data_8BUE
#
_model_server_result.job_id            sq53ShDLEmRgNfmfR4MOug 
_model_server_result.datetime_utc      '2024-10-19 08:31:22' 
_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          8bue 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":1101}' 
#
_entry.id    8BUE 
#
_exptl.entry_id    8BUE 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              364.398 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            ~{N}-(1~{H}-benzimidazol-2-yl)-1-(2-methoxy-5-methyl-phenyl)-5-oxidanylidene-pyrrolidine-3-carboxamide 
_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            8BUE 
_cell.length_a            249.329 
_cell.length_b            249.329 
_cell.length_c            218.681 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8BUE 
_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,O,P,Q,R,S,T,U,V 1 1 
D,E,F,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA 2 1 
G,H,I,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB 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 Q N N 
? 5 GA N N 
? 5 VA 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf2 G SG CYS 22 G CYS 18 1_555 G SG CYS 317 G CYS 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
covale ? covale1 B C TYR 184 B TYR 892 1_555 B N TPO 185 B TPO 893 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 
covale ? covale2 B C TPO 185 B TPO 893 1_555 B N ASN 186 B ASN 894 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
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 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? 
covale ? covale5 H C TYR 184 H TYR 892 1_555 H N TPO 185 H TPO 893 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale6 H C TPO 185 H TPO 893 1_555 H N ASN 186 H ASN 894 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
#
_chem_comp.formula           'C20 H20 N4 O3' 
_chem_comp.formula_weight    364.398 
_chem_comp.id                RVU 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              ~{N}-(1~{H}-benzimidazol-2-yl)-1-(2-methoxy-5-methyl-phenyl)-5-oxidanylidene-pyrrolidine-3-carboxamide 
_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
C19 C20 RVU doub 275 n y 
C19 C18 RVU sing 276 n y 
C20 C16 RVU sing 277 n y 
C18 C17 RVU doub 278 n y 
C16 C15 RVU doub 279 n y 
C16 N4 RVU sing 280 n y 
C17 C15 RVU sing 281 n y 
C15 N3 RVU sing 282 n y 
N4 C3 RVU doub 283 n y 
N3 C3 RVU sing 284 n y 
C3 N1 RVU sing 285 n n 
N1 C2 RVU sing 286 n n 
C2 O3 RVU doub 287 n n 
C2 C1 RVU sing 288 n n 
C1 C4 RVU sing 289 n n 
C1 C6 RVU sing 290 n n 
C4 N2 RVU sing 291 n n 
C6 C5 RVU sing 292 n n 
N2 C5 RVU sing 293 n n 
N2 C7 RVU sing 294 n n 
C5 O1 RVU doub 295 n n 
O2 C14 RVU sing 296 n n 
O2 C8 RVU sing 297 n n 
C7 C12 RVU doub 298 n y 
C7 C8 RVU sing 299 n y 
C12 C11 RVU sing 300 n y 
C8 C9 RVU doub 301 n y 
C9 C10 RVU sing 302 n y 
C11 C10 RVU doub 303 n y 
C11 C13 RVU sing 304 n n 
C9 H91 RVU sing 305 n n 
C1 H11 RVU sing 306 n n 
C4 H41 RVU sing 307 n n 
C4 H42 RVU sing 308 n n 
C6 H62 RVU sing 309 n n 
C6 H61 RVU sing 310 n n 
C10 H101 RVU sing 311 n n 
C12 H121 RVU sing 312 n n 
C13 H131 RVU sing 313 n n 
C13 H133 RVU sing 314 n n 
C13 H132 RVU sing 315 n n 
C14 H141 RVU sing 316 n n 
C14 H142 RVU sing 317 n n 
C14 H143 RVU sing 318 n n 
C17 H171 RVU sing 319 n n 
C18 H181 RVU sing 320 n n 
C19 H191 RVU sing 321 n n 
C20 H201 RVU sing 322 n n 
N1 H12 RVU sing 323 n n 
N3 H31 RVU sing 324 n n 
#
_atom_sites.entry_id                     8BUE 
_atom_sites.fract_transf_matrix[1][1]    0.004011 
_atom_sites.fract_transf_matrix[1][2]    0.002316 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.004631 
_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]    0.004573 
_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 3 SO4 SO4 . 
K 4 SO4 A 1 1202 5 SO4 SO4 . 
L 4 SO4 A 1 1203 10 SO4 SO4 . 
M 4 SO4 A 1 1204 41 SO4 SO4 . 
N 4 SO4 A 1 1205 47 SO4 SO4 . 
O 4 SO4 A 1 1206 75 SO4 SO4 . 
P 4 SO4 A 1 1207 76 SO4 SO4 . 
Q 5 RVU B 1 1101 1101 RVU 11S . 
R 4 SO4 B 1 1102 44 SO4 SO4 . 
S 4 SO4 B 1 1103 71 SO4 SO4 . 
T 4 SO4 C 1 301 4 SO4 SO4 . 
U 4 SO4 C 1 302 30 SO4 SO4 . 
V 4 SO4 C 1 303 78 SO4 SO4 . 
W 4 SO4 D 1 1201 2 SO4 SO4 . 
X 4 SO4 D 1 1202 7 SO4 SO4 . 
Y 4 SO4 D 1 1203 9 SO4 SO4 . 
Z 4 SO4 D 1 1204 20 SO4 SO4 . 
AA 4 SO4 D 1 1205 29 SO4 SO4 . 
BA 4 SO4 D 1 1206 34 SO4 SO4 . 
CA 4 SO4 D 1 1207 36 SO4 SO4 . 
DA 4 SO4 D 1 1208 46 SO4 SO4 . 
EA 4 SO4 D 1 1209 68 SO4 SO4 . 
FA 4 SO4 D 1 1210 74 SO4 SO4 . 
GA 5 RVU E 1 1101 1101 RVU 11S . 
HA 4 SO4 E 1 1102 40 SO4 SO4 . 
IA 4 SO4 E 1 1103 43 SO4 SO4 . 
JA 4 SO4 F 1 301 21 SO4 SO4 . 
KA 4 SO4 F 1 302 26 SO4 SO4 . 
LA 4 SO4 F 1 303 31 SO4 SO4 . 
MA 4 SO4 F 1 304 73 SO4 SO4 . 
NA 4 SO4 G 1 1201 1 SO4 SO4 . 
OA 4 SO4 G 1 1202 8 SO4 SO4 . 
PA 4 SO4 G 1 1203 13 SO4 SO4 . 
QA 4 SO4 G 1 1204 14 SO4 SO4 . 
RA 4 SO4 G 1 1205 15 SO4 SO4 . 
SA 4 SO4 G 1 1206 28 SO4 SO4 . 
TA 4 SO4 G 1 1207 42 SO4 SO4 . 
UA 4 SO4 G 1 1208 54 SO4 SO4 . 
VA 5 RVU H 1 1101 1101 RVU 11S . 
WA 4 SO4 H 1 1102 33 SO4 SO4 . 
XA 4 SO4 H 1 1103 38 SO4 SO4 . 
YA 4 SO4 H 1 1104 39 SO4 SO4 . 
ZA 4 SO4 H 1 1105 79 SO4 SO4 . 
AB 4 SO4 I 1 301 12 SO4 SO4 . 
BB 4 SO4 I 1 302 32 SO4 SO4 . 
CB 4 SO4 I 1 303 77 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 C8 RVU . . . Q 5 -66.351 25.468 0.637 1 119.04 ? C8 RVU 1101 B 1 
HETATM 2 C C9 RVU . . . Q 5 -66.329 26.532 1.529 1 121.34 ? C9 RVU 1101 B 1 
HETATM 3 C C1 RVU . . . Q 5 -65.03 22.875 -2.808 1 111.42 ? C1 RVU 1101 B 1 
HETATM 4 C C2 RVU . . . Q 5 -64.049 23.168 -3.908 1 115.96 ? C2 RVU 1101 B 1 
HETATM 5 C C3 RVU . . . Q 5 -63.916 23.732 -6.279 1 118.44 ? C3 RVU 1101 B 1 
HETATM 6 C C4 RVU . . . Q 5 -65.534 24.095 -2.067 1 114.94 ? C4 RVU 1101 B 1 
HETATM 7 C C5 RVU . . . Q 5 -64.636 22.607 -0.446 1 137.24 ? C5 RVU 1101 B 1 
HETATM 8 C C6 RVU . . . Q 5 -64.377 21.942 -1.769 1 130.4 ? C6 RVU 1101 B 1 
HETATM 9 C C10 RVU . . . Q 5 -65.13 27.059 1.959 1 125.75 ? C10 RVU 1101 B 1 
HETATM 10 C C11 RVU . . . Q 5 -63.897 26.557 1.529 1 123.94 ? C11 RVU 1101 B 1 
HETATM 11 C C12 RVU . . . Q 5 -63.92 25.496 0.634 1 121.89 ? C12 RVU 1101 B 1 
HETATM 12 C C13 RVU . . . Q 5 -62.588 27.151 2.006 1 132.79 ? C13 RVU 1101 B 1 
HETATM 13 C C14 RVU . . . Q 5 -68.746 25.475 0.446 1 119.9 ? C14 RVU 1101 B 1 
HETATM 14 C C15 RVU . . . Q 5 -62.327 24.33 -7.675 1 116.66 ? C15 RVU 1101 B 1 
HETATM 15 C C16 RVU . . . Q 5 -63.488 23.959 -8.365 1 115.11 ? C16 RVU 1101 B 1 
HETATM 16 C C17 RVU . . . Q 5 -61.181 24.75 -8.33 1 116.72 ? C17 RVU 1101 B 1 
HETATM 17 C C18 RVU . . . Q 5 -61.23 24.791 -9.707 1 115 ? C18 RVU 1101 B 1 
HETATM 18 C C19 RVU . . . Q 5 -62.381 24.424 -10.409 1 116.37 ? C19 RVU 1101 B 1 
HETATM 19 C C20 RVU . . . Q 5 -63.517 24.007 -9.756 1 116.32 ? C20 RVU 1101 B 1 
HETATM 20 C C7 RVU . . . Q 5 -65.122 24.947 0.188 1 122.62 ? C7 RVU 1101 B 1 
HETATM 21 N N1 RVU . . . Q 5 -64.594 23.452 -5.113 1 115.39 ? N1 RVU 1101 B 1 
HETATM 22 N N2 RVU . . . Q 5 -65.106 23.858 -0.706 1 130.72 ? N2 RVU 1101 B 1 
HETATM 23 N N3 RVU . . . Q 5 -62.632 24.171 -6.336 1 120.82 ? N3 RVU 1101 B 1 
HETATM 24 N N4 RVU . . . Q 5 -64.48 23.579 -7.462 1 119.13 ? N4 RVU 1101 B 1 
HETATM 25 O O1 RVU . . . Q 5 -64.467 22.159 0.674 1 139.27 ? O1 RVU 1101 B 1 
HETATM 26 O O2 RVU . . . Q 5 -67.483 24.878 0.15 1 125.48 ? O2 RVU 1101 B 1 
HETATM 27 O O3 RVU . . . Q 5 -62.841 23.119 -3.734 1 126.42 ? O3 RVU 1101 B 1 
HETATM 28 H H91 RVU . . . Q 5 -67.147 26.894 1.84 0 146.02 ? H91 RVU 1101 B 1 
HETATM 29 H H11 RVU . . . Q 5 -65.86 22.471 -3.166 0 134.13 ? H11 RVU 1101 B 1 
HETATM 30 H H41 RVU . . . Q 5 -66.517 24.163 -2.125 0 138.35 ? H41 RVU 1101 B 1 
HETATM 31 H H42 RVU . . . Q 5 -65.131 24.921 -2.428 0 138.35 ? H42 RVU 1101 B 1 
HETATM 32 H H62 RVU . . . Q 5 -63.419 21.855 -1.93 0 156.9 ? H62 RVU 1101 B 1 
HETATM 33 H H61 RVU . . . Q 5 -64.781 21.055 -1.793 0 156.9 ? H61 RVU 1101 B 1 
HETATM 34 H H101 RVU . . . Q 5 -65.141 27.783 2.564 0 151.31 ? H101 RVU 1101 B 1 
HETATM 35 H H121 RVU . . . Q 5 -63.099 25.136 0.318 0 146.69 ? H121 RVU 1101 B 1 
HETATM 36 H H131 RVU . . . Q 5 -61.874 26.504 1.885 0 159.76 ? H131 RVU 1101 B 1 
HETATM 37 H H133 RVU . . . Q 5 -62.659 27.38 2.947 0 159.76 ? H133 RVU 1101 B 1 
HETATM 38 H H132 RVU . . . Q 5 -62.388 27.951 1.494 0 159.76 ? H132 RVU 1101 B 1 
HETATM 39 H H141 RVU . . . Q 5 -69.45 24.985 -0.008 0 144.3 ? H141 RVU 1101 B 1 
HETATM 40 H H142 RVU . . . Q 5 -68.746 26.398 0.143 0 144.3 ? H142 RVU 1101 B 1 
HETATM 41 H H143 RVU . . . Q 5 -68.899 25.449 1.405 0 144.3 ? H143 RVU 1101 B 1 
HETATM 42 H H171 RVU . . . Q 5 -60.409 24.995 -7.861 0 140.49 ? H171 RVU 1101 B 1 
HETATM 43 H H181 RVU . . . Q 5 -60.47 25.072 -10.185 0 138.41 ? H181 RVU 1101 B 1 
HETATM 44 H H191 RVU . . . Q 5 -62.379 24.463 -11.347 0 140.06 ? H191 RVU 1101 B 1 
HETATM 45 H H201 RVU . . . Q 5 -64.29 23.761 -10.23 0 140 ? H201 RVU 1101 B 1 
HETATM 46 H H12 RVU . . . Q 5 -65.47 23.459 -5.163 0 138.88 ? H12 RVU 1101 B 1 
HETATM 47 H H31 RVU . . . Q 5 -62.12 24.317 -5.639 0 145.4 ? H31 RVU 1101 B 1 
#
_model_server_stats.io_time_ms              123 
_model_server_stats.parse_time_ms           26 
_model_server_stats.create_model_time_ms    77 
_model_server_stats.query_time_ms           304 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           47 
#