data_A1D9M
# 
_chem_comp.id                                    A1D9M 
_chem_comp.name                                  "5-ethyl-1-[[3-[(3~{R})-4-ethyl-3-(2-hydroxyethyl)piperazin-1-yl]carbonyl-4-fluoranyl-phenyl]methyl]pyrimidine-2,4-dione" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C22 H29 F N4 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-07-02 
_chem_comp.pdbx_modified_date                    2025-07-04 
_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                        432.488 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1D9M 
_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        9ILN 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBC 
_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_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_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 
A1D9M C10 C1  C 0 1 Y N N N N N -36.592 5.126 -11.371 0.214  3.309  -0.708 C10 A1D9M 1  
A1D9M C13 C2  C 0 1 N N N N N N -38.053 3.302 -10.341 1.808  1.924  0.617  C13 A1D9M 2  
A1D9M C15 C3  C 0 1 N N N N N N -39.814 4.996 -10.750 1.101  -0.413 0.386  C15 A1D9M 3  
A1D9M C17 C4  C 0 1 N N R N N N -41.515 2.921 -9.598  3.912  -0.789 -0.271 C17 A1D9M 4  
A1D9M C20 C5  C 0 1 N N N N N N -42.243 2.298 -7.254  6.327  -0.255 0.084  C20 A1D9M 5  
A1D9M C21 C6  C 0 1 N N N N N N -42.726 4.405 -11.111 3.358  -2.909 -1.302 C21 A1D9M 6  
A1D9M C22 C7  C 0 1 N N N N N N -43.463 5.720 -11.297 2.538  -4.181 -1.076 C22 A1D9M 7  
A1D9M C01 C8  C 0 1 N N N N N N -32.946 2.602 -6.322  -3.433 -1.937 0.338  C01 A1D9M 8  
A1D9M C02 C9  C 0 1 N N N N N N -33.211 3.711 -7.043  -3.021 -0.828 0.991  C02 A1D9M 9  
A1D9M C03 C10 C 0 1 N N N N N N -35.276 4.180 -5.907  -4.490 0.489  -0.298 C03 A1D9M 10 
A1D9M C04 C11 C 0 1 N N N N N N -33.904 2.212 -5.298  -4.415 -1.815 -0.674 C04 A1D9M 11 
A1D9M C05 C12 C 0 1 N N N N N N -31.736 1.727 -6.498  -2.849 -3.284 0.678  C05 A1D9M 12 
A1D9M C06 C13 C 0 1 N N N N N N -30.866 2.116 -7.682  -3.754 -3.991 1.690  C06 A1D9M 13 
A1D9M C07 C14 C 0 1 Y N N N N N -35.264 5.476 -8.984  -1.936 2.194  0.647  C07 A1D9M 14 
A1D9M C08 C15 C 0 1 Y N N N N N -34.919 6.238 -10.102 -2.148 3.136  -0.344 C08 A1D9M 15 
A1D9M C09 C16 C 0 1 Y N N N N N -35.584 6.067 -11.309 -1.077 3.696  -1.015 C09 A1D9M 16 
A1D9M C11 C17 C 0 1 Y N N N N N -36.973 4.349 -10.287 0.433  2.348  0.285  C11 A1D9M 17 
A1D9M C12 C18 C 0 1 Y N N N N N -36.283 4.531 -9.089  -0.655 1.793  0.962  C12 A1D9M 18 
A1D9M C14 C19 C 0 1 N N N N N N -34.527 5.689 -7.686  -3.111 1.590  1.373  C14 A1D9M 19 
A1D9M C16 C20 C 0 1 N N N N N N -40.929 5.288 -9.756  1.596  -1.355 -0.717 C16 A1D9M 20 
A1D9M C18 C21 C 0 1 N N N N N N -40.424 2.637 -10.631 3.512  0.176  0.850  C18 A1D9M 21 
A1D9M C19 C22 C 0 1 N N N N N N -41.067 2.610 -8.162  5.291  -1.380 0.031  C19 A1D9M 22 
A1D9M F01 F1  F 0 1 N N N N N N -37.238 4.957 -12.536 1.260  3.852  -1.368 F01 A1D9M 23 
A1D9M N01 N1  N 0 1 N N N N N N -34.332 4.491 -6.857  -3.557 0.388  0.665  N01 A1D9M 24 
A1D9M N02 N2  N 0 1 N N N N N N -35.005 3.045 -5.178  -4.919 -0.599 -0.965 N02 A1D9M 25 
A1D9M N03 N3  N 0 1 N N N N N N -39.346 3.620 -10.560 2.128  0.615  0.618  N03 A1D9M 26 
A1D9M N04 N4  N 0 1 N N N N N N -42.005 4.290 -9.837  2.923  -1.872 -0.357 N04 A1D9M 27 
A1D9M O01 O1  O 0 1 N N N N N N -33.787 1.231 -4.576  -4.802 -2.801 -1.276 O01 A1D9M 28 
A1D9M O02 O2  O 0 1 N N N N N N -36.282 4.843 -5.707  -4.954 1.580  -0.571 O02 A1D9M 29 
A1D9M O03 O3  O 0 1 N N N N N N -37.717 2.128 -10.187 2.652  2.756  0.889  O03 A1D9M 30 
A1D9M O04 O4  O 0 1 N N N N N N -41.974 2.879 -5.977  7.600  -0.797 0.441  O04 A1D9M 31 
A1D9M H14 H1  H 0 1 N N N N N N -38.981 5.694 -10.583 0.172  0.062  0.072  H14 A1D9M 32 
A1D9M H13 H2  H 0 1 N N N N N N -40.194 5.117 -11.775 0.932  -0.979 1.302  H13 A1D9M 33 
A1D9M H17 H3  H 0 1 N N N N N N -42.345 2.235 -9.822  3.946  -0.251 -1.219 H17 A1D9M 34 
A1D9M H22 H4  H 0 1 N N N N N N -43.164 2.727 -7.674  6.396  0.221  -0.894 H22 A1D9M 35 
A1D9M H23 H5  H 0 1 N N N N N N -42.359 1.209 -7.153  6.024  0.483  0.827  H23 A1D9M 36 
A1D9M H25 H6  H 0 1 N N N N N N -41.998 4.299 -11.929 4.415  -3.125 -1.143 H25 A1D9M 37 
A1D9M H24 H7  H 0 1 N N N N N N -43.460 3.588 -11.166 3.209  -2.557 -2.322 H24 A1D9M 38 
A1D9M H27 H8  H 0 1 N N N N N N -43.972 5.721 -12.272 2.688  -4.534 -0.056 H27 A1D9M 39 
A1D9M H28 H9  H 0 1 N N N N N N -44.206 5.840 -10.495 1.482  -3.965 -1.235 H28 A1D9M 40 
A1D9M H26 H10 H 0 1 N N N N N N -42.744 6.552 -11.258 2.862  -4.951 -1.777 H26 A1D9M 41 
A1D9M H01 H11 H 0 1 N N N N N N -32.506 4.004 -7.807  -2.273 -0.902 1.766  H01 A1D9M 42 
A1D9M H04 H12 H 0 1 N N N N N N -31.127 1.789 -5.584  -2.776 -3.887 -0.226 H04 A1D9M 43 
A1D9M H03 H13 H 0 1 N N N N N N -32.075 0.691 -6.642  -1.857 -3.152 1.109  H03 A1D9M 44 
A1D9M H07 H14 H 0 1 N N N N N N -30.005 1.434 -7.745  -3.827 -3.387 2.595  H07 A1D9M 45 
A1D9M H05 H15 H 0 1 N N N N N N -31.456 2.049 -8.608  -4.746 -4.123 1.260  H05 A1D9M 46 
A1D9M H06 H16 H 0 1 N N N N N N -30.507 3.147 -7.550  -3.332 -4.965 1.936  H06 A1D9M 47 
A1D9M H08 H17 H 0 1 N N N N N N -34.127 6.968 -10.027 -3.155 3.446  -0.585 H08 A1D9M 48 
A1D9M H09 H18 H 0 1 N N N N N N -35.320 6.654 -12.176 -1.250 4.438  -1.781 H09 A1D9M 49 
A1D9M H10 H19 H 0 1 N N N N N N -36.542 3.931 -8.229  -0.493 1.058  1.736  H10 A1D9M 50 
A1D9M H11 H20 H 0 1 N N N N N N -35.094 6.422 -7.092  -2.814 1.325  2.388  H11 A1D9M 51 
A1D9M H12 H21 H 0 1 N N N N N N -33.535 6.099 -7.925  -3.926 2.313  1.410  H12 A1D9M 52 
A1D9M H16 H22 H 0 1 N N N N N N -40.511 5.279 -8.739  0.899  -2.185 -0.826 H16 A1D9M 53 
A1D9M H15 H23 H 0 1 N N N N N N -41.348 6.282 -9.972  1.662  -0.809 -1.659 H15 A1D9M 54 
A1D9M H18 H24 H 0 1 N N N N N N -40.868 2.667 -11.637 3.578  -0.333 1.812  H18 A1D9M 55 
A1D9M H19 H25 H 0 1 N N N N N N -40.007 1.636 -10.444 4.178  1.038  0.846  H19 A1D9M 56 
A1D9M H21 H26 H 0 1 N N N N N N -40.393 1.741 -8.181  5.263  -1.894 0.992  H21 A1D9M 57 
A1D9M H20 H27 H 0 1 N N N N N N -40.530 3.482 -7.761  5.562  -2.087 -0.752 H20 A1D9M 58 
A1D9M H02 H28 H 0 1 N N N N N N -35.678 2.793 -4.483  -5.593 -0.508 -1.656 H02 A1D9M 59 
A1D9M H29 H30 H 0 1 N N N N N N -42.697 2.698 -5.388  8.307  -0.139 0.493  H29 A1D9M 60 
# 
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 
A1D9M C01 C02 DOUB N N 1  
A1D9M C01 C04 SING N N 2  
A1D9M C01 C05 SING N N 3  
A1D9M C02 N01 SING N N 4  
A1D9M N01 C03 SING N N 5  
A1D9M N01 C14 SING N N 6  
A1D9M C03 N02 SING N N 7  
A1D9M C03 O02 DOUB N N 8  
A1D9M N02 C04 SING N N 9  
A1D9M C04 O01 DOUB N N 10 
A1D9M C05 C06 SING N N 11 
A1D9M C07 C08 DOUB Y N 12 
A1D9M C07 C12 SING Y N 13 
A1D9M C07 C14 SING N N 14 
A1D9M C08 C09 SING Y N 15 
A1D9M C09 C10 DOUB Y N 16 
A1D9M C10 C11 SING Y N 17 
A1D9M C10 F01 SING N N 18 
A1D9M C11 C12 DOUB Y N 19 
A1D9M C11 C13 SING N N 20 
A1D9M C13 O03 DOUB N N 21 
A1D9M C13 N03 SING N N 22 
A1D9M N03 C15 SING N N 23 
A1D9M N03 C18 SING N N 24 
A1D9M C15 C16 SING N N 25 
A1D9M C16 N04 SING N N 26 
A1D9M N04 C17 SING N N 27 
A1D9M N04 C21 SING N N 28 
A1D9M C17 C18 SING N N 29 
A1D9M C17 C19 SING N N 30 
A1D9M C19 C20 SING N N 31 
A1D9M C20 O04 SING N N 32 
A1D9M C21 C22 SING N N 33 
A1D9M C15 H14 SING N N 34 
A1D9M C15 H13 SING N N 35 
A1D9M C17 H17 SING N N 36 
A1D9M C20 H22 SING N N 37 
A1D9M C20 H23 SING N N 38 
A1D9M C21 H25 SING N N 39 
A1D9M C21 H24 SING N N 40 
A1D9M C22 H27 SING N N 41 
A1D9M C22 H28 SING N N 42 
A1D9M C22 H26 SING N N 43 
A1D9M C02 H01 SING N N 44 
A1D9M C05 H04 SING N N 45 
A1D9M C05 H03 SING N N 46 
A1D9M C06 H07 SING N N 47 
A1D9M C06 H05 SING N N 48 
A1D9M C06 H06 SING N N 49 
A1D9M C08 H08 SING N N 50 
A1D9M C09 H09 SING N N 51 
A1D9M C12 H10 SING N N 52 
A1D9M C14 H11 SING N N 53 
A1D9M C14 H12 SING N N 54 
A1D9M C16 H16 SING N N 55 
A1D9M C16 H15 SING N N 56 
A1D9M C18 H18 SING N N 57 
A1D9M C18 H19 SING N N 58 
A1D9M C19 H21 SING N N 59 
A1D9M C19 H20 SING N N 60 
A1D9M N02 H02 SING N N 61 
A1D9M O04 H29 SING N N 62 
# 
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 
A1D9M InChI            InChI                1.06  "InChI=1S/C22H29FN4O4/c1-3-16-13-27(22(31)24-20(16)29)12-15-5-6-19(23)18(11-15)21(30)26-9-8-25(4-2)17(14-26)7-10-28/h5-6,11,13,17,28H,3-4,7-10,12,14H2,1-2H3,(H,24,29,31)/t17-/m0/s1" 
A1D9M InChIKey         InChI                1.06  LLSYINGLAVMEEM-KRWDZBQOSA-N                                                                                                                                                           
A1D9M SMILES_CANONICAL CACTVS               3.385 "CCN1CCN(C[C@H]1CCO)C(=O)c2cc(CN3C=C(CC)C(=O)NC3=O)ccc2F"                                                                                                                             
A1D9M SMILES           CACTVS               3.385 "CCN1CCN(C[CH]1CCO)C(=O)c2cc(CN3C=C(CC)C(=O)NC3=O)ccc2F"                                                                                                                              
A1D9M SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCC1=CN(C(=O)NC1=O)Cc2ccc(c(c2)C(=O)N3CCN([C@@H](C3)CCO)CC)F"                                                                                                                        
A1D9M SMILES           "OpenEye OEToolkits" 2.0.7 "CCC1=CN(C(=O)NC1=O)Cc2ccc(c(c2)C(=O)N3CCN(C(C3)CCO)CC)F"                                                                                                                             
# 
_pdbx_chem_comp_identifier.comp_id           A1D9M 
_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        "5-ethyl-1-[[3-[(3~{R})-4-ethyl-3-(2-hydroxyethyl)piperazin-1-yl]carbonyl-4-fluoranyl-phenyl]methyl]pyrimidine-2,4-dione" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1D9M "Create component" 2024-07-02 PDBC 
A1D9M "Initial release"  2025-07-09 RCSB 
# 
