data_6VKQ
#
_model_server_result.job_id            v6T2b4oSL_LmKMpVi3Xgpw 
_model_server_result.datetime_utc      '2024-12-11 21:19:51' 
_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":"I","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 . . . I 2 13.223 9.075 89.378 1 55.49 ? C01 UHB 2001 B 1 
HETATM 2 C C02 UHB . . . I 2 14.173 8.521 88.531 1 55.46 ? C02 UHB 2001 B 1 
HETATM 3 C C03 UHB . . . I 2 13.799 7.679 87.491 1 56.73 ? C03 UHB 2001 B 1 
HETATM 4 C C04 UHB . . . I 2 12.449 7.388 87.296 1 58.3 ? C04 UHB 2001 B 1 
HETATM 5 C C05 UHB . . . I 2 11.487 7.934 88.155 1 57.15 ? C05 UHB 2001 B 1 
HETATM 6 C C06 UHB . . . I 2 11.876 8.773 89.179 1 55.99 ? C06 UHB 2001 B 1 
HETATM 7 C C07 UHB . . . I 2 10.658 9.222 89.896 1 54.73 ? C07 UHB 2001 B 1 
HETATM 8 C C08 UHB . . . I 2 9.998 7.751 88.181 1 56.77 ? C08 UHB 2001 B 1 
HETATM 9 N N09 UHB . . . I 2 9.621 8.619 89.287 1 55.12 ? N09 UHB 2001 B 1 
HETATM 10 O O10 UHB . . . I 2 10.576 9.98 90.859 1 51.09 ? O10 UHB 2001 B 1 
HETATM 11 N N11 UHB . . . I 2 12.031 6.594 86.201 1 61.49 ? N11 UHB 2001 B 1 
HETATM 12 C C12 UHB . . . I 2 11.297 5.46 86.228 1 66.66 ? C12 UHB 2001 B 1 
HETATM 13 O O13 UHB . . . I 2 11.011 4.857 87.256 1 66.65 ? O13 UHB 2001 B 1 
HETATM 14 C C14 UHB . . . I 2 10.861 4.96 84.86 1 72.65 ? C14 UHB 2001 B 1 
HETATM 15 N N15 UHB . . . I 2 9.531 4.345 84.778 1 78.52 ? N15 UHB 2001 B 1 
HETATM 16 C C16 UHB . . . I 2 8.464 5.253 85.212 1 81.12 ? C16 UHB 2001 B 1 
HETATM 17 C C17 UHB . . . I 2 7.102 4.617 84.965 1 83.05 ? C17 UHB 2001 B 1 
HETATM 18 N N18 UHB . . . I 2 7.007 3.333 85.676 1 84.92 ? N18 UHB 2001 B 1 
HETATM 19 C C19 UHB . . . I 2 8.103 2.426 85.31 1 83.17 ? C19 UHB 2001 B 1 
HETATM 20 C C20 UHB . . . I 2 9.444 3.098 85.546 1 81.82 ? C20 UHB 2001 B 1 
HETATM 21 C C21 UHB . . . I 2 6.04 2.944 86.536 1 83.83 ? C21 UHB 2001 B 1 
HETATM 22 C C22 UHB . . . I 2 4.856 3.876 86.806 1 84.27 ? C22 UHB 2001 B 1 
HETATM 23 C C23 UHB . . . I 2 5.227 5.112 87.637 1 82.04 ? C23 UHB 2001 B 1 
HETATM 24 C C24 UHB . . . I 2 4.841 4.674 89.047 1 80.93 ? C24 UHB 2001 B 1 
HETATM 25 C C25 UHB . . . I 2 3.572 3.879 88.753 1 83.45 ? C25 UHB 2001 B 1 
HETATM 26 O O26 UHB . . . I 2 3.811 3.206 87.532 1 86.51 ? O26 UHB 2001 B 1 
HETATM 27 O O27 UHB . . . I 2 6.087 1.87 87.112 1 79.23 ? O27 UHB 2001 B 1 
HETATM 28 O O28 UHB . . . I 2 4.46 6.231 87.212 1 83.47 ? O28 UHB 2001 B 1 
HETATM 29 O O29 UHB . . . I 2 4.563 5.795 89.875 1 78.72 ? O29 UHB 2001 B 1 
HETATM 30 N N30 UHB . . . I 2 3.218 2.899 89.775 1 85.26 ? N30 UHB 2001 B 1 
HETATM 31 C C31 UHB . . . I 2 2.343 1.208 90.881 1 88.84 ? C31 UHB 2001 B 1 
HETATM 32 C C32 UHB . . . I 2 2.551 1.709 89.606 1 87.48 ? C32 UHB 2001 B 1 
HETATM 33 C C33 UHB . . . I 2 3.403 3.03 91.127 1 87.09 ? C33 UHB 2001 B 1 
HETATM 34 N N34 UHB . . . I 2 2.896 2.05 91.834 1 88.45 ? N34 UHB 2001 B 1 
HETATM 35 N N35 UHB . . . I 2 1.265 -0.614 89.833 1 86.71 ? N35 UHB 2001 B 1 
HETATM 36 C C36 UHB . . . I 2 1.555 -0.022 88.671 1 87.66 ? C36 UHB 2001 B 1 
HETATM 37 N N37 UHB . . . I 2 2.183 1.138 88.454 1 88.82 ? N37 UHB 2001 B 1 
HETATM 38 C C38 UHB . . . I 2 1.643 -0.01 90.981 1 88.38 ? C38 UHB 2001 B 1 
HETATM 39 N N39 UHB . . . I 2 1.3 -0.578 92.141 1 88.84 ? N39 UHB 2001 B 1 
#
_model_server_stats.io_time_ms              100 
_model_server_stats.parse_time_ms           23 
_model_server_stats.create_model_time_ms    38 
_model_server_stats.query_time_ms           295 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           39 
#