data_6VKQ
#
_model_server_result.job_id            3KTj9VO3oj4AQmSFTL1sZw 
_model_server_result.datetime_utc      '2024-12-11 21:21:37' 
_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          6vkq 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":2001}' 
#
_entry.id    6VKQ 
#
_exptl.entry_id    6VKQ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              537.528 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          111.25 
_cell.angle_gamma         90 
_cell.entry_id            6VKQ 
_cell.length_a            140.219 
_cell.length_b            130.31 
_cell.length_c            101.87 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6VKQ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
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 
? monomeric 1 author_defined_assembly 3 
? monomeric 1 author_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,G,H 1 1 
B,I,J,K,L 2 1 
C,M,N,O,P 3 1 
D,Q,R,S,T 4 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
? 2 E N N 
? 2 I N N 
? 2 M N N 
? 2 Q 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 206 A CYS 845 1_555 A SG CYS 206 A CYS 845 2_657 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? 
disulf ? disulf2 B SG CYS 206 B CYS 845 1_555 D SG CYS 206 D CYS 845 2_658 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? 
disulf ? disulf3 C SG CYS 206 C CYS 845 1_555 C SG CYS 206 C CYS 845 2_658 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? 
#
_chem_comp.formula           'C24 H27 N9 O6' 
_chem_comp.formula_weight    537.528 
_chem_comp.id                UHB 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide 
_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 UHB doub 360 n y 
C01 C06 UHB sing 361 n y 
C02 C03 UHB sing 362 n y 
C03 C04 UHB doub 363 n y 
C04 C05 UHB sing 364 n y 
C04 N11 UHB sing 365 n n 
C05 C06 UHB doub 366 n y 
C05 C08 UHB sing 367 n n 
C06 C07 UHB sing 368 n n 
C07 N09 UHB sing 369 n n 
C07 O10 UHB doub 370 n n 
C08 N09 UHB sing 371 n n 
N11 C12 UHB sing 372 n n 
C12 O13 UHB doub 373 n n 
C12 C14 UHB sing 374 n n 
C14 N15 UHB sing 375 n n 
N15 C16 UHB sing 376 n n 
N15 C20 UHB sing 377 n n 
C16 C17 UHB sing 378 n n 
C17 N18 UHB sing 379 n n 
N18 C19 UHB sing 380 n n 
N18 C21 UHB sing 381 n n 
C19 C20 UHB sing 382 n n 
C21 C22 UHB sing 383 n n 
C21 O27 UHB doub 384 n n 
C22 C23 UHB sing 385 n n 
C22 O26 UHB sing 386 n n 
C23 C24 UHB sing 387 n n 
C23 O28 UHB sing 388 n n 
C24 C25 UHB sing 389 n n 
C24 O29 UHB sing 390 n n 
C25 O26 UHB sing 391 n n 
C25 N30 UHB sing 392 n n 
N30 C32 UHB sing 393 n y 
N30 C33 UHB sing 394 n y 
C31 C32 UHB doub 395 n y 
C31 N34 UHB sing 396 n y 
C31 C38 UHB sing 397 n y 
C32 N37 UHB sing 398 n y 
C33 N34 UHB doub 399 n y 
N35 C36 UHB sing 400 n y 
N35 C38 UHB doub 401 n y 
C36 N37 UHB doub 402 n y 
C38 N39 UHB sing 403 n n 
C01 H01 UHB sing 404 n n 
C02 H02 UHB sing 405 n n 
C03 H03 UHB sing 406 n n 
C08 H081 UHB sing 407 n n 
C08 H082 UHB sing 408 n n 
N09 HN09 UHB sing 409 n n 
C14 H14 UHB sing 410 n n 
C14 H14A UHB sing 411 n n 
C16 H16 UHB sing 412 n n 
C16 H16A UHB sing 413 n n 
C17 H17 UHB sing 414 n n 
C17 H17A UHB sing 415 n n 
C19 H19 UHB sing 416 n n 
C19 H19A UHB sing 417 n n 
C20 H20 UHB sing 418 n n 
C20 H20A UHB sing 419 n n 
C22 H22 UHB sing 420 n n 
C23 H23 UHB sing 421 n n 
C24 H24 UHB sing 422 n n 
C25 H25 UHB sing 423 n n 
O28 HO28 UHB sing 424 n n 
O29 HO29 UHB sing 425 n n 
C33 H33 UHB sing 426 n n 
C36 H36 UHB sing 427 n n 
N39 HN39 UHB sing 428 n n 
N39 HN3A UHB sing 429 n n 
N11 HN11 UHB sing 430 n n 
#
_atom_sites.entry_id                     6VKQ 
_atom_sites.fract_transf_matrix[1][1]    0.007132 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002773 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007674 
_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]    0.010533 
_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
E 2 UHB A 1 2001 2001 UHB UHB . 
F 3 SO4 A 1 2002 4 SO4 SO4 . 
G 3 SO4 A 1 2003 5 SO4 SO4 . 
H 3 SO4 A 1 2004 9 SO4 SO4 . 
I 2 UHB B 1 2001 2001 UHB UHB . 
J 3 SO4 B 1 2002 3 SO4 SO4 . 
K 3 SO4 B 1 2003 8 SO4 SO4 . 
L 3 SO4 B 1 2004 12 SO4 SO4 . 
M 2 UHB C 1 2001 2001 UHB UHB . 
N 3 SO4 C 1 2002 1 SO4 SO4 . 
O 3 SO4 C 1 2003 6 SO4 SO4 . 
P 3 SO4 C 1 2004 10 SO4 SO4 . 
Q 2 UHB D 1 2001 2001 UHB UHB . 
R 3 SO4 D 1 2002 2 SO4 SO4 . 
S 3 SO4 D 1 2003 7 SO4 SO4 . 
T 3 SO4 D 1 2004 11 SO4 SO4 . 
#
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 C01 UHB . . . M 2 33.422 18.827 124.569 1 41.04 ? C01 UHB 2001 C 1 
HETATM 2 C C02 UHB . . . M 2 33.291 18.211 123.331 1 41.9 ? C02 UHB 2001 C 1 
HETATM 3 C C03 UHB . . . M 2 32.747 18.889 122.247 1 42.14 ? C03 UHB 2001 C 1 
HETATM 4 C C04 UHB . . . M 2 32.326 20.209 122.401 1 42.95 ? C04 UHB 2001 C 1 
HETATM 5 C C05 UHB . . . M 2 32.46 20.839 123.648 1 41.89 ? C05 UHB 2001 C 1 
HETATM 6 C C06 UHB . . . M 2 33.007 20.15 124.712 1 41.61 ? C06 UHB 2001 C 1 
HETATM 7 C C07 UHB . . . M 2 33.055 21.064 125.878 1 41.08 ? C07 UHB 2001 C 1 
HETATM 8 C C08 UHB . . . M 2 32.107 22.235 124.069 1 42.07 ? C08 UHB 2001 C 1 
HETATM 9 N N09 UHB . . . M 2 32.537 22.234 125.46 1 41.33 ? N09 UHB 2001 C 1 
HETATM 10 O O10 UHB . . . M 2 33.466 20.831 127.013 1 38.94 ? O10 UHB 2001 C 1 
HETATM 11 N N11 UHB . . . M 2 31.805 20.913 121.289 1 46.92 ? N11 UHB 2001 C 1 
HETATM 12 C C12 UHB . . . M 2 30.687 21.673 121.209 1 53.27 ? C12 UHB 2001 C 1 
HETATM 13 O O13 UHB . . . M 2 29.833 21.73 122.085 1 53.65 ? O13 UHB 2001 C 1 
HETATM 14 C C14 UHB . . . M 2 30.552 22.463 119.917 1 60.69 ? C14 UHB 2001 C 1 
HETATM 15 N N15 UHB . . . M 2 29.892 23.769 120.032 1 69.27 ? N15 UHB 2001 C 1 
HETATM 16 C C16 UHB . . . M 2 30.518 24.62 121.053 1 74.37 ? C16 UHB 2001 C 1 
HETATM 17 C C17 UHB . . . M 2 29.876 25.999 121.06 1 75.93 ? C17 UHB 2001 C 1 
HETATM 18 N N18 UHB . . . M 2 28.433 25.88 121.31 1 77.18 ? N18 UHB 2001 C 1 
HETATM 19 C C19 UHB . . . M 2 27.791 25.004 120.323 1 74.22 ? C19 UHB 2001 C 1 
HETATM 20 C C20 UHB . . . M 2 28.458 23.639 120.321 1 72.59 ? C20 UHB 2001 C 1 
HETATM 21 C C21 UHB . . . M 2 27.725 26.504 122.276 1 79.11 ? C21 UHB 2001 C 1 
HETATM 22 C C22 UHB . . . M 2 28.435 27.488 123.208 1 81.36 ? C22 UHB 2001 C 1 
HETATM 23 C C23 UHB . . . M 2 29.352 26.821 124.243 1 79.85 ? C23 UHB 2001 C 1 
HETATM 24 C C24 UHB . . . M 2 28.455 26.754 125.479 1 78.05 ? C24 UHB 2001 C 1 
HETATM 25 C C25 UHB . . . M 2 27.647 28.043 125.338 1 79.21 ? C25 UHB 2001 C 1 
HETATM 26 O O26 UHB . . . M 2 27.492 28.273 123.952 1 82.48 ? O26 UHB 2001 C 1 
HETATM 27 O O27 UHB . . . M 2 26.532 26.3 122.43 1 76.73 ? O27 UHB 2001 C 1 
HETATM 28 O O28 UHB . . . M 2 30.515 27.606 124.476 1 81.49 ? O28 UHB 2001 C 1 
HETATM 29 O O29 UHB . . . M 2 29.229 26.786 126.672 1 74.93 ? O29 UHB 2001 C 1 
HETATM 30 N N30 UHB . . . M 2 26.324 27.995 125.955 1 79.68 ? N30 UHB 2001 C 1 
HETATM 31 C C31 UHB . . . M 2 24.243 28.403 126.543 1 81.15 ? C31 UHB 2001 C 1 
HETATM 32 C C32 UHB . . . M 2 25.178 28.634 125.547 1 80.55 ? C32 UHB 2001 C 1 
HETATM 33 C C33 UHB . . . M 2 26.006 27.384 127.139 1 80.43 ? C33 UHB 2001 C 1 
HETATM 34 N N34 UHB . . . M 2 24.776 27.599 127.539 1 80.62 ? N34 UHB 2001 C 1 
HETATM 35 N N35 UHB . . . M 2 22.756 29.706 125.249 1 81.07 ? N35 UHB 2001 C 1 
HETATM 36 C C36 UHB . . . M 2 23.748 29.821 124.36 1 82.02 ? C36 UHB 2001 C 1 
HETATM 37 N N37 UHB . . . M 2 24.99 29.333 124.422 1 81.71 ? N37 UHB 2001 C 1 
HETATM 38 C C38 UHB . . . M 2 22.977 28.999 126.379 1 81.26 ? C38 UHB 2001 C 1 
HETATM 39 N N39 UHB . . . M 2 22.006 28.948 127.298 1 80.78 ? N39 UHB 2001 C 1 
#
_model_server_stats.io_time_ms              29 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           325 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           39 
#