data_8XGY
#
_model_server_result.job_id            GIh7yb8NChRSmakGtkwJmg 
_model_server_result.datetime_utc      '2024-12-18 09:55:54' 
_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          8xgy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"V","auth_seq_id":402}' 
#
_entry.id    8XGY 
#
_exptl.entry_id    8XGY 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              388.419 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (3~{Z})-3-(1~{H}-benzimidazol-5-ylmethylidene)-4-[(3~{R})-1-ethanoylpyrrolidin-3-yl]oxy-1~{H}-indol-2-one 
_entity.pdbx_number_of_molecules    12 
_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            8XGY 
_cell.length_a            83.722 
_cell.length_b            217.245 
_cell.length_c            242.303 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8XGY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dodecameric 
_pdbx_struct_assembly.oligomeric_count      12 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H,I,J,K,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,KA,LA,MA,NA,OA,PA,QA,RA,SA 1 1 
L,IA,JA,TA 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_554 -x+1/2,-y,z-1/2 -1 0 0 0 -1 0 0 0 1 41.861 0 -121.1515 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 N N N 
? 3 P N N 
? 3 R N N 
? 3 T N N 
? 3 V N N 
? 3 X N N 
? 3 Z N N 
? 3 BA N N 
? 3 DA N N 
? 3 FA N N 
? 3 HA N N 
? 3 JA 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 298 B HIS 330 1_555 M ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.819 ? 
metalc ? metalc2 M ZN ZN . B ZN 401 1_555 N N26 A1D5C . B A1D5C 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
metalc ? metalc3 B NE2 HIS 298 A HIS 330 1_555 O ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.785 ? 
metalc ? metalc4 O ZN ZN . A ZN 401 1_555 P N26 A1D5C . A A1D5C 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.903 ? 
metalc ? metalc5 C NE2 HIS 298 C HIS 330 1_555 Q ZN ZN . C ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.847 ? 
metalc ? metalc6 D NE2 HIS 298 D HIS 330 1_555 S ZN ZN . D ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.936 ? 
metalc ? metalc7 S ZN ZN . D ZN 401 1_555 T N26 A1D5C . D A1D5C 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.769 ? 
metalc ? metalc8 E NE2 HIS 298 E HIS 330 1_555 U ZN ZN . E ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? 
metalc ? metalc9 U ZN ZN . E ZN 401 1_555 V N26 A1D5C . E A1D5C 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.711 ? 
metalc ? metalc10 F NE2 HIS 298 F HIS 330 1_555 W ZN ZN . F ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.87 ? 
metalc ? metalc11 W ZN ZN . F ZN 401 1_555 X N26 A1D5C . F A1D5C 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.733 ? 
metalc ? metalc12 G OE2 GLU 170 G GLU 202 1_555 Y ZN ZN . G ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.742 ? 
metalc ? metalc13 G NE2 HIS 298 G HIS 330 1_555 Y ZN ZN . G ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.895 ? 
metalc ? metalc14 Y ZN ZN . G ZN 401 1_555 Z N26 A1D5C . G A1D5C 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? 
metalc ? metalc15 H NE2 HIS 298 H HIS 330 1_555 AA ZN ZN . H ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.783 ? 
metalc ? metalc16 I NE2 HIS 298 I HIS 330 1_555 CA ZN ZN . I ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.706 ? 
metalc ? metalc17 CA ZN ZN . I ZN 401 1_555 DA N26 A1D5C . I A1D5C 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.731 ? 
metalc ? metalc18 J OD2 ASP 127 J ASP 159 1_555 EA ZN ZN . J ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.793 ? 
metalc ? metalc19 J OE2 GLU 170 J GLU 202 1_555 EA ZN ZN . J ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.725 ? 
metalc ? metalc20 J NE2 HIS 298 J HIS 330 1_555 EA ZN ZN . J ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.862 ? 
metalc ? metalc21 K OE2 GLU 170 K GLU 202 1_555 GA ZN ZN . K ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.822 ? 
metalc ? metalc22 K NE2 HIS 298 K HIS 330 1_555 GA ZN ZN . K ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.726 ? 
#
_chem_comp.formula           'C22 H20 N4 O3' 
_chem_comp.formula_weight    388.419 
_chem_comp.id                A1D5C 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (3~{Z})-3-(1~{H}-benzimidazol-5-ylmethylidene)-4-[(3~{R})-1-ethanoylpyrrolidin-3-yl]oxy-1~{H}-indol-2-one 
_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
C01 C02 A1D5C sing 1 n n 
O03 C02 A1D5C doub 2 n n 
C02 N04 A1D5C sing 3 n n 
C22 C21 A1D5C doub 4 n y 
C22 C23 A1D5C sing 5 n y 
N24 C23 A1D5C sing 6 n y 
N24 C25 A1D5C sing 7 n y 
C21 C20 A1D5C sing 8 n y 
C23 C27 A1D5C doub 9 n y 
N04 C08 A1D5C sing 10 n n 
N04 C05 A1D5C sing 11 n n 
C08 C07 A1D5C sing 12 n n 
C25 N26 A1D5C doub 13 n y 
C05 C06 A1D5C sing 14 n n 
C20 C28 A1D5C doub 15 n y 
C20 C19 A1D5C sing 16 n n 
C27 N26 A1D5C sing 17 n y 
C27 C28 A1D5C sing 18 n y 
C19 C18 A1D5C doub 19 z n 
C07 C06 A1D5C sing 20 n n 
C07 O09 A1D5C sing 21 n n 
O09 C10 A1D5C sing 22 n n 
C18 C16 A1D5C sing 23 n n 
C18 C29 A1D5C sing 24 n n 
O17 C16 A1D5C doub 25 n n 
C10 C29 A1D5C doub 26 n y 
C10 C11 A1D5C sing 27 n y 
C16 N15 A1D5C sing 28 n n 
C29 C14 A1D5C sing 29 n y 
C11 C12 A1D5C doub 30 n y 
C14 N15 A1D5C sing 31 n n 
C14 C13 A1D5C doub 32 n y 
C12 C13 A1D5C sing 33 n y 
C28 H1 A1D5C sing 34 n n 
C01 H2 A1D5C sing 35 n n 
C01 H3 A1D5C sing 36 n n 
C01 H4 A1D5C sing 37 n n 
C05 H5 A1D5C sing 38 n n 
C05 H6 A1D5C sing 39 n n 
C06 H7 A1D5C sing 40 n n 
C06 H8 A1D5C sing 41 n n 
C07 H9 A1D5C sing 42 n n 
C08 H10 A1D5C sing 43 n n 
C08 H11 A1D5C sing 44 n n 
C11 H12 A1D5C sing 45 n n 
C12 H13 A1D5C sing 46 n n 
C13 H14 A1D5C sing 47 n n 
N15 H15 A1D5C sing 48 n n 
C19 H16 A1D5C sing 49 n n 
C21 H17 A1D5C sing 50 n n 
C22 H18 A1D5C sing 51 n n 
N24 H19 A1D5C sing 52 n n 
C25 H20 A1D5C sing 53 n n 
#
_atom_sites.entry_id                     8XGY 
_atom_sites.fract_transf_matrix[1][1]    0.011944 
_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]    0.004603 
_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]    0.004127 
_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
M 2 ZN B 1 401 1 ZN ZN . 
N 3 A1D5C B 1 402 1 A1D5C M24 . 
O 2 ZN A 1 401 2 ZN ZN . 
P 3 A1D5C A 1 402 2 A1D5C M24 . 
Q 2 ZN C 1 401 3 ZN ZN . 
R 3 A1D5C C 1 402 3 A1D5C M24 . 
S 2 ZN D 1 401 4 ZN ZN . 
T 3 A1D5C D 1 402 4 A1D5C M24 . 
U 2 ZN E 1 401 5 ZN ZN . 
V 3 A1D5C E 1 402 5 A1D5C M24 . 
W 2 ZN F 1 401 6 ZN ZN . 
X 3 A1D5C F 1 402 6 A1D5C M24 . 
Y 2 ZN G 1 401 7 ZN ZN . 
Z 3 A1D5C G 1 402 7 A1D5C M24 . 
AA 2 ZN H 1 401 8 ZN ZN . 
BA 3 A1D5C H 1 402 8 A1D5C M24 . 
CA 2 ZN I 1 401 9 ZN ZN . 
DA 3 A1D5C I 1 402 9 A1D5C M24 . 
EA 2 ZN J 1 401 10 ZN ZN . 
FA 3 A1D5C J 1 402 10 A1D5C M24 . 
GA 2 ZN K 1 401 11 ZN ZN . 
HA 3 A1D5C K 1 402 11 A1D5C M24 . 
IA 2 ZN L 1 401 12 ZN ZN . 
JA 3 A1D5C L 1 402 12 A1D5C M24 . 
KA 4 HOH B 1 501 35 HOH HOH . 
KA 4 HOH B 2 502 15 HOH HOH . 
KA 4 HOH B 3 503 89 HOH HOH . 
KA 4 HOH B 4 504 9 HOH HOH . 
KA 4 HOH B 5 505 21 HOH HOH . 
LA 4 HOH A 1 501 25 HOH HOH . 
MA 4 HOH C 1 501 4 HOH HOH . 
MA 4 HOH C 2 502 12 HOH HOH . 
MA 4 HOH C 3 503 44 HOH HOH . 
NA 4 HOH D 1 501 77 HOH HOH . 
OA 4 HOH E 1 501 3 HOH HOH . 
OA 4 HOH E 2 502 42 HOH HOH . 
PA 4 HOH F 1 501 63 HOH HOH . 
PA 4 HOH F 2 502 34 HOH HOH . 
PA 4 HOH F 3 503 10 HOH HOH . 
QA 4 HOH G 1 501 65 HOH HOH . 
RA 4 HOH H 1 501 6 HOH HOH . 
SA 4 HOH K 1 501 74 HOH HOH . 
SA 4 HOH K 2 502 8 HOH HOH . 
SA 4 HOH K 3 503 56 HOH HOH . 
TA 4 HOH L 1 501 5 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 C27 A1D5C . . . V 3 28.421 -3.532 5.348 1 38.88 ? C27 A1D5C 402 E 1 
HETATM 2 C C28 A1D5C . . . V 3 27.545 -2.784 6.152 1 45.36 ? C28 A1D5C 402 E 1 
HETATM 3 C C29 A1D5C . . . V 3 24.939 -0.727 9.028 1 63.45 ? C29 A1D5C 402 E 1 
HETATM 4 C C01 A1D5C . . . V 3 22.541 -7.974 10.237 1 66.99 ? C01 A1D5C 402 E 1 
HETATM 5 C C02 A1D5C . . . V 3 21.516 -6.913 10.638 1 91.1 ? C02 A1D5C 402 E 1 
HETATM 6 O O03 A1D5C . . . V 3 20.731 -7.301 11.506 1 96.67 ? O03 A1D5C 402 E 1 
HETATM 7 N N04 A1D5C . . . V 3 21.401 -5.529 10.062 1 93.96 ? N04 A1D5C 402 E 1 
HETATM 8 C C05 A1D5C . . . V 3 20.392 -4.344 10.446 1 94.82 ? C05 A1D5C 402 E 1 
HETATM 9 C C06 A1D5C . . . V 3 21.358 -3.043 10.388 1 86.85 ? C06 A1D5C 402 E 1 
HETATM 10 C C07 A1D5C . . . V 3 22.055 -3.177 9.247 1 89.58 ? C07 A1D5C 402 E 1 
HETATM 11 C C08 A1D5C . . . V 3 22.143 -4.898 9.106 1 91.77 ? C08 A1D5C 402 E 1 
HETATM 12 O O09 A1D5C . . . V 3 23.379 -2.553 9.11 1 67.49 ? O09 A1D5C 402 E 1 
HETATM 13 C C10 A1D5C . . . V 3 23.859 -1.342 9.683 1 64.28 ? C10 A1D5C 402 E 1 
HETATM 14 C C11 A1D5C . . . V 3 23.387 -0.736 10.822 1 61.7 ? C11 A1D5C 402 E 1 
HETATM 15 C C12 A1D5C . . . V 3 23.957 0.465 11.325 1 73.38 ? C12 A1D5C 402 E 1 
HETATM 16 C C13 A1D5C . . . V 3 25.012 1.034 10.664 1 75.64 ? C13 A1D5C 402 E 1 
HETATM 17 C C14 A1D5C . . . V 3 25.512 0.461 9.519 1 65.17 ? C14 A1D5C 402 E 1 
HETATM 18 N N15 A1D5C . . . V 3 26.599 0.863 8.6 1 72.23 ? N15 A1D5C 402 E 1 
HETATM 19 C C16 A1D5C . . . V 3 26.664 -0.122 7.554 1 64.76 ? C16 A1D5C 402 E 1 
HETATM 20 O O17 A1D5C . . . V 3 27.439 -0.1 6.642 1 60.19 ? O17 A1D5C 402 E 1 
HETATM 21 C C18 A1D5C . . . V 3 25.634 -1.121 7.798 1 57.65 ? C18 A1D5C 402 E 1 
HETATM 22 C C19 A1D5C . . . V 3 25.263 -2.213 7.101 1 51.35 ? C19 A1D5C 402 E 1 
HETATM 23 C C20 A1D5C . . . V 3 26.183 -2.997 6.217 1 44.73 ? C20 A1D5C 402 E 1 
HETATM 24 C C21 A1D5C . . . V 3 25.6 -3.998 5.459 1 44.54 ? C21 A1D5C 402 E 1 
HETATM 25 C C22 A1D5C . . . V 3 26.38 -4.732 4.652 1 40.15 ? C22 A1D5C 402 E 1 
HETATM 26 C C23 A1D5C . . . V 3 27.805 -4.513 4.604 1 38.9 ? C23 A1D5C 402 E 1 
HETATM 27 N N24 A1D5C . . . V 3 28.765 -5.099 3.881 1 41.15 ? N24 A1D5C 402 E 1 
HETATM 28 C C25 A1D5C . . . V 3 29.949 -4.476 4.24 1 40.91 ? C25 A1D5C 402 E 1 
HETATM 29 N N26 A1D5C . . . V 3 29.805 -3.493 5.133 1 36.31 ? N26 A1D5C 402 E 1 
#
_model_server_stats.io_time_ms              26 
_model_server_stats.parse_time_ms           25 
_model_server_stats.create_model_time_ms    66 
_model_server_stats.query_time_ms           411 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           29 
#