data_Z53 # _chem_comp.id Z53 _chem_comp.name "(6S,9aS)-6-[(2S)-butan-2-yl]-4,7-bis(oxidanylidene)-8-(phenanthren-9-ylmethyl)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C31 H35 F3 N4 O3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "2-(4-(3-tert-butyl-5-(3-thiazol-2-ylureido)-1H-pyrazol-1-yl)phenyl)acetic acid" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-02-10 _chem_comp.pdbx_modified_date 2024-10-18 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 568.630 _chem_comp.one_letter_code ? _chem_comp.three_letter_code Z53 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 8I7K _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ _chem_comp.pdbx_pcm ? # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal Z53 C2 C1 C 0 1 N N N N N N 25.129 8.423 45.106 -2.680 1.215 -2.099 C2 Z53 1 Z53 C4 C2 C 0 1 N N N N N N 27.185 7.939 43.832 -0.796 2.638 -2.717 C4 Z53 2 Z53 C5 C3 C 0 1 N N N N N N 28.165 8.813 44.610 -0.565 3.991 -2.034 C5 Z53 3 Z53 C6 C4 C 0 1 N N N N N N 28.686 8.034 45.806 0.070 3.759 -0.692 C6 Z53 4 Z53 C8 C5 C 0 1 N N S N N N 28.479 6.088 47.321 0.479 2.531 1.362 C8 Z53 5 Z53 C9 C6 C 0 1 N N S N N N 27.566 6.181 48.557 -0.599 2.751 2.426 C9 Z53 6 Z53 C10 C7 C 0 1 N N N N N N 27.309 7.583 49.108 -1.280 4.101 2.190 C10 Z53 7 Z53 C11 C8 C 0 1 N N N N N N 26.244 7.505 50.192 -2.439 4.266 3.175 C11 Z53 8 Z53 C17 C9 C 0 1 N N S N N N 26.638 6.647 45.794 -0.911 1.505 -0.453 C17 Z53 9 Z53 C18 C10 C 0 1 N N N N N N 26.790 5.321 45.019 0.008 0.283 -0.539 C18 Z53 10 Z53 C20 C11 C 0 1 N N N N N N 27.304 2.910 45.509 1.365 -1.163 0.985 C20 Z53 11 Z53 C21 C12 C 0 1 Y N N N N N 25.858 2.490 45.676 2.769 -1.256 0.443 C21 Z53 12 Z53 C22 C13 C 0 1 Y N N N N N 25.334 2.288 46.952 3.467 -2.482 0.538 C22 Z53 13 Z53 C23 C14 C 0 1 Y N N N N N 26.135 2.482 48.071 2.873 -3.608 1.126 C23 Z53 14 Z53 C24 C15 C 0 1 Y N N N N N 25.615 2.300 49.353 3.570 -4.778 1.203 C24 Z53 15 Z53 C25 C16 C 0 1 Y N N N N N 24.283 1.924 49.512 4.865 -4.872 0.707 C25 Z53 16 Z53 C26 C17 C 0 1 Y N N N N N 23.474 1.732 48.394 5.471 -3.793 0.128 C26 Z53 17 Z53 C27 C18 C 0 1 Y N N N N N 23.996 1.918 47.111 4.784 -2.582 0.034 C27 Z53 18 Z53 C28 C19 C 0 1 Y N N N N N 23.181 1.724 45.991 5.395 -1.399 -0.579 C28 Z53 19 Z53 C29 C20 C 0 1 Y N N N N N 23.707 1.899 44.712 4.645 -0.203 -0.643 C29 Z53 20 Z53 C30 C21 C 0 1 Y N N N N N 25.046 2.276 44.554 3.329 -0.169 -0.126 C30 Z53 21 Z53 C31 C22 C 0 1 N N N N N N 28.415 4.666 46.810 1.065 1.155 1.516 C31 Z53 22 Z53 C35 C23 C 0 1 N N N N N N 23.860 10.420 44.602 -4.504 -0.343 -1.674 C35 Z53 23 Z53 C36 C24 C 0 1 N N N N N N 22.656 10.179 43.721 -4.964 -1.281 -0.557 C36 Z53 24 Z53 C37 C25 C 0 1 N N N N N N 21.839 9.164 43.968 -6.251 -1.989 -0.982 C37 Z53 25 Z53 C38 C26 C 0 1 N N N N N N 20.644 8.933 43.072 -6.711 -2.927 0.136 C38 Z53 26 Z53 C46 C27 C 0 1 N N N N N N 28.096 5.317 49.697 0.044 2.740 3.814 C46 Z53 27 Z53 C51 C28 C 0 1 Y N N N N N 21.845 1.353 46.145 6.691 -1.432 -1.096 C51 Z53 28 Z53 C52 C29 C 0 1 Y N N N N N 21.033 1.172 45.025 7.224 -0.308 -1.659 C52 Z53 29 Z53 C53 C30 C 0 1 Y N N N N N 21.554 1.337 43.742 6.489 0.871 -1.724 C53 Z53 30 Z53 C54 C31 C 0 1 Y N N N N N 22.889 1.707 43.597 5.221 0.934 -1.227 C54 Z53 31 Z53 F40 F1 F 0 1 N N N N N N 20.079 7.798 43.432 -5.716 -3.879 0.385 F40 Z53 32 Z53 F41 F2 F 0 1 N N N N N N 19.794 9.934 43.170 -6.949 -2.186 1.298 F41 Z53 33 Z53 F42 F3 F 0 1 N N N N N N 21.025 8.848 41.808 -7.888 -3.575 -0.253 F42 Z53 34 Z53 N3 N1 N 0 1 N N N N N N 26.221 7.710 44.892 -1.497 1.768 -1.764 N3 Z53 35 Z53 N7 N2 N 0 1 N N N N N N 27.968 6.988 46.289 -0.122 2.644 0.020 N7 Z53 36 Z53 N19 N3 N 0 1 N N N N N N 27.530 4.336 45.843 0.807 0.155 0.672 N19 Z53 37 Z53 N34 N4 N 0 1 N N N N N N 24.916 9.469 44.311 -3.271 0.335 -1.267 N34 Z53 38 Z53 O1 O1 O 0 1 N N N N N N 24.351 8.143 45.998 -3.215 1.514 -3.149 O1 Z53 39 Z53 O32 O2 O 0 1 N N N N N N 29.184 3.829 47.269 1.807 0.944 2.452 O32 Z53 40 Z53 O33 O3 O 0 1 N N N N N N 29.763 8.396 46.273 0.789 4.622 -0.234 O33 Z53 41 Z53 H1 H1 H 0 1 N N N N N N 26.743 8.471 42.976 -1.406 2.774 -3.610 H1 Z53 42 Z53 H2 H2 H 0 1 N N N N N N 27.649 7.004 43.483 0.161 2.193 -2.988 H2 Z53 43 Z53 H3 H3 H 0 1 N N N N N N 29.006 9.093 43.958 0.095 4.602 -2.649 H3 Z53 44 Z53 H4 H4 H 0 1 N N N N N N 27.652 9.722 44.958 -1.519 4.501 -1.903 H4 Z53 45 Z53 H5 H5 H 0 1 N N N N N N 29.511 6.349 47.597 1.263 3.279 1.477 H5 Z53 46 Z53 H6 H6 H 0 1 N N N N N N 26.590 5.766 48.265 -1.340 1.954 2.362 H6 Z53 47 Z53 H7 H7 H 0 1 N N N N N N 28.239 7.987 49.534 -0.557 4.903 2.341 H7 Z53 48 Z53 H8 H8 H 0 1 N N N N N N 26.961 8.239 48.297 -1.661 4.142 1.170 H8 Z53 49 Z53 H9 H9 H 0 1 N N N N N N 26.054 8.511 50.593 -2.058 4.225 4.195 H9 Z53 50 Z53 H10 H10 H 0 1 N N N N N N 25.315 7.099 49.765 -2.924 5.228 3.007 H10 Z53 51 Z53 H11 H11 H 0 1 N N N N N N 26.593 6.847 51.002 -3.161 3.464 3.024 H11 Z53 52 Z53 H12 H12 H 0 1 N N N N N N 25.924 6.521 46.621 -1.714 1.302 0.256 H12 Z53 53 Z53 H13 H13 H 0 1 N N N N N N 25.793 4.922 44.781 -0.598 -0.614 -0.667 H13 Z53 54 Z53 H14 H14 H 0 1 N N N N N N 27.343 5.505 44.086 0.672 0.392 -1.398 H14 Z53 55 Z53 H15 H15 H 0 1 N N N N N N 27.928 2.291 46.170 0.748 -1.937 0.528 H15 Z53 56 Z53 H16 H16 H 0 1 N N N N N N 27.600 2.743 44.463 1.383 -1.303 2.066 H16 Z53 57 Z53 H17 H17 H 0 1 N N N N N N 27.167 2.776 47.948 1.868 -3.549 1.516 H17 Z53 58 Z53 H18 H18 H 0 1 N N N N N N 26.243 2.450 50.219 3.109 -5.643 1.657 H18 Z53 59 Z53 H19 H19 H 0 1 N N N N N N 23.877 1.781 50.503 5.398 -5.808 0.780 H19 Z53 60 Z53 H20 H20 H 0 1 N N N N N N 22.442 1.439 48.519 6.477 -3.877 -0.255 H20 Z53 61 Z53 H21 H21 H 0 1 N N N N N N 25.455 2.403 43.563 2.764 0.750 -0.180 H21 Z53 62 Z53 H22 H22 H 0 1 N N N N N N 24.235 11.439 44.427 -4.319 -0.920 -2.580 H22 Z53 63 Z53 H23 H23 H 0 1 N N N N N N 23.562 10.315 45.656 -5.280 0.398 -1.868 H23 Z53 64 Z53 H24 H24 H 0 1 N N N N N N 23.036 10.038 42.698 -4.188 -2.022 -0.363 H24 Z53 65 Z53 H25 H25 H 0 1 N N N N N N 21.451 9.307 44.987 -7.027 -1.248 -1.176 H25 Z53 66 Z53 H26 H26 H 0 1 N N N N N N 27.426 5.403 50.565 0.848 3.475 3.848 H26 Z53 67 Z53 H27 H27 H 0 1 N N N N N N 28.141 4.267 49.371 -0.707 2.986 4.564 H27 Z53 68 Z53 H28 H28 H 0 1 N N N N N N 29.104 5.658 49.977 0.450 1.749 4.018 H28 Z53 69 Z53 H29 H29 H 0 1 N N N N N N 21.438 1.205 47.134 7.271 -2.343 -1.051 H29 Z53 70 Z53 H30 H30 H 0 1 N N N N N N 19.995 0.903 45.152 8.227 -0.334 -2.059 H30 Z53 71 Z53 H31 H31 H 0 1 N N N N N N 20.931 1.180 42.874 6.930 1.748 -2.173 H31 Z53 72 Z53 H32 H32 H 0 1 N N N N N N 23.297 1.847 42.607 4.662 1.856 -1.284 H32 Z53 73 Z53 H33 H33 H 0 1 N N N N N N 25.491 9.601 43.503 -2.881 0.151 -0.398 H33 Z53 74 Z53 H34 H34 H 0 1 N N N N N N 22.046 11.093 43.762 -5.149 -0.704 0.349 H34 Z53 75 Z53 H35 H35 H 0 1 N N N N N N 22.447 8.248 43.932 -6.066 -2.567 -1.888 H35 Z53 76 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal Z53 F42 C38 SING N N 1 Z53 C38 F41 SING N N 2 Z53 C38 F40 SING N N 3 Z53 C38 C37 SING N N 4 Z53 C54 C53 DOUB Y N 5 Z53 C54 C29 SING Y N 6 Z53 C36 C37 SING N N 7 Z53 C36 C35 SING N N 8 Z53 C53 C52 SING Y N 9 Z53 C4 C5 SING N N 10 Z53 C4 N3 SING N N 11 Z53 N34 C35 SING N N 12 Z53 N34 C2 SING N N 13 Z53 C30 C29 DOUB Y N 14 Z53 C30 C21 SING Y N 15 Z53 C5 C6 SING N N 16 Z53 C29 C28 SING Y N 17 Z53 N3 C2 SING N N 18 Z53 N3 C17 SING N N 19 Z53 C18 C17 SING N N 20 Z53 C18 N19 SING N N 21 Z53 C52 C51 DOUB Y N 22 Z53 C2 O1 DOUB N N 23 Z53 C20 C21 SING N N 24 Z53 C20 N19 SING N N 25 Z53 C21 C22 DOUB Y N 26 Z53 C17 N7 SING N N 27 Z53 C6 O33 DOUB N N 28 Z53 C6 N7 SING N N 29 Z53 N19 C31 SING N N 30 Z53 C28 C51 SING Y N 31 Z53 C28 C27 DOUB Y N 32 Z53 N7 C8 SING N N 33 Z53 C31 O32 DOUB N N 34 Z53 C31 C8 SING N N 35 Z53 C22 C27 SING Y N 36 Z53 C22 C23 SING Y N 37 Z53 C27 C26 SING Y N 38 Z53 C8 C9 SING N N 39 Z53 C23 C24 DOUB Y N 40 Z53 C26 C25 DOUB Y N 41 Z53 C9 C10 SING N N 42 Z53 C9 C46 SING N N 43 Z53 C10 C11 SING N N 44 Z53 C24 C25 SING Y N 45 Z53 C4 H1 SING N N 46 Z53 C4 H2 SING N N 47 Z53 C5 H3 SING N N 48 Z53 C5 H4 SING N N 49 Z53 C8 H5 SING N N 50 Z53 C9 H6 SING N N 51 Z53 C10 H7 SING N N 52 Z53 C10 H8 SING N N 53 Z53 C11 H9 SING N N 54 Z53 C11 H10 SING N N 55 Z53 C11 H11 SING N N 56 Z53 C17 H12 SING N N 57 Z53 C18 H13 SING N N 58 Z53 C18 H14 SING N N 59 Z53 C20 H15 SING N N 60 Z53 C20 H16 SING N N 61 Z53 C23 H17 SING N N 62 Z53 C24 H18 SING N N 63 Z53 C25 H19 SING N N 64 Z53 C26 H20 SING N N 65 Z53 C30 H21 SING N N 66 Z53 C35 H22 SING N N 67 Z53 C35 H23 SING N N 68 Z53 C36 H24 SING N N 69 Z53 C37 H25 SING N N 70 Z53 C46 H26 SING N N 71 Z53 C46 H27 SING N N 72 Z53 C46 H28 SING N N 73 Z53 C51 H29 SING N N 74 Z53 C52 H30 SING N N 75 Z53 C53 H31 SING N N 76 Z53 C54 H32 SING N N 77 Z53 N34 H33 SING N N 78 Z53 C36 H34 SING N N 79 Z53 C37 H35 SING N N 80 # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor Z53 InChI InChI 1.06 "InChI=1S/C31H35F3N4O3/c1-3-20(2)28-29(40)36(18-22-17-21-9-4-5-10-23(21)25-12-7-6-11-24(22)25)19-26-37(16-13-27(39)38(26)28)30(41)35-15-8-14-31(32,33)34/h4-7,9-12,17,20,26,28H,3,8,13-16,18-19H2,1-2H3,(H,35,41)/t20-,26+,28-/m0/s1" Z53 InChIKey InChI 1.06 LRRHDBKPDZEZJJ-GFNGZDJJSA-N Z53 SMILES_CANONICAL CACTVS 3.385 "CC[C@H](C)[C@@H]1N2[C@H](CN(Cc3cc4ccccc4c5ccccc35)C1=O)N(CCC2=O)C(=O)NCCCC(F)(F)F" Z53 SMILES CACTVS 3.385 "CC[CH](C)[CH]1N2[CH](CN(Cc3cc4ccccc4c5ccccc35)C1=O)N(CCC2=O)C(=O)NCCCC(F)(F)F" Z53 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC[C@H](C)[C@H]1C(=O)N(C[C@H]2N1C(=O)CCN2C(=O)NCCCC(F)(F)F)Cc3cc4ccccc4c5c3cccc5" Z53 SMILES "OpenEye OEToolkits" 2.0.7 "CCC(C)C1C(=O)N(CC2N1C(=O)CCN2C(=O)NCCCC(F)(F)F)Cc3cc4ccccc4c5c3cccc5" # _pdbx_chem_comp_identifier.comp_id Z53 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "(6~{S},9~{a}~{S})-6-[(2~{S})-butan-2-yl]-4,7-bis(oxidanylidene)-8-(phenanthren-9-ylmethyl)-~{N}-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9~{a}-tetrahydro-2~{H}-pyrazino[1,2-a]pyrimidine-1-carboxamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site Z53 "Create component" 2023-02-10 PDBJ Z53 "Initial release" 2024-10-23 RCSB #