data_4YNB
#
_model_server_result.job_id            ysQKSw3TgrpG3C_sihIj4g 
_model_server_result.datetime_utc      '2024-11-20 15:24:05' 
_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          4ynb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":301}' 
#
_entry.id    4YNB 
#
_exptl.entry_id    4YNB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              357.433 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(pyrazin-2-ylsulfanyl)methyl]pyrrolidin-3-ol 
_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            4YNB 
_cell.length_a            157.512 
_cell.length_b            157.512 
_cell.length_c            157.512 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4YNB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        211 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 4 3 2' 
#
_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,F 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 19_555 -x,-z,-y -1 0 0 0 0 -1 0 -1 0 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C16 H19 N7 O S' 
_chem_comp.formula_weight    357.433 
_chem_comp.id                4EH 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(pyrazin-2-ylsulfanyl)methyl]pyrrolidin-3-ol 
_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
C7' N2' 4EH doub 1 n y 
C7' C8' 4EH sing 2 n y 
N2' C6' 4EH sing 3 n y 
C8' N3' 4EH doub 4 n y 
C6' S 4EH sing 5 n n 
C6' C9' 4EH doub 6 n y 
S C5' 4EH sing 7 n n 
N3' C9' 4EH sing 8 n y 
N1 C2 4EH doub 9 n y 
N1 C6 4EH sing 10 n y 
N6 C6 4EH sing 11 n n 
C2 N3 4EH sing 12 n y 
C6 C5 4EH doub 13 n y 
C5' C4' 4EH sing 14 n n 
N3 C4 4EH doub 15 n y 
C5 C4 4EH sing 16 n y 
C5 N7 4EH sing 17 n y 
C4 C9 4EH sing 18 n y 
C4' C3' 4EH sing 19 n n 
C4' C1' 4EH sing 20 n n 
C3' C2' 4EH sing 21 n n 
C3' O3' 4EH sing 22 n n 
N7 C8 4EH sing 23 n y 
C2' N1' 4EH sing 24 n n 
C1' N1' 4EH sing 25 n n 
C9 C8 4EH doub 26 n y 
C9 C10 4EH sing 27 n n 
N1' C10 4EH sing 28 n n 
O3' H1 4EH sing 29 n n 
C3' H2 4EH sing 30 n n 
C4' H3 4EH sing 31 n n 
C5' H4 4EH sing 32 n n 
C5' H5 4EH sing 33 n n 
C2' H6 4EH sing 34 n n 
C2' H7 4EH sing 35 n n 
C1' H9 4EH sing 36 n n 
C1' H10 4EH sing 37 n n 
C10 H11 4EH sing 38 n n 
C10 H12 4EH sing 39 n n 
C2 H13 4EH sing 40 n n 
C8 H14 4EH sing 41 n n 
N7 H15 4EH sing 42 n n 
N6 H16 4EH sing 43 n n 
N6 H17 4EH sing 44 n n 
C9' H18 4EH sing 45 n n 
C8' H19 4EH sing 46 n n 
C7' H20 4EH sing 47 n n 
#
_atom_sites.entry_id                     4YNB 
_atom_sites.fract_transf_matrix[1][1]    0.006349 
_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]    0.006349 
_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]    0.006349 
_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
B 2 4EH A 1 301 1 4EH ZDI . 
C 3 GOL A 1 302 2 GOL GOL . 
D 3 GOL A 1 303 3 GOL GOL . 
E 4 PEG A 1 304 1 PEG PEG . 
F 5 HOH A 1 401 73 HOH HOH . 
F 5 HOH A 2 402 152 HOH HOH . 
F 5 HOH A 3 403 110 HOH HOH . 
F 5 HOH A 4 404 82 HOH HOH . 
F 5 HOH A 5 405 10 HOH HOH . 
F 5 HOH A 6 406 95 HOH HOH . 
F 5 HOH A 7 407 12 HOH HOH . 
F 5 HOH A 8 408 4 HOH HOH . 
F 5 HOH A 9 409 14 HOH HOH . 
F 5 HOH A 10 410 39 HOH HOH . 
F 5 HOH A 11 411 151 HOH HOH . 
F 5 HOH A 12 412 25 HOH HOH . 
F 5 HOH A 13 413 56 HOH HOH . 
F 5 HOH A 14 414 111 HOH HOH . 
F 5 HOH A 15 415 76 HOH HOH . 
F 5 HOH A 16 416 163 HOH HOH . 
F 5 HOH A 17 417 26 HOH HOH . 
F 5 HOH A 18 418 99 HOH HOH . 
F 5 HOH A 19 419 79 HOH HOH . 
F 5 HOH A 20 420 9 HOH HOH . 
F 5 HOH A 21 421 172 HOH HOH . 
F 5 HOH A 22 422 3 HOH HOH . 
F 5 HOH A 23 423 158 HOH HOH . 
F 5 HOH A 24 424 13 HOH HOH . 
F 5 HOH A 25 425 52 HOH HOH . 
F 5 HOH A 26 426 134 HOH HOH . 
F 5 HOH A 27 427 44 HOH HOH . 
F 5 HOH A 28 428 18 HOH HOH . 
F 5 HOH A 29 429 31 HOH HOH . 
F 5 HOH A 30 430 77 HOH HOH . 
F 5 HOH A 31 431 7 HOH HOH . 
F 5 HOH A 32 432 94 HOH HOH . 
F 5 HOH A 33 433 2 HOH HOH . 
F 5 HOH A 34 434 69 HOH HOH . 
F 5 HOH A 35 435 128 HOH HOH . 
F 5 HOH A 36 436 114 HOH HOH . 
F 5 HOH A 37 437 74 HOH HOH . 
F 5 HOH A 38 438 22 HOH HOH . 
F 5 HOH A 39 439 116 HOH HOH . 
F 5 HOH A 40 440 102 HOH HOH . 
F 5 HOH A 41 441 185 HOH HOH . 
F 5 HOH A 42 442 58 HOH HOH . 
F 5 HOH A 43 443 59 HOH HOH . 
F 5 HOH A 44 444 38 HOH HOH . 
F 5 HOH A 45 445 45 HOH HOH . 
F 5 HOH A 46 446 179 HOH HOH . 
F 5 HOH A 47 447 16 HOH HOH . 
F 5 HOH A 48 448 80 HOH HOH . 
F 5 HOH A 49 449 143 HOH HOH . 
F 5 HOH A 50 450 193 HOH HOH . 
F 5 HOH A 51 451 84 HOH HOH . 
F 5 HOH A 52 452 182 HOH HOH . 
F 5 HOH A 53 453 92 HOH HOH . 
F 5 HOH A 54 454 190 HOH HOH . 
F 5 HOH A 55 455 131 HOH HOH . 
F 5 HOH A 56 456 165 HOH HOH . 
F 5 HOH A 57 457 175 HOH HOH . 
F 5 HOH A 58 458 138 HOH HOH . 
F 5 HOH A 59 459 29 HOH HOH . 
F 5 HOH A 60 460 86 HOH HOH . 
F 5 HOH A 61 461 127 HOH HOH . 
F 5 HOH A 62 462 167 HOH HOH . 
F 5 HOH A 63 463 180 HOH HOH . 
F 5 HOH A 64 464 1 HOH HOH . 
F 5 HOH A 65 465 5 HOH HOH . 
F 5 HOH A 66 466 6 HOH HOH . 
F 5 HOH A 67 467 8 HOH HOH . 
F 5 HOH A 68 468 11 HOH HOH . 
F 5 HOH A 69 469 15 HOH HOH . 
F 5 HOH A 70 470 17 HOH HOH . 
F 5 HOH A 71 471 19 HOH HOH . 
F 5 HOH A 72 472 20 HOH HOH . 
F 5 HOH A 73 473 21 HOH HOH . 
F 5 HOH A 74 474 23 HOH HOH . 
F 5 HOH A 75 475 24 HOH HOH . 
F 5 HOH A 76 476 27 HOH HOH . 
F 5 HOH A 77 477 28 HOH HOH . 
F 5 HOH A 78 478 30 HOH HOH . 
F 5 HOH A 79 479 32 HOH HOH . 
F 5 HOH A 80 480 33 HOH HOH . 
F 5 HOH A 81 481 34 HOH HOH . 
F 5 HOH A 82 482 35 HOH HOH . 
F 5 HOH A 83 483 36 HOH HOH . 
F 5 HOH A 84 484 37 HOH HOH . 
F 5 HOH A 85 485 40 HOH HOH . 
F 5 HOH A 86 486 41 HOH HOH . 
F 5 HOH A 87 487 42 HOH HOH . 
F 5 HOH A 88 488 43 HOH HOH . 
F 5 HOH A 89 489 46 HOH HOH . 
F 5 HOH A 90 490 47 HOH HOH . 
F 5 HOH A 91 491 48 HOH HOH . 
F 5 HOH A 92 492 49 HOH HOH . 
F 5 HOH A 93 493 50 HOH HOH . 
F 5 HOH A 94 494 51 HOH HOH . 
F 5 HOH A 95 495 53 HOH HOH . 
F 5 HOH A 96 496 54 HOH HOH . 
F 5 HOH A 97 497 55 HOH HOH . 
F 5 HOH A 98 498 57 HOH HOH . 
F 5 HOH A 99 499 60 HOH HOH . 
F 5 HOH A 100 500 61 HOH HOH . 
F 5 HOH A 101 501 62 HOH HOH . 
F 5 HOH A 102 502 63 HOH HOH . 
F 5 HOH A 103 503 64 HOH HOH . 
F 5 HOH A 104 504 65 HOH HOH . 
F 5 HOH A 105 505 66 HOH HOH . 
F 5 HOH A 106 506 67 HOH HOH . 
F 5 HOH A 107 507 68 HOH HOH . 
F 5 HOH A 108 508 70 HOH HOH . 
F 5 HOH A 109 509 71 HOH HOH . 
F 5 HOH A 110 510 72 HOH HOH . 
F 5 HOH A 111 511 75 HOH HOH . 
F 5 HOH A 112 512 78 HOH HOH . 
F 5 HOH A 113 513 81 HOH HOH . 
F 5 HOH A 114 514 83 HOH HOH . 
F 5 HOH A 115 515 85 HOH HOH . 
F 5 HOH A 116 516 87 HOH HOH . 
F 5 HOH A 117 517 88 HOH HOH . 
F 5 HOH A 118 518 89 HOH HOH . 
F 5 HOH A 119 519 90 HOH HOH . 
F 5 HOH A 120 520 91 HOH HOH . 
F 5 HOH A 121 521 93 HOH HOH . 
F 5 HOH A 122 522 96 HOH HOH . 
F 5 HOH A 123 523 97 HOH HOH . 
F 5 HOH A 124 524 98 HOH HOH . 
F 5 HOH A 125 525 100 HOH HOH . 
F 5 HOH A 126 526 101 HOH HOH . 
F 5 HOH A 127 527 103 HOH HOH . 
F 5 HOH A 128 528 104 HOH HOH . 
F 5 HOH A 129 529 105 HOH HOH . 
F 5 HOH A 130 530 106 HOH HOH . 
F 5 HOH A 131 531 107 HOH HOH . 
F 5 HOH A 132 532 108 HOH HOH . 
F 5 HOH A 133 533 109 HOH HOH . 
F 5 HOH A 134 534 112 HOH HOH . 
F 5 HOH A 135 535 113 HOH HOH . 
F 5 HOH A 136 536 115 HOH HOH . 
F 5 HOH A 137 537 117 HOH HOH . 
F 5 HOH A 138 538 118 HOH HOH . 
F 5 HOH A 139 539 119 HOH HOH . 
F 5 HOH A 140 540 120 HOH HOH . 
F 5 HOH A 141 541 121 HOH HOH . 
F 5 HOH A 142 542 122 HOH HOH . 
F 5 HOH A 143 543 123 HOH HOH . 
F 5 HOH A 144 544 124 HOH HOH . 
F 5 HOH A 145 545 125 HOH HOH . 
F 5 HOH A 146 546 126 HOH HOH . 
F 5 HOH A 147 547 129 HOH HOH . 
F 5 HOH A 148 548 130 HOH HOH . 
F 5 HOH A 149 549 132 HOH HOH . 
F 5 HOH A 150 550 133 HOH HOH . 
F 5 HOH A 151 551 135 HOH HOH . 
F 5 HOH A 152 552 136 HOH HOH . 
F 5 HOH A 153 553 137 HOH HOH . 
F 5 HOH A 154 554 139 HOH HOH . 
F 5 HOH A 155 555 140 HOH HOH . 
F 5 HOH A 156 556 141 HOH HOH . 
F 5 HOH A 157 557 142 HOH HOH . 
F 5 HOH A 158 558 144 HOH HOH . 
F 5 HOH A 159 559 145 HOH HOH . 
F 5 HOH A 160 560 146 HOH HOH . 
F 5 HOH A 161 561 147 HOH HOH . 
F 5 HOH A 162 562 148 HOH HOH . 
F 5 HOH A 163 563 149 HOH HOH . 
F 5 HOH A 164 564 150 HOH HOH . 
F 5 HOH A 165 565 153 HOH HOH . 
F 5 HOH A 166 566 154 HOH HOH . 
F 5 HOH A 167 567 155 HOH HOH . 
F 5 HOH A 168 568 156 HOH HOH . 
F 5 HOH A 169 569 157 HOH HOH . 
F 5 HOH A 170 570 159 HOH HOH . 
F 5 HOH A 171 571 160 HOH HOH . 
F 5 HOH A 172 572 161 HOH HOH . 
F 5 HOH A 173 573 162 HOH HOH . 
F 5 HOH A 174 574 164 HOH HOH . 
F 5 HOH A 175 575 166 HOH HOH . 
F 5 HOH A 176 576 168 HOH HOH . 
F 5 HOH A 177 577 169 HOH HOH . 
F 5 HOH A 178 578 170 HOH HOH . 
F 5 HOH A 179 579 171 HOH HOH . 
F 5 HOH A 180 580 173 HOH HOH . 
F 5 HOH A 181 581 174 HOH HOH . 
F 5 HOH A 182 582 176 HOH HOH . 
F 5 HOH A 183 583 177 HOH HOH . 
F 5 HOH A 184 584 178 HOH HOH . 
F 5 HOH A 185 585 181 HOH HOH . 
F 5 HOH A 186 586 183 HOH HOH . 
F 5 HOH A 187 587 184 HOH HOH . 
F 5 HOH A 188 588 186 HOH HOH . 
F 5 HOH A 189 589 187 HOH HOH . 
F 5 HOH A 190 590 188 HOH HOH . 
F 5 HOH A 191 591 189 HOH HOH . 
F 5 HOH A 192 592 191 HOH HOH . 
F 5 HOH A 193 593 192 HOH HOH . 
F 5 HOH A 194 594 194 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 O O3' 4EH . . . B 2 10.916 43.501 -34.169 1 27.02 ? O3' 4EH 301 A 1 
HETATM 2 C C3' 4EH . . . B 2 10.76 44.531 -35.153 1 27.78 ? C3' 4EH 301 A 1 
HETATM 3 C C4' 4EH . . . B 2 12.097 45.211 -35.386 1 28.97 ? C4' 4EH 301 A 1 
HETATM 4 C C5' 4EH . . . B 2 12.272 45.936 -36.719 1 32.91 ? C5' 4EH 301 A 1 
HETATM 5 S S 4EH . . . B 2 12.468 44.846 -38.108 1 40.36 ? S 4EH 301 A 1 
HETATM 6 C C2' 4EH . . . B 2 9.866 45.606 -34.554 1 26.29 ? C2' 4EH 301 A 1 
HETATM 7 N N1' 4EH . . . B 2 10.815 46.288 -33.656 1 25.95 ? N1' 4EH 301 A 1 
HETATM 8 C C1' 4EH . . . B 2 12.149 46.281 -34.291 1 27.23 ? C1' 4EH 301 A 1 
HETATM 9 C C10 4EH . . . B 2 10.397 47.635 -33.281 1 24.33 ? C10 4EH 301 A 1 
HETATM 10 C C9 4EH . . . B 2 10.427 48.812 -34.249 1 20.12 ? C9 4EH 301 A 1 
HETATM 11 C C4 4EH . . . B 2 9.584 49.13 -35.419 1 18.84 ? C4 4EH 301 A 1 
HETATM 12 N N3 4EH . . . B 2 8.614 48.423 -36.041 1 18.66 ? N3 4EH 301 A 1 
HETATM 13 C C2 4EH . . . B 2 8.025 48.959 -37.133 1 19.53 ? C2 4EH 301 A 1 
HETATM 14 C C8 4EH . . . B 2 11.241 49.933 -34.102 1 19.46 ? C8 4EH 301 A 1 
HETATM 15 N N7 4EH . . . B 2 10.994 50.86 -35.076 1 18.22 ? N7 4EH 301 A 1 
HETATM 16 C C5 4EH . . . B 2 10.026 50.441 -35.888 1 18.23 ? C5 4EH 301 A 1 
HETATM 17 C C6 4EH . . . B 2 9.352 50.948 -37.075 1 19.3 ? C6 4EH 301 A 1 
HETATM 18 N N1 4EH . . . B 2 8.375 50.17 -37.651 1 18.87 ? N1 4EH 301 A 1 
HETATM 19 N N6 4EH . . . B 2 9.715 52.152 -37.572 1 18.7 ? N6 4EH 301 A 1 
HETATM 20 C C6' 4EH . . . B 2 14.089 44.37 -38.385 1 36.7 ? C6' 4EH 301 A 1 
HETATM 21 C C9' 4EH . . . B 2 15.151 44.825 -37.612 1 34.57 ? C9' 4EH 301 A 1 
HETATM 22 N N3' 4EH . . . B 2 16.396 44.398 -37.901 1 37.05 ? N3' 4EH 301 A 1 
HETATM 23 C C8' 4EH . . . B 2 16.65 43.543 -38.908 1 35.94 ? C8' 4EH 301 A 1 
HETATM 24 C C7' 4EH . . . B 2 15.596 43.089 -39.677 1 36.5 ? C7' 4EH 301 A 1 
HETATM 25 N N2' 4EH . . . B 2 14.353 43.516 -39.408 1 38.06 ? N2' 4EH 301 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           297 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           25 
#