data_1Y6Q
#
_model_server_result.job_id            oBYWdiS_PapH2QLZk8hStA 
_model_server_result.datetime_utc      '2024-11-08 06:53:59' 
_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          1y6q 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":234}' 
#
_entry.id    1Y6Q 
#
_exptl.entry_id    1Y6Q 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              293.388 
_entity.id                          3 
_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-[(METHYLSULFANYL)METHYL]PYRROLIDIN-3-OL 
_entity.pdbx_number_of_molecules    2 
_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            1Y6Q 
_cell.length_a            51.71 
_cell.length_b            69.79 
_cell.length_c            128.34 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1Y6Q 
_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,F,G,H 
_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 
#
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 
#
_chem_comp.formula           'C13 H19 N5 O S' 
_chem_comp.formula_weight    293.388 
_chem_comp.id                TDI 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (3R,4S)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-[(METHYLSULFANYL)METHYL]PYRROLIDIN-3-OL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     (3R,4S)-1-[9-DEAZAADENIN-9-YL)METHYL]-3-HYDROXY-4-(METHYLTHIOMETHYL)PYRROLIDINE 
#
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
C2 N1 TDI doub 290 n y 
C2 N3 TDI sing 291 n y 
C2 H2 TDI sing 292 n n 
C4 C5 TDI sing 293 n y 
C4 C9 TDI sing 294 n y 
C4 N3 TDI doub 295 n y 
C5 C6 TDI doub 296 n y 
C5 N7 TDI sing 297 n y 
C6 N6 TDI sing 298 n n 
C6 N1 TDI sing 299 n y 
CS5 S TDI sing 300 n n 
CS5 HS51 TDI sing 301 n n 
CS5 HS52 TDI sing 302 n n 
CS5 HS53 TDI sing 303 n n 
S C5' TDI sing 304 n n 
C5' C4' TDI sing 305 n n 
C5' "H5'1" TDI sing 306 n n 
C5' "H5'2" TDI sing 307 n n 
C4' C1' TDI sing 308 n n 
C4' C3' TDI sing 309 n n 
C4' H4' TDI sing 310 n n 
C1' N1' TDI sing 311 n n 
C1' "H1'1" TDI sing 312 n n 
C1' "H1'2" TDI sing 313 n n 
N1' C10 TDI sing 314 n n 
N1' C2' TDI sing 315 n n 
C10 C9 TDI sing 316 n n 
C10 H101 TDI sing 317 n n 
C10 H102 TDI sing 318 n n 
C9 C8 TDI doub 319 n y 
C8 N7 TDI sing 320 n y 
C8 H8 TDI sing 321 n n 
N7 HN7 TDI sing 322 n n 
N6 HN61 TDI sing 323 n n 
N6 HN62 TDI sing 324 n n 
C2' C3' TDI sing 325 n n 
C2' "H2'1" TDI sing 326 n n 
C2' "H2'2" TDI sing 327 n n 
C3' O3' TDI sing 328 n n 
C3' H3' TDI sing 329 n n 
O3' H1 TDI sing 330 n n 
#
_atom_sites.entry_id                     1Y6Q 
_atom_sites.fract_transf_matrix[1][1]    0.019339 
_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]    0.014329 
_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]    0.007792 
_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 2 CL A 1 302 302 CL CL . 
D 3 TDI A 1 233 233 TDI TDI . 
E 2 CL B 1 301 301 CL CL . 
F 3 TDI B 1 234 234 TDI TDI . 
G 4 HOH A 1 402 402 HOH WAT . 
G 4 HOH A 2 403 403 HOH WAT . 
G 4 HOH A 3 408 408 HOH WAT . 
G 4 HOH A 4 410 410 HOH WAT . 
G 4 HOH A 5 411 411 HOH WAT . 
G 4 HOH A 6 412 412 HOH WAT . 
G 4 HOH A 7 416 416 HOH WAT . 
G 4 HOH A 8 417 417 HOH WAT . 
G 4 HOH A 9 418 418 HOH WAT . 
G 4 HOH A 10 422 422 HOH WAT . 
G 4 HOH A 11 424 424 HOH WAT . 
G 4 HOH A 12 425 425 HOH WAT . 
G 4 HOH A 13 426 426 HOH WAT . 
G 4 HOH A 14 431 431 HOH WAT . 
G 4 HOH A 15 432 432 HOH WAT . 
G 4 HOH A 16 433 433 HOH WAT . 
G 4 HOH A 17 434 434 HOH WAT . 
G 4 HOH A 18 438 438 HOH WAT . 
G 4 HOH A 19 439 439 HOH WAT . 
G 4 HOH A 20 440 440 HOH WAT . 
G 4 HOH A 21 441 441 HOH WAT . 
G 4 HOH A 22 442 442 HOH WAT . 
G 4 HOH A 23 447 447 HOH WAT . 
G 4 HOH A 24 448 448 HOH WAT . 
G 4 HOH A 25 449 449 HOH WAT . 
G 4 HOH A 26 451 451 HOH WAT . 
G 4 HOH A 27 452 452 HOH WAT . 
G 4 HOH A 28 454 454 HOH WAT . 
G 4 HOH A 29 455 455 HOH WAT . 
G 4 HOH A 30 457 457 HOH WAT . 
G 4 HOH A 31 463 463 HOH WAT . 
G 4 HOH A 32 464 464 HOH WAT . 
G 4 HOH A 33 467 467 HOH WAT . 
G 4 HOH A 34 468 468 HOH WAT . 
G 4 HOH A 35 469 469 HOH WAT . 
G 4 HOH A 36 470 470 HOH WAT . 
G 4 HOH A 37 471 471 HOH WAT . 
G 4 HOH A 38 472 472 HOH WAT . 
G 4 HOH A 39 475 475 HOH WAT . 
G 4 HOH A 40 478 478 HOH WAT . 
G 4 HOH A 41 479 479 HOH WAT . 
G 4 HOH A 42 481 481 HOH WAT . 
G 4 HOH A 43 483 483 HOH WAT . 
G 4 HOH A 44 487 487 HOH WAT . 
G 4 HOH A 45 488 488 HOH WAT . 
G 4 HOH A 46 489 489 HOH WAT . 
G 4 HOH A 47 490 490 HOH WAT . 
G 4 HOH A 48 491 491 HOH WAT . 
G 4 HOH A 49 492 492 HOH WAT . 
G 4 HOH A 50 493 493 HOH WAT . 
G 4 HOH A 51 494 494 HOH WAT . 
G 4 HOH A 52 495 495 HOH WAT . 
G 4 HOH A 53 496 496 HOH WAT . 
G 4 HOH A 54 497 497 HOH WAT . 
G 4 HOH A 55 509 509 HOH WAT . 
G 4 HOH A 56 510 510 HOH WAT . 
G 4 HOH A 57 511 511 HOH WAT . 
G 4 HOH A 58 512 512 HOH WAT . 
G 4 HOH A 59 513 513 HOH WAT . 
G 4 HOH A 60 523 523 HOH WAT . 
G 4 HOH A 61 524 524 HOH WAT . 
G 4 HOH A 62 526 526 HOH WAT . 
G 4 HOH A 63 529 529 HOH WAT . 
G 4 HOH A 64 535 535 HOH WAT . 
G 4 HOH A 65 537 537 HOH WAT . 
G 4 HOH A 66 538 538 HOH WAT . 
G 4 HOH A 67 543 543 HOH WAT . 
G 4 HOH A 68 544 544 HOH WAT . 
G 4 HOH A 69 545 545 HOH WAT . 
G 4 HOH A 70 546 546 HOH WAT . 
G 4 HOH A 71 560 560 HOH WAT . 
G 4 HOH A 72 561 561 HOH WAT . 
G 4 HOH A 73 562 562 HOH WAT . 
G 4 HOH A 74 563 563 HOH WAT . 
G 4 HOH A 75 570 570 HOH WAT . 
G 4 HOH A 76 571 571 HOH WAT . 
G 4 HOH A 77 572 572 HOH WAT . 
G 4 HOH A 78 590 590 HOH WAT . 
G 4 HOH A 79 593 593 HOH WAT . 
G 4 HOH A 80 594 594 HOH WAT . 
G 4 HOH A 81 598 598 HOH WAT . 
G 4 HOH A 82 599 599 HOH WAT . 
G 4 HOH A 83 600 600 HOH WAT . 
G 4 HOH A 84 601 601 HOH WAT . 
G 4 HOH A 85 602 602 HOH WAT . 
G 4 HOH A 86 603 603 HOH WAT . 
G 4 HOH A 87 604 604 HOH WAT . 
G 4 HOH A 88 605 605 HOH WAT . 
G 4 HOH A 89 608 608 HOH WAT . 
G 4 HOH A 90 609 609 HOH WAT . 
G 4 HOH A 91 610 610 HOH WAT . 
G 4 HOH A 92 612 612 HOH WAT . 
G 4 HOH A 93 613 613 HOH WAT . 
G 4 HOH A 94 614 614 HOH WAT . 
G 4 HOH A 95 618 618 HOH WAT . 
G 4 HOH A 96 619 619 HOH WAT . 
H 4 HOH B 1 401 401 HOH WAT . 
H 4 HOH B 2 404 404 HOH WAT . 
H 4 HOH B 3 405 405 HOH WAT . 
H 4 HOH B 4 406 406 HOH WAT . 
H 4 HOH B 5 407 407 HOH WAT . 
H 4 HOH B 6 409 409 HOH WAT . 
H 4 HOH B 7 413 413 HOH WAT . 
H 4 HOH B 8 414 414 HOH WAT . 
H 4 HOH B 9 415 415 HOH WAT . 
H 4 HOH B 10 419 419 HOH WAT . 
H 4 HOH B 11 420 420 HOH WAT . 
H 4 HOH B 12 421 421 HOH WAT . 
H 4 HOH B 13 423 423 HOH WAT . 
H 4 HOH B 14 427 427 HOH WAT . 
H 4 HOH B 15 428 428 HOH WAT . 
H 4 HOH B 16 429 429 HOH WAT . 
H 4 HOH B 17 430 430 HOH WAT . 
H 4 HOH B 18 435 435 HOH WAT . 
H 4 HOH B 19 436 436 HOH WAT . 
H 4 HOH B 20 437 437 HOH WAT . 
H 4 HOH B 21 443 443 HOH WAT . 
H 4 HOH B 22 444 444 HOH WAT . 
H 4 HOH B 23 445 445 HOH WAT . 
H 4 HOH B 24 446 446 HOH WAT . 
H 4 HOH B 25 450 450 HOH WAT . 
H 4 HOH B 26 453 453 HOH WAT . 
H 4 HOH B 27 456 456 HOH WAT . 
H 4 HOH B 28 458 458 HOH WAT . 
H 4 HOH B 29 459 459 HOH WAT . 
H 4 HOH B 30 460 460 HOH WAT . 
H 4 HOH B 31 461 461 HOH WAT . 
H 4 HOH B 32 462 462 HOH WAT . 
H 4 HOH B 33 465 465 HOH WAT . 
H 4 HOH B 34 466 466 HOH WAT . 
H 4 HOH B 35 473 473 HOH WAT . 
H 4 HOH B 36 474 474 HOH WAT . 
H 4 HOH B 37 476 476 HOH WAT . 
H 4 HOH B 38 477 477 HOH WAT . 
H 4 HOH B 39 480 480 HOH WAT . 
H 4 HOH B 40 482 482 HOH WAT . 
H 4 HOH B 41 484 484 HOH WAT . 
H 4 HOH B 42 485 485 HOH WAT . 
H 4 HOH B 43 486 486 HOH WAT . 
H 4 HOH B 44 498 498 HOH WAT . 
H 4 HOH B 45 499 499 HOH WAT . 
H 4 HOH B 46 500 500 HOH WAT . 
H 4 HOH B 47 501 501 HOH WAT . 
H 4 HOH B 48 502 502 HOH WAT . 
H 4 HOH B 49 503 503 HOH WAT . 
H 4 HOH B 50 504 504 HOH WAT . 
H 4 HOH B 51 505 505 HOH WAT . 
H 4 HOH B 52 506 506 HOH WAT . 
H 4 HOH B 53 507 507 HOH WAT . 
H 4 HOH B 54 508 508 HOH WAT . 
H 4 HOH B 55 514 514 HOH WAT . 
H 4 HOH B 56 515 515 HOH WAT . 
H 4 HOH B 57 516 516 HOH WAT . 
H 4 HOH B 58 517 517 HOH WAT . 
H 4 HOH B 59 518 518 HOH WAT . 
H 4 HOH B 60 519 519 HOH WAT . 
H 4 HOH B 61 520 520 HOH WAT . 
H 4 HOH B 62 521 521 HOH WAT . 
H 4 HOH B 63 522 522 HOH WAT . 
H 4 HOH B 64 525 525 HOH WAT . 
H 4 HOH B 65 527 527 HOH WAT . 
H 4 HOH B 66 528 528 HOH WAT . 
H 4 HOH B 67 530 530 HOH WAT . 
H 4 HOH B 68 531 531 HOH WAT . 
H 4 HOH B 69 532 532 HOH WAT . 
H 4 HOH B 70 533 533 HOH WAT . 
H 4 HOH B 71 534 534 HOH WAT . 
H 4 HOH B 72 536 536 HOH WAT . 
H 4 HOH B 73 539 539 HOH WAT . 
H 4 HOH B 74 540 540 HOH WAT . 
H 4 HOH B 75 541 541 HOH WAT . 
H 4 HOH B 76 542 542 HOH WAT . 
H 4 HOH B 77 547 547 HOH WAT . 
H 4 HOH B 78 548 548 HOH WAT . 
H 4 HOH B 79 549 549 HOH WAT . 
H 4 HOH B 80 550 550 HOH WAT . 
H 4 HOH B 81 551 551 HOH WAT . 
H 4 HOH B 82 552 552 HOH WAT . 
H 4 HOH B 83 553 553 HOH WAT . 
H 4 HOH B 84 554 554 HOH WAT . 
H 4 HOH B 85 555 555 HOH WAT . 
H 4 HOH B 86 556 556 HOH WAT . 
H 4 HOH B 87 557 557 HOH WAT . 
H 4 HOH B 88 558 558 HOH WAT . 
H 4 HOH B 89 559 559 HOH WAT . 
H 4 HOH B 90 564 564 HOH WAT . 
H 4 HOH B 91 565 565 HOH WAT . 
H 4 HOH B 92 566 566 HOH WAT . 
H 4 HOH B 93 567 567 HOH WAT . 
H 4 HOH B 94 568 568 HOH WAT . 
H 4 HOH B 95 569 569 HOH WAT . 
H 4 HOH B 96 573 573 HOH WAT . 
H 4 HOH B 97 574 574 HOH WAT . 
H 4 HOH B 98 575 575 HOH WAT . 
H 4 HOH B 99 576 576 HOH WAT . 
H 4 HOH B 100 577 577 HOH WAT . 
H 4 HOH B 101 578 578 HOH WAT . 
H 4 HOH B 102 579 579 HOH WAT . 
H 4 HOH B 103 580 580 HOH WAT . 
H 4 HOH B 104 581 581 HOH WAT . 
H 4 HOH B 105 582 582 HOH WAT . 
H 4 HOH B 106 583 583 HOH WAT . 
H 4 HOH B 107 584 584 HOH WAT . 
H 4 HOH B 108 585 585 HOH WAT . 
H 4 HOH B 109 586 586 HOH WAT . 
H 4 HOH B 110 587 587 HOH WAT . 
H 4 HOH B 111 588 588 HOH WAT . 
H 4 HOH B 112 589 589 HOH WAT . 
H 4 HOH B 113 591 591 HOH WAT . 
H 4 HOH B 114 592 592 HOH WAT . 
H 4 HOH B 115 595 595 HOH WAT . 
H 4 HOH B 116 596 596 HOH WAT . 
H 4 HOH B 117 597 597 HOH WAT . 
H 4 HOH B 118 606 606 HOH WAT . 
H 4 HOH B 119 607 607 HOH WAT . 
H 4 HOH B 120 611 611 HOH WAT . 
H 4 HOH B 121 615 615 HOH WAT . 
H 4 HOH B 122 616 616 HOH WAT . 
H 4 HOH B 123 617 617 HOH WAT . 
#
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 C2 TDI . . . F 3 44.401 84.682 40.051 1 18.78 ? C2 TDI 234 B 1 
HETATM 2 C C4 TDI . . . F 3 44.606 85.488 42.239 1 20.07 ? C4 TDI 234 B 1 
HETATM 3 C C5 TDI . . . F 3 43.208 85.758 42.284 1 18.61 ? C5 TDI 234 B 1 
HETATM 4 C C6 TDI . . . F 3 42.45 85.452 41.149 1 15.1 ? C6 TDI 234 B 1 
HETATM 5 C CS5 TDI . . . F 3 47.676 91.494 40.541 1 18.58 ? CS5 TDI 234 B 1 
HETATM 6 S S TDI . . . F 3 47.504 89.857 39.755 1 25.94 ? S TDI 234 B 1 
HETATM 7 C C5' TDI . . . F 3 47.424 89.126 41.397 1 23.34 ? C5' TDI 234 B 1 
HETATM 8 C C4' TDI . . . F 3 48.128 88.543 42.616 1 24.54 ? C4' TDI 234 B 1 
HETATM 9 C C1' TDI . . . F 3 47.316 87.815 43.699 1 22.23 ? C1' TDI 234 B 1 
HETATM 10 N N1' TDI . . . F 3 47.869 86.426 43.726 1 28.6 ? N1' TDI 234 B 1 
HETATM 11 C C10 TDI . . . F 3 46.546 85.805 43.977 1 22.48 ? C10 TDI 234 B 1 
HETATM 12 C C9 TDI . . . F 3 45.113 85.892 43.53 1 21.53 ? C9 TDI 234 B 1 
HETATM 13 C C8 TDI . . . F 3 44.077 86.365 44.246 1 21.23 ? C8 TDI 234 B 1 
HETATM 14 N N7 TDI . . . F 3 42.929 86.289 43.513 1 19.82 ? N7 TDI 234 B 1 
HETATM 15 N N6 TDI . . . F 3 41.094 85.691 41.144 1 20.9 ? N6 TDI 234 B 1 
HETATM 16 N N1 TDI . . . F 3 43.07 84.927 40.067 1 17.98 ? N1 TDI 234 B 1 
HETATM 17 N N3 TDI . . . F 3 45.161 84.951 41.113 1 21.67 ? N3 TDI 234 B 1 
HETATM 18 C C2' TDI . . . F 3 48.207 86.114 42.298 1 20.38 ? C2' TDI 234 B 1 
HETATM 19 C C3' TDI . . . F 3 48.796 87.424 41.762 1 23.02 ? C3' TDI 234 B 1 
HETATM 20 O O3' TDI . . . F 3 50.071 87.488 42.431 1 22.05 ? O3' TDI 234 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           340 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           20 
#