data_Y3R
# 
_chem_comp.id                                    Y3R 
_chem_comp.name                                  "ethyl 4-oxo-4-(2-{3-[2-({(1S)-1-[(3P)-3-(thiophen-3-yl)phenyl]ethyl}carbamoyl)phenyl]propanoyl}hydrazinyl)butanoate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C28 H31 N3 O5 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-11-17 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        521.628 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y3R 
_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        8UVM 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              Y 
# 
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 
Y3R C10  C1  C 0 1 Y N N N N N -30.056 -74.128 -9.139  6.202   1.673  -0.484 C10  Y3R 1  
Y3R C15  C2  C 0 1 Y N N N N N -27.345 -74.497 -9.096  8.036   3.312  0.094  C15  Y3R 2  
Y3R C17  C3  C 0 1 Y N N N N N -30.045 -71.949 -3.365  1.604   -3.611 0.109  C17  Y3R 3  
Y3R C20  C4  C 0 1 N N N N N N -32.772 -72.466 -1.466  -1.518  -2.830 0.331  C20  Y3R 4  
Y3R C21  C5  C 0 1 N N N N N N -34.023 -72.427 -0.483  -2.557  -1.907 0.913  C21  Y3R 5  
Y3R C24  C6  C 0 1 N N N N N N -35.079 -73.282 2.863   -5.517  -0.113 -0.098 C24  Y3R 6  
Y3R C26  C7  C 0 1 N N N N N N -37.451 -73.023 3.074   -7.566  1.190  -0.600 C26  Y3R 7  
Y3R C02  C8  C 0 1 N N N N N N -31.052 -72.662 -4.332  1.726   -2.151 -0.089 C02  Y3R 8  
Y3R C04  C9  C 0 1 N N R N N N -31.844 -74.812 -5.634  2.937   -0.195 -0.890 C04  Y3R 9  
Y3R C05  C10 C 0 1 N N N N N N -31.649 -76.341 -5.435  2.215   0.208  -2.177 C05  Y3R 10 
Y3R C06  C11 C 0 1 Y N N N N N -31.629 -74.388 -7.144  4.394   0.178  -0.994 C06  Y3R 11 
Y3R C07  C12 C 0 1 Y N N N N N -32.673 -73.879 -7.920  5.266   -0.633 -1.697 C07  Y3R 12 
Y3R C08  C13 C 0 1 Y N N N N N -32.447 -73.508 -9.250  6.605   -0.299 -1.792 C08  Y3R 13 
Y3R C09  C14 C 0 1 Y N N N N N -31.181 -73.632 -9.827  7.076   0.852  -1.194 C09  Y3R 14 
Y3R C11  C15 C 0 1 Y N N N N N -28.641 -74.273 -9.760  6.702   2.912  0.161  C11  Y3R 15 
Y3R C12  C16 C 0 1 Y N N N N N -28.314 -74.217 -11.074 5.906   3.743  0.858  C12  Y3R 16 
Y3R C14  C17 C 0 1 Y N N N N N -26.255 -74.586 -9.860  8.313   4.448  0.728  C14  Y3R 17 
Y3R C16  C18 C 0 1 Y N N N N N -30.370 -74.483 -7.793  4.855   1.329  -0.387 C16  Y3R 18 
Y3R C18  C19 C 0 1 Y N N N N N -30.357 -71.338 -2.108  0.531   -4.133 0.832  C18  Y3R 19 
Y3R C19  C20 C 0 1 N N N N N N -31.761 -71.255 -1.455  -0.508  -3.210 1.415  C19  Y3R 20 
Y3R C25  C21 C 0 1 N N N N N N -36.360 -73.568 3.563   -6.556  0.810  0.484  C25  Y3R 21 
Y3R C27  C22 C 0 1 N N N N N N -38.821 -73.230 3.659   -8.605  2.114  -0.018 C27  Y3R 22 
Y3R C29  C23 C 0 1 N N N N N N -41.123 -72.674 3.651   -10.563 3.464  -0.163 C29  Y3R 23 
Y3R C30  C24 C 0 1 N N N N N N -42.227 -73.690 3.933   -11.612 3.888  -1.193 C30  Y3R 24 
Y3R C34  C25 C 0 1 Y N N N N N -29.283 -70.747 -1.396  0.423   -5.497 1.013  C34  Y3R 25 
Y3R C35  C26 C 0 1 Y N N N N N -27.968 -70.745 -1.865  1.376   -6.346 0.479  C35  Y3R 26 
Y3R C36  C27 C 0 1 Y N N N N N -27.669 -71.334 -3.071  2.442   -5.835 -0.240 C36  Y3R 27 
Y3R C37  C28 C 0 1 Y N N N N N -28.699 -71.931 -3.814  2.559   -4.474 -0.433 C37  Y3R 28 
Y3R N03  N1  N 0 1 N N N N N N -30.949 -74.033 -4.698  2.817   -1.641 -0.695 N03  Y3R 29 
Y3R N22  N2  N 0 1 N N N N N N -34.115 -73.464 0.527   -3.554  -1.439 0.137  N22  Y3R 30 
Y3R N23  N3  N 0 1 N N N N N N -35.137 -73.599 1.470   -4.520  -0.581 0.678  N23  Y3R 31 
Y3R O01  O1  O 0 1 N N N N N N -31.955 -72.003 -4.801  0.842   -1.410 0.296  O01  Y3R 32 
Y3R O28  O2  O 0 1 N N N N N N -39.975 -73.204 2.984   -9.599  2.579  -0.791 O28  Y3R 33 
Y3R O31  O3  O 0 1 N N N N N N -38.794 -73.451 4.860   -8.544  2.435  1.145  O31  Y3R 34 
Y3R O32  O4  O 0 1 N N N N N N -34.111 -72.844 3.390   -5.579  -0.436 -1.266 O32  Y3R 35 
Y3R O33  O5  O 0 1 N N N N N N -34.818 -71.588 -0.583  -2.495  -1.584 2.081  O33  Y3R 36 
Y3R S13  S1  S 0 1 Y N N N N N -26.652 -74.409 -11.498 6.854   5.094  1.466  S13  Y3R 37 
Y3R H151 H1  H 0 0 N N N N N N -27.279 -74.587 -8.022  8.788   2.739  -0.428 H151 Y3R 38 
Y3R H202 H2  H 0 0 N N N N N N -33.167 -72.549 -2.489  -2.003  -3.731 -0.046 H202 Y3R 39 
Y3R H201 H3  H 0 0 N N N N N N -32.196 -73.371 -1.221  -1.002  -2.326 -0.487 H201 Y3R 40 
Y3R H261 H4  H 0 0 N N N N N N -37.278 -71.937 3.093   -7.050  1.694  -1.418 H261 Y3R 41 
Y3R H041 H5  H 0 0 N N N N N N -32.888 -74.577 -5.378  2.489   0.325  -0.044 H041 Y3R 42 
Y3R H051 H6  H 0 0 N N N N N N -32.309 -76.888 -6.125  2.305   1.285  -2.323 H051 Y3R 43 
Y3R H053 H7  H 0 0 N N N N N N -30.602 -76.607 -5.641  2.664   -0.312 -3.024 H053 Y3R 44 
Y3R H052 H8  H 0 0 N N N N N N -31.898 -76.610 -4.398  1.161   -0.062 -2.102 H052 Y3R 45 
Y3R H071 H9  H 0 0 N N N N N N -33.659 -73.771 -7.492  4.900   -1.532 -2.171 H071 Y3R 46 
Y3R H081 H10 H 0 0 N N N N N N -33.264 -73.120 -9.840  7.281   -0.936 -2.342 H081 Y3R 47 
Y3R H091 H11 H 0 0 N N N N N N -31.058 -73.331 -10.857 8.120   1.116  -1.277 H091 Y3R 48 
Y3R H121 H12 H 0 0 N N N N N N -29.068 -74.058 -11.830 4.847   3.602  1.019  H121 Y3R 49 
Y3R H141 H13 H 0 0 N N N N N N -25.255 -74.749 -9.485  9.290   4.904  0.785  H141 Y3R 50 
Y3R H161 H14 H 0 0 N N N N N N -29.555 -74.869 -7.199  4.173   1.962  0.162  H161 Y3R 51 
Y3R H192 H15 H 0 0 N N N N N N -32.279 -70.420 -1.949  -0.023  -2.309 1.792  H192 Y3R 52 
Y3R H191 H16 H 0 0 N N N N N N -31.592 -71.007 -0.397  -1.024  -3.714 2.232  H191 Y3R 53 
Y3R H251 H17 H 0 0 N N N N N N -36.254 -73.220 4.601   -7.073  0.307  1.301  H251 Y3R 54 
Y3R H291 H18 H 0 0 N N N N N N -40.795 -72.250 4.612   -10.052 4.347  0.219  H291 Y3R 55 
Y3R H292 H19 H 0 0 N N N N N N -41.545 -71.876 3.023   -11.053 2.943  0.660  H292 Y3R 56 
Y3R H302 H20 H 0 0 N N N N N N -43.063 -73.191 4.445   -12.336 4.553  -0.722 H302 Y3R 57 
Y3R H301 H21 H 0 0 N N N N N N -42.582 -74.119 2.984   -11.123 4.410  -2.016 H301 Y3R 58 
Y3R H303 H22 H 0 0 N N N N N N -41.832 -74.493 4.573   -12.124 3.005  -1.576 H303 Y3R 59 
Y3R H341 H23 H 0 0 N N N N N N -29.492 -70.276 -0.447  -0.406  -5.903 1.573  H341 Y3R 60 
Y3R H351 H24 H 0 0 N N N N N N -27.187 -70.281 -1.281  1.287   -7.413 0.623  H351 Y3R 61 
Y3R H361 H25 H 0 0 N N N N N N -26.655 -71.337 -3.442  3.182   -6.503 -0.655 H361 Y3R 62 
Y3R H371 H26 H 0 0 N N N N N N -28.459 -72.393 -4.760  3.389   -4.076 -0.998 H371 Y3R 63 
Y3R H031 H27 H 0 0 N N N N N N -30.193 -74.543 -4.286  3.522   -2.233 -1.001 H031 Y3R 64 
Y3R H221 H28 H 0 0 N N N N N N -33.381 -74.143 0.550   -3.603  -1.697 -0.797 H221 Y3R 65 
Y3R H231 H29 H 0 0 N N N N N N -36.007 -73.958 1.133   -4.471  -0.323 1.612  H231 Y3R 66 
Y3R H262 H30 H 0 1 N N N N N N -37.516 -73.366 2.031   -8.051  0.289  -0.977 H1   Y3R 67 
Y3R H252 H31 H 0 1 N Y N N N N -36.504 -74.659 3.555   -6.071  1.711  0.861  H2   Y3R 68 
# 
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 
Y3R C02 O01  DOUB N N 1  
Y3R C04 N03  SING N N 2  
Y3R C05 C04  SING N N 3  
Y3R C06 C04  SING N N 4  
Y3R C07 C06  DOUB Y N 5  
Y3R C08 C07  SING Y N 6  
Y3R C09 C08  DOUB Y N 7  
Y3R C10 C09  SING Y N 8  
Y3R C12 C11  DOUB Y N 9  
Y3R S13 C12  SING Y N 10 
Y3R C14 S13  SING Y N 11 
Y3R C15 C14  DOUB Y N 12 
Y3R C11 C10  SING N N 13 
Y3R C16 C10  DOUB Y N 14 
Y3R N03 C02  SING N N 15 
Y3R C17 C02  SING N N 16 
Y3R C18 C17  DOUB Y N 17 
Y3R C20 C19  SING N N 18 
Y3R C21 C20  SING N N 19 
Y3R N23 N22  SING N N 20 
Y3R C24 N23  SING N N 21 
Y3R C26 C25  SING N N 22 
Y3R C27 C26  SING N N 23 
Y3R C29 O28  SING N N 24 
Y3R C30 C29  SING N N 25 
Y3R O28 C27  SING N N 26 
Y3R O31 C27  DOUB N N 27 
Y3R C25 C24  SING N N 28 
Y3R O32 C24  DOUB N N 29 
Y3R N22 C21  SING N N 30 
Y3R O33 C21  DOUB N N 31 
Y3R C19 C18  SING N N 32 
Y3R C34 C18  SING Y N 33 
Y3R C35 C34  DOUB Y N 34 
Y3R C36 C35  SING Y N 35 
Y3R C37 C36  DOUB Y N 36 
Y3R C06 C16  SING Y N 37 
Y3R C11 C15  SING Y N 38 
Y3R C17 C37  SING Y N 39 
Y3R C15 H151 SING N N 40 
Y3R C20 H202 SING N N 41 
Y3R C20 H201 SING N N 42 
Y3R C26 H261 SING N N 43 
Y3R C04 H041 SING N N 44 
Y3R C05 H051 SING N N 45 
Y3R C05 H053 SING N N 46 
Y3R C05 H052 SING N N 47 
Y3R C07 H071 SING N N 48 
Y3R C08 H081 SING N N 49 
Y3R C09 H091 SING N N 50 
Y3R C12 H121 SING N N 51 
Y3R C14 H141 SING N N 52 
Y3R C16 H161 SING N N 53 
Y3R C19 H192 SING N N 54 
Y3R C19 H191 SING N N 55 
Y3R C25 H251 SING N N 56 
Y3R C29 H291 SING N N 57 
Y3R C29 H292 SING N N 58 
Y3R C30 H302 SING N N 59 
Y3R C30 H301 SING N N 60 
Y3R C30 H303 SING N N 61 
Y3R C34 H341 SING N N 62 
Y3R C35 H351 SING N N 63 
Y3R C36 H361 SING N N 64 
Y3R C37 H371 SING N N 65 
Y3R N03 H031 SING N N 66 
Y3R N22 H221 SING N N 67 
Y3R N23 H231 SING N N 68 
Y3R C26 H262 SING N N 69 
Y3R C25 H252 SING N N 70 
# 
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 
Y3R SMILES           ACDLabs              12.01 "O=C(OCC)CCC(=O)NNC(=O)CCc1ccccc1C(=O)NC(C)c1cccc(c1)c1ccsc1"                                                                                                                                   
Y3R InChI            InChI                1.06  "InChI=1S/C28H31N3O5S/c1-3-36-27(34)14-13-26(33)31-30-25(32)12-11-20-7-4-5-10-24(20)28(35)29-19(2)21-8-6-9-22(17-21)23-15-16-37-18-23/h4-10,15-19H,3,11-14H2,1-2H3,(H,29,35)(H,30,32)(H,31,33)" 
Y3R InChIKey         InChI                1.06  VCEOCCSGIGLDNU-UHFFFAOYSA-N                                                                                                                                                                     
Y3R SMILES_CANONICAL CACTVS               3.385 "CCOC(=O)CCC(=O)NNC(=O)CCc1ccccc1C(=O)N[C@H](C)c2cccc(c2)c3cscc3"                                                                                                                               
Y3R SMILES           CACTVS               3.385 "CCOC(=O)CCC(=O)NNC(=O)CCc1ccccc1C(=O)N[CH](C)c2cccc(c2)c3cscc3"                                                                                                                                
Y3R SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCOC(=O)CCC(=O)NNC(=O)CCc1ccccc1C(=O)N[C@H](C)c2cccc(c2)c3ccsc3"                                                                                                                               
Y3R SMILES           "OpenEye OEToolkits" 2.0.7 "CCOC(=O)CCC(=O)NNC(=O)CCc1ccccc1C(=O)NC(C)c2cccc(c2)c3ccsc3"                                                                                                                                   
# 
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 
Y3R "SYSTEMATIC NAME" ACDLabs              12.01 "ethyl 4-oxo-4-(2-{3-[2-({(1S)-1-[(3P)-3-(thiophen-3-yl)phenyl]ethyl}carbamoyl)phenyl]propanoyl}hydrazinyl)butanoate"       
Y3R "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "ethyl 4-oxidanylidene-4-[2-[3-[2-[[(1~{R})-1-(3-thiophen-3-ylphenyl)ethyl]carbamoyl]phenyl]propanoyl]hydrazinyl]butanoate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
Y3R "Create component" 2023-11-17 RCSB 
Y3R "Initial release"  2024-04-03 RCSB 
Y3R "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            Y3R 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               C25 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
