data_Y0I
# 
_chem_comp.id                                    Y0I 
_chem_comp.name                                  "(3Z)-N-([1,1'-biphenyl]-4-yl)-3-imino-N-[(1R)-2-oxo-2-{[(1S)-1-phenylethyl]amino}-1-(pyridin-3-yl)ethyl]propanamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C30 H28 N4 O2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-12-19 
_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                        476.569 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y0I 
_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        8FIV 
_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_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 
Y0I C10 C1  C 0 1 Y N N N N N 11.137 2.103  23.052 6.588  -0.133 -1.126 C10 Y0I 1  
Y0I C13 C2  C 0 1 Y N N N N N 10.798 1.958  25.783 6.802  1.962  0.665  C13 Y0I 2  
Y0I C17 C3  C 0 1 Y N N N N N 6.718  0.119  18.910 -0.222 1.539  -0.079 C17 Y0I 3  
Y0I C20 C4  C 0 1 Y N N N N N 4.599  1.875  18.668 0.172  2.978  2.194  C20 Y0I 4  
Y0I C21 C5  C 0 1 Y N N N N N 5.080  1.596  19.962 0.657  1.681  2.136  C21 Y0I 5  
Y0I C22 C6  C 0 1 Y N N N N N 8.441  -1.326 22.403 -1.415 -0.844 0.313  C22 Y0I 6  
Y0I C24 C7  C 0 1 Y N N N N N 10.835 -1.569 22.568 -3.219 -0.399 -1.203 C24 Y0I 7  
Y0I C26 C8  C 0 1 Y N N N N N 11.940 -2.201 24.848 -5.307 0.711  -0.414 C26 Y0I 8  
Y0I C28 C9  C 0 1 Y N N N N N 12.878 -2.911 26.974 -7.301 1.782  0.386  C28 Y0I 9  
Y0I O01 O1  O 0 1 N N N N N N 5.380  -2.174 20.592 1.156  -3.148 0.794  O01 Y0I 10 
Y0I C02 C10 C 0 1 N N N N N N 6.401  -2.263 21.202 0.069  -2.692 0.506  C02 Y0I 11 
Y0I N03 N1  N 0 1 N N N N N N 7.182  -1.066 21.659 -0.138 -1.362 0.553  N03 Y0I 12 
Y0I C04 C11 C 0 1 N N R N N N 6.758  0.347  21.443 0.974  -0.457 0.856  C04 Y0I 13 
Y0I C05 C12 C 0 1 N N N N N N 7.899  1.358  21.660 1.995  -0.529 -0.250 C05 Y0I 14 
Y0I N06 N2  N 0 1 N N N N N N 7.811  2.457  22.653 3.112  0.223  -0.185 N06 Y0I 15 
Y0I C07 C13 C 0 1 N N S N N N 8.968  3.353  22.737 4.105  0.154  -1.260 C07 Y0I 16 
Y0I C08 C14 C 0 1 N N N N N N 8.581  4.749  23.186 3.704  1.108  -2.387 C08 Y0I 17 
Y0I C09 C15 C 0 1 Y N N N N N 10.008 2.668  23.635 5.456  0.550  -0.723 C09 Y0I 18 
Y0I C11 C16 C 0 1 Y N N N N N 12.098 1.472  23.838 7.827  0.230  -0.633 C11 Y0I 19 
Y0I C12 C17 C 0 1 Y N N N N N 11.927 1.405  25.205 7.934  1.278  0.263  C12 Y0I 20 
Y0I C14 C18 C 0 1 Y N N N N N 9.839  2.584  24.997 5.563  1.597  0.173  C14 Y0I 21 
Y0I O15 O2  O 0 1 N N N N N N 8.870  1.252  20.951 1.812  -1.263 -1.198 O15 Y0I 22 
Y0I C16 C19 C 0 1 Y N N N N N 6.142  0.688  20.064 0.457  0.953  0.972  C16 Y0I 23 
Y0I N18 N3  N 0 1 Y N N N N N 6.244  0.400  17.700 -0.673 2.774  0.013  N18 Y0I 24 
Y0I C19 C20 C 0 1 Y N N N N N 5.214  1.251  17.571 -0.498 3.497  1.102  C19 Y0I 25 
Y0I C23 C21 C 0 1 Y N N N N N 9.695  -1.305 21.791 -1.958 -0.904 -0.965 C23 Y0I 26 
Y0I C25 C22 C 0 1 Y N N N N N 10.706 -1.861 23.952 -3.948 0.172  -0.161 C25 Y0I 27 
Y0I C27 C23 C 0 1 Y N N N N N 11.771 -2.591 26.184 -6.037 1.282  0.627  C27 Y0I 28 
Y0I C29 C24 C 0 1 Y N N N N N 14.153 -2.877 26.443 -7.843 1.718  -0.885 C29 Y0I 29 
Y0I C30 C25 C 0 1 Y N N N N N 14.332 -2.517 25.113 -7.118 1.161  -1.924 C30 Y0I 30 
Y0I C31 C26 C 0 1 Y N N N N N 13.233 -2.184 24.318 -5.856 0.654  -1.693 C31 Y0I 31 
Y0I C32 C27 C 0 1 Y N N N N N 9.439  -1.892 24.531 -3.399 0.235  1.118  C32 Y0I 32 
Y0I C33 C28 C 0 1 Y N N N N N 8.302  -1.621 23.758 -2.140 -0.275 1.353  C33 Y0I 33 
Y0I C34 C29 C 0 1 N N N N N N 6.931  -3.689 21.474 -1.049 -3.615 0.094  C34 Y0I 34 
Y0I C35 C30 C 0 1 N N N N N N 7.064  -4.426 20.118 -0.605 -5.046 0.254  C35 Y0I 35 
Y0I N37 N4  N 0 1 N N N N N N 6.135  -5.242 19.889 -1.294 -5.855 0.966  N37 Y0I 36 
Y0I H1  H1  H 0 1 N N N N N N 11.270 2.154  21.981 6.503  -0.955 -1.822 H1  Y0I 37 
Y0I H2  H2  H 0 1 N N N N N N 10.661 1.903  26.853 6.886  2.780  1.365  H2  Y0I 38 
Y0I H3  H3  H 0 1 N N N N N N 7.556  -0.555 19.010 -0.381 0.979  -0.989 H3  Y0I 39 
Y0I H4  H4  H 0 1 N N N N N N 3.773  2.556  18.522 0.309  3.573  3.085  H4  Y0I 40 
Y0I H5  H5  H 0 1 N N N N N N 4.649  2.061  20.836 1.177  1.246  2.977  H5  Y0I 41 
Y0I H6  H6  H 0 1 N N N N N N 11.813 -1.550 22.111 -3.643 -0.449 -2.195 H6  Y0I 42 
Y0I H7  H7  H 0 1 N N N N N N 12.736 -3.187 28.008 -7.868 2.225  1.192  H7  Y0I 43 
Y0I H8  H8  H 0 1 N N N N N N 5.988  0.574  22.195 1.437  -0.753 1.798  H8  Y0I 44 
Y0I H9  H9  H 0 1 N N N N N N 7.006  2.580  23.233 3.259  0.810  0.573  H9  Y0I 45 
Y0I H10 H10 H 0 1 N N N N N N 9.409  3.438  21.733 4.152  -0.865 -1.646 H10 Y0I 46 
Y0I H11 H11 H 0 1 N N N N N N 9.480  5.382  23.233 3.657  2.126  -2.001 H11 Y0I 47 
Y0I H12 H12 H 0 1 N N N N N N 7.867  5.180  22.469 4.443  1.056  -3.187 H12 Y0I 48 
Y0I H13 H13 H 0 1 N N N N N N 8.116  4.698  24.181 2.727  0.821  -2.776 H13 Y0I 49 
Y0I H14 H14 H 0 1 N N N N N N 12.974 1.037  23.379 8.711  -0.304 -0.948 H14 Y0I 50 
Y0I H15 H15 H 0 1 N N N N N N 12.671 0.923  25.822 8.902  1.562  0.648  H15 Y0I 51 
Y0I H16 H16 H 0 1 N N N N N N 8.958  3.006  25.457 4.679  2.131  0.488  H16 Y0I 52 
Y0I H17 H17 H 0 1 N N N N N N 4.842  1.465  16.580 -0.882 4.505  1.141  H17 Y0I 53 
Y0I H18 H18 H 0 1 N N N N N N 9.787  -1.089 20.737 -1.393 -1.345 -1.772 H18 Y0I 54 
Y0I H19 H19 H 0 1 N N N N N N 10.778 -2.644 26.605 -5.616 1.333  1.620  H19 Y0I 55 
Y0I H20 H20 H 0 1 N N N N N N 15.005 -3.129 27.058 -8.832 2.110  -1.069 H20 Y0I 56 
Y0I H21 H21 H 0 1 N N N N N N 15.326 -2.495 24.692 -7.546 1.114  -2.914 H21 Y0I 57 
Y0I H22 H22 H 0 1 N N N N N N 13.384 -1.911 23.284 -5.294 0.212  -2.503 H22 Y0I 58 
Y0I H23 H23 H 0 1 N N N N N N 9.333  -2.126 25.580 -3.962 0.678  1.927  H23 Y0I 59 
Y0I H24 H24 H 0 1 N N N N N N 7.322  -1.641 24.211 -1.717 -0.233 2.346  H24 Y0I 60 
Y0I H25 H25 H 0 1 N N N N N N 6.227  -4.230 22.124 -1.921 -3.433 0.723  H25 Y0I 61 
Y0I H26 H26 H 0 1 N N N N N N 7.914  -3.633 21.965 -1.309 -3.429 -0.948 H26 Y0I 62 
Y0I H27 H27 H 0 1 N N N N N N 7.880  -4.255 19.432 0.296  -5.389 -0.233 H27 Y0I 63 
Y0I H29 H29 H 0 1 N N N N N N 6.248  -5.701 19.008 -1.008 -6.776 1.068  H29 Y0I 64 
# 
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 
Y0I C19 N18 DOUB Y N 1  
Y0I C19 C20 SING Y N 2  
Y0I N18 C17 SING Y N 3  
Y0I C20 C21 DOUB Y N 4  
Y0I C17 C16 DOUB Y N 5  
Y0I N37 C35 DOUB N N 6  
Y0I C21 C16 SING Y N 7  
Y0I C16 C04 SING N N 8  
Y0I C35 C34 SING N N 9  
Y0I O01 C02 DOUB N N 10 
Y0I O15 C05 DOUB N N 11 
Y0I C02 C34 SING N N 12 
Y0I C02 N03 SING N N 13 
Y0I C04 N03 SING N N 14 
Y0I C04 C05 SING N N 15 
Y0I N03 C22 SING N N 16 
Y0I C05 N06 SING N N 17 
Y0I C23 C22 DOUB Y N 18 
Y0I C23 C24 SING Y N 19 
Y0I C22 C33 SING Y N 20 
Y0I C24 C25 DOUB Y N 21 
Y0I N06 C07 SING N N 22 
Y0I C07 C08 SING N N 23 
Y0I C07 C09 SING N N 24 
Y0I C10 C09 DOUB Y N 25 
Y0I C10 C11 SING Y N 26 
Y0I C09 C14 SING Y N 27 
Y0I C33 C32 DOUB Y N 28 
Y0I C11 C12 DOUB Y N 29 
Y0I C25 C32 SING Y N 30 
Y0I C25 C26 SING N N 31 
Y0I C31 C26 DOUB Y N 32 
Y0I C31 C30 SING Y N 33 
Y0I C26 C27 SING Y N 34 
Y0I C14 C13 DOUB Y N 35 
Y0I C30 C29 DOUB Y N 36 
Y0I C12 C13 SING Y N 37 
Y0I C27 C28 DOUB Y N 38 
Y0I C29 C28 SING Y N 39 
Y0I C10 H1  SING N N 40 
Y0I C13 H2  SING N N 41 
Y0I C17 H3  SING N N 42 
Y0I C20 H4  SING N N 43 
Y0I C21 H5  SING N N 44 
Y0I C24 H6  SING N N 45 
Y0I C28 H7  SING N N 46 
Y0I C04 H8  SING N N 47 
Y0I N06 H9  SING N N 48 
Y0I C07 H10 SING N N 49 
Y0I C08 H11 SING N N 50 
Y0I C08 H12 SING N N 51 
Y0I C08 H13 SING N N 52 
Y0I C11 H14 SING N N 53 
Y0I C12 H15 SING N N 54 
Y0I C14 H16 SING N N 55 
Y0I C19 H17 SING N N 56 
Y0I C23 H18 SING N N 57 
Y0I C27 H19 SING N N 58 
Y0I C29 H20 SING N N 59 
Y0I C30 H21 SING N N 60 
Y0I C31 H22 SING N N 61 
Y0I C32 H23 SING N N 62 
Y0I C33 H24 SING N N 63 
Y0I C34 H25 SING N N 64 
Y0I C34 H26 SING N N 65 
Y0I C35 H27 SING N N 66 
Y0I N37 H29 SING N N 67 
# 
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 
Y0I SMILES           ACDLabs              12.01 "CC(NC(=O)C(N(C(=O)CC=N)c1ccc(cc1)c1ccccc1)c1cccnc1)c1ccccc1"                                                                                                                              
Y0I InChI            InChI                1.06  "InChI=1S/C30H28N4O2/c1-22(23-9-4-2-5-10-23)33-30(36)29(26-13-8-20-32-21-26)34(28(35)18-19-31)27-16-14-25(15-17-27)24-11-6-3-7-12-24/h2-17,19-22,29,31H,18H2,1H3,(H,33,36)/t22-,29+/m0/s1" 
Y0I InChIKey         InChI                1.06  WSBQTFUCGVUNEH-PZGXJGMVSA-N                                                                                                                                                                
Y0I SMILES_CANONICAL CACTVS               3.385 "C[C@H](NC(=O)[C@H](N(C(=O)CC=N)c1ccc(cc1)c2ccccc2)c3cccnc3)c4ccccc4"                                                                                                                      
Y0I SMILES           CACTVS               3.385 "C[CH](NC(=O)[CH](N(C(=O)CC=N)c1ccc(cc1)c2ccccc2)c3cccnc3)c4ccccc4"                                                                                                                        
Y0I SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H](c1ccccc1)NC(=O)[C@@H](c2cccnc2)N(c3ccc(cc3)c4ccccc4)C(=O)CC=N"                                                                                                                    
Y0I SMILES           "OpenEye OEToolkits" 2.0.7 "CC(c1ccccc1)NC(=O)C(c2cccnc2)N(c3ccc(cc3)c4ccccc4)C(=O)CC=N"                                                                                                                              
# 
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 
Y0I "SYSTEMATIC NAME" ACDLabs              12.01 "(3Z)-N-([1,1'-biphenyl]-4-yl)-3-imino-N-[(1R)-2-oxo-2-{[(1S)-1-phenylethyl]amino}-1-(pyridin-3-yl)ethyl]propanamide"                 
Y0I "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "3-azanylidene-~{N}-[(1~{R})-2-oxidanylidene-2-[[(1~{S})-1-phenylethyl]amino]-1-pyridin-3-yl-ethyl]-~{N}-(4-phenylphenyl)propanamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
Y0I "Create component" 2022-12-19 RCSB 
Y0I "Initial release"  2023-08-09 RCSB 
Y0I "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            Y0I 
_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               C35 
_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      ? 
# 
