data_YDF
# 
_chem_comp.id                                    YDF 
_chem_comp.name                                  "4-(2-fluoranylethyl)-1,6-dimethyl-7-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-3~{H}-1,4-benzodiazepine-2,5-dione" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C20 H21 F N2 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-11-30 
_chem_comp.pdbx_modified_date                    2024-11-15 
_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                        388.390 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YDF 
_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        8X69 
_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_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 
YDF C13 C1  C 0 1 N N N N N N 1.469  -3.389 81.557 2.380  -1.060 0.153  C13 YDF 1  
YDF C17 C2  C 0 1 N N N N N N 4.592  -5.807 81.722 6.031  0.100  0.682  C17 YDF 2  
YDF C20 C3  C 0 1 N N N N N N 1.894  -5.531 83.013 4.000  0.123  -1.412 C20 YDF 3  
YDF C24 C4  C 0 1 N N N N N N -5.878 -3.961 82.633 -4.863 -0.967 0.082  C24 YDF 4  
YDF C26 C5  C 0 1 N N N N N N -2.626 0.076  85.569 -1.937 3.555  1.171  C26 YDF 5  
YDF C01 C6  C 0 1 Y N N N N N 0.265  -2.929 82.330 1.187  -0.191 0.209  C01 YDF 6  
YDF C02 C7  C 0 1 Y N N N N N 0.551  -1.798 83.286 1.327  1.199  0.131  C02 YDF 7  
YDF C03 C8  C 0 1 Y N N N N N -0.621 -1.239 84.038 0.216  2.004  0.186  C03 YDF 8  
YDF C04 C9  C 0 1 Y N N N N N -2.020 -1.823 83.818 -1.064 1.455  0.320  C04 YDF 9  
YDF C05 C10 C 0 1 Y N N N N N -2.381 -2.930 82.855 -1.214 0.068  0.393  C05 YDF 10 
YDF C06 C11 C 0 1 Y N N N N N -1.131 -3.503 82.066 -0.079 -0.751 0.334  C06 YDF 11 
YDF C08 C12 C 0 1 N N N N N N -4.800 -1.281 84.763 -3.299 2.177  -0.221 C08 YDF 12 
YDF C09 C13 C 0 1 N N N N N N -5.368 -2.408 83.941 -3.627 0.943  -1.016 C09 YDF 13 
YDF C11 C14 C 0 1 N N N N N N -3.599 -3.410 82.682 -2.519 -0.592 0.522  C11 YDF 14 
YDF C12 C15 C 0 1 N N N N N N -1.159 -4.636 81.034 -0.232 -2.249 0.411  C12 YDF 15 
YDF C14 C16 C 0 1 N N N N N N 2.332  -4.554 81.940 3.704  -0.475 -0.105 C14 YDF 16 
YDF C16 C17 C 0 1 N N N N N N 3.556  -4.879 81.106 4.665  -0.490 0.878  C16 YDF 17 
YDF C18 C18 C 0 1 N N N N N N 4.383  -6.002 83.223 6.380  0.194  -0.802 C18 YDF 18 
YDF C19 C19 C 0 1 N N N N N N 2.967  -6.456 83.585 5.264  0.947  -1.539 C19 YDF 19 
YDF C27 C20 C 0 1 N N N N N N -6.408 -3.628 81.223 -4.949 -2.089 -0.955 C27 YDF 20 
YDF F28 F1  F 0 1 N N N N N N -6.112 -2.377 80.754 -6.133 -2.810 -0.765 F28 YDF 21 
YDF N07 N1  N 0 1 N N N N N N -3.144 -1.008 84.755 -2.124 2.337  0.379  N07 YDF 22 
YDF N10 N2  N 0 1 N N N N N N -4.827 -3.097 83.168 -3.624 -0.212 -0.118 N10 YDF 23 
YDF O15 O1  O 0 1 N N N N N N 1.734  -2.743 80.591 2.267  -2.260 0.324  O15 YDF 24 
YDF O21 O2  O 0 1 N N N N N N 3.849  -4.162 79.948 4.370  -1.054 2.059  O21 YDF 25 
YDF O22 O3  O 0 1 N N N N N N 0.768  -5.572 83.385 3.257  -0.037 -2.358 O22 YDF 26 
YDF O23 O4  O 0 1 N N N N N N -3.676 -4.309 81.927 -2.597 -1.552 1.265  O23 YDF 27 
YDF O25 O5  O 0 1 N N N N N N -5.486 -0.615 85.454 -4.133 3.053  -0.125 O25 YDF 28 
YDF H1  H1  H 0 1 N N N N N N 4.527  -6.787 81.226 6.055  1.099  1.119  H1  YDF 29 
YDF H2  H2  H 0 1 N N N N N N 5.592  -5.379 81.558 6.767  -0.527 1.184  H2  YDF 30 
YDF H3  H3  H 0 1 N N N N N N -6.730 -3.916 83.327 -5.717 -0.300 -0.033 H3  YDF 31 
YDF H4  H4  H 0 1 N N N N N N -5.482 -4.987 82.605 -4.869 -1.397 1.083  H4  YDF 32 
YDF H5  H5  H 0 1 N N N N N N -3.449 0.534  86.137 -1.532 4.343  0.535  H5  YDF 33 
YDF H6  H6  H 0 1 N N N N N N -1.873 -0.318 86.268 -2.897 3.874  1.578  H6  YDF 34 
YDF H7  H7  H 0 1 N N N N N N -2.163 0.833  84.919 -1.244 3.355  1.987  H7  YDF 35 
YDF H8  H8  H 0 1 N N N N N N 1.550  -1.410 83.422 2.308  1.639  0.027  H8  YDF 36 
YDF H9  H9  H 0 1 N N N N N N -0.478 -0.425 84.734 0.333  3.076  0.126  H9  YDF 37 
YDF H11 H11 H 0 1 N N N N N N -5.787 -3.104 84.683 -4.612 1.051  -1.468 H11 YDF 38 
YDF H12 H12 H 0 1 N N N N N N -1.017 -5.600 81.544 -0.077 -2.577 1.439  H12 YDF 39 
YDF H13 H13 H 0 1 N N N N N N -2.129 -4.635 80.515 -1.234 -2.529 0.087  H13 YDF 40 
YDF H14 H14 H 0 1 N N N N N N -0.351 -4.486 80.303 0.505  -2.723 -0.237 H14 YDF 41 
YDF H17 H17 H 0 1 N N N N N N 5.094  -6.762 83.578 7.321  0.732  -0.921 H17 YDF 42 
YDF H18 H18 H 0 1 N N N N N N 4.583  -5.047 83.730 6.478  -0.809 -1.218 H18 YDF 43 
YDF H19 H19 H 0 1 N N N N N N 2.871  -6.473 84.681 5.527  1.062  -2.590 H19 YDF 44 
YDF H20 H20 H 0 1 N N N N N N 2.808  -7.469 83.187 5.115  1.926  -1.084 H20 YDF 45 
YDF H21 H21 H 0 1 N N N N N N -5.983 -4.361 80.521 -4.943 -1.659 -1.957 H21 YDF 46 
YDF H22 H22 H 0 1 N N N N N N -7.503 -3.731 81.241 -4.095 -2.756 -0.841 H22 YDF 47 
YDF H24 H24 H 0 1 N N N N N N 3.209  -3.469 79.834 3.475  -1.403 2.167  H24 YDF 48 
YDF H10 H10 H 0 1 N N N N N N -6.186 -1.945 83.370 -2.878 0.802  -1.795 H10 YDF 49 
# 
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 
YDF C13 C01 SING N N 1  
YDF C13 C14 SING N N 2  
YDF C13 O15 DOUB N N 3  
YDF C17 C16 SING N N 4  
YDF C17 C18 SING N N 5  
YDF C20 C14 SING N N 6  
YDF C20 C19 SING N N 7  
YDF C20 O22 DOUB N N 8  
YDF C24 C27 SING N N 9  
YDF C24 N10 SING N N 10 
YDF C26 N07 SING N N 11 
YDF C01 C02 DOUB Y N 12 
YDF C01 C06 SING Y N 13 
YDF C02 C03 SING Y N 14 
YDF C03 C04 DOUB Y N 15 
YDF C04 C05 SING Y N 16 
YDF C04 N07 SING N N 17 
YDF C05 C06 DOUB Y N 18 
YDF C05 C11 SING N N 19 
YDF C06 C12 SING N N 20 
YDF C08 C09 SING N N 21 
YDF C08 O25 DOUB N N 22 
YDF C09 N10 SING N N 23 
YDF C11 N10 SING N N 24 
YDF C11 O23 DOUB N N 25 
YDF C14 C16 DOUB N N 26 
YDF C16 O21 SING N N 27 
YDF C18 C19 SING N N 28 
YDF C27 F28 SING N N 29 
YDF C17 H1  SING N N 30 
YDF C17 H2  SING N N 31 
YDF C24 H3  SING N N 32 
YDF C24 H4  SING N N 33 
YDF C26 H5  SING N N 34 
YDF C26 H6  SING N N 35 
YDF C26 H7  SING N N 36 
YDF C02 H8  SING N N 37 
YDF C03 H9  SING N N 38 
YDF C09 H11 SING N N 39 
YDF C12 H12 SING N N 40 
YDF C12 H13 SING N N 41 
YDF C12 H14 SING N N 42 
YDF C18 H17 SING N N 43 
YDF C18 H18 SING N N 44 
YDF C19 H19 SING N N 45 
YDF C19 H20 SING N N 46 
YDF C27 H21 SING N N 47 
YDF C27 H22 SING N N 48 
YDF O21 H24 SING N N 49 
YDF C08 N07 SING N N 50 
YDF C09 H10 SING N N 51 
# 
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 
YDF InChI            InChI                1.06  "InChI=1S/C20H21FN2O5/c1-11-12(19(27)18-14(24)4-3-5-15(18)25)6-7-13-17(11)20(28)23(9-8-21)10-16(26)22(13)2/h6-7,24H,3-5,8-10H2,1-2H3" 
YDF InChIKey         InChI                1.06  VBRGYJMIQKGTST-UHFFFAOYSA-N                                                                                                           
YDF SMILES_CANONICAL CACTVS               3.385 "CN1C(=O)CN(CCF)C(=O)c2c(C)c(ccc12)C(=O)C3=C(O)CCCC3=O"                                                                               
YDF SMILES           CACTVS               3.385 "CN1C(=O)CN(CCF)C(=O)c2c(C)c(ccc12)C(=O)C3=C(O)CCCC3=O"                                                                               
YDF SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(ccc2c1C(=O)N(CC(=O)N2C)CCF)C(=O)C3=C(CCCC3=O)O"                                                                                 
YDF SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1c(ccc2c1C(=O)N(CC(=O)N2C)CCF)C(=O)C3=C(CCCC3=O)O"                                                                                 
# 
_pdbx_chem_comp_identifier.comp_id           YDF 
_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        "4-(2-fluoranylethyl)-1,6-dimethyl-7-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-3~{H}-1,4-benzodiazepine-2,5-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 
YDF "Create component" 2023-11-30 PDBJ 
YDF "Initial release"  2024-11-20 RCSB 
# 
