data_4YML # _model_server_result.job_id nCFBH4RJvN2kK4XRwlbsDw _model_server_result.datetime_utc '2025-03-04 17:59:54' _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 4yml # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 4YML # _exptl.entry_id 4YML _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 293.388 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (3S,4R)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(methylsulfanyl)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 4YML _cell.length_a 71.95 _cell.length_b 91.95 _cell.length_c 69.58 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YML _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 _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' 3_454 -x-1,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 -71.95 0 -34.79 # _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 'C13 H19 N5 O S' _chem_comp.formula_weight 293.388 _chem_comp.id 4F0 _chem_comp.mon_nstd_flag . _chem_comp.name (3S,4R)-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 ? # 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 CS5 S 4F0 sing 1 n n S C5' 4F0 sing 2 n n C5' C4' 4F0 sing 3 n n C1' C4' 4F0 sing 4 n n C1' N1' 4F0 sing 5 n n C4' C3' 4F0 sing 6 n n N1' C2' 4F0 sing 7 n n N1' C10 4F0 sing 8 n n C2' C3' 4F0 sing 9 n n C3' O3' 4F0 sing 10 n n C8 N7 4F0 sing 11 n y C8 C9 4F0 doub 12 n y N7 C5 4F0 sing 13 n y C9 C10 4F0 sing 14 n n C9 C4 4F0 sing 15 n y C5 C6 4F0 doub 16 n y C5 C4 4F0 sing 17 n y N6 C6 4F0 sing 18 n n C6 N1 4F0 sing 19 n y C4 N3 4F0 doub 20 n y N1 C2 4F0 doub 21 n y N3 C2 4F0 sing 22 n y C2 H1 4F0 sing 23 n n CS5 H2 4F0 sing 24 n n CS5 H3 4F0 sing 25 n n CS5 H4 4F0 sing 26 n n C5' H5 4F0 sing 27 n n C5' H6 4F0 sing 28 n n C4' H7 4F0 sing 29 n n C1' H8 4F0 sing 30 n n C1' H9 4F0 sing 31 n n C10 H11 4F0 sing 32 n n C10 H12 4F0 sing 33 n n C8 H13 4F0 sing 34 n n N7 H14 4F0 sing 35 n n N6 H15 4F0 sing 36 n n N6 H16 4F0 sing 37 n n C2' H17 4F0 sing 38 n n C2' H18 4F0 sing 39 n n C3' H19 4F0 sing 40 n n O3' H20 4F0 sing 41 n n # _atom_sites.entry_id 4YML _atom_sites.fract_transf_matrix[1][1] 0.013899 _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] 0.010875 _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] 0.014372 _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 4F0 A 1 301 1 4F0 eMT . C 3 PO4 A 1 302 1 PO4 PO4 . D 4 HOH A 1 401 77 HOH HOH . D 4 HOH A 2 402 76 HOH HOH . D 4 HOH A 3 403 23 HOH HOH . D 4 HOH A 4 404 7 HOH HOH . D 4 HOH A 5 405 34 HOH HOH . D 4 HOH A 6 406 62 HOH HOH . D 4 HOH A 7 407 46 HOH HOH . D 4 HOH A 8 408 72 HOH HOH . D 4 HOH A 9 409 1 HOH HOH . D 4 HOH A 10 410 60 HOH HOH . D 4 HOH A 11 411 18 HOH HOH . D 4 HOH A 12 412 22 HOH HOH . D 4 HOH A 13 413 36 HOH HOH . D 4 HOH A 14 414 84 HOH HOH . D 4 HOH A 15 415 21 HOH HOH . D 4 HOH A 16 416 33 HOH HOH . D 4 HOH A 17 417 29 HOH HOH . D 4 HOH A 18 418 93 HOH HOH . D 4 HOH A 19 419 17 HOH HOH . D 4 HOH A 20 420 100 HOH HOH . D 4 HOH A 21 421 89 HOH HOH . D 4 HOH A 22 422 2 HOH HOH . D 4 HOH A 23 423 31 HOH HOH . D 4 HOH A 24 424 122 HOH HOH . D 4 HOH A 25 425 27 HOH HOH . D 4 HOH A 26 426 86 HOH HOH . D 4 HOH A 27 427 52 HOH HOH . D 4 HOH A 28 428 53 HOH HOH . D 4 HOH A 29 429 15 HOH HOH . D 4 HOH A 30 430 70 HOH HOH . D 4 HOH A 31 431 95 HOH HOH . D 4 HOH A 32 432 99 HOH HOH . D 4 HOH A 33 433 117 HOH HOH . D 4 HOH A 34 434 16 HOH HOH . D 4 HOH A 35 435 116 HOH HOH . D 4 HOH A 36 436 51 HOH HOH . D 4 HOH A 37 437 25 HOH HOH . D 4 HOH A 38 438 90 HOH HOH . D 4 HOH A 39 439 128 HOH HOH . D 4 HOH A 40 440 79 HOH HOH . D 4 HOH A 41 441 71 HOH HOH . D 4 HOH A 42 442 119 HOH HOH . D 4 HOH A 43 443 66 HOH HOH . D 4 HOH A 44 444 87 HOH HOH . D 4 HOH A 45 445 24 HOH HOH . D 4 HOH A 46 446 68 HOH HOH . D 4 HOH A 47 447 94 HOH HOH . D 4 HOH A 48 448 57 HOH HOH . D 4 HOH A 49 449 3 HOH HOH . D 4 HOH A 50 450 4 HOH HOH . D 4 HOH A 51 451 5 HOH HOH . D 4 HOH A 52 452 6 HOH HOH . D 4 HOH A 53 453 8 HOH HOH . D 4 HOH A 54 454 9 HOH HOH . D 4 HOH A 55 455 10 HOH HOH . D 4 HOH A 56 456 11 HOH HOH . D 4 HOH A 57 457 12 HOH HOH . D 4 HOH A 58 458 13 HOH HOH . D 4 HOH A 59 459 14 HOH HOH . D 4 HOH A 60 460 19 HOH HOH . D 4 HOH A 61 461 20 HOH HOH . D 4 HOH A 62 462 26 HOH HOH . D 4 HOH A 63 463 28 HOH HOH . D 4 HOH A 64 464 30 HOH HOH . D 4 HOH A 65 465 32 HOH HOH . D 4 HOH A 66 466 35 HOH HOH . D 4 HOH A 67 467 37 HOH HOH . D 4 HOH A 68 468 38 HOH HOH . D 4 HOH A 69 469 39 HOH HOH . D 4 HOH A 70 470 40 HOH HOH . D 4 HOH A 71 471 41 HOH HOH . D 4 HOH A 72 472 42 HOH HOH . D 4 HOH A 73 473 43 HOH HOH . D 4 HOH A 74 474 44 HOH HOH . D 4 HOH A 75 475 45 HOH HOH . D 4 HOH A 76 476 47 HOH HOH . D 4 HOH A 77 477 48 HOH HOH . D 4 HOH A 78 478 49 HOH HOH . D 4 HOH A 79 479 50 HOH HOH . D 4 HOH A 80 480 54 HOH HOH . D 4 HOH A 81 481 55 HOH HOH . D 4 HOH A 82 482 56 HOH HOH . D 4 HOH A 83 483 58 HOH HOH . D 4 HOH A 84 484 59 HOH HOH . D 4 HOH A 85 485 61 HOH HOH . D 4 HOH A 86 486 63 HOH HOH . D 4 HOH A 87 487 64 HOH HOH . D 4 HOH A 88 488 65 HOH HOH . D 4 HOH A 89 489 67 HOH HOH . D 4 HOH A 90 490 69 HOH HOH . D 4 HOH A 91 491 73 HOH HOH . D 4 HOH A 92 492 74 HOH HOH . D 4 HOH A 93 493 75 HOH HOH . D 4 HOH A 94 494 78 HOH HOH . D 4 HOH A 95 495 80 HOH HOH . D 4 HOH A 96 496 81 HOH HOH . D 4 HOH A 97 497 82 HOH HOH . D 4 HOH A 98 498 83 HOH HOH . D 4 HOH A 99 499 85 HOH HOH . D 4 HOH A 100 500 88 HOH HOH . D 4 HOH A 101 501 91 HOH HOH . D 4 HOH A 102 502 92 HOH HOH . D 4 HOH A 103 503 96 HOH HOH . D 4 HOH A 104 504 97 HOH HOH . D 4 HOH A 105 505 98 HOH HOH . D 4 HOH A 106 506 101 HOH HOH . D 4 HOH A 107 507 102 HOH HOH . D 4 HOH A 108 508 103 HOH HOH . D 4 HOH A 109 509 104 HOH HOH . D 4 HOH A 110 510 105 HOH HOH . D 4 HOH A 111 511 106 HOH HOH . D 4 HOH A 112 512 107 HOH HOH . D 4 HOH A 113 513 108 HOH HOH . D 4 HOH A 114 514 109 HOH HOH . D 4 HOH A 115 515 110 HOH HOH . D 4 HOH A 116 516 111 HOH HOH . D 4 HOH A 117 517 112 HOH HOH . D 4 HOH A 118 518 113 HOH HOH . D 4 HOH A 119 519 114 HOH HOH . D 4 HOH A 120 520 115 HOH HOH . D 4 HOH A 121 521 118 HOH HOH . D 4 HOH A 122 522 120 HOH HOH . D 4 HOH A 123 523 121 HOH HOH . D 4 HOH A 124 524 123 HOH HOH . D 4 HOH A 125 525 124 HOH HOH . D 4 HOH A 126 526 125 HOH HOH . D 4 HOH A 127 527 126 HOH HOH . D 4 HOH A 128 528 127 HOH HOH . D 4 HOH A 129 529 129 HOH HOH . D 4 HOH A 130 530 130 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 C C2 4F0 . . . B 2 -25.043 2.5 -21.942 1 15.65 ? C2 4F0 301 A 1 HETATM 2 C C4 4F0 . . . B 2 -23.199 1.302 -22.589 1 18.15 ? C4 4F0 301 A 1 HETATM 3 C C5 4F0 . . . B 2 -22.456 2.522 -22.897 1 17.45 ? C5 4F0 301 A 1 HETATM 4 C C6 4F0 . . . B 2 -23.164 3.781 -22.624 1 16.79 ? C6 4F0 301 A 1 HETATM 5 C CS5 4F0 . . . B 2 -26.783 -0.572 -28.436 1 37.27 ? CS5 4F0 301 A 1 HETATM 6 S S 4F0 . . . B 2 -26.186 -0.427 -26.788 1 34.66 ? S 4F0 301 A 1 HETATM 7 C C5' 4F0 . . . B 2 -25.785 -1.996 -26.045 1 32.65 ? C5' 4F0 301 A 1 HETATM 8 C C4' 4F0 . . . B 2 -25.016 -1.81 -24.737 1 31.58 ? C4' 4F0 301 A 1 HETATM 9 C C1' 4F0 . . . B 2 -23.678 -1.186 -25.036 1 29.56 ? C1' 4F0 301 A 1 HETATM 10 N N1' 4F0 . . . B 2 -22.744 -1.867 -24.142 1 27.57 ? N1' 4F0 301 A 1 HETATM 11 C C10 4F0 . . . B 2 -22.697 -1.262 -22.792 1 22.91 ? C10 4F0 301 A 1 HETATM 12 C C9 4F0 . . . B 2 -22.33 0.189 -22.911 1 19.93 ? C9 4F0 301 A 1 HETATM 13 C C8 4F0 . . . B 2 -21.146 0.772 -23.369 1 18.63 ? C8 4F0 301 A 1 HETATM 14 N N7 4F0 . . . B 2 -21.229 2.141 -23.35 1 17.66 ? N7 4F0 301 A 1 HETATM 15 N N6 4F0 . . . B 2 -22.582 4.992 -22.855 1 16.18 ? N6 4F0 301 A 1 HETATM 16 N N1 4F0 . . . B 2 -24.441 3.687 -22.171 1 15.98 ? N1 4F0 301 A 1 HETATM 17 N N3 4F0 . . . B 2 -24.472 1.3 -22.132 1 16.61 ? N3 4F0 301 A 1 HETATM 18 C C2' 4F0 . . . B 2 -23.208 -3.262 -24.067 1 30.45 ? C2' 4F0 301 A 1 HETATM 19 C C3' 4F0 . . . B 2 -24.711 -3.116 -23.993 1 31.8 ? C3' 4F0 301 A 1 HETATM 20 O O3' 4F0 . . . B 2 -25.09 -3.058 -22.603 1 35.22 ? O3' 4F0 301 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #