data_2XH5
#
_model_server_result.job_id            xMRW2EfS_cBT4uVRXR-l8w 
_model_server_result.datetime_utc      '2025-05-21 02:21:40' 
_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          2xh5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1480}' 
#
_entry.id    2XH5 
#
_exptl.entry_id    2XH5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              364.507 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            4-(4-tert-butylbenzyl)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-4-aminium 
_entity.pdbx_number_of_molecules    1 
_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            2XH5 
_cell.length_a            44.948 
_cell.length_b            61.233 
_cell.length_c            135.671 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2XH5 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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
covale ? covale1 A C LYS 168 A LYS 308 1_555 A N TPO 169 A TPO 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
covale ? covale2 A C TPO 169 A TPO 309 1_555 A N PHE 170 A PHE 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
#
_chem_comp.formula           'C22 H30 N5 1' 
_chem_comp.formula_weight    364.507 
_chem_comp.id                X37 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              4-(4-tert-butylbenzyl)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-4-aminium 
_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
N1 C2 X37 sing 397 n n 
N1 C21 X37 sing 398 n n 
N1 C22 X37 sing 399 n n 
C2 C3 X37 sing 400 n n 
C2 H2 X37 sing 401 n n 
C2 H2A X37 sing 402 n n 
C3 C4 X37 sing 403 n n 
C3 H3 X37 sing 404 n n 
C3 H3A X37 sing 405 n n 
C4 N5 X37 sing 406 n n 
C4 C9 X37 sing 407 n n 
C4 C20 X37 sing 408 n n 
N5 HN5 X37 sing 409 n n 
N5 HN5A X37 sing 410 n n 
N5 HN5B X37 sing 411 n n 
C9 C10 X37 sing 412 n n 
C9 H9 X37 sing 413 n n 
C9 H9A X37 sing 414 n n 
C10 C11 X37 doub 415 n y 
C10 C15 X37 sing 416 n y 
C11 C12 X37 sing 417 n y 
C11 H11 X37 sing 418 n n 
C12 C13 X37 doub 419 n y 
C12 H12 X37 sing 420 n n 
C13 C14 X37 sing 421 n y 
C13 C16 X37 sing 422 n n 
C14 C15 X37 doub 423 n y 
C14 H14 X37 sing 424 n n 
C15 H15 X37 sing 425 n n 
C16 C17 X37 sing 426 n n 
C16 C18 X37 sing 427 n n 
C16 C19 X37 sing 428 n n 
C17 H17 X37 sing 429 n n 
C17 H17A X37 sing 430 n n 
C17 H17B X37 sing 431 n n 
C18 H18 X37 sing 432 n n 
C18 H18A X37 sing 433 n n 
C18 H18B X37 sing 434 n n 
C19 H19 X37 sing 435 n n 
C19 H19A X37 sing 436 n n 
C19 H19B X37 sing 437 n n 
C20 C21 X37 sing 438 n n 
C20 H20 X37 sing 439 n n 
C20 H20A X37 sing 440 n n 
C21 H21 X37 sing 441 n n 
C21 H21A X37 sing 442 n n 
C22 N23 X37 doub 443 n y 
C22 C31 X37 sing 444 n y 
N23 C24 X37 sing 445 n y 
C24 N25 X37 doub 446 n y 
C24 H24 X37 sing 447 n n 
N25 C26 X37 sing 448 n y 
C26 N27 X37 sing 449 n y 
C26 C31 X37 doub 450 n y 
N27 C29 X37 sing 451 n y 
N27 HN27 X37 sing 452 n n 
C29 C30 X37 doub 453 n y 
C29 H29 X37 sing 454 n n 
C30 C31 X37 sing 455 n y 
C30 H30 X37 sing 456 n n 
#
_atom_sites.entry_id                     2XH5 
_atom_sites.fract_transf_matrix[1][1]    0.022248 
_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]    0.016331 
_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]    0.007371 
_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 3 X37 A 1 1480 1480 X37 X37 . 
D 4 HOH A 1 2001 2001 HOH HOH . 
D 4 HOH A 2 2002 2002 HOH HOH . 
D 4 HOH A 3 2003 2003 HOH HOH . 
D 4 HOH A 4 2004 2004 HOH HOH . 
D 4 HOH A 5 2005 2005 HOH HOH . 
D 4 HOH A 6 2006 2006 HOH HOH . 
D 4 HOH A 7 2007 2007 HOH HOH . 
D 4 HOH A 8 2008 2008 HOH HOH . 
D 4 HOH A 9 2009 2009 HOH HOH . 
D 4 HOH A 10 2010 2010 HOH HOH . 
D 4 HOH A 11 2011 2011 HOH HOH . 
D 4 HOH A 12 2012 2012 HOH HOH . 
D 4 HOH A 13 2013 2013 HOH HOH . 
D 4 HOH A 14 2014 2014 HOH HOH . 
D 4 HOH A 15 2015 2015 HOH HOH . 
D 4 HOH A 16 2016 2016 HOH HOH . 
D 4 HOH A 17 2017 2017 HOH HOH . 
D 4 HOH A 18 2018 2018 HOH HOH . 
D 4 HOH A 19 2019 2019 HOH HOH . 
D 4 HOH A 20 2020 2020 HOH HOH . 
D 4 HOH A 21 2021 2021 HOH HOH . 
D 4 HOH A 22 2022 2022 HOH HOH . 
D 4 HOH A 23 2023 2023 HOH HOH . 
D 4 HOH A 24 2024 2024 HOH HOH . 
D 4 HOH A 25 2025 2025 HOH HOH . 
D 4 HOH A 26 2026 2026 HOH HOH . 
D 4 HOH A 27 2027 2027 HOH HOH . 
D 4 HOH A 28 2028 2028 HOH HOH . 
D 4 HOH A 29 2029 2029 HOH HOH . 
D 4 HOH A 30 2030 2030 HOH HOH . 
D 4 HOH A 31 2031 2031 HOH HOH . 
D 4 HOH A 32 2032 2032 HOH HOH . 
D 4 HOH A 33 2033 2033 HOH HOH . 
D 4 HOH A 34 2034 2034 HOH HOH . 
D 4 HOH A 35 2035 2035 HOH HOH . 
D 4 HOH A 36 2036 2036 HOH HOH . 
D 4 HOH A 37 2037 2037 HOH HOH . 
D 4 HOH A 38 2038 2038 HOH HOH . 
D 4 HOH A 39 2039 2039 HOH HOH . 
D 4 HOH A 40 2040 2040 HOH HOH . 
D 4 HOH A 41 2041 2041 HOH HOH . 
E 4 HOH C 1 2001 2001 HOH HOH . 
E 4 HOH C 2 2002 2002 HOH HOH . 
E 4 HOH C 3 2003 2003 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 X37 . . . C 3 44.602 33.727 113.939 1 26.44 ? N1 X37 1480 A 1 
HETATM 2 C C2 X37 . . . C 3 43.255 33.168 113.892 1 25.21 ? C2 X37 1480 A 1 
HETATM 3 C C3 X37 . . . C 3 42.934 32.49 115.199 1 25.14 ? C3 X37 1480 A 1 
HETATM 4 C C4 X37 . . . C 3 44.016 31.49 115.639 1 27.4 ? C4 X37 1480 A 1 
HETATM 5 N N5 X37 . . . C 3 43.925 31.436 117.144 1 27.58 ? N5 X37 1480 A 1 
HETATM 6 C C9 X37 . . . C 3 43.736 30.026 115.258 1 29.21 ? C9 X37 1480 A 1 
HETATM 7 C C10 X37 . . . C 3 43.293 29.68 113.856 1 30.97 ? C10 X37 1480 A 1 
HETATM 8 C C11 X37 . . . C 3 41.942 29.647 113.534 1 30.72 ? C11 X37 1480 A 1 
HETATM 9 C C12 X37 . . . C 3 41.527 29.311 112.262 1 31.17 ? C12 X37 1480 A 1 
HETATM 10 C C13 X37 . . . C 3 42.454 28.982 111.272 1 32.07 ? C13 X37 1480 A 1 
HETATM 11 C C14 X37 . . . C 3 43.814 29.003 111.603 1 29.52 ? C14 X37 1480 A 1 
HETATM 12 C C15 X37 . . . C 3 44.225 29.342 112.876 1 28.8 ? C15 X37 1480 A 1 
HETATM 13 C C16 X37 . . . C 3 41.985 28.595 109.846 1 32.04 ? C16 X37 1480 A 1 
HETATM 14 C C17 X37 . . . C 3 40.698 27.784 109.902 1 31.44 ? C17 X37 1480 A 1 
HETATM 15 C C18 X37 . . . C 3 41.719 29.838 108.993 1 31.96 ? C18 X37 1480 A 1 
HETATM 16 C C19 X37 . . . C 3 43.044 27.733 109.146 1 31.82 ? C19 X37 1480 A 1 
HETATM 17 C C20 X37 . . . C 3 45.468 31.918 115.341 1 26.86 ? C20 X37 1480 A 1 
HETATM 18 C C21 X37 . . . C 3 45.618 32.671 114.037 1 27.46 ? C21 X37 1480 A 1 
HETATM 19 C C22 X37 . . . C 3 44.868 35.033 114.392 1 25.17 ? C22 X37 1480 A 1 
HETATM 20 N N23 X37 . . . C 3 46.155 35.3 114.673 1 23.4 ? N23 X37 1480 A 1 
HETATM 21 C C24 X37 . . . C 3 46.436 36.533 115.098 1 21.99 ? C24 X37 1480 A 1 
HETATM 22 N N25 X37 . . . C 3 45.595 37.547 115.275 1 20.88 ? N25 X37 1480 A 1 
HETATM 23 C C26 X37 . . . C 3 44.341 37.261 114.988 1 22.11 ? C26 X37 1480 A 1 
HETATM 24 N N27 X37 . . . C 3 43.265 38.088 115.068 1 22.17 ? N27 X37 1480 A 1 
HETATM 25 C C29 X37 . . . C 3 42.161 37.419 114.68 1 23.7 ? C29 X37 1480 A 1 
HETATM 26 C C30 X37 . . . C 3 42.529 36.161 114.353 1 24.25 ? C30 X37 1480 A 1 
HETATM 27 C C31 X37 . . . C 3 43.882 36.029 114.537 1 24.7 ? C31 X37 1480 A 1 
HETATM 28 H HN5 X37 . . . C 3 44.455 30.791 117.466 1 27.52 ? HN5 X37 1480 A 1 
HETATM 29 H HN5A X37 . . . C 3 44.187 32.241 117.515 1 27.52 ? HN5A X37 1480 A 1 
HETATM 30 H HN5B X37 . . . C 3 43.054 31.261 117.411 1 27.52 ? HN5B X37 1480 A 1 
HETATM 31 H HN27 X37 . . . C 3 43.288 38.945 115.334 1 22.64 ? HN27 X37 1480 A 1 
HETATM 32 H H2 X37 . . . C 3 42.616 33.868 113.722 1 25.47 ? H2 X37 1480 A 1 
HETATM 33 H H2A X37 . . . C 3 43.199 32.518 113.163 1 25.47 ? H2A X37 1480 A 1 
HETATM 34 H H3 X37 . . . C 3 42.831 33.17 115.894 1 25.67 ? H3 X37 1480 A 1 
HETATM 35 H H3A X37 . . . C 3 42.087 32.016 115.112 1 25.67 ? H3A X37 1480 A 1 
HETATM 36 H H9 X37 . . . C 3 44.549 29.518 115.445 1 29.17 ? H9 X37 1480 A 1 
HETATM 37 H H9A X37 . . . C 3 43.053 29.691 115.875 1 29.17 ? H9A X37 1480 A 1 
HETATM 38 H H11 X37 . . . C 3 41.301 29.866 114.194 1 30.78 ? H11 X37 1480 A 1 
HETATM 39 H H12 X37 . . . C 3 40.605 29.3 112.058 1 31.12 ? H12 X37 1480 A 1 
HETATM 40 H H14 X37 . . . C 3 44.457 28.784 110.948 1 30.06 ? H14 X37 1480 A 1 
HETATM 41 H H15 X37 . . . C 3 45.148 29.351 113.086 1 29.66 ? H15 X37 1480 A 1 
HETATM 42 H H17 X37 . . . C 3 39.953 28.361 110.143 1 31.62 ? H17 X37 1480 A 1 
HETATM 43 H H17A X37 . . . C 3 40.521 27.383 109.034 1 31.62 ? H17A X37 1480 A 1 
HETATM 44 H H17B X37 . . . C 3 40.781 27.079 110.567 1 31.62 ? H17B X37 1480 A 1 
HETATM 45 H H18 X37 . . . C 3 42.331 30.549 109.246 1 31.98 ? H18 X37 1480 A 1 
HETATM 46 H H18A X37 . . . C 3 41.849 29.628 108.052 1 31.98 ? H18A X37 1480 A 1 
HETATM 47 H H18B X37 . . . C 3 40.807 30.143 109.126 1 31.98 ? H18B X37 1480 A 1 
HETATM 48 H H19 X37 . . . C 3 43.357 27.036 109.749 1 31.88 ? H19 X37 1480 A 1 
HETATM 49 H H19A X37 . . . C 3 42.662 27.318 108.353 1 31.88 ? H19A X37 1480 A 1 
HETATM 50 H H19B X37 . . . C 3 43.799 28.287 108.88 1 31.88 ? H19B X37 1480 A 1 
HETATM 51 H H20 X37 . . . C 3 45.785 32.485 116.072 1 27.12 ? H20 X37 1480 A 1 
HETATM 52 H H20A X37 . . . C 3 46.032 31.121 115.314 1 27.12 ? H20A X37 1480 A 1 
HETATM 53 H H21 X37 . . . C 3 45.517 32.052 113.288 1 27.07 ? H21 X37 1480 A 1 
HETATM 54 H H21A X37 . . . C 3 46.509 33.068 113.988 1 27.07 ? H21A X37 1480 A 1 
HETATM 55 H H24 X37 . . . C 3 47.345 36.707 115.3 1 22.26 ? H24 X37 1480 A 1 
HETATM 56 H H29 X37 . . . C 3 41.289 37.787 114.655 1 23.43 ? H29 X37 1480 A 1 
HETATM 57 H H30 X37 . . . C 3 41.947 35.487 114.054 1 24.06 ? H30 X37 1480 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           291 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           57 
#