data_4Y46 # _model_server_result.job_id glROCyNFUDgk2ORDQ96g2Q _model_server_result.datetime_utc '2024-11-04 22:40:31' _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 4y46 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 4Y46 # _exptl.entry_id 4Y46 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 412.528 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-{trans-4-[(8-cyclopentyl-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-2-yl)amino]cyclohexyl}-3-propan-2-ylurea _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 4Y46 _cell.length_a 53.8 _cell.length_b 72.14 _cell.length_c 107.94 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Y46 _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 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 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C22 H32 N6 O2' _chem_comp.formula_weight 412.528 _chem_comp.id 4F2 _chem_comp.mon_nstd_flag . _chem_comp.name 1-{trans-4-[(8-cyclopentyl-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-2-yl)amino]cyclohexyl}-3-propan-2-ylurea _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 C19 C20 4F2 doub 1 n n C19 C18 4F2 sing 2 n n C20 C21 4F2 sing 3 n n C17 C18 4F2 doub 4 n y C17 N16 4F2 sing 5 n y C18 C29 4F2 sing 6 n y N16 C15 4F2 doub 7 n y C21 O22 4F2 doub 8 n n C21 N23 4F2 sing 9 n n C29 N23 4F2 sing 10 n n C29 N30 4F2 doub 11 n y N23 C24 4F2 sing 12 n n C15 N30 4F2 sing 13 n y C15 N14 4F2 sing 14 n n C28 C24 4F2 sing 15 n n C28 C27 4F2 sing 16 n n N14 C11 4F2 sing 17 n n C12 C11 4F2 sing 18 n n C12 C13 4F2 sing 19 n n C24 C25 4F2 sing 20 n n C11 C10 4F2 sing 21 n n C13 C08 4F2 sing 22 n n C27 C26 4F2 sing 23 n n C25 C26 4F2 sing 24 n n C01 C02 4F2 sing 25 n n C10 C09 4F2 sing 26 n n C08 C09 4F2 sing 27 n n C08 N07 4F2 sing 28 n n C03 C02 4F2 sing 29 n n N04 C02 4F2 sing 30 n n N04 C05 4F2 sing 31 n n N07 C05 4F2 sing 32 n n C05 O06 4F2 doub 33 n n C10 H101 4F2 sing 34 n n C10 H102 4F2 sing 35 n n C11 H111 4F2 sing 36 n n C12 H121 4F2 sing 37 n n C12 H122 4F2 sing 38 n n C13 H131 4F2 sing 39 n n C13 H132 4F2 sing 40 n n C19 H191 4F2 sing 41 n n C20 H201 4F2 sing 42 n n C24 H241 4F2 sing 43 n n C25 H252 4F2 sing 44 n n C25 H251 4F2 sing 45 n n C26 H262 4F2 sing 46 n n C26 H261 4F2 sing 47 n n C28 H281 4F2 sing 48 n n C28 H282 4F2 sing 49 n n C01 H013 4F2 sing 50 n n C01 H012 4F2 sing 51 n n C01 H011 4F2 sing 52 n n C02 H021 4F2 sing 53 n n C03 H033 4F2 sing 54 n n C03 H031 4F2 sing 55 n n C03 H032 4F2 sing 56 n n N04 H041 4F2 sing 57 n n N07 H071 4F2 sing 58 n n C08 H081 4F2 sing 59 n n C09 H091 4F2 sing 60 n n C09 H092 4F2 sing 61 n n N14 H141 4F2 sing 62 n n C17 H171 4F2 sing 63 n n C27 H271 4F2 sing 64 n n C27 H272 4F2 sing 65 n n # _atom_sites.entry_id 4Y46 _atom_sites.fract_transf_matrix[1][1] 0.018587 _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] 0.013862 _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] 0.009264 _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 4F2 A 1 501 1 4F2 736 . C 3 HOH A 1 601 1 HOH HOH . C 3 HOH A 2 602 46 HOH HOH . C 3 HOH A 3 603 45 HOH HOH . C 3 HOH A 4 604 3 HOH HOH . C 3 HOH A 5 605 21 HOH HOH . C 3 HOH A 6 606 16 HOH HOH . C 3 HOH A 7 607 44 HOH HOH . C 3 HOH A 8 608 19 HOH HOH . C 3 HOH A 9 609 4 HOH HOH . C 3 HOH A 10 610 22 HOH HOH . C 3 HOH A 11 611 6 HOH HOH . C 3 HOH A 12 612 9 HOH HOH . C 3 HOH A 13 613 5 HOH HOH . C 3 HOH A 14 614 18 HOH HOH . C 3 HOH A 15 615 48 HOH HOH . C 3 HOH A 16 616 11 HOH HOH . C 3 HOH A 17 617 49 HOH HOH . C 3 HOH A 18 618 59 HOH HOH . C 3 HOH A 19 619 23 HOH HOH . C 3 HOH A 20 620 36 HOH HOH . C 3 HOH A 21 621 27 HOH HOH . C 3 HOH A 22 622 34 HOH HOH . C 3 HOH A 23 623 2 HOH HOH . C 3 HOH A 24 624 61 HOH HOH . C 3 HOH A 25 625 67 HOH HOH . C 3 HOH A 26 626 29 HOH HOH . C 3 HOH A 27 627 13 HOH HOH . C 3 HOH A 28 628 8 HOH HOH . C 3 HOH A 29 629 24 HOH HOH . C 3 HOH A 30 630 35 HOH HOH . C 3 HOH A 31 631 56 HOH HOH . C 3 HOH A 32 632 25 HOH HOH . C 3 HOH A 33 633 63 HOH HOH . C 3 HOH A 34 634 32 HOH HOH . C 3 HOH A 35 635 28 HOH HOH . C 3 HOH A 36 636 26 HOH HOH . C 3 HOH A 37 637 57 HOH HOH . C 3 HOH A 38 638 10 HOH HOH . C 3 HOH A 39 639 41 HOH HOH . C 3 HOH A 40 640 58 HOH HOH . C 3 HOH A 41 641 47 HOH HOH . C 3 HOH A 42 642 7 HOH HOH . C 3 HOH A 43 643 14 HOH HOH . C 3 HOH A 44 644 70 HOH HOH . C 3 HOH A 45 645 33 HOH HOH . C 3 HOH A 46 646 66 HOH HOH . C 3 HOH A 47 647 17 HOH HOH . C 3 HOH A 48 648 40 HOH HOH . C 3 HOH A 49 649 42 HOH HOH . C 3 HOH A 50 650 20 HOH HOH . C 3 HOH A 51 651 30 HOH HOH . C 3 HOH A 52 652 62 HOH HOH . C 3 HOH A 53 653 15 HOH HOH . C 3 HOH A 54 654 72 HOH HOH . C 3 HOH A 55 655 60 HOH HOH . C 3 HOH A 56 656 52 HOH HOH . C 3 HOH A 57 657 73 HOH HOH . C 3 HOH A 58 658 54 HOH HOH . C 3 HOH A 59 659 38 HOH HOH . C 3 HOH A 60 660 31 HOH HOH . C 3 HOH A 61 661 43 HOH HOH . C 3 HOH A 62 662 50 HOH HOH . C 3 HOH A 63 663 71 HOH HOH . C 3 HOH A 64 664 64 HOH HOH . C 3 HOH A 65 665 37 HOH HOH . C 3 HOH A 66 666 39 HOH HOH . C 3 HOH A 67 667 12 HOH HOH . C 3 HOH A 68 668 69 HOH HOH . C 3 HOH A 69 669 51 HOH HOH . C 3 HOH A 70 670 68 HOH HOH . C 3 HOH A 71 671 53 HOH HOH . C 3 HOH A 72 672 55 HOH HOH . C 3 HOH A 73 673 65 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 C10 4F2 . . . B 2 2.284 -30.382 -29.693 1 40.6 ? C10 4F2 501 A 1 HETATM 2 C C11 4F2 . . . B 2 2.294 -30.51 -31.2 1 39.87 ? C11 4F2 501 A 1 HETATM 3 C C12 4F2 . . . B 2 1.397 -31.72 -31.579 1 37.09 ? C12 4F2 501 A 1 HETATM 4 C C13 4F2 . . . B 2 0.005 -31.71 -30.961 1 41.58 ? C13 4F2 501 A 1 HETATM 5 C C18 4F2 . . . B 2 6.039 -27.317 -32.817 1 31.31 ? C18 4F2 501 A 1 HETATM 6 C C19 4F2 . . . B 2 6.778 -26.173 -33.165 1 34.65 ? C19 4F2 501 A 1 HETATM 7 C C20 4F2 . . . B 2 6.32 -24.907 -32.982 1 34.95 ? C20 4F2 501 A 1 HETATM 8 C C21 4F2 . . . B 2 4.995 -24.618 -32.406 1 33.98 ? C21 4F2 501 A 1 HETATM 9 C C24 4F2 . . . B 2 2.928 -25.544 -31.41 1 38.14 ? C24 4F2 501 A 1 HETATM 10 C C25 4F2 . . . B 2 2.972 -25.875 -29.873 1 39.46 ? C25 4F2 501 A 1 HETATM 11 C C26 4F2 . . . B 2 1.776 -26.724 -29.48 1 39.92 ? C26 4F2 501 A 1 HETATM 12 C C28 4F2 . . . B 2 1.692 -26.276 -31.847 1 42.27 ? C28 4F2 501 A 1 HETATM 13 C C29 4F2 . . . B 2 4.749 -27.124 -32.255 1 31.54 ? C29 4F2 501 A 1 HETATM 14 C C15 4F2 . . . B 2 4.486 -29.484 -32.047 1 33.46 ? C15 4F2 501 A 1 HETATM 15 C C01 4F2 . . . B 2 -2.542 -35.789 -29.739 1 66.95 ? C01 4F2 501 A 1 HETATM 16 C C02 4F2 . . . B 2 -3.07 -34.595 -28.893 1 64.91 ? C02 4F2 501 A 1 HETATM 17 C C03 4F2 . . . B 2 -4.557 -34.33 -29.312 1 62.13 ? C03 4F2 501 A 1 HETATM 18 N N04 4F2 . . . B 2 -2.123 -33.461 -29.041 1 62.76 ? N04 4F2 501 A 1 HETATM 19 C C05 4F2 . . . B 2 -2.367 -32.066 -28.655 1 60.4 ? C05 4F2 501 A 1 HETATM 20 O O06 4F2 . . . B 2 -3.434 -31.707 -28.158 1 63.16 ? O06 4F2 501 A 1 HETATM 21 N N07 4F2 . . . B 2 -1.36 -31.096 -28.875 1 53.22 ? N07 4F2 501 A 1 HETATM 22 C C08 4F2 . . . B 2 -0.017 -31.391 -29.448 1 46 ? C08 4F2 501 A 1 HETATM 23 C C09 4F2 . . . B 2 0.921 -30.211 -29.121 1 42.05 ? C09 4F2 501 A 1 HETATM 24 N N14 4F2 . . . B 2 3.683 -30.575 -31.71 1 37.89 ? N14 4F2 501 A 1 HETATM 25 N N16 4F2 . . . B 2 5.743 -29.692 -32.588 1 29.26 ? N16 4F2 501 A 1 HETATM 26 C C17 4F2 . . . B 2 6.441 -28.617 -32.946 1 30.32 ? C17 4F2 501 A 1 HETATM 27 O O22 4F2 . . . B 2 4.594 -23.474 -32.252 1 41.01 ? O22 4F2 501 A 1 HETATM 28 N N23 4F2 . . . B 2 4.262 -25.807 -32.076 1 33.6 ? N23 4F2 501 A 1 HETATM 29 C C27 4F2 . . . B 2 0.815 -26.37 -30.598 1 42.97 ? C27 4F2 501 A 1 HETATM 30 N N30 4F2 . . . B 2 4.013 -28.208 -31.893 1 33.97 ? N30 4F2 501 A 1 HETATM 31 H H101 4F2 . . . B 2 2.974 -29.567 -29.394 1 40.25 ? H101 4F2 501 A 1 HETATM 32 H H102 4F2 . . . B 2 2.75 -31.258 -29.207 1 41.14 ? H102 4F2 501 A 1 HETATM 33 H H111 4F2 . . . B 2 1.811 -29.606 -31.656 1 40.24 ? H111 4F2 501 A 1 HETATM 34 H H121 4F2 . . . B 2 1.278 -31.835 -32.688 1 37.33 ? H121 4F2 501 A 1 HETATM 35 H H122 4F2 . . . B 2 1.916 -32.665 -31.328 1 37.29 ? H122 4F2 501 A 1 HETATM 36 H H131 4F2 . . . B 2 -0.635 -31.01 -31.537 1 41.63 ? H131 4F2 501 A 1 HETATM 37 H H132 4F2 . . . B 2 -0.536 -32.67 -31.123 1 41.63 ? H132 4F2 501 A 1 HETATM 38 H H191 4F2 . . . B 2 7.794 -26.272 -33.614 1 35.09 ? H191 4F2 501 A 1 HETATM 39 H H201 4F2 . . . B 2 6.872 -23.974 -33.254 1 35.78 ? H201 4F2 501 A 1 HETATM 40 H H241 4F2 . . . B 2 2.592 -24.506 -31.591 1 37.96 ? H241 4F2 501 A 1 HETATM 41 H H252 4F2 . . . B 2 3.839 -26.48 -29.597 1 38.63 ? H252 4F2 501 A 1 HETATM 42 H H251 4F2 . . . B 2 2.947 -25.004 -29.233 1 39.65 ? H251 4F2 501 A 1 HETATM 43 H H262 4F2 . . . B 2 2.097 -27.786 -29.475 1 39.05 ? H262 4F2 501 A 1 HETATM 44 H H261 4F2 . . . B 2 1.457 -26.51 -28.432 1 40.27 ? H261 4F2 501 A 1 HETATM 45 H H281 4F2 . . . B 2 1.254 -25.68 -32.668 1 43.3 ? H281 4F2 501 A 1 HETATM 46 H H282 4F2 . . . B 2 2.019 -27.215 -32.303 1 42.05 ? H282 4F2 501 A 1 HETATM 47 H H013 4F2 . . . B 2 -2.908 -35.769 -30.781 1 67.17 ? H013 4F2 501 A 1 HETATM 48 H H012 4F2 . . . B 2 -1.447 -35.848 -29.817 1 66.98 ? H012 4F2 501 A 1 HETATM 49 H H011 4F2 . . . B 2 -2.876 -36.75 -29.338 1 67.24 ? H011 4F2 501 A 1 HETATM 50 H H021 4F2 . . . B 2 -3.048 -34.941 -27.842 1 65.23 ? H021 4F2 501 A 1 HETATM 51 H H033 4F2 . . . B 2 -4.723 -34.573 -30.36 1 61.8 ? H033 4F2 501 A 1 HETATM 52 H H031 4F2 . . . B 2 -4.856 -33.27 -29.214 1 61.8 ? H031 4F2 501 A 1 HETATM 53 H H032 4F2 . . . B 2 -5.334 -34.881 -28.748 1 62.02 ? H032 4F2 501 A 1 HETATM 54 H H041 4F2 . . . B 2 -1.247 -33.738 -29.442 1 62.94 ? H041 4F2 501 A 1 HETATM 55 H H071 4F2 . . . B 2 -1.462 -30.134 -28.627 1 53.1 ? H071 4F2 501 A 1 HETATM 56 H H081 4F2 . . . B 2 0.404 -32.26 -28.889 1 46.07 ? H081 4F2 501 A 1 HETATM 57 H H091 4F2 . . . B 2 0.459 -29.247 -29.447 1 41.69 ? H091 4F2 501 A 1 HETATM 58 H H092 4F2 . . . B 2 1.027 -30.048 -28.023 1 42.76 ? H092 4F2 501 A 1 HETATM 59 H H141 4F2 . . . B 2 3.978 -31.554 -31.783 1 38.3 ? H141 4F2 501 A 1 HETATM 60 H H171 4F2 . . . B 2 7.44 -28.89 -33.396 1 30.33 ? H171 4F2 501 A 1 HETATM 61 H H271 4F2 . . . B 2 0.04 -27.138 -30.718 1 43.08 ? H271 4F2 501 A 1 HETATM 62 H H272 4F2 . . . B 2 0.306 -25.442 -30.335 1 42.98 ? H272 4F2 501 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 62 #