5 -134.729 15.518 8.268 1 215.23 ? S1 RKO 1101 H 1 
HETATM 21 CL CL1 RKO . . . V 5 -128.15 8.82 10.338 1 102.1 ? CL1 RKO 1101 H 1 
HETATM 22 H H7 RKO . . . V 5 -135.801 17.877 13.127 0 164.29 ? H7 RKO 1101 H 1 
HETATM 23 H H8 RKO . . . V 5 -134.697 19.755 13.944 0 189.57 ? H8 RKO 1101 H 1 
HETATM 24 H H9 RKO . . . V 5 -133.021 20.771 12.709 0 196.8 ? H9 RKO 1101 H 1 
HETATM 25 H H10 RKO . . . V 5 -132.377 19.938 10.643 0 178.51 ? H10 RKO 1101 H 1 
HETATM 26 H H2 RKO . . . V 5 -127.753 11.229 8.992 0 158.98 ? H2 RKO 1101 H 1 
HETATM 27 H H3 RKO . . . V 5 -130.923 9.277 10.514 0 131.62 ? H3 RKO 1101 H 1 
HETATM 28 H H4 RKO . . . V 5 -132.286 11.033 9.775 0 148.58 ? H4 RKO 1101 H 1 
HETATM 29 H H5 RKO . . . V 5 -132.93 14.756 7.047 0 213.82 ? H5 RKO 1101 H 1 
HETATM 30 H H6 RKO . . . V 5 -132.435 15.726 8.192 0 213.82 ? H6 RKO 1101 H 1 
HETATM 31 H H1 RKO . . . V 5 -131.016 13.668 7.829 0 165.77 ? H1 RKO 1101 H 1 
HETATM 32 H H11 RKO . . . V 5 -135.799 16.184 10.842 0 155.2 ? H11 RKO 1101 H 1 
#
_model_server_stats.io_time_ms              179 
_model_server_stats.parse_time_ms           45 
_model_server_stats.create_model_time_ms    119 
_model_server_stats.query_time_ms           332 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           32 
#