data_8EQX
#
_model_server_result.job_id            3ZrFaLEbLDq1YoC7PF-yVQ 
_model_server_result.datetime_utc      '2024-11-27 18:05:43' 
_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          8eqx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1201}' 
#
_entry.id    8EQX 
#
_exptl.entry_id    8EQX 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              438.519 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (2R,3R,4R,5S)-2-(hydroxymethyl)-1-{[6-({[(5M)-3-methyl-5-(1H-pyrrol-2-yl)phenyl]amino}methyl)pyridin-2-yl]methyl}piperidine-3,4,5-triol 
_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         90 
_cell.entry_id            8EQX 
_cell.length_a            141.392 
_cell.length_b            179.82 
_cell.length_c            180.861 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8EQX 
_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,D,E,F,G,H,I,J,K,S 1 1 
B,C,L,M,N,O,P,Q,R,T 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 F N N 
? 3 L N N 
#
_pdbx_entity_branch.entity_id    2 
_pdbx_entity_branch.type         oligosaccharide 
#
_pdbx_entity_branch_link.link_id                     1 
_pdbx_entity_branch_link.details                     ? 
_pdbx_entity_branch_link.entity_id                   2 
_pdbx_entity_branch_link.entity_branch_list_num_1    2 
_pdbx_entity_branch_link.entity_branch_list_num_2    1 
_pdbx_entity_branch_link.comp_id_1                   NAG 
_pdbx_entity_branch_link.comp_id_2                   NAG 
_pdbx_entity_branch_link.atom_id_1                   C1 
_pdbx_entity_branch_link.leaving_atom_id_1           O1 
_pdbx_entity_branch_link.atom_stereo_config_1        . 
_pdbx_entity_branch_link.atom_id_2                   O4 
_pdbx_entity_branch_link.leaving_atom_id_2           HO4 
_pdbx_entity_branch_link.atom_stereo_config_2        . 
_pdbx_entity_branch_link.value_order                 sing 
#
loop_
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.hetero
_pdbx_branch_scheme.asym_id
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
_pdbx_branch_scheme.pdb_asym_id
_pdbx_branch_scheme.pdb_seq_num
_pdbx_branch_scheme.pdb_mon_id
_pdbx_branch_scheme.auth_asym_id
_pdbx_branch_scheme.auth_seq_num
_pdbx_branch_scheme.auth_mon_id
2 n C NAG 1 C 1 NAG B 1601 NAG 
2 n C NAG 2 C 2 NAG B 1701 NAG 
#
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 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
disulf ? disulf2 B SG CYS 656 B CYS 654 1_555 B SG CYS 670 B CYS 668 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
covale ? covale1 B ND2 ASN 47 B ASN 45 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? 
covale ? covale2 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? 
#
_chem_comp.formula           'C24 H30 N4 O4' 
_chem_comp.formula_weight    438.519 
_chem_comp.id                WT5 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (2R,3R,4R,5S)-2-(hydroxymethyl)-1-{[6-({[(5M)-3-methyl-5-(1H-pyrrol-2-yl)phenyl]amino}methyl)pyridin-2-yl]methyl}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
O2 C2 WT5 sing 423 n n 
O3 C3 WT5 sing 424 n n 
C3 C2 WT5 sing 425 n n 
C3 C4 WT5 sing 426 n n 
C2 C1 WT5 sing 427 n n 
O4 C6 WT5 sing 428 n n 
C1 O1 WT5 sing 429 n n 
C1 C5 WT5 sing 430 n n 
C4 N1 WT5 sing 431 n n 
N1 C5 WT5 sing 432 n n 
N1 C7 WT5 sing 433 n n 
C23 C24 WT5 doub 434 n y 
C23 C22 WT5 sing 435 n y 
C24 C8 WT5 sing 436 n y 
C5 C6 WT5 sing 437 n n 
C22 C9 WT5 doub 438 n y 
C8 C7 WT5 sing 439 n n 
C8 N2 WT5 doub 440 n y 
C9 N2 WT5 sing 441 n y 
C9 C10 WT5 sing 442 n n 
C10 N3 WT5 sing 443 n n 
N3 C11 WT5 sing 444 n n 
C21 C11 WT5 doub 445 n y 
C21 C16 WT5 sing 446 n y 
C11 C12 WT5 sing 447 n y 
N4 C20 WT5 sing 448 n y 
N4 C17 WT5 sing 449 n y 
C20 C19 WT5 doub 450 n y 
C16 C17 WT5 sing 451 n n 
C16 C15 WT5 doub 452 n y 
C12 C13 WT5 doub 453 n y 
C17 C18 WT5 doub 454 n y 
C15 C13 WT5 sing 455 n y 
C13 C14 WT5 sing 456 n n 
C19 C18 WT5 sing 457 n y 
N3 H2 WT5 sing 458 n n 
C4 H3 WT5 sing 459 n n 
C4 H4 WT5 sing 460 n n 
C5 H5 WT5 sing 461 n n 
C6 H6 WT5 sing 462 n n 
C6 H7 WT5 sing 463 n n 
C7 H8 WT5 sing 464 n n 
C7 H9 WT5 sing 465 n n 
C10 H10 WT5 sing 466 n n 
C10 H11 WT5 sing 467 n n 
C15 H12 WT5 sing 468 n n 
C20 H13 WT5 sing 469 n n 
C21 H14 WT5 sing 470 n n 
C22 H15 WT5 sing 471 n n 
C24 H16 WT5 sing 472 n n 
C1 H17 WT5 sing 473 n n 
C12 H18 WT5 sing 474 n n 
C14 H19 WT5 sing 475 n n 
C14 H20 WT5 sing 476 n n 
C14 H21 WT5 sing 477 n n 
C18 H22 WT5 sing 478 n n 
C19 H23 WT5 sing 479 n n 
C2 H24 WT5 sing 480 n n 
C23 H25 WT5 sing 481 n n 
C3 H26 WT5 sing 482 n n 
N4 H27 WT5 sing 483 n n 
O1 H28 WT5 sing 484 n n 
O2 H29 WT5 sing 485 n n 
O3 H30 WT5 sing 486 n n 
O4 H31 WT5 sing 487 n n 
#
_atom_sites.entry_id                     8EQX 
_atom_sites.fract_transf_matrix[1][1]    0.007073 
_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]    0.005561 
_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]    0.005529 
_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
D 3 WT5 A 1 1201 1201 WT5 LIG . 
E 4 GOL A 1 1202 1301 GOL GOL . 
F 3 WT5 A 1 1203 1401 WT5 LIG . 
G 5 SO4 A 1 1204 2 SO4 SO4 . 
H 5 SO4 A 1 1205 3 SO4 SO4 . 
I 5 SO4 A 1 1206 6 SO4 SO4 . 
J 5 SO4 A 1 1207 7 SO4 SO4 . 
K 5 SO4 A 1 1208 8 SO4 SO4 . 
L 3 WT5 B 1 1501 1501 WT5 LIG . 
M 4 GOL B 1 1502 1801 GOL GOL . 
N 4 GOL B 1 1503 1901 GOL GOL . 
O 4 GOL B 1 1504 2001 GOL GOL . 
P 5 SO4 B 1 1505 1 SO4 SO4 . 
Q 5 SO4 B 1 1506 4 SO4 SO4 . 
R 5 SO4 B 1 1507 5 SO4 SO4 . 
S 6 HOH A 1 1301 4 HOH HOH . 
S 6 HOH A 2 1302 24 HOH HOH . 
S 6 HOH A 3 1303 21 HOH HOH . 
S 6 HOH A 4 1304 28 HOH HOH . 
S 6 HOH A 5 1305 13 HOH HOH . 
S 6 HOH A 6 1306 29 HOH HOH . 
S 6 HOH A 7 1307 19 HOH HOH . 
S 6 HOH A 8 1308 27 HOH HOH . 
S 6 HOH A 9 1309 16 HOH HOH . 
S 6 HOH A 10 1310 2 HOH HOH . 
S 6 HOH A 11 1311 25 HOH HOH . 
T 6 HOH B 1 1601 23 HOH HOH . 
T 6 HOH B 2 1602 11 HOH HOH . 
T 6 HOH B 3 1603 22 HOH HOH . 
T 6 HOH B 4 1604 26 HOH HOH . 
T 6 HOH B 5 1605 18 HOH HOH . 
T 6 HOH B 6 1606 3 HOH HOH . 
T 6 HOH B 7 1607 10 HOH HOH . 
T 6 HOH B 8 1608 9 HOH HOH . 
T 6 HOH B 9 1609 14 HOH HOH . 
T 6 HOH B 10 1610 8 HOH HOH . 
T 6 HOH B 11 1611 1 HOH HOH . 
T 6 HOH B 12 1612 5 HOH HOH . 
T 6 HOH B 13 1613 7 HOH HOH . 
T 6 HOH B 14 1614 12 HOH HOH . 
T 6 HOH B 15 1615 17 HOH HOH . 
T 6 HOH B 16 1616 6 HOH HOH . 
T 6 HOH B 17 1617 15 HOH HOH . 
T 6 HOH B 18 1618 20 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 WT5 . . . D 3 -38.379 -30.988 -67.655 1 59.42 ? N1 WT5 1201 A 1 
HETATM 2 N N3 WT5 . . . D 3 -44.336 -33.337 -65.27 1 64.48 ? N3 WT5 1201 A 1 
HETATM 3 C C4 WT5 . . . D 3 -38.648 -32.37 -67.937 1 52.86 ? C4 WT5 1201 A 1 
HETATM 4 C C5 WT5 . . . D 3 -36.986 -30.804 -67.383 1 52.08 ? C5 WT5 1201 A 1 
HETATM 5 C C6 WT5 . . . D 3 -36.706 -29.328 -67.32 1 48.35 ? C6 WT5 1201 A 1 
HETATM 6 C C7 WT5 . . . D 3 -38.965 -30.659 -66.666 1 70.36 ? C7 WT5 1201 A 1 
HETATM 7 C C8 WT5 . . . D 3 -40.471 -30.934 -66.699 1 66.54 ? C8 WT5 1201 A 1 
HETATM 8 C C10 WT5 . . . D 3 -42.887 -33.358 -65.315 1 68.43 ? C10 WT5 1201 A 1 
HETATM 9 C C13 WT5 . . . D 3 -44.929 -30.963 -62.53 1 65.88 ? C13 WT5 1201 A 1 
HETATM 10 C C15 WT5 . . . D 3 -46.285 -30.91 -62.496 1 64.88 ? C15 WT5 1201 A 1 
HETATM 11 C C17 WT5 . . . D 3 -48.539 -31.531 -63.265 1 75.81 ? C17 WT5 1201 A 1 
HETATM 12 C C20 WT5 . . . D 3 -50.613 -31.778 -63.669 1 65.6 ? C20 WT5 1201 A 1 
HETATM 13 C C21 WT5 . . . D 3 -46.408 -32.449 -64.289 1 64.4 ? C21 WT5 1201 A 1 
HETATM 14 C C22 WT5 . . . D 3 -43.126 -31.379 -66.806 1 74.61 ? C22 WT5 1201 A 1 
HETATM 15 C C24 WT5 . . . D 3 -41.258 -30.098 -67.434 1 66.83 ? C24 WT5 1201 A 1 
HETATM 16 C C1 WT5 . . . D 3 -36.037 -31.48 -68.38 1 45.66 ? C1 WT5 1201 A 1 
HETATM 17 C C11 WT5 . . . D 3 -45.036 -32.505 -64.316 1 73.12 ? C11 WT5 1201 A 1 
HETATM 18 C C12 WT5 . . . D 3 -44.301 -31.761 -63.437 1 65.11 ? C12 WT5 1201 A 1 
HETATM 19 C C14 WT5 . . . D 3 -44.128 -30.135 -61.555 1 64.91 ? C14 WT5 1201 A 1 
HETATM 20 C C16 WT5 . . . D 3 -47.029 -31.642 -63.369 1 67.08 ? C16 WT5 1201 A 1 
HETATM 21 C C18 WT5 . . . D 3 -49.207 -30.834 -62.293 1 64 ? C18 WT5 1201 A 1 
HETATM 22 C C19 WT5 . . . D 3 -50.536 -30.993 -62.556 1 61.69 ? C19 WT5 1201 A 1 
HETATM 23 C C2 WT5 . . . D 3 -36.366 -32.855 -68.565 1 48.23 ? C2 WT5 1201 A 1 
HETATM 24 C C23 WT5 . . . D 3 -42.61 -30.315 -67.501 1 66.61 ? C23 WT5 1201 A 1 
HETATM 25 C C3 WT5 . . . D 3 -37.719 -32.942 -69.013 1 54.21 ? C3 WT5 1201 A 1 
HETATM 26 C C9 WT5 . . . D 3 -42.285 -32.178 -66.079 1 68.46 ? C9 WT5 1201 A 1 
HETATM 27 N N2 WT5 . . . D 3 -40.998 -31.94 -66.041 1 64.64 ? N2 WT5 1201 A 1 
HETATM 28 N N4 WT5 . . . D 3 -49.409 -32.079 -64.051 1 68.01 ? N4 WT5 1201 A 1 
HETATM 29 O O1 WT5 . . . D 3 -34.754 -31.494 -67.803 1 53.11 ? O1 WT5 1201 A 1 
HETATM 30 O O2 WT5 . . . D 3 -35.463 -33.387 -69.588 1 42.12 ? O2 WT5 1201 A 1 
HETATM 31 O O3 WT5 . . . D 3 -38.092 -34.283 -69.223 1 43.67 ? O3 WT5 1201 A 1 
HETATM 32 O O4 WT5 . . . D 3 -36.858 -28.855 -68.592 1 45.31 ? O4 WT5 1201 A 1 
#
_model_server_stats.io_time_ms              74 
_model_server_stats.parse_time_ms           30 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           308 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           32 
#