data_Y2R
# 
_chem_comp.id                                    Y2R 
_chem_comp.name                                  "N-{(1R)-1-[(3P,5P)-3-[5-(aminomethyl)thiophen-2-yl]-5-(thiophen-2-yl)phenyl]ethyl}-5-[2-(dimethylamino)ethoxy]-2-methylbenzamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C29 H33 N3 O2 S2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-11-14 
_chem_comp.pdbx_modified_date                    2024-03-29 
_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                        519.721 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y2R 
_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        8UUY 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
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 
Y2R C1   C1  C 0 1 N N N N N N 46.841 32.565 1.333  3.157   5.161  0.396  C1   Y2R 1  
Y2R C2   C2  C 0 1 Y N N N N N 48.011 33.426 0.930  3.708   3.772  0.204  C2   Y2R 2  
Y2R C3   C3  C 0 1 Y N N N N N 47.927 34.809 1.070  5.037   3.597  -0.123 C3   Y2R 3  
Y2R C4   C4  C 0 1 Y N N N N N 48.971 35.645 0.720  5.548   2.324  -0.301 C4   Y2R 4  
Y2R C5   C5  C 0 1 Y N N N N N 50.137 35.103 0.215  4.727   1.214  -0.150 C5   Y2R 5  
Y2R C7   C6  C 0 1 N N N N N N 52.382 35.367 -0.604 6.620   -0.130 -0.663 C7   Y2R 6  
Y2R C8   C7  C 0 1 N N N N N N 53.179 36.497 -1.189 7.006   -1.602 -0.819 C8   Y2R 7  
Y2R C10  C8  C 0 1 N N N N N N 54.260 36.480 1.042  6.792   -1.775 -3.224 C10  Y2R 8  
Y2R C11  C9  C 0 1 N N N N N N 53.276 38.550 0.183  6.210   -3.658 -1.819 C11  Y2R 9  
Y2R C12  C10 C 0 1 Y N N N N N 50.259 33.731 0.061  3.392   1.379  0.177  C12  Y2R 10 
Y2R C13  C11 C 0 1 Y N N N N N 49.201 32.886 0.414  2.877   2.662  0.363  C13  Y2R 11 
Y2R C14  C12 C 0 1 N N N N N N 49.340 31.411 0.197  1.452   2.846  0.713  C14  Y2R 12 
Y2R C17  C13 C 0 1 N N R N N N 50.302 29.289 0.961  -0.737  1.956  1.304  C17  Y2R 13 
Y2R C18  C14 C 0 1 N N N N N N 50.696 28.734 2.325  -0.864  2.206  2.808  C18  Y2R 14 
Y2R C19  C15 C 0 1 Y N N N N N 51.311 28.930 -0.115 -1.510  0.716  0.934  C19  Y2R 15 
Y2R C20  C16 C 0 1 Y N N N N N 50.944 28.148 -1.204 -0.957  -0.530 1.155  C20  Y2R 16 
Y2R C21  C17 C 0 1 Y N N N N N 51.868 27.801 -2.185 -1.668  -1.683 0.814  C21  Y2R 17 
Y2R C22  C18 C 0 1 Y N N N N N 51.457 26.962 -3.320 -1.074  -3.016 1.050  C22  Y2R 18 
Y2R C23  C19 C 0 1 Y N N N N N 52.227 26.518 -4.379 -1.664  -4.193 0.762  C23  Y2R 19 
Y2R C24  C20 C 0 1 Y N N N N N 51.485 25.715 -5.293 -0.912  -5.307 1.074  C24  Y2R 20 
Y2R C25  C21 C 0 1 Y N N N N N 50.199 25.568 -4.919 0.284   -5.050 1.613  C25  Y2R 21 
Y2R C27  C22 C 0 1 Y N N N N N 53.182 28.246 -2.078 -2.937  -1.574 0.251  C27  Y2R 22 
Y2R C28  C23 C 0 1 Y N N N N N 53.567 29.031 -0.994 -3.489  -0.314 0.031  C28  Y2R 23 
Y2R C29  C24 C 0 1 Y N N N N N 54.948 29.525 -0.890 -4.836  -0.189 -0.566 C29  Y2R 24 
Y2R C30  C25 C 0 1 Y N N N N N 55.535 30.235 0.138  -5.622  -1.219 -0.937 C30  Y2R 25 
Y2R C31  C26 C 0 1 Y N N N N N 56.878 30.569 -0.110 -6.840  -0.853 -1.472 C31  Y2R 26 
Y2R C32  C27 C 0 1 Y N N N N N 57.338 30.120 -1.329 -7.055  0.465  -1.539 C32  Y2R 27 
Y2R C33  C28 C 0 1 N N N N N N 58.682 30.297 -1.905 -8.303  1.112  -2.080 C33  Y2R 28 
Y2R C36  C29 C 0 1 Y N N N N N 52.628 29.366 -0.022 -2.770  0.831  0.382  C36  Y2R 29 
Y2R N16  N1  N 0 1 N N N N N N 50.105 30.738 1.066  0.674   1.773  0.957  N16  Y2R 30 
Y2R N34  N2  N 0 1 N N N N N N 58.968 29.271 -2.930 -9.271  1.296  -0.990 N34  Y2R 31 
Y2R N9   N3  N 0 1 N N N N N N 53.958 37.277 -0.178 6.245   -2.194 -1.927 N9   Y2R 32 
Y2R O15  O1  O 0 1 N N N N N N 48.771 30.856 -0.740 0.983   3.966  0.781  O15  Y2R 33 
Y2R O6   O2  O 0 1 N N N N N N 51.160 35.948 -0.129 5.235   -0.034 -0.326 O6   Y2R 34 
Y2R S26  S1  S 0 1 Y N N N N N 49.849 26.386 -3.469 0.515   -3.311 1.744  S26  Y2R 35 
Y2R S35  S2  S 0 1 Y N N N N N 56.087 29.274 -2.173 -5.665  1.328  -0.894 S35  Y2R 36 
Y2R H1B  H1  H 0 1 N N N N N N 46.172 32.428 0.471  2.670   5.489  -0.523 H1B  Y2R 37 
Y2R H1C  H2  H 0 1 N N N N N N 47.207 31.585 1.672  2.431   5.155  1.209  H1C  Y2R 38 
Y2R H1A  H3  H 0 1 N N N N N N 46.291 33.054 2.150  3.970   5.845  0.640  H1A  Y2R 39 
Y2R H3   H4  H 0 1 N N N N N N 47.019 35.241 1.464  5.681   4.456  -0.242 H3   Y2R 40 
Y2R H4   H5  H 0 1 N N N N N N 48.876 36.714 0.841  6.589   2.193  -0.557 H4   Y2R 41 
Y2R H7A  H6  H 0 1 N N N N N N 52.932 34.902 0.227  7.219   0.321  0.128  H7A  Y2R 42 
Y2R H7B  H7  H 0 1 N N N N N N 52.171 34.610 -1.374 6.803   0.395  -1.601 H7B  Y2R 43 
Y2R H8A  H8  H 0 1 N N N N N N 53.884 36.080 -1.923 8.073   -1.678 -1.030 H8A  Y2R 44 
Y2R H8B  H9  H 0 1 N N N N N N 52.485 37.184 -1.696 6.780   -2.137 0.104  H8B  Y2R 45 
Y2R H10B H10 H 0 0 N N N N N N 54.832 37.097 1.751  7.830   -2.097 -3.302 H10B Y2R 46 
Y2R H10A H11 H 0 0 N N N N N N 53.319 36.158 1.512  6.210   -2.227 -4.027 H10A Y2R 47 
Y2R H10C H12 H 0 0 N N N N N N 54.852 35.596 0.765  6.742   -0.689 -3.306 H10C Y2R 48 
Y2R H11B H13 H 0 0 N N N N N N 53.879 39.092 0.926  5.813   -3.941 -0.844 H11B Y2R 49 
Y2R H11C H14 H 0 0 N N N N N N 53.159 39.171 -0.717 5.572   -4.065 -2.603 H11C Y2R 50 
Y2R H11A H15 H 0 0 N N N N N N 52.285 38.328 0.607  7.219   -4.055 -1.929 H11A Y2R 51 
Y2R H12  H16 H 0 1 N N N N N N 51.174 33.313 -0.333 2.753   0.517  0.294  H12  Y2R 52 
Y2R H17  H17 H 0 1 N N N N N N 49.342 28.831 0.682  -1.138  2.810  0.759  H17  Y2R 53 
Y2R H18C H18 H 0 0 N N N N N N 50.845 27.647 2.250  -0.463  1.352  3.354  H18C Y2R 54 
Y2R H18B H19 H 0 0 N N N N N N 51.630 29.210 2.658  -0.305  3.103  3.076  H18B Y2R 55 
Y2R H18A H20 H 0 0 N N N N N N 49.897 28.946 3.051  -1.914  2.342  3.067  H18A Y2R 56 
Y2R H20  H21 H 0 1 N N N N N N 49.924 27.804 -1.290 0.027   -0.613 1.591  H20  Y2R 57 
Y2R H23  H22 H 0 1 N N N N N N 53.274 26.753 -4.500 -2.648  -4.259 0.323  H23  Y2R 58 
Y2R H24  H23 H 0 1 N N N N N N 51.906 25.274 -6.185 -1.264  -6.312 0.897  H24  Y2R 59 
Y2R H25  H24 H 0 1 N N N N N N 49.473 24.996 -5.477 1.002   -5.797 1.917  H25  Y2R 60 
Y2R H27  H25 H 0 1 N N N N N N 53.904 27.982 -2.836 -3.490  -2.463 -0.015 H27  Y2R 61 
Y2R H30  H26 H 0 1 N N N N N N 55.014 30.507 1.044  -5.321  -2.250 -0.826 H30  Y2R 62 
Y2R H31  H27 H 0 1 N N N N N N 57.489 31.123 0.587  -7.565  -1.577 -1.811 H31  Y2R 63 
Y2R H33B H28 H 0 0 N N N N N N 58.745 31.293 -2.368 -8.052  2.082  -2.510 H33B Y2R 64 
Y2R H33A H29 H 0 0 N N N N N N 59.429 30.218 -1.101 -8.739  0.475  -2.849 H33A Y2R 65 
Y2R H36  H30 H 0 1 N N N N N N 52.928 29.975 0.818  -3.197  1.809  0.212  H36  Y2R 66 
Y2R H16  H31 H 0 1 N N N N N N 50.554 31.237 1.807  1.049   0.880  0.902  H16  Y2R 67 
Y2R H34B H32 H 0 0 N N N N N N 59.885 29.417 -3.302 -8.868  1.830  -0.234 H34B Y2R 68 
Y2R H34C H33 H 0 0 N N N N N N 58.917 28.362 -2.515 -10.118 1.729  -1.327 H34C Y2R 69 
# 
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 
Y2R C1  C2   SING N N 1  
Y2R C2  C3   DOUB Y N 2  
Y2R C3  C4   SING Y N 3  
Y2R C4  C5   DOUB Y N 4  
Y2R C5  O6   SING N N 5  
Y2R O6  C7   SING N N 6  
Y2R C7  C8   SING N N 7  
Y2R C8  N9   SING N N 8  
Y2R N9  C10  SING N N 9  
Y2R N9  C11  SING N N 10 
Y2R C5  C12  SING Y N 11 
Y2R C12 C13  DOUB Y N 12 
Y2R C13 C14  SING N N 13 
Y2R C14 O15  DOUB N N 14 
Y2R C14 N16  SING N N 15 
Y2R N16 C17  SING N N 16 
Y2R C17 C18  SING N N 17 
Y2R C17 C19  SING N N 18 
Y2R C19 C20  DOUB Y N 19 
Y2R C20 C21  SING Y N 20 
Y2R C21 C22  SING N N 21 
Y2R C22 C23  DOUB Y N 22 
Y2R C23 C24  SING Y N 23 
Y2R C24 C25  DOUB Y N 24 
Y2R C25 S26  SING Y N 25 
Y2R C21 C27  DOUB Y N 26 
Y2R C27 C28  SING Y N 27 
Y2R C28 C29  SING N N 28 
Y2R C29 C30  DOUB Y N 29 
Y2R C30 C31  SING Y N 30 
Y2R C31 C32  DOUB Y N 31 
Y2R C32 C33  SING N N 32 
Y2R C33 N34  SING N N 33 
Y2R C32 S35  SING Y N 34 
Y2R C28 C36  DOUB Y N 35 
Y2R C13 C2   SING Y N 36 
Y2R C36 C19  SING Y N 37 
Y2R S26 C22  SING Y N 38 
Y2R S35 C29  SING Y N 39 
Y2R C1  H1B  SING N N 40 
Y2R C1  H1C  SING N N 41 
Y2R C1  H1A  SING N N 42 
Y2R C3  H3   SING N N 43 
Y2R C4  H4   SING N N 44 
Y2R C7  H7A  SING N N 45 
Y2R C7  H7B  SING N N 46 
Y2R C8  H8A  SING N N 47 
Y2R C8  H8B  SING N N 48 
Y2R C10 H10B SING N N 49 
Y2R C10 H10A SING N N 50 
Y2R C10 H10C SING N N 51 
Y2R C11 H11B SING N N 52 
Y2R C11 H11C SING N N 53 
Y2R C11 H11A SING N N 54 
Y2R C12 H12  SING N N 55 
Y2R C17 H17  SING N N 56 
Y2R C18 H18C SING N N 57 
Y2R C18 H18B SING N N 58 
Y2R C18 H18A SING N N 59 
Y2R C20 H20  SING N N 60 
Y2R C23 H23  SING N N 61 
Y2R C24 H24  SING N N 62 
Y2R C25 H25  SING N N 63 
Y2R C27 H27  SING N N 64 
Y2R C30 H30  SING N N 65 
Y2R C31 H31  SING N N 66 
Y2R C33 H33B SING N N 67 
Y2R C33 H33A SING N N 68 
Y2R C36 H36  SING N N 69 
Y2R N16 H16  SING N N 70 
Y2R N34 H34B SING N N 71 
Y2R N34 H34C SING N N 72 
# 
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 
Y2R SMILES           ACDLabs              12.01 "NCc1ccc(s1)c1cc(cc(c1)c1cccs1)C(C)NC(=O)c1cc(OCCN(C)C)ccc1C"                                                                                                                         
Y2R InChI            InChI                1.06  "InChI=1S/C29H33N3O2S2/c1-19-7-8-24(34-12-11-32(3)4)17-26(19)29(33)31-20(2)21-14-22(27-6-5-13-35-27)16-23(15-21)28-10-9-25(18-30)36-28/h5-10,13-17,20H,11-12,18,30H2,1-4H3,(H,31,33)" 
Y2R InChIKey         InChI                1.06  LNRHXFDDRMUVPS-UHFFFAOYSA-N                                                                                                                                                           
Y2R SMILES_CANONICAL CACTVS               3.385 "C[C@@H](NC(=O)c1cc(OCCN(C)C)ccc1C)c2cc(cc(c2)c3sc(CN)cc3)c4sccc4"                                                                                                                    
Y2R SMILES           CACTVS               3.385 "C[CH](NC(=O)c1cc(OCCN(C)C)ccc1C)c2cc(cc(c2)c3sc(CN)cc3)c4sccc4"                                                                                                                      
Y2R SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1ccc(cc1C(=O)N[C@H](C)c2cc(cc(c2)c3ccc(s3)CN)c4cccs4)OCCN(C)C"                                                                                                                     
Y2R SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1ccc(cc1C(=O)NC(C)c2cc(cc(c2)c3ccc(s3)CN)c4cccs4)OCCN(C)C"                                                                                                                         
# 
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 
Y2R "SYSTEMATIC NAME" ACDLabs              12.01 "N-{(1R)-1-[(3P,5P)-3-[5-(aminomethyl)thiophen-2-yl]-5-(thiophen-2-yl)phenyl]ethyl}-5-[2-(dimethylamino)ethoxy]-2-methylbenzamide" 
Y2R "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "~{N}-[(1~{R})-1-[3-[5-(aminomethyl)thiophen-2-yl]-5-thiophen-2-yl-phenyl]ethyl]-5-[2-(dimethylamino)ethoxy]-2-methyl-benzamide"   
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
Y2R "Create component" 2023-11-14 RCSB 
Y2R "Initial release"  2024-04-03 RCSB 
# 
