data_YDH
# 
_chem_comp.id                                    YDH 
_chem_comp.name                                  "1-[2-(cyclohexylmethyl)-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl]-N-[(4-methyl-1,2,5-oxadiazol-3-yl)methyl]piperidine-4-carboxamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C25 H31 N5 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-06-13 
_chem_comp.pdbx_modified_date                    2024-12-13 
_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                        465.545 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YDH 
_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        7G5G 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_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 
YDH C02 C1  C 0 1 N N N N N N -12.089 7.642  44.653 -2.940 0.626  -0.613 C02 YDH 1  
YDH C04 C2  C 0 1 N N N N N N -11.091 7.923  42.607 -4.050 1.783  0.920  C04 YDH 2  
YDH C05 C3  C 0 1 Y N N N N N -10.772 9.080  43.422 -2.625 2.124  1.108  C05 YDH 3  
YDH C06 C4  C 0 1 Y N N N N N -16.558 13.168 47.931 6.555  -0.589 0.411  C06 YDH 4  
YDH C07 C5  C 0 1 Y N N N N N -11.208 9.943  45.622 -0.533 1.482  0.060  C07 YDH 5  
YDH O08 O1  O 0 1 Y N N N N N -16.938 12.902 45.871 8.187  -2.018 0.728  O08 YDH 6  
YDH N09 N1  N 0 1 Y N N N N N -16.861 12.244 47.071 7.605  -1.087 -0.171 N09 YDH 7  
YDH C13 C6  C 0 1 N N N N N N -14.134 11.778 49.381 3.606  0.485  -1.545 C13 YDH 8  
YDH C18 C7  C 0 1 N N N N N N -16.324 12.944 49.387 5.631  0.439  -0.191 C18 YDH 9  
YDH C19 C8  C 0 1 N N N N N N -13.497 10.440 49.184 2.500  -0.212 -2.295 C19 YDH 10 
YDH C20 C9  C 0 1 N N N N N N -11.360 10.890 47.934 0.918  1.651  -1.786 C20 YDH 11 
YDH C21 C10 C 0 1 N N N N N N -12.948 9.077  47.137 1.059  -0.222 -0.255 C21 YDH 12 
YDH C23 C11 C 0 1 N N N N N N -11.952 10.505 49.291 1.561  0.831  -2.907 C23 YDH 13 
YDH C24 C12 C 0 1 N N N N N N -13.993 9.937  47.818 1.707  -1.098 -1.330 C24 YDH 14 
YDH C25 C13 C 0 1 Y N N N N N -10.001 10.188 43.080 -1.934 2.953  1.974  C25 YDH 15 
YDH C26 C14 C 0 1 Y N N N N N -10.397 11.052 45.306 0.145  2.318  0.950  C26 YDH 16 
YDH C27 C15 C 0 1 N N N N N N -11.038 4.733  43.072 -5.716 -0.948 0.170  C27 YDH 17 
YDH C28 C16 C 0 1 N N N N N N -16.037 15.692 47.938 5.314  -0.841 2.671  C28 YDH 18 
YDH N01 N2  N 0 1 N N N N N N -11.867 7.035  43.404 -4.150 0.911  -0.099 N01 YDH 19 
YDH C03 C17 C 0 1 Y N N N N N -11.380 8.929  44.669 -1.921 1.382  0.135  C03 YDH 20 
YDH N10 N3  N 0 1 N N N N N N -11.768 9.907  46.901 0.170  0.758  -0.891 N10 YDH 21 
YDH N11 N4  N 0 1 Y N N N N N -16.658 14.230 46.002 7.374  -2.013 1.891  N11 YDH 22 
YDH C12 C18 C 0 1 Y N N N N N -16.415 14.398 47.272 6.412  -1.163 1.689  C12 YDH 23 
YDH C14 C19 C 0 1 N N N N N N -12.257 5.676  42.996 -5.411 0.346  -0.586 C14 YDH 24 
YDH N15 N5  N 0 1 N N N N N N -15.504 11.729 49.454 4.556  -0.238 -0.920 N15 YDH 25 
YDH O16 O2  O 0 1 N N N N N N -12.653 6.990  45.505 -2.723 -0.133 -1.536 O16 YDH 26 
YDH O17 O3  O 0 1 N N N N N N -10.796 7.673  41.450 -4.977 2.223  1.572  O17 YDH 27 
YDH O22 O4  O 0 1 N N N N N N -13.512 12.848 49.473 3.640  1.696  -1.503 O22 YDH 28 
YDH C29 C20 C 0 1 Y N N N N N -9.815  11.177 44.046 -0.552 3.052  1.885  C29 YDH 29 
YDH C30 C21 C 0 1 N N N N N N -10.855 4.168  44.489 -7.091 -1.472 -0.249 C30 YDH 30 
YDH C31 C22 C 0 1 N N N N N N -11.225 3.583  42.069 -4.650 -1.995 -0.160 C31 YDH 31 
YDH C32 C23 C 0 1 N N N N N N -10.185 2.461  42.178 -4.955 -3.289 0.596  C32 YDH 32 
YDH C33 C24 C 0 1 N N N N N N -9.688  3.175  44.488 -7.396 -2.767 0.507  C33 YDH 33 
YDH C34 C25 C 0 1 N N N N N N -10.009 1.964  43.611 -6.330 -3.813 0.177  C34 YDH 34 
YDH H38 H1  H 0 1 N N N N N N -15.789 13.797 49.829 5.202  1.051  0.603  H38 YDH 35 
YDH H39 H2  H 0 1 N N N N N N -17.278 12.797 49.914 6.192  1.074  -0.877 H39 YDH 36 
YDH H40 H3  H 0 1 N N N N N N -13.866 9.753  49.960 2.928  -0.826 -3.087 H40 YDH 37 
YDH H42 H4  H 0 1 N N N N N N -10.263 10.906 48.007 1.694  2.165  -1.220 H42 YDH 38 
YDH H41 H5  H 0 1 N N N N N N -11.723 11.889 47.649 0.237  2.385  -2.218 H41 YDH 39 
YDH H44 H6  H 0 1 N N N N N N -13.339 8.702  46.180 0.482  -0.849 0.424  H44 YDH 40 
YDH H43 H7  H 0 1 N N N N N N -12.684 8.227  47.784 1.836  0.301  0.303  H43 YDH 41 
YDH H45 H8  H 0 1 N N N N N N -11.668 11.258 50.041 2.128  1.492  -3.562 H45 YDH 42 
YDH H46 H9  H 0 1 N N N N N N -11.564 9.521  49.594 0.783  0.328  -3.482 H46 YDH 43 
YDH H47 H10 H 0 1 N N N N N N -14.907 9.342  47.965 0.932  -1.632 -1.880 H47 YDH 44 
YDH H48 H11 H 0 1 N N N N N N -14.218 10.802 47.177 2.379  -1.816 -0.859 H48 YDH 45 
YDH H49 H12 H 0 1 N N N N N N -9.561  10.279 42.098 -2.470 3.523  2.719  H49 YDH 46 
YDH H50 H13 H 0 1 N N N N N N -10.224 11.815 46.051 1.221  2.400  0.897  H50 YDH 47 
YDH H51 H14 H 0 1 N N N N N N -10.136 5.299  42.797 -5.713 -0.752 1.242  H51 YDH 48 
YDH H52 H15 H 0 1 N N N N N N -15.994 16.493 47.186 4.472  -1.513 2.506  H52 YDH 49 
YDH H54 H16 H 0 1 N N N N N N -16.789 15.945 48.700 5.687  -0.968 3.687  H54 YDH 50 
YDH H53 H17 H 0 1 N N N N N N -15.052 15.584 48.416 4.990  0.190  2.528  H53 YDH 51 
YDH H35 H18 H 0 1 N N N N N N -13.046 5.306  43.667 -5.326 0.133  -1.652 H35 YDH 52 
YDH H36 H19 H 0 1 N N N N N N -12.635 5.700  41.963 -6.217 1.061  -0.422 H36 YDH 53 
YDH H37 H20 H 0 1 N N N N N N -15.955 10.842 49.555 4.529  -1.207 -0.954 H37 YDH 54 
YDH H55 H21 H 0 1 N N N N N N -9.216  12.046 43.816 -0.018 3.701  2.564  H55 YDH 55 
YDH H56 H22 H 0 1 N N N N N N -10.639 4.990  45.188 -7.851 -0.726 -0.014 H56 YDH 56 
YDH H57 H23 H 0 1 N N N N N N -11.776 3.654  44.802 -7.094 -1.668 -1.321 H57 YDH 57 
YDH H58 H24 H 0 1 N N N N N N -12.220 3.144  42.233 -4.653 -2.191 -1.232 H58 YDH 58 
YDH H59 H25 H 0 1 N N N N N N -11.171 4.002  41.053 -3.670 -1.622 0.138  H59 YDH 59 
YDH H61 H26 H 0 1 N N N N N N -10.508 1.618  41.549 -4.195 -4.035 0.361  H61 YDH 60 
YDH H60 H27 H 0 1 N N N N N N -9.218  2.840  41.815 -4.952 -3.093 1.668  H60 YDH 61 
YDH H63 H28 H 0 1 N N N N N N -8.789  3.675  44.098 -7.393 -2.571 1.579  H63 YDH 62 
YDH H62 H29 H 0 1 N N N N N N -9.502  2.836  45.518 -8.376 -3.140 0.208  H62 YDH 63 
YDH H65 H30 H 0 1 N N N N N N -10.937 1.486  43.958 -6.333 -4.009 -0.895 H65 YDH 64 
YDH H64 H31 H 0 1 N N N N N N -9.183  1.239  43.657 -6.547 -4.735 0.715  H64 YDH 65 
# 
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 
YDH N01 C02 SING N N 1  
YDH N01 C04 SING N N 2  
YDH N01 C14 SING N N 3  
YDH C02 C03 SING N N 4  
YDH C02 O16 DOUB N N 5  
YDH C03 C05 DOUB Y N 6  
YDH C03 C07 SING Y N 7  
YDH C04 C05 SING N N 8  
YDH C04 O17 DOUB N N 9  
YDH C05 C25 SING Y N 10 
YDH C06 N09 DOUB Y N 11 
YDH C06 C12 SING Y N 12 
YDH C06 C18 SING N N 13 
YDH C07 N10 SING N N 14 
YDH C07 C26 DOUB Y N 15 
YDH O08 N09 SING Y N 16 
YDH O08 N11 SING Y N 17 
YDH N10 C20 SING N N 18 
YDH N10 C21 SING N N 19 
YDH N11 C12 DOUB Y N 20 
YDH C12 C28 SING N N 21 
YDH C13 N15 SING N N 22 
YDH C13 C19 SING N N 23 
YDH C13 O22 DOUB N N 24 
YDH C14 C27 SING N N 25 
YDH N15 C18 SING N N 26 
YDH C19 C23 SING N N 27 
YDH C19 C24 SING N N 28 
YDH C20 C23 SING N N 29 
YDH C21 C24 SING N N 30 
YDH C25 C29 DOUB Y N 31 
YDH C26 C29 SING Y N 32 
YDH C27 C30 SING N N 33 
YDH C27 C31 SING N N 34 
YDH C30 C33 SING N N 35 
YDH C31 C32 SING N N 36 
YDH C32 C34 SING N N 37 
YDH C33 C34 SING N N 38 
YDH C18 H38 SING N N 39 
YDH C18 H39 SING N N 40 
YDH C19 H40 SING N N 41 
YDH C20 H42 SING N N 42 
YDH C20 H41 SING N N 43 
YDH C21 H44 SING N N 44 
YDH C21 H43 SING N N 45 
YDH C23 H45 SING N N 46 
YDH C23 H46 SING N N 47 
YDH C24 H47 SING N N 48 
YDH C24 H48 SING N N 49 
YDH C25 H49 SING N N 50 
YDH C26 H50 SING N N 51 
YDH C27 H51 SING N N 52 
YDH C28 H52 SING N N 53 
YDH C28 H54 SING N N 54 
YDH C28 H53 SING N N 55 
YDH C14 H35 SING N N 56 
YDH C14 H36 SING N N 57 
YDH N15 H37 SING N N 58 
YDH C29 H55 SING N N 59 
YDH C30 H56 SING N N 60 
YDH C30 H57 SING N N 61 
YDH C31 H58 SING N N 62 
YDH C31 H59 SING N N 63 
YDH C32 H61 SING N N 64 
YDH C32 H60 SING N N 65 
YDH C33 H63 SING N N 66 
YDH C33 H62 SING N N 67 
YDH C34 H65 SING N N 68 
YDH C34 H64 SING N N 69 
# 
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 
YDH SMILES           ACDLabs              12.01 "O=C(NCc1nonc1C)C1CCN(CC1)c1cccc2C(=O)N(CC3CCCCC3)C(=O)c21"                                                                                                                    
YDH InChI            InChI                1.06  "InChI=1S/C25H31N5O4/c1-16-20(28-34-27-16)14-26-23(31)18-10-12-29(13-11-18)21-9-5-8-19-22(21)25(33)30(24(19)32)15-17-6-3-2-4-7-17/h5,8-9,17-18H,2-4,6-7,10-15H2,1H3,(H,26,31)" 
YDH InChIKey         InChI                1.06  LIYHDVZZLXQJCD-UHFFFAOYSA-N                                                                                                                                                    
YDH SMILES_CANONICAL CACTVS               3.385 "Cc1nonc1CNC(=O)C2CCN(CC2)c3cccc4C(=O)N(CC5CCCCC5)C(=O)c34"                                                                                                                    
YDH SMILES           CACTVS               3.385 "Cc1nonc1CNC(=O)C2CCN(CC2)c3cccc4C(=O)N(CC5CCCCC5)C(=O)c34"                                                                                                                    
YDH SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(non1)CNC(=O)C2CCN(CC2)c3cccc4c3C(=O)N(C4=O)CC5CCCCC5"                                                                                                                    
YDH SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1c(non1)CNC(=O)C2CCN(CC2)c3cccc4c3C(=O)N(C4=O)CC5CCCCC5"                                                                                                                    
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
YDH "SYSTEMATIC NAME" ACDLabs              12.01 "1-[2-(cyclohexylmethyl)-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl]-N-[(4-methyl-1,2,5-oxadiazol-3-yl)methyl]piperidine-4-carboxamide" 
YDH "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "1-[2-(cyclohexylmethyl)-1,3-bis(oxidanylidene)isoindol-4-yl]-~{N}-[(4-methyl-1,2,5-oxadiazol-3-yl)methyl]piperidine-4-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 
YDH "Create component" 2023-06-13 RCSB 
YDH "Initial release"  2024-12-18 RCSB 
# 
