data_8EQX # _model_server_result.job_id dvAbm0HzpQ1LMxet0_z6dg _model_server_result.datetime_utc '2024-11-13 11:57:00' _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 13 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #