data_3Q77 # _model_server_result.job_id 1HD8e8zUiLJprwmzkZ917w _model_server_result.datetime_utc '2025-07-31 18:19:51' _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 3q77 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 3Q77 # _exptl.entry_id 3Q77 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 445.391 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-hydroxyethyl (4R)-4-(4-cyanophenyl)-6-methyl-2-oxo-1-[3-(trifluoromethyl)phenyl]-1,2,3,4-tetrahydropyrimidine-5-carboxylate' _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 120 _cell.entry_id 3Q77 _cell.length_a 73.732 _cell.length_b 73.732 _cell.length_c 70.658 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3Q77 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 1 FUC NAG C1 O1 . O6 HO6 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B NAG 1 B 1 NAG A 401 NAG 2 n B NAG 2 B 2 NAG A 403 NAG 2 n B FUC 3 B 3 FUC A 402 FUC # 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 26 A CYS 42 1_555 A SG CYS 42 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 122 A CYS 136 1_555 A SG CYS 179 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 A SG CYS 152 A CYS 168 1_555 A SG CYS 158 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 A SG CYS 169 A CYS 191 1_555 A SG CYS 194 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? covale ? covale1 A ND2 ASN 95 A ASN 109 1_555 C C1 NAG . A NAG 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale2 A ND2 ASN 144 A ASN 159 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? covale ? covale3 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale4 B O6 NAG . B NAG 1 1_555 B C1 FUC . B FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? # _chem_comp.formula 'C22 H18 F3 N3 O4' _chem_comp.formula_weight 445.391 _chem_comp.id 2HY _chem_comp.mon_nstd_flag . _chem_comp.name '2-hydroxyethyl (4R)-4-(4-cyanophenyl)-6-methyl-2-oxo-1-[3-(trifluoromethyl)phenyl]-1,2,3,4-tetrahydropyrimidine-5-carboxylate' _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 C1 N1 2HY sing 1 n n C1 O1 2HY doub 2 n n C1 N2 2HY sing 3 n n F1 C11 2HY sing 4 n n N1 C4 2HY sing 5 n n N1 C5 2HY sing 6 n n C2 N2 2HY sing 7 n n C2 C3 2HY sing 8 n n C2 C13 2HY sing 9 n n F2 C11 2HY sing 10 n n O2 C20 2HY doub 11 n n C3 C4 2HY doub 12 n n C3 C20 2HY sing 13 n n F3 C11 2HY sing 14 n n N3 C19 2HY trip 15 n n O3 C20 2HY sing 16 n n O3 C21 2HY sing 17 n n C4 C23 2HY sing 18 n n C5 C6 2HY doub 19 n y C5 C10 2HY sing 20 n y C6 C7 2HY sing 21 n y C7 C8 2HY doub 22 n y C7 C11 2HY sing 23 n n C8 C9 2HY sing 24 n y C9 C10 2HY doub 25 n y C13 C14 2HY doub 26 n y C13 C18 2HY sing 27 n y C14 C15 2HY sing 28 n y C15 C16 2HY doub 29 n y C16 C17 2HY sing 30 n y C16 C19 2HY sing 31 n n C17 C18 2HY doub 32 n y C21 C22 2HY sing 33 n n C22 O33 2HY sing 34 n n C2 H2 2HY sing 35 n n N2 HN2 2HY sing 36 n n C6 H6 2HY sing 37 n n C8 H8 2HY sing 38 n n C9 H9 2HY sing 39 n n C10 H10 2HY sing 40 n n C14 H14 2HY sing 41 n n C15 H15 2HY sing 42 n n C17 H17 2HY sing 43 n n C18 H18 2HY sing 44 n n C21 H21 2HY sing 45 n n C21 H21A 2HY sing 46 n n C22 H22 2HY sing 47 n n C22 H22A 2HY sing 48 n n C23 H23 2HY sing 49 n n C23 H23A 2HY sing 50 n n C23 H23B 2HY sing 51 n n O33 HO33 2HY sing 52 n n # _atom_sites.entry_id 3Q77 _atom_sites.fract_transf_matrix[1][1] 0.013563 _atom_sites.fract_transf_matrix[1][2] 0.00783 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015661 _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] 0.014153 _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 3 NAG A 1 411 411 NAG NAG . D 4 2HY A 1 500 500 2HY 2HY . E 5 HOH A 1 501 501 HOH HOH . E 5 HOH A 2 502 502 HOH HOH . E 5 HOH A 3 503 503 HOH HOH . E 5 HOH A 4 504 504 HOH HOH . E 5 HOH A 5 505 505 HOH HOH . E 5 HOH A 6 506 506 HOH HOH . E 5 HOH A 7 507 507 HOH HOH . E 5 HOH A 8 508 508 HOH HOH . E 5 HOH A 9 509 509 HOH HOH . E 5 HOH A 10 510 510 HOH HOH . E 5 HOH A 11 511 511 HOH HOH . E 5 HOH A 12 512 512 HOH HOH . E 5 HOH A 13 513 513 HOH HOH . E 5 HOH A 14 514 514 HOH HOH . E 5 HOH A 15 515 515 HOH HOH . E 5 HOH A 16 516 516 HOH HOH . E 5 HOH A 17 517 517 HOH HOH . E 5 HOH A 18 518 518 HOH HOH . E 5 HOH A 19 519 519 HOH HOH . E 5 HOH A 20 520 520 HOH HOH . E 5 HOH A 21 521 521 HOH HOH . E 5 HOH A 22 522 522 HOH HOH . E 5 HOH A 23 523 523 HOH HOH . E 5 HOH A 24 524 524 HOH HOH . E 5 HOH A 25 525 525 HOH HOH . E 5 HOH A 26 526 526 HOH HOH . E 5 HOH A 27 527 527 HOH HOH . E 5 HOH A 28 528 528 HOH HOH . E 5 HOH A 29 529 529 HOH HOH . E 5 HOH A 30 530 530 HOH HOH . E 5 HOH A 31 531 531 HOH HOH . E 5 HOH A 32 532 532 HOH HOH . E 5 HOH A 33 533 533 HOH HOH . E 5 HOH A 34 534 534 HOH HOH . E 5 HOH A 35 535 535 HOH HOH . E 5 HOH A 36 536 536 HOH HOH . E 5 HOH A 37 537 537 HOH HOH . E 5 HOH A 38 538 538 HOH HOH . E 5 HOH A 39 539 539 HOH HOH . E 5 HOH A 40 540 540 HOH HOH . E 5 HOH A 41 541 541 HOH HOH . E 5 HOH A 42 542 542 HOH HOH . E 5 HOH A 43 543 543 HOH HOH . E 5 HOH A 44 544 544 HOH HOH . E 5 HOH A 45 545 545 HOH HOH . E 5 HOH A 46 546 546 HOH HOH . E 5 HOH A 47 547 547 HOH HOH . E 5 HOH A 48 548 548 HOH HOH . E 5 HOH A 49 549 549 HOH HOH . E 5 HOH A 50 550 550 HOH HOH . E 5 HOH A 51 551 551 HOH HOH . E 5 HOH A 52 552 552 HOH HOH . E 5 HOH A 53 553 553 HOH HOH . E 5 HOH A 54 554 554 HOH HOH . E 5 HOH A 55 555 555 HOH HOH . E 5 HOH A 56 556 556 HOH HOH . E 5 HOH A 57 557 557 HOH HOH . E 5 HOH A 58 558 558 HOH HOH . E 5 HOH A 59 559 559 HOH HOH . E 5 HOH A 60 560 560 HOH HOH . E 5 HOH A 61 561 561 HOH HOH . E 5 HOH A 62 562 562 HOH HOH . E 5 HOH A 63 563 563 HOH HOH . E 5 HOH A 64 564 564 HOH HOH . E 5 HOH A 65 565 565 HOH HOH . E 5 HOH A 66 566 566 HOH HOH . E 5 HOH A 67 567 567 HOH HOH . E 5 HOH A 68 568 568 HOH HOH . E 5 HOH A 69 569 569 HOH HOH . E 5 HOH A 70 570 570 HOH HOH . E 5 HOH A 71 571 571 HOH HOH . E 5 HOH A 72 572 572 HOH HOH . E 5 HOH A 73 573 573 HOH HOH . E 5 HOH A 74 574 574 HOH HOH . E 5 HOH A 75 575 575 HOH HOH . E 5 HOH A 76 576 576 HOH HOH . E 5 HOH A 77 577 577 HOH HOH . E 5 HOH A 78 578 578 HOH HOH . E 5 HOH A 79 579 579 HOH HOH . E 5 HOH A 80 580 580 HOH HOH . E 5 HOH A 81 581 581 HOH HOH . E 5 HOH A 82 582 582 HOH HOH . E 5 HOH A 83 583 583 HOH HOH . E 5 HOH A 84 584 584 HOH HOH . E 5 HOH A 85 585 585 HOH HOH . E 5 HOH A 86 586 586 HOH HOH . E 5 HOH A 87 587 587 HOH HOH . E 5 HOH A 88 588 588 HOH HOH . E 5 HOH A 89 589 589 HOH HOH . E 5 HOH A 90 590 590 HOH HOH . E 5 HOH A 91 591 591 HOH HOH . E 5 HOH A 92 592 592 HOH HOH . E 5 HOH A 93 593 593 HOH HOH . E 5 HOH A 94 594 594 HOH HOH . E 5 HOH A 95 595 595 HOH HOH . E 5 HOH A 96 596 596 HOH HOH . E 5 HOH A 97 597 597 HOH HOH . E 5 HOH A 98 598 598 HOH HOH . E 5 HOH A 99 599 599 HOH HOH . E 5 HOH A 100 600 600 HOH HOH . E 5 HOH A 101 601 601 HOH HOH . E 5 HOH A 102 602 602 HOH HOH . E 5 HOH A 103 603 603 HOH HOH . E 5 HOH A 104 604 604 HOH HOH . E 5 HOH A 105 605 605 HOH HOH . E 5 HOH A 106 606 606 HOH HOH . E 5 HOH A 107 607 607 HOH HOH . E 5 HOH A 108 608 608 HOH HOH . E 5 HOH A 109 609 609 HOH HOH . E 5 HOH A 110 610 610 HOH HOH . E 5 HOH A 111 611 611 HOH HOH . E 5 HOH A 112 612 612 HOH HOH . E 5 HOH A 113 613 613 HOH HOH . E 5 HOH A 114 614 614 HOH HOH . E 5 HOH A 115 615 615 HOH HOH . E 5 HOH A 116 616 616 HOH HOH . E 5 HOH A 117 617 617 HOH HOH . E 5 HOH A 118 618 618 HOH HOH . E 5 HOH A 119 619 619 HOH HOH . E 5 HOH A 120 620 620 HOH HOH . E 5 HOH A 121 621 621 HOH HOH . E 5 HOH A 122 622 622 HOH HOH . E 5 HOH A 123 623 623 HOH HOH . E 5 HOH A 124 624 624 HOH HOH . E 5 HOH A 125 625 625 HOH HOH . E 5 HOH A 126 626 626 HOH HOH . E 5 HOH A 127 627 627 HOH HOH . E 5 HOH A 128 628 628 HOH HOH . E 5 HOH A 129 629 629 HOH HOH . E 5 HOH A 130 630 630 HOH HOH . E 5 HOH A 131 631 631 HOH HOH . E 5 HOH A 132 632 632 HOH HOH . E 5 HOH A 133 633 633 HOH HOH . E 5 HOH A 134 634 634 HOH HOH . E 5 HOH A 135 635 635 HOH HOH . E 5 HOH A 136 636 636 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 C1 2HY . . . D 4 38.2 -13.221 2.243 1 12.59 ? C1 2HY 500 A 1 HETATM 2 F F1 2HY . . . D 4 39.139 -7.832 -1.726 1 11.44 ? F1 2HY 500 A 1 HETATM 3 N N1 2HY . . . D 4 39.295 -12.689 1.663 1 13.89 ? N1 2HY 500 A 1 HETATM 4 O O1 2HY . . . D 4 37.096 -13.17 1.664 1 10.92 ? O1 2HY 500 A 1 HETATM 5 C C2 2HY . . . D 4 39.429 -13.909 4.278 1 15.92 ? C2 2HY 500 A 1 HETATM 6 F F2 2HY . . . D 4 37.325 -8.251 -0.65 1 9.39 ? F2 2HY 500 A 1 HETATM 7 N N2 2HY . . . D 4 38.238 -13.833 3.441 1 16.53 ? N2 2HY 500 A 1 HETATM 8 O O2 2HY . . . D 4 42.999 -13.228 3.928 1 20.99 ? O2 2HY 500 A 1 HETATM 9 C C3 2HY . . . D 4 40.614 -13.385 3.6 1 14.97 ? C3 2HY 500 A 1 HETATM 10 F F3 2HY . . . D 4 39.104 -7.85 0.424 1 13.81 ? F3 2HY 500 A 1 HETATM 11 N N3 2HY . . . D 4 37.81 -9.196 8.87 1 21.22 ? N3 2HY 500 A 1 HETATM 12 O O3 2HY . . . D 4 41.762 -13.994 5.728 1 34.98 ? O3 2HY 500 A 1 HETATM 13 C C4 2HY . . . D 4 40.497 -12.732 2.273 1 14.48 ? C4 2HY 500 A 1 HETATM 14 C C5 2HY . . . D 4 39.143 -12.052 0.41 1 12.71 ? C5 2HY 500 A 1 HETATM 15 C C6 2HY . . . D 4 38.986 -10.66 0.442 1 13.39 ? C6 2HY 500 A 1 HETATM 16 C C7 2HY . . . D 4 38.821 -9.921 -0.726 1 7.73 ? C7 2HY 500 A 1 HETATM 17 C C8 2HY . . . D 4 38.804 -10.589 -1.949 1 10.71 ? C8 2HY 500 A 1 HETATM 18 C C9 2HY . . . D 4 38.946 -11.983 -1.981 1 10.83 ? C9 2HY 500 A 1 HETATM 19 C C10 2HY . . . D 4 39.115 -12.717 -0.807 1 12.12 ? C10 2HY 500 A 1 HETATM 20 C C11 2HY . . . D 4 38.627 -8.424 -0.664 1 13.29 ? C11 2HY 500 A 1 HETATM 21 C C13 2HY . . . D 4 39.09 -12.88 5.319 1 21.07 ? C13 2HY 500 A 1 HETATM 22 C C14 2HY . . . D 4 38.838 -11.55 4.944 1 20.3 ? C14 2HY 500 A 1 HETATM 23 C C15 2HY . . . D 4 38.502 -10.578 5.887 1 20.65 ? C15 2HY 500 A 1 HETATM 24 C C16 2HY . . . D 4 38.414 -10.921 7.232 1 26.68 ? C16 2HY 500 A 1 HETATM 25 C C17 2HY . . . D 4 38.665 -12.244 7.623 1 28.01 ? C17 2HY 500 A 1 HETATM 26 C C18 2HY . . . D 4 39.001 -13.209 6.67 1 24.05 ? C18 2HY 500 A 1 HETATM 27 C C19 2HY . . . D 4 38.097 -10.023 8.101 1 25.99 ? C19 2HY 500 A 1 HETATM 28 C C20 2HY . . . D 4 41.891 -13.5 4.375 1 22.89 ? C20 2HY 500 A 1 HETATM 29 C C21 2HY . . . D 4 42.883 -14.583 6.367 1 43.35 ? C21 2HY 500 A 1 HETATM 30 C C22 2HY . . . D 4 43.021 -13.929 7.728 1 52.06 ? C22 2HY 500 A 1 HETATM 31 C C23 2HY . . . D 4 41.724 -12.149 1.61 1 12.37 ? C23 2HY 500 A 1 HETATM 32 O O33 2HY . . . D 4 43.953 -14.683 8.51 1 61.21 ? O33 2HY 500 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #