data_5VD2 # _model_server_result.job_id BB_IA6TncyLiss3tgsbK-Q _model_server_result.datetime_utc '2024-10-18 16:27:34' _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 5vd2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 5VD2 # _exptl.entry_id 5VD2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 474.479 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-{2-[(1S,4R)-6-{[4-(cyclobutylamino)-5-(trifluoromethyl)pyrimidin-2-yl]amino}-1,2,3,4-tetrahydro-1,4-epiminonaphthalen-9-yl]-2-oxoethyl}acetamide _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 102.52 _cell.angle_gamma 90 _cell.entry_id 5VD2 _cell.length_a 50.52 _cell.length_b 45.71 _cell.length_c 59.44 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VD2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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,F _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 'C23 H25 F3 N6 O2' _chem_comp.formula_weight 474.479 _chem_comp.id 34W _chem_comp.mon_nstd_flag . _chem_comp.name N-{2-[(1S,4R)-6-{[4-(cyclobutylamino)-5-(trifluoromethyl)pyrimidin-2-yl]amino}-1,2,3,4-tetrahydro-1,4-epiminonaphthalen-9-yl]-2-oxoethyl}acetamide _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 C11 C10 34W sing 1 n n C11 C12 34W sing 2 n n C10 C09 34W sing 3 n n C12 N08 34W sing 4 n n C12 C13 34W sing 5 n n O03 C02 34W doub 6 n n N08 C09 34W sing 7 n n N08 C06 34W sing 8 n n C13 C18 34W doub 9 n y C13 C14 34W sing 10 n y C05 C06 34W sing 11 n n C05 N04 34W sing 12 n n C18 C17 34W sing 13 n y C09 C14 34W sing 14 n n C02 N04 34W sing 15 n n C02 C01 34W sing 16 n n C06 O07 34W doub 17 n n C14 C15 34W doub 18 n y C17 N19 34W sing 19 n n C17 C16 34W doub 20 n y N19 C20 34W sing 21 n n C15 C16 34W sing 22 n y N21 C20 34W doub 23 n y N21 C22 34W sing 24 n y C20 N25 34W sing 25 n y C22 C23 34W doub 26 n y N25 C24 34W doub 27 n y C23 C24 34W sing 28 n y C23 C31 34W sing 29 n n C24 N26 34W sing 30 n n F34 C31 34W sing 31 n n C30 C27 34W sing 32 n n C30 C29 34W sing 33 n n C31 F32 34W sing 34 n n C31 F33 34W sing 35 n n N26 C27 34W sing 36 n n C27 C28 34W sing 37 n n C29 C28 34W sing 38 n n C01 H1 34W sing 39 n n C01 H2 34W sing 40 n n C01 H3 34W sing 41 n n N04 H4 34W sing 42 n n C05 H5 34W sing 43 n n C05 H6 34W sing 44 n n C09 H7 34W sing 45 n n C10 H8 34W sing 46 n n C10 H9 34W sing 47 n n C11 H10 34W sing 48 n n C11 H11 34W sing 49 n n C12 H12 34W sing 50 n n C15 H13 34W sing 51 n n C16 H14 34W sing 52 n n C18 H15 34W sing 53 n n N19 H16 34W sing 54 n n C22 H17 34W sing 55 n n N26 H18 34W sing 56 n n C27 H19 34W sing 57 n n C28 H20 34W sing 58 n n C28 H21 34W sing 59 n n C29 H22 34W sing 60 n n C29 H23 34W sing 61 n n C30 H24 34W sing 62 n n C30 H25 34W sing 63 n n # _atom_sites.entry_id 5VD2 _atom_sites.fract_transf_matrix[1][1] 0.019794 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004394 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021877 _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] 0.017233 _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 34W A 1 601 1 34W 34W . C 3 PO4 A 1 602 1 PO4 PO4 . D 4 CL A 1 603 1 CL CL . E 4 CL A 1 604 2 CL CL . F 5 HOH A 1 701 41 HOH HOH . F 5 HOH A 2 702 26 HOH HOH . F 5 HOH A 3 703 38 HOH HOH . F 5 HOH A 4 704 33 HOH HOH . F 5 HOH A 5 705 5 HOH HOH . F 5 HOH A 6 706 18 HOH HOH . F 5 HOH A 7 707 39 HOH HOH . F 5 HOH A 8 708 13 HOH HOH . F 5 HOH A 9 709 8 HOH HOH . F 5 HOH A 10 710 9 HOH HOH . F 5 HOH A 11 711 7 HOH HOH . F 5 HOH A 12 712 32 HOH HOH . F 5 HOH A 13 713 23 HOH HOH . F 5 HOH A 14 714 44 HOH HOH . F 5 HOH A 15 715 12 HOH HOH . F 5 HOH A 16 716 19 HOH HOH . F 5 HOH A 17 717 25 HOH HOH . F 5 HOH A 18 718 43 HOH HOH . F 5 HOH A 19 719 15 HOH HOH . F 5 HOH A 20 720 1 HOH HOH . F 5 HOH A 21 721 11 HOH HOH . F 5 HOH A 22 722 4 HOH HOH . F 5 HOH A 23 723 34 HOH HOH . F 5 HOH A 24 724 3 HOH HOH . F 5 HOH A 25 725 17 HOH HOH . F 5 HOH A 26 726 21 HOH HOH . F 5 HOH A 27 727 6 HOH HOH . F 5 HOH A 28 728 10 HOH HOH . F 5 HOH A 29 729 2 HOH HOH . F 5 HOH A 30 730 16 HOH HOH . F 5 HOH A 31 731 45 HOH HOH . F 5 HOH A 32 732 27 HOH HOH . F 5 HOH A 33 733 31 HOH HOH . F 5 HOH A 34 734 49 HOH HOH . F 5 HOH A 35 735 35 HOH HOH . F 5 HOH A 36 736 20 HOH HOH . F 5 HOH A 37 737 14 HOH HOH . F 5 HOH A 38 738 22 HOH HOH . F 5 HOH A 39 739 37 HOH HOH . F 5 HOH A 40 740 29 HOH HOH . F 5 HOH A 41 741 28 HOH HOH . F 5 HOH A 42 742 36 HOH HOH . F 5 HOH A 43 743 42 HOH HOH . F 5 HOH A 44 744 47 HOH HOH . F 5 HOH A 45 745 30 HOH HOH . F 5 HOH A 46 746 24 HOH HOH . F 5 HOH A 47 747 40 HOH HOH . F 5 HOH A 48 748 48 HOH HOH . F 5 HOH A 49 749 46 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 C01 34W . . . B 2 -14.427 10.796 7.23 1 70.95 ? C01 34W 601 A 1 HETATM 2 C C02 34W . . . B 2 -13.28 10.437 8.086 1 70.17 ? C02 34W 601 A 1 HETATM 3 O O03 34W . . . B 2 -13.503 9.829 9.17 1 70.6 ? O03 34W 601 A 1 HETATM 4 N N04 34W . . . B 2 -12.009 10.759 7.699 1 69.51 ? N04 34W 601 A 1 HETATM 5 C C05 34W . . . B 2 -10.904 10.807 8.607 1 66.36 ? C05 34W 601 A 1 HETATM 6 C C06 34W . . . B 2 -9.621 10.303 8.041 1 62.39 ? C06 34W 601 A 1 HETATM 7 O O07 34W . . . B 2 -9.584 9.958 6.828 1 65.75 ? O07 34W 601 A 1 HETATM 8 N N08 34W . . . B 2 -8.473 10.206 8.797 1 49.59 ? N08 34W 601 A 1 HETATM 9 C C09 34W . . . B 2 -7.113 10.341 8.357 1 48.02 ? C09 34W 601 A 1 HETATM 10 C C10 34W . . . B 2 -6.665 11.684 9.03 1 44.18 ? C10 34W 601 A 1 HETATM 11 C C11 34W . . . B 2 -7.573 11.746 10.289 1 44.38 ? C11 34W 601 A 1 HETATM 12 C C12 34W . . . B 2 -8.327 10.38 10.207 1 46.83 ? C12 34W 601 A 1 HETATM 13 C C13 34W . . . B 2 -7.427 9.208 10.312 1 48.56 ? C13 34W 601 A 1 HETATM 14 C C14 34W . . . B 2 -6.662 9.185 9.144 1 47.8 ? C14 34W 601 A 1 HETATM 15 C C15 34W . . . B 2 -5.698 8.198 8.915 1 47.08 ? C15 34W 601 A 1 HETATM 16 C C16 34W . . . B 2 -5.526 7.216 9.915 1 45.59 ? C16 34W 601 A 1 HETATM 17 C C17 34W . . . B 2 -6.295 7.211 11.109 1 41.61 ? C17 34W 601 A 1 HETATM 18 C C18 34W . . . B 2 -7.258 8.233 11.306 1 42.59 ? C18 34W 601 A 1 HETATM 19 N N19 34W . . . B 2 -6.104 6.26 12.069 1 34.82 ? N19 34W 601 A 1 HETATM 20 C C20 34W . . . B 2 -5.341 5.132 12.173 1 29.5 ? C20 34W 601 A 1 HETATM 21 N N21 34W . . . B 2 -5.412 4.348 13.273 1 25.14 ? N21 34W 601 A 1 HETATM 22 C C22 34W . . . B 2 -4.688 3.223 13.422 1 23.55 ? C22 34W 601 A 1 HETATM 23 C C23 34W . . . B 2 -3.793 2.807 12.424 1 25.95 ? C23 34W 601 A 1 HETATM 24 C C24 34W . . . B 2 -3.723 3.633 11.273 1 29.04 ? C24 34W 601 A 1 HETATM 25 N N25 34W . . . B 2 -4.489 4.751 11.198 1 27.52 ? N25 34W 601 A 1 HETATM 26 N N26 34W . . . B 2 -2.896 3.337 10.237 1 33.09 ? N26 34W 601 A 1 HETATM 27 C C27 34W . . . B 2 -2.547 4.304 9.244 1 38.9 ? C27 34W 601 A 1 HETATM 28 C C28 34W . . . B 2 -3.54 4.326 8.066 1 39.82 ? C28 34W 601 A 1 HETATM 29 C C29 34W . . . B 2 -2.333 4.445 7.129 1 39.88 ? C29 34W 601 A 1 HETATM 30 C C30 34W . . . B 2 -1.499 3.782 8.238 1 40.04 ? C30 34W 601 A 1 HETATM 31 C C31 34W . . . B 2 -3.01 1.554 12.605 1 27.8 ? C31 34W 601 A 1 HETATM 32 F F32 34W . . . B 2 -1.643 1.734 12.575 1 30.76 ? F32 34W 601 A 1 HETATM 33 F F33 34W . . . B 2 -3.335 0.685 11.612 1 27.17 ? F33 34W 601 A 1 HETATM 34 F F34 34W . . . B 2 -3.286 0.942 13.789 1 27.43 ? F34 34W 601 A 1 HETATM 35 H H1 34W . . . B 2 -14.461 11.887 7.101 1 85.15 ? H1 34W 601 A 1 HETATM 36 H H2 34W . . . B 2 -14.317 10.313 6.248 1 85.15 ? H2 34W 601 A 1 HETATM 37 H H3 34W . . . B 2 -15.359 10.453 7.704 1 85.15 ? H3 34W 601 A 1 HETATM 38 H H4 34W . . . B 2 -11.889 11.175 6.798 1 83.42 ? H4 34W 601 A 1 HETATM 39 H H5 34W . . . B 2 -11.154 10.2 9.489 1 79.64 ? H5 34W 601 A 1 HETATM 40 H H6 34W . . . B 2 -10.756 11.853 8.916 1 79.64 ? H6 34W 601 A 1 HETATM 41 H H7 34W . . . B 2 -6.932 10.291 7.274 1 57.62 ? H7 34W 601 A 1 HETATM 42 H H8 34W . . . B 2 -5.601 11.654 9.308 1 53.01 ? H8 34W 601 A 1 HETATM 43 H H9 34W . . . B 2 -6.847 12.542 8.366 1 53.01 ? H9 34W 601 A 1 HETATM 44 H H10 34W . . . B 2 -8.272 12.593 10.237 1 53.26 ? H10 34W 601 A 1 HETATM 45 H H11 34W . . . B 2 -6.976 11.819 11.211 1 53.26 ? H11 34W 601 A 1 HETATM 46 H H12 34W . . . B 2 -9.245 10.332 10.811 1 56.2 ? H12 34W 601 A 1 HETATM 47 H H13 34W . . . B 2 -5.11 8.186 8.009 1 56.5 ? H13 34W 601 A 1 HETATM 48 H H14 34W . . . B 2 -4.789 6.441 9.764 1 54.72 ? H14 34W 601 A 1 HETATM 49 H H15 34W . . . B 2 -7.854 8.26 12.206 1 51.11 ? H15 34W 601 A 1 HETATM 50 H H16 34W . . . B 2 -6.653 6.428 12.888 1 41.78 ? H16 34W 601 A 1 HETATM 51 H H17 34W . . . B 2 -4.793 2.636 14.322 1 28.26 ? H17 34W 601 A 1 HETATM 52 H H18 34W . . . B 2 -2.03 3.067 10.658 1 39.71 ? H18 34W 601 A 1 HETATM 53 H H19 34W . . . B 2 -2.313 5.307 9.63 1 46.69 ? H19 34W 601 A 1 HETATM 54 H H20 34W . . . B 2 -4.125 3.403 7.944 1 47.79 ? H20 34W 601 A 1 HETATM 55 H H21 34W . . . B 2 -4.216 5.193 8.053 1 47.79 ? H21 34W 601 A 1 HETATM 56 H H22 34W . . . B 2 -2.039 5.477 6.888 1 47.86 ? H22 34W 601 A 1 HETATM 57 H H23 34W . . . B 2 -2.412 3.859 6.202 1 47.86 ? H23 34W 601 A 1 HETATM 58 H H24 34W . . . B 2 -1.435 2.686 8.171 1 48.06 ? H24 34W 601 A 1 HETATM 59 H H25 34W . . . B 2 -0.49 4.202 8.366 1 48.06 ? H25 34W 601 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 59 #