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 
# 
