data_8E3J
#
_model_server_result.job_id            fgGTdrH1SwBJtGSv0Q9hbA 
_model_server_result.datetime_utc      '2024-11-15 07:12:23' 
_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          8e3j 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"R","auth_seq_id":906}' 
#
_entry.id    8E3J 
#
_exptl.entry_id    8E3J 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              462.519 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (2R,3R,4R,5S)-2-(hydroxymethyl)-1-{6-[2-nitro-4-(pyrimidin-2-yl)anilino]hexyl}piperidine-3,4,5-triol 
_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            8E3J 
_cell.length_a            135.207 
_cell.length_b            179.208 
_cell.length_c            180.59 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8E3J 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,G,H,I,J,K,L,X 1 1 
B,M,N,O,P,Q,R,S,T,U,V,W,Y 2 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
? 3 D N N 
? 3 R 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 656 A CYS 654 1_555 A SG CYS 670 A CYS 668 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf2 B SG CYS 656 B CYS 654 1_555 B SG CYS 670 B CYS 668 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? 
covale ? covale1 B ND2 ASN 47 B ASN 45 1_555 M C1 NAG . B NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? 
#
_chem_comp.formula           'C22 H32 N5 O6' 
_chem_comp.formula_weight    462.519 
_chem_comp.id                UGO 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (2R,3R,4R,5S)-2-(hydroxymethyl)-1-{6-[2-nitro-4-(pyrimidin-2-yl)anilino]hexyl}piperidine-3,4,5-triol 
_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
O1 C1 UGO sing 405 n n 
O6 C22 UGO sing 406 n n 
C22 C1 UGO sing 407 n n 
C22 C21 UGO sing 408 n n 
C16 C17 UGO doub 409 n y 
C16 N4 UGO sing 410 n y 
O3 C4 UGO sing 411 n n 
C1 C2 UGO sing 412 n n 
C17 C18 UGO sing 413 n y 
N4 C15 UGO doub 414 n y 
C21 N1 UGO sing 415 n n 
C2 O2 UGO sing 416 n n 
C2 C3 UGO sing 417 n n 
N1 C5 UGO sing 418 n n 
N1 C3 UGO sing 419 n n 
C5 C6 UGO sing 420 n n 
C3 C4 UGO sing 421 n n 
C15 N5 UGO sing 422 n y 
C15 C14 UGO sing 423 n n 
C18 N5 UGO doub 424 n y 
C19 C14 UGO doub 425 n y 
C19 C20 UGO sing 426 n y 
C14 C13 UGO sing 427 n y 
C6 C7 UGO sing 428 n n 
C20 C11 UGO doub 429 n y 
C7 C8 UGO sing 430 n n 
C13 C12 UGO doub 431 n y 
C11 C12 UGO sing 432 n y 
C11 N2 UGO sing 433 n n 
C12 N3 UGO sing 434 n n 
C10 N2 UGO sing 435 n n 
C10 C9 UGO sing 436 n n 
C8 C9 UGO sing 437 n n 
N3 O5 UGO sing 438 n n 
N3 O4 UGO doub 439 n n 
C4 H2 UGO sing 440 n n 
C4 H3 UGO sing 441 n n 
C5 H4 UGO sing 442 n n 
C5 H5 UGO sing 443 n n 
C6 H6 UGO sing 444 n n 
C6 H7 UGO sing 445 n n 
C7 H8 UGO sing 446 n n 
C7 H9 UGO sing 447 n n 
C8 H10 UGO sing 448 n n 
C8 H11 UGO sing 449 n n 
C10 H12 UGO sing 450 n n 
C10 H13 UGO sing 451 n n 
C13 H14 UGO sing 452 n n 
C17 H15 UGO sing 453 n n 
C20 H16 UGO sing 454 n n 
C21 H17 UGO sing 455 n n 
C21 H18 UGO sing 456 n n 
C22 H19 UGO sing 457 n n 
O1 H20 UGO sing 458 n n 
C1 H21 UGO sing 459 n n 
C2 H22 UGO sing 460 n n 
O2 H23 UGO sing 461 n n 
C3 H24 UGO sing 462 n n 
O3 H25 UGO sing 463 n n 
C9 H26 UGO sing 464 n n 
C9 H27 UGO sing 465 n n 
N2 H28 UGO sing 466 n n 
C16 H29 UGO sing 467 n n 
C18 H30 UGO sing 468 n n 
C19 H31 UGO sing 469 n n 
O6 H32 UGO sing 470 n n 
O5 H1 UGO sing 471 n n 
#
_atom_sites.entry_id                     8E3J 
_atom_sites.fract_transf_matrix[1][1]    0.007396 
_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]    0.00558 
_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]    0.005537 
_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 GOL A 1 1101 1101 GOL GOL . 
D 3 UGO A 1 1102 1201 UGO LIG . 
E 4 SO4 A 1 1103 1 SO4 SO4 . 
F 4 SO4 A 1 1104 5 SO4 SO4 . 
G 4 SO4 A 1 1105 7 SO4 SO4 . 
H 4 SO4 A 1 1106 8 SO4 SO4 . 
I 4 SO4 A 1 1107 9 SO4 SO4 . 
J 4 SO4 A 1 1108 10 SO4 SO4 . 
K 4 SO4 A 1 1109 11 SO4 SO4 . 
L 4 SO4 A 1 1110 12 SO4 SO4 . 
M 5 NAG B 1 901 1001 NAG NAG . 
N 2 GOL B 1 902 1101 GOL GOL . 
O 2 GOL B 1 903 1201 GOL GOL . 
P 2 GOL B 1 904 1301 GOL GOL . 
Q 2 GOL B 1 905 1401 GOL GOL . 
R 3 UGO B 1 906 1501 UGO LIG . 
S 4 SO4 B 1 907 2 SO4 SO4 . 
T 4 SO4 B 1 908 3 SO4 SO4 . 
U 4 SO4 B 1 909 4 SO4 SO4 . 
V 4 SO4 B 1 910 6 SO4 SO4 . 
W 4 SO4 B 1 911 13 SO4 SO4 . 
X 6 HOH A 1 1201 16 HOH HOH . 
X 6 HOH A 2 1202 19 HOH HOH . 
X 6 HOH A 3 1203 21 HOH HOH . 
X 6 HOH A 4 1204 10 HOH HOH . 
X 6 HOH A 5 1205 12 HOH HOH . 
X 6 HOH A 6 1206 17 HOH HOH . 
X 6 HOH A 7 1207 20 HOH HOH . 
X 6 HOH A 8 1208 8 HOH HOH . 
X 6 HOH A 9 1209 2 HOH HOH . 
X 6 HOH A 10 1210 18 HOH HOH . 
Y 6 HOH B 1 1001 6 HOH HOH . 
Y 6 HOH B 2 1002 8 HOH HOH . 
Y 6 HOH B 3 1003 23 HOH HOH . 
Y 6 HOH B 4 1004 25 HOH HOH . 
Y 6 HOH B 5 1005 8 HOH HOH . 
Y 6 HOH B 6 1006 3 HOH HOH . 
Y 6 HOH B 7 1007 4 HOH HOH . 
Y 6 HOH B 8 1008 1 HOH HOH . 
Y 6 HOH B 9 1009 11 HOH HOH . 
Y 6 HOH B 10 1010 14 HOH HOH . 
Y 6 HOH B 11 1011 13 HOH HOH . 
Y 6 HOH B 12 1012 45 HOH HOH . 
Y 6 HOH B 13 1013 82 HOH HOH . 
Y 6 HOH B 14 1014 22 HOH HOH . 
Y 6 HOH B 15 1015 9 HOH HOH . 
Y 6 HOH B 16 1016 7 HOH HOH . 
Y 6 HOH B 17 1017 5 HOH HOH . 
Y 6 HOH B 18 1018 24 HOH HOH . 
Y 6 HOH B 19 1019 26 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 N N1 UGO . . . R 3 -7.119 -40.442 -32.908 1 47.9 ? N1 UGO 906 B 1 
HETATM 2 N N3 UGO . . . R 3 -13.156 -37.734 -39.022 1 106.62 1 N3 UGO 906 B 1 
HETATM 3 C C4 UGO . . . R 3 -8.951 -41.539 -31.709 1 43.96 ? C4 UGO 906 B 1 
HETATM 4 C C5 UGO . . . R 3 -7.795 -39.52 -33.349 1 57.62 ? C5 UGO 906 B 1 
HETATM 5 C C6 UGO . . . R 3 -8.493 -39.812 -34.739 1 62.37 ? C6 UGO 906 B 1 
HETATM 6 C C7 UGO . . . R 3 -9.018 -38.507 -35.493 1 75.87 ? C7 UGO 906 B 1 
HETATM 7 C C8 UGO . . . R 3 -9.01 -38.667 -37.073 1 89.79 ? C8 UGO 906 B 1 
HETATM 8 C C10 UGO . . . R 3 -10.526 -39.571 -39.014 1 99.79 ? C10 UGO 906 B 1 
HETATM 9 C C13 UGO . . . R 3 -12.728 -35.442 -39.877 1 89.27 ? C13 UGO 906 B 1 
HETATM 10 C C15 UGO . . . R 3 -12.466 -33.106 -40.617 1 118.46 ? C15 UGO 906 B 1 
HETATM 11 C C17 UGO . . . R 3 -13.447 -30.597 -40.74 1 132.83 ? C17 UGO 906 B 1 
HETATM 12 C C20 UGO . . . R 3 -10.179 -36.229 -40.932 1 96.79 ? C20 UGO 906 B 1 
HETATM 13 C C21 UGO . . . R 3 -5.898 -40.629 -33.64 1 43.23 ? C21 UGO 906 B 1 
HETATM 14 C C22 UGO . . . R 3 -4.97 -41.572 -32.92 1 43.28 ? C22 UGO 906 B 1 
HETATM 15 O O1 UGO . . . R 3 -4.7 -43.687 -31.823 1 37.55 ? O1 UGO 906 B 1 
HETATM 16 C C1 UGO . . . R 3 -5.605 -42.827 -32.677 1 41.39 ? C1 UGO 906 B 1 
HETATM 17 C C2 UGO . . . R 3 -6.842 -42.696 -31.949 1 40.52 ? C2 UGO 906 B 1 
HETATM 18 O O2 UGO . . . R 3 -7.453 -43.99 -31.94 1 41.4 ? O2 UGO 906 B 1 
HETATM 19 C C3 UGO . . . R 3 -7.868 -41.731 -32.636 1 40.96 ? C3 UGO 906 B 1 
HETATM 20 O O3 UGO . . . R 3 -8.464 -40.729 -30.664 1 46.83 ? O3 UGO 906 B 1 
HETATM 21 C C9 UGO . . . R 3 -10.483 -38.9 -37.638 1 104.02 ? C9 UGO 906 B 1 
HETATM 22 N N2 UGO . . . R 3 -10.443 -38.651 -40.149 1 103.41 ? N2 UGO 906 B 1 
HETATM 23 C C11 UGO . . . R 3 -10.989 -37.221 -40.246 1 100.11 ? C11 UGO 906 B 1 
HETATM 24 C C12 UGO . . . R 3 -12.253 -36.822 -39.745 1 97.88 ? C12 UGO 906 B 1 
HETATM 25 O O4 UGO . . . R 3 -13.311 -39.085 -39.395 1 104.36 -1 O4 UGO 906 B 1 
HETATM 26 O O5 UGO . . . R 3 -13.847 -37.201 -37.958 1 90.86 ? O5 UGO 906 B 1 
HETATM 27 C C14 UGO . . . R 3 -11.947 -34.509 -40.52 1 102.82 ? C14 UGO 906 B 1 
HETATM 28 N N4 UGO . . . R 3 -13.759 -32.893 -40.401 1 119.98 ? N4 UGO 906 B 1 
HETATM 29 C C16 UGO . . . R 3 -14.282 -31.638 -40.465 1 130.83 ? C16 UGO 906 B 1 
HETATM 30 C C18 UGO . . . R 3 -12.046 -30.858 -40.951 1 128.93 ? C18 UGO 906 B 1 
HETATM 31 N N5 UGO . . . R 3 -11.61 -32.112 -40.878 1 124.38 ? N5 UGO 906 B 1 
HETATM 32 C C19 UGO . . . R 3 -10.638 -34.894 -41.062 1 98.72 ? C19 UGO 906 B 1 
HETATM 33 O O6 UGO . . . R 3 -3.738 -41.748 -33.74 1 42.51 ? O6 UGO 906 B 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    31 
_model_server_stats.query_time_ms           285 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           33 
#