data_7R4P # _model_server_result.job_id v70jaWL497VaE8AfpQHxLw _model_server_result.datetime_utc '2025-02-24 18:21:31' _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 7r4p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 7R4P # _exptl.entry_id 7R4P _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 248.281 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 6-amino-1-benzyl-5-(methylamino)pyrimidine-2,4(1H,3H)-dione _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 7R4P _cell.length_a 97.13 _cell.length_b 97.13 _cell.length_c 80.84 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7R4P _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 1,2,3,4 # 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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C12 H16 N4 O2' _chem_comp.formula_weight 248.281 _chem_comp.id I2Z _chem_comp.mon_nstd_flag . _chem_comp.name 6-amino-1-benzyl-5-(methylamino)pyrimidine-2,4(1H,3H)-dione _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 O1 C10 I2Z doub 206 n n N3 C10 I2Z sing 207 n n N3 C11 I2Z sing 208 n n C10 N2 I2Z sing 209 n n O C11 I2Z doub 210 n n C11 C1 I2Z sing 211 n n N2 C3 I2Z sing 212 n n N2 C2 I2Z sing 213 n n C1 C2 I2Z sing 214 n n C1 N I2Z sing 215 n n C3 C4 I2Z sing 216 n n C2 N1 I2Z sing 217 n n N C I2Z sing 218 n n C5 C4 I2Z doub 219 n y C5 C6 I2Z sing 220 n y C4 C9 I2Z sing 221 n y C6 C7 I2Z doub 222 n y C9 C8 I2Z doub 223 n y C8 C7 I2Z sing 224 n y N1 H1 I2Z sing 225 n n N1 H2 I2Z sing 226 n n N3 H4 I2Z sing 227 n n C5 H5 I2Z sing 228 n n C6 H6 I2Z sing 229 n n C7 H7 I2Z sing 230 n n C8 H8 I2Z sing 231 n n C1 H9 I2Z sing 232 n n N H10 I2Z sing 233 n n C H12 I2Z sing 234 n n C H13 I2Z sing 235 n n C H14 I2Z sing 236 n n C2 H15 I2Z sing 237 n n C3 H16 I2Z sing 238 n n C3 H17 I2Z sing 239 n n C9 H18 I2Z sing 240 n n # _atom_sites.entry_id 7R4P _atom_sites.fract_transf_matrix[1][1] 0.010295 _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] 0.010295 _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] 0.01237 _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 FMN A 1 401 1 FMN FMN . C 3 I2Z A 1 402 1 I2Z LIG . D 4 HOH A 1 501 427 HOH HOH . D 4 HOH A 2 502 409 HOH HOH . D 4 HOH A 3 503 511 HOH HOH . D 4 HOH A 4 504 67 HOH HOH . D 4 HOH A 5 505 393 HOH HOH . D 4 HOH A 6 506 160 HOH HOH . D 4 HOH A 7 507 423 HOH HOH . D 4 HOH A 8 508 504 HOH HOH . D 4 HOH A 9 509 419 HOH HOH . D 4 HOH A 10 510 31 HOH HOH . D 4 HOH A 11 511 390 HOH HOH . D 4 HOH A 12 512 501 HOH HOH . D 4 HOH A 13 513 497 HOH HOH . D 4 HOH A 14 514 436 HOH HOH . D 4 HOH A 15 515 73 HOH HOH . D 4 HOH A 16 516 6 HOH HOH . D 4 HOH A 17 517 498 HOH HOH . D 4 HOH A 18 518 33 HOH HOH . D 4 HOH A 19 519 439 HOH HOH . D 4 HOH A 20 520 83 HOH HOH . D 4 HOH A 21 521 482 HOH HOH . D 4 HOH A 22 522 387 HOH HOH . D 4 HOH A 23 523 86 HOH HOH . D 4 HOH A 24 524 398 HOH HOH . D 4 HOH A 25 525 528 HOH HOH . D 4 HOH A 26 526 115 HOH HOH . D 4 HOH A 27 527 412 HOH HOH . D 4 HOH A 28 528 70 HOH HOH . D 4 HOH A 29 529 21 HOH HOH . D 4 HOH A 30 530 8 HOH HOH . D 4 HOH A 31 531 346 HOH HOH . D 4 HOH A 32 532 512 HOH HOH . D 4 HOH A 33 533 13 HOH HOH . D 4 HOH A 34 534 100 HOH HOH . D 4 HOH A 35 535 416 HOH HOH . D 4 HOH A 36 536 19 HOH HOH . D 4 HOH A 37 537 448 HOH HOH . D 4 HOH A 38 538 155 HOH HOH . D 4 HOH A 39 539 16 HOH HOH . D 4 HOH A 40 540 472 HOH HOH . D 4 HOH A 41 541 17 HOH HOH . D 4 HOH A 42 542 28 HOH HOH . D 4 HOH A 43 543 38 HOH HOH . D 4 HOH A 44 544 108 HOH HOH . D 4 HOH A 45 545 81 HOH HOH . D 4 HOH A 46 546 392 HOH HOH . D 4 HOH A 47 547 406 HOH HOH . D 4 HOH A 48 548 85 HOH HOH . D 4 HOH A 49 549 232 HOH HOH . D 4 HOH A 50 550 120 HOH HOH . D 4 HOH A 51 551 405 HOH HOH . D 4 HOH A 52 552 72 HOH HOH . D 4 HOH A 53 553 438 HOH HOH . D 4 HOH A 54 554 14 HOH HOH . D 4 HOH A 55 555 381 HOH HOH . D 4 HOH A 56 556 48 HOH HOH . D 4 HOH A 57 557 22 HOH HOH . D 4 HOH A 58 558 162 HOH HOH . D 4 HOH A 59 559 36 HOH HOH . D 4 HOH A 60 560 42 HOH HOH . D 4 HOH A 61 561 199 HOH HOH . D 4 HOH A 62 562 513 HOH HOH . D 4 HOH A 63 563 20 HOH HOH . D 4 HOH A 64 564 340 HOH HOH . D 4 HOH A 65 565 304 HOH HOH . D 4 HOH A 66 566 98 HOH HOH . D 4 HOH A 67 567 400 HOH HOH . D 4 HOH A 68 568 524 HOH HOH . D 4 HOH A 69 569 128 HOH HOH . D 4 HOH A 70 570 94 HOH HOH . D 4 HOH A 71 571 415 HOH HOH . D 4 HOH A 72 572 486 HOH HOH . D 4 HOH A 73 573 49 HOH HOH . D 4 HOH A 74 574 385 HOH HOH . D 4 HOH A 75 575 383 HOH HOH . D 4 HOH A 76 576 394 HOH HOH . D 4 HOH A 77 577 129 HOH HOH . D 4 HOH A 78 578 101 HOH HOH . D 4 HOH A 79 579 97 HOH HOH . D 4 HOH A 80 580 9 HOH HOH . D 4 HOH A 81 581 2 HOH HOH . D 4 HOH A 82 582 7 HOH HOH . D 4 HOH A 83 583 99 HOH HOH . D 4 HOH A 84 584 502 HOH HOH . D 4 HOH A 85 585 12 HOH HOH . D 4 HOH A 86 586 499 HOH HOH . D 4 HOH A 87 587 62 HOH HOH . D 4 HOH A 88 588 10 HOH HOH . D 4 HOH A 89 589 40 HOH HOH . D 4 HOH A 90 590 23 HOH HOH . D 4 HOH A 91 591 32 HOH HOH . D 4 HOH A 92 592 78 HOH HOH . D 4 HOH A 93 593 71 HOH HOH . D 4 HOH A 94 594 39 HOH HOH . D 4 HOH A 95 595 117 HOH HOH . D 4 HOH A 96 596 110 HOH HOH . D 4 HOH A 97 597 30 HOH HOH . D 4 HOH A 98 598 140 HOH HOH . D 4 HOH A 99 599 417 HOH HOH . D 4 HOH A 100 600 388 HOH HOH . D 4 HOH A 101 601 107 HOH HOH . D 4 HOH A 102 602 503 HOH HOH . D 4 HOH A 103 603 401 HOH HOH . D 4 HOH A 104 604 399 HOH HOH . D 4 HOH A 105 605 52 HOH HOH . D 4 HOH A 106 606 59 HOH HOH . D 4 HOH A 107 607 377 HOH HOH . D 4 HOH A 108 608 485 HOH HOH . D 4 HOH A 109 609 80 HOH HOH . D 4 HOH A 110 610 408 HOH HOH . D 4 HOH A 111 611 404 HOH HOH . D 4 HOH A 112 612 119 HOH HOH . D 4 HOH A 113 613 44 HOH HOH . D 4 HOH A 114 614 428 HOH HOH . D 4 HOH A 115 615 382 HOH HOH . D 4 HOH A 116 616 425 HOH HOH . D 4 HOH A 117 617 61 HOH HOH . D 4 HOH A 118 618 389 HOH HOH . D 4 HOH A 119 619 66 HOH HOH . D 4 HOH A 120 620 43 HOH HOH . D 4 HOH A 121 621 118 HOH HOH . D 4 HOH A 122 622 488 HOH HOH . D 4 HOH A 123 623 104 HOH HOH . D 4 HOH A 124 624 505 HOH HOH . D 4 HOH A 125 625 54 HOH HOH . D 4 HOH A 126 626 136 HOH HOH . D 4 HOH A 127 627 58 HOH HOH . D 4 HOH A 128 628 522 HOH HOH . D 4 HOH A 129 629 241 HOH HOH . D 4 HOH A 130 630 506 HOH HOH . D 4 HOH A 131 631 391 HOH HOH . D 4 HOH A 132 632 145 HOH HOH . D 4 HOH A 133 633 414 HOH HOH . D 4 HOH A 134 634 441 HOH HOH . D 4 HOH A 135 635 154 HOH HOH . D 4 HOH A 136 636 65 HOH HOH . D 4 HOH A 137 637 411 HOH HOH . D 4 HOH A 138 638 126 HOH HOH . D 4 HOH A 139 639 207 HOH HOH . D 4 HOH A 140 640 384 HOH HOH . D 4 HOH A 141 641 18 HOH HOH . D 4 HOH A 142 642 190 HOH HOH . D 4 HOH A 143 643 24 HOH HOH . D 4 HOH A 144 644 429 HOH HOH . D 4 HOH A 145 645 50 HOH HOH . D 4 HOH A 146 646 114 HOH HOH . D 4 HOH A 147 647 443 HOH HOH . D 4 HOH A 148 648 93 HOH HOH . D 4 HOH A 149 649 116 HOH HOH . D 4 HOH A 150 650 51 HOH HOH . D 4 HOH A 151 651 424 HOH HOH . D 4 HOH A 152 652 34 HOH HOH . D 4 HOH A 153 653 467 HOH HOH . D 4 HOH A 154 654 76 HOH HOH . D 4 HOH A 155 655 37 HOH HOH . D 4 HOH A 156 656 477 HOH HOH . D 4 HOH A 157 657 102 HOH HOH . D 4 HOH A 158 658 113 HOH HOH . D 4 HOH A 159 659 402 HOH HOH . D 4 HOH A 160 660 41 HOH HOH . D 4 HOH A 161 661 57 HOH HOH . D 4 HOH A 162 662 508 HOH HOH . D 4 HOH A 163 663 181 HOH HOH . D 4 HOH A 164 664 410 HOH HOH . D 4 HOH A 165 665 77 HOH HOH . D 4 HOH A 166 666 218 HOH HOH . D 4 HOH A 167 667 45 HOH HOH . D 4 HOH A 168 668 440 HOH HOH . D 4 HOH A 169 669 122 HOH HOH . D 4 HOH A 170 670 84 HOH HOH . D 4 HOH A 171 671 466 HOH HOH . D 4 HOH A 172 672 135 HOH HOH . D 4 HOH A 173 673 29 HOH HOH . D 4 HOH A 174 674 123 HOH HOH . D 4 HOH A 175 675 317 HOH HOH . D 4 HOH A 176 676 3 HOH HOH . D 4 HOH A 177 677 89 HOH HOH . D 4 HOH A 178 678 178 HOH HOH . D 4 HOH A 179 679 509 HOH HOH . D 4 HOH A 180 680 11 HOH HOH . D 4 HOH A 181 681 442 HOH HOH . D 4 HOH A 182 682 376 HOH HOH . D 4 HOH A 183 683 246 HOH HOH . D 4 HOH A 184 684 175 HOH HOH . D 4 HOH A 185 685 487 HOH HOH . D 4 HOH A 186 686 396 HOH HOH . D 4 HOH A 187 687 60 HOH HOH . D 4 HOH A 188 688 46 HOH HOH . D 4 HOH A 189 689 283 HOH HOH . D 4 HOH A 190 690 421 HOH HOH . D 4 HOH A 191 691 91 HOH HOH . D 4 HOH A 192 692 156 HOH HOH . D 4 HOH A 193 693 270 HOH HOH . D 4 HOH A 194 694 139 HOH HOH . D 4 HOH A 195 695 184 HOH HOH . D 4 HOH A 196 696 447 HOH HOH . D 4 HOH A 197 697 74 HOH HOH . D 4 HOH A 198 698 185 HOH HOH . D 4 HOH A 199 699 82 HOH HOH . D 4 HOH A 200 700 127 HOH HOH . D 4 HOH A 201 701 437 HOH HOH . D 4 HOH A 202 702 238 HOH HOH . D 4 HOH A 203 703 500 HOH HOH . D 4 HOH A 204 704 47 HOH HOH . D 4 HOH A 205 705 451 HOH HOH . D 4 HOH A 206 706 354 HOH HOH . D 4 HOH A 207 707 159 HOH HOH . D 4 HOH A 208 708 303 HOH HOH . D 4 HOH A 209 709 96 HOH HOH . D 4 HOH A 210 710 166 HOH HOH . D 4 HOH A 211 711 152 HOH HOH . D 4 HOH A 212 712 164 HOH HOH . D 4 HOH A 213 713 150 HOH HOH . D 4 HOH A 214 714 141 HOH HOH . D 4 HOH A 215 715 491 HOH HOH . D 4 HOH A 216 716 63 HOH HOH . D 4 HOH A 217 717 490 HOH HOH . D 4 HOH A 218 718 235 HOH HOH . D 4 HOH A 219 719 68 HOH HOH . D 4 HOH A 220 720 489 HOH HOH . D 4 HOH A 221 721 514 HOH HOH . D 4 HOH A 222 722 27 HOH HOH . D 4 HOH A 223 723 349 HOH HOH . D 4 HOH A 224 724 496 HOH HOH . D 4 HOH A 225 725 170 HOH HOH . D 4 HOH A 226 726 88 HOH HOH . D 4 HOH A 227 727 510 HOH HOH . D 4 HOH A 228 728 492 HOH HOH . D 4 HOH A 229 729 147 HOH HOH . D 4 HOH A 230 730 180 HOH HOH . D 4 HOH A 231 731 111 HOH HOH . D 4 HOH A 232 732 527 HOH HOH . D 4 HOH A 233 733 25 HOH HOH . D 4 HOH A 234 734 142 HOH HOH . D 4 HOH A 235 735 375 HOH HOH . D 4 HOH A 236 736 87 HOH HOH . D 4 HOH A 237 737 149 HOH HOH . D 4 HOH A 238 738 494 HOH HOH . D 4 HOH A 239 739 179 HOH HOH . D 4 HOH A 240 740 210 HOH HOH . D 4 HOH A 241 741 79 HOH HOH . D 4 HOH A 242 742 176 HOH HOH . D 4 HOH A 243 743 358 HOH HOH . D 4 HOH A 244 744 157 HOH HOH . D 4 HOH A 245 745 189 HOH HOH . D 4 HOH A 246 746 347 HOH HOH . D 4 HOH A 247 747 220 HOH HOH . D 4 HOH A 248 748 351 HOH HOH . D 4 HOH A 249 749 265 HOH HOH . D 4 HOH A 250 750 112 HOH HOH . D 4 HOH A 251 751 132 HOH HOH . D 4 HOH A 252 752 507 HOH HOH . D 4 HOH A 253 753 328 HOH HOH . D 4 HOH A 254 754 493 HOH HOH . D 4 HOH A 255 755 364 HOH HOH . D 4 HOH A 256 756 248 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 N N1 I2Z . . . C 3 6.231 31.486 32.146 0.5 47.19 ? N1 I2Z 402 A 1 HETATM 2 N N3 I2Z . . . C 3 5.497 31.035 28.205 0.5 26.62 ? N3 I2Z 402 A 1 HETATM 3 C C4 I2Z . . . C 3 4.908 33.982 31.813 0.5 38.97 ? C4 I2Z 402 A 1 HETATM 4 C C5 I2Z . . . C 3 3.631 33.424 31.792 0.5 42.34 ? C5 I2Z 402 A 1 HETATM 5 C C6 I2Z . . . C 3 2.853 33.461 32.927 0.5 44.58 ? C6 I2Z 402 A 1 HETATM 6 C C7 I2Z . . . C 3 3.358 34.11 34.098 0.5 48.24 ? C7 I2Z 402 A 1 HETATM 7 C C8 I2Z . . . C 3 4.605 34.693 34.096 0.5 48.29 ? C8 I2Z 402 A 1 HETATM 8 C C10 I2Z . . . C 3 5.615 32.372 28.655 0.5 29.55 ? C10 I2Z 402 A 1 HETATM 9 O O1 I2Z . . . C 3 5.582 33.334 27.929 0.5 32.39 ? O1 I2Z 402 A 1 HETATM 10 C C11 I2Z . . . C 3 5.442 30.011 29.189 0.5 26.12 ? C11 I2Z 402 A 1 HETATM 11 O O I2Z . . . C 3 5.281 28.853 28.975 0.5 26.37 ? O I2Z 402 A 1 HETATM 12 C C1 I2Z . . . C 3 5.578 30.4 30.422 0.5 30.37 ? C1 I2Z 402 A 1 HETATM 13 N N I2Z . . . C 3 5.157 29.824 31.418 0.5 33.64 ? N I2Z 402 A 1 HETATM 14 C C I2Z . . . C 3 3.714 30.084 31.507 0.5 43.95 ? C I2Z 402 A 1 HETATM 15 N N2 I2Z . . . C 3 5.75 32.508 30.029 0.5 31.02 ? N2 I2Z 402 A 1 HETATM 16 C C2 I2Z . . . C 3 5.803 31.478 30.838 0.5 34.83 ? C2 I2Z 402 A 1 HETATM 17 C C3 I2Z . . . C 3 5.752 33.896 30.599 0.5 34.85 ? C3 I2Z 402 A 1 HETATM 18 C C9 I2Z . . . C 3 5.411 34.622 32.961 0.5 43.57 ? C9 I2Z 402 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 18 #