data_Y3B
# 
_chem_comp.id                                    Y3B 
_chem_comp.name                                  "[4-cyano-2-(2,2-dimethylpropanamido)phenyl]methyl (3aR,6aS)-5-(1H-benzotriazole-5-carbonyl)hexahydropyrrolo[3,4-c]pyrrole-2(1H)-carboxylate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C27 H29 N7 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-06-09 
_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                        515.564 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y3B 
_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        7G63 
_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 
Y3B C11 C1  C 0 1 N N N N N N -11.028 12.360 51.193 5.724  1.535  0.177  C11 Y3B 1  
Y3B C15 C2  C 0 1 Y N N N N N -7.496  13.348 52.014 7.740  -1.544 0.876  C15 Y3B 2  
Y3B C16 C3  C 0 1 Y N N N N N -9.330  11.145 52.720 7.991  0.841  -0.556 C16 Y3B 3  
Y3B C17 C4  C 0 1 Y N N N N N -7.993  11.218 53.222 9.035  -0.087 -0.571 C17 Y3B 4  
Y3B C18 C5  C 0 1 Y N N N N N -7.106  12.302 52.889 8.902  -1.287 0.153  C18 Y3B 5  
Y3B C22 C6  C 0 1 N N N N N N -14.397 7.574  47.140 -1.004 -0.804 0.177  C22 Y3B 6  
Y3B C25 C7  C 0 1 N N N N N N -13.408 5.399  46.100 -3.365 -0.458 0.212  C25 Y3B 7  
Y3B C26 C8  C 0 1 Y N N N N N -12.616 4.684  44.915 -4.363 0.668  0.125  C26 Y3B 8  
Y3B C27 C9  C 0 1 Y N N N N N -11.988 5.368  43.827 -5.723 0.395  0.194  C27 Y3B 9  
Y3B C28 C10 C 0 1 Y N N N N N -11.306 4.681  42.821 -6.643 1.430  0.115  C28 Y3B 10 
Y3B C1  C11 C 0 1 N N N N N N -12.369 8.553  48.237 1.493  -1.225 0.146  C1  Y3B 11 
Y3B N2  N1  N 0 1 N N N N N N -13.783 8.601  47.914 0.270  -0.372 0.094  N2  Y3B 12 
Y3B C3  C12 C 0 1 N N N N N N -14.380 9.778  48.545 0.711  1.051  -0.067 C3  Y3B 13 
Y3B C4  C13 C 0 1 N N S N N N -12.157 9.990  48.703 2.625  -0.292 -0.175 C4  Y3B 14 
Y3B C5  C14 C 0 1 N N S N N N -13.379 9.991  49.680 2.095  1.023  0.528  C5  Y3B 15 
Y3B C6  C15 C 0 1 N N N N N N -13.123 11.447 50.079 3.227  1.956  0.208  C6  Y3B 16 
Y3B N7  N2  N 0 1 N N N N N N -11.699 11.372 50.432 4.450  1.103  0.260  N7  Y3B 17 
Y3B C8  C16 C 0 1 N N N N N N -11.141 10.172 49.831 4.009  -0.320 0.420  C8  Y3B 18 
Y3B C12 C17 C 0 1 Y N N N N N -9.693  12.197 51.832 6.835  0.561  0.162  C12 Y3B 19 
Y3B O13 O1  O 0 1 N N N N N N -11.576 13.444 51.339 5.959  2.726  0.109  O13 Y3B 20 
Y3B C14 C18 C 0 1 Y N N N N N -8.781  13.284 51.506 6.723  -0.637 0.882  C14 Y3B 21 
Y3B N19 N3  N 0 1 Y N N N N N -5.917  12.036 53.580 10.068 -1.984 -0.049 N19 Y3B 22 
Y3B N20 N4  N 0 1 Y N N N N N -6.039  10.908 54.266 10.870 -1.193 -0.883 N20 Y3B 23 
Y3B N21 N5  N 0 1 Y N N N N N -7.248  10.403 54.090 10.250 -0.104 -1.170 N21 Y3B 24 
Y3B O23 O2  O 0 1 N N N N N N -13.534 6.893  46.148 -2.020 0.078  0.116  O23 Y3B 25 
Y3B O24 O3  O 0 1 N N N N N N -15.569 7.227  47.380 -1.236 -1.990 0.306  O24 Y3B 26 
Y3B C29 C19 C 0 1 Y N N N N N -11.220 3.318  42.871 -6.197 2.743  -0.034 C29 Y3B 27 
Y3B C30 C20 C 0 1 Y N N N N N -11.789 2.602  43.917 -4.827 3.007  -0.102 C30 Y3B 28 
Y3B C31 C21 C 0 1 Y N N N N N -12.478 3.286  44.919 -3.920 1.970  -0.017 C31 Y3B 29 
Y3B N32 N6  N 0 1 N N N N N N -12.093 6.764  43.733 -6.166 -0.924 0.343  N32 Y3B 30 
Y3B C33 C22 C 0 1 N N N N N N -11.508 7.622  42.831 -7.311 -1.321 -0.246 C33 Y3B 31 
Y3B O34 O4  O 0 1 N N N N N N -10.729 7.254  41.974 -7.995 -0.519 -0.845 O34 Y3B 32 
Y3B C35 C23 C 0 1 N N N N N N -11.925 9.073  43.088 -7.741 -2.763 -0.161 C35 Y3B 33 
Y3B C36 C24 C 0 1 N N N N N N -11.279 9.518  44.402 -9.065 -2.945 -0.907 C36 Y3B 34 
Y3B C37 C25 C 0 1 N N N N N N -11.549 10.037 41.967 -6.671 -3.653 -0.796 C37 Y3B 35 
Y3B C38 C26 C 0 1 N N N N N N -13.440 9.072  43.264 -7.925 -3.155 1.306  C38 Y3B 36 
Y3B C39 C27 C 0 1 N N N N N N -10.523 2.639  41.829 -7.140 3.817  -0.117 C39 Y3B 37 
Y3B N40 N7  N 0 1 N N N N N N -9.948  2.125  40.962 -7.889 4.669  -0.183 N40 Y3B 38 
Y3B H50 H1  H 0 1 N N N N N N -6.824  14.153 51.757 7.642  -2.467 1.429  H50 Y3B 39 
Y3B H51 H2  H 0 1 N N N N N N -10.012 10.353 52.993 8.078  1.766  -1.107 H51 Y3B 40 
Y3B H53 H3  H 0 1 N N N N N N -12.914 5.096  47.035 -3.484 -0.975 1.164  H53 Y3B 41 
Y3B H54 H4  H 0 1 N N N N N N -14.432 4.998  46.079 -3.536 -1.159 -0.606 H54 Y3B 42 
Y3B H55 H5  H 0 1 N N N N N N -10.849 5.224  42.007 -7.701 1.219  0.168  H55 Y3B 43 
Y3B H42 H6  H 0 1 N N N N N N -11.756 8.315  47.355 1.620  -1.647 1.143  H42 Y3B 44 
Y3B H41 H7  H 0 1 N N N N N N -12.157 7.829  49.037 1.434  -2.020 -0.599 H41 Y3B 45 
Y3B H44 H8  H 0 1 N N N N N N -14.413 10.638 47.860 0.746  1.329  -1.120 H44 Y3B 46 
Y3B H43 H9  H 0 1 N N N N N N -15.392 9.572  48.924 0.061  1.724  0.492  H43 Y3B 47 
Y3B H9  H10 H 0 1 N N N N N N -12.167 10.766 47.923 2.689  -0.139 -1.252 H9  Y3B 48 
Y3B H10 H11 H 0 1 N N N N N N -13.365 9.241  50.484 2.036  0.872  1.606  H10 Y3B 49 
Y3B H46 H12 H 0 1 N N N N N N -13.299 12.137 49.240 3.100  2.378  -0.789 H46 Y3B 50 
Y3B H45 H13 H 0 1 N N N N N N -13.740 11.749 50.938 3.286  2.750  0.952  H45 Y3B 51 
Y3B H47 H14 H 0 1 N N N N N N -11.139 9.321  50.529 3.973  -0.598 1.474  H47 Y3B 52 
Y3B H48 H15 H 0 1 N N N N N N -10.122 10.335 49.449 4.659  -0.993 -0.139 H48 Y3B 53 
Y3B H49 H16 H 0 1 N N N N N N -9.120  14.068 50.844 5.824  -0.843 1.444  H49 Y3B 54 
Y3B H52 H17 H 0 1 N N N N N N -5.099  12.611 53.559 10.292 -2.855 0.316  H52 Y3B 55 
Y3B H56 H18 H 0 1 N N N N N N -11.699 1.526  43.954 -4.477 4.022  -0.218 H56 Y3B 56 
Y3B H57 H19 H 0 1 N N N N N N -12.921 2.721  45.726 -2.861 2.177  -0.066 H57 Y3B 57 
Y3B H58 H20 H 0 1 N N N N N N -12.677 7.197  44.420 -5.648 -1.553 0.870  H58 Y3B 58 
Y3B H59 H21 H 0 1 N N N N N N -11.560 10.560 44.615 -8.934 -2.666 -1.953 H59 Y3B 59 
Y3B H61 H22 H 0 1 N N N N N N -11.627 8.870  45.220 -9.376 -3.988 -0.845 H61 Y3B 60 
Y3B H60 H23 H 0 1 N N N N N N -10.185 9.444  44.316 -9.827 -2.311 -0.454 H60 Y3B 61 
Y3B H63 H24 H 0 1 N N N N N N -11.882 11.052 42.229 -5.728 -3.523 -0.265 H63 Y3B 62 
Y3B H64 H25 H 0 1 N N N N N N -10.457 10.033 41.831 -6.982 -4.696 -0.735 H64 Y3B 63 
Y3B H62 H26 H 0 1 N N N N N N -12.036 9.721  41.033 -6.540 -3.374 -1.842 H62 Y3B 64 
Y3B H67 H27 H 0 1 N N N N N N -13.788 10.098 43.452 -8.687 -2.521 1.759  H67 Y3B 65 
Y3B H65 H28 H 0 1 N N N N N N -13.915 8.685  42.350 -8.236 -4.198 1.368  H65 Y3B 66 
Y3B H66 H29 H 0 1 N N N N N N -13.710 8.431  44.117 -6.982 -3.025 1.838  H66 Y3B 67 
# 
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 
Y3B C1  C4  SING N N 1  
Y3B C1  N2  SING N N 2  
Y3B N2  C3  SING N N 3  
Y3B N2  C22 SING N N 4  
Y3B C3  C5  SING N N 5  
Y3B C4  C5  SING N N 6  
Y3B C4  C8  SING N N 7  
Y3B C5  C6  SING N N 8  
Y3B C6  N7  SING N N 9  
Y3B N7  C8  SING N N 10 
Y3B N7  C11 SING N N 11 
Y3B C11 C12 SING N N 12 
Y3B C11 O13 DOUB N N 13 
Y3B C12 C14 DOUB Y N 14 
Y3B C12 C16 SING Y N 15 
Y3B C14 C15 SING Y N 16 
Y3B C15 C18 DOUB Y N 17 
Y3B C16 C17 DOUB Y N 18 
Y3B C17 C18 SING Y N 19 
Y3B C17 N21 SING Y N 20 
Y3B C18 N19 SING Y N 21 
Y3B N19 N20 SING Y N 22 
Y3B N20 N21 DOUB Y N 23 
Y3B C22 O23 SING N N 24 
Y3B C22 O24 DOUB N N 25 
Y3B O23 C25 SING N N 26 
Y3B C25 C26 SING N N 27 
Y3B C26 C27 DOUB Y N 28 
Y3B C26 C31 SING Y N 29 
Y3B C27 C28 SING Y N 30 
Y3B C27 N32 SING N N 31 
Y3B C28 C29 DOUB Y N 32 
Y3B C29 C30 SING Y N 33 
Y3B C29 C39 SING N N 34 
Y3B C30 C31 DOUB Y N 35 
Y3B N32 C33 SING N N 36 
Y3B C33 O34 DOUB N N 37 
Y3B C33 C35 SING N N 38 
Y3B C35 C36 SING N N 39 
Y3B C35 C37 SING N N 40 
Y3B C35 C38 SING N N 41 
Y3B C39 N40 TRIP N N 42 
Y3B C15 H50 SING N N 43 
Y3B C16 H51 SING N N 44 
Y3B C25 H53 SING N N 45 
Y3B C25 H54 SING N N 46 
Y3B C28 H55 SING N N 47 
Y3B C1  H42 SING N N 48 
Y3B C1  H41 SING N N 49 
Y3B C3  H44 SING N N 50 
Y3B C3  H43 SING N N 51 
Y3B C4  H9  SING N N 52 
Y3B C5  H10 SING N N 53 
Y3B C6  H46 SING N N 54 
Y3B C6  H45 SING N N 55 
Y3B C8  H47 SING N N 56 
Y3B C8  H48 SING N N 57 
Y3B C14 H49 SING N N 58 
Y3B N19 H52 SING N N 59 
Y3B C30 H56 SING N N 60 
Y3B C31 H57 SING N N 61 
Y3B N32 H58 SING N N 62 
Y3B C36 H59 SING N N 63 
Y3B C36 H61 SING N N 64 
Y3B C36 H60 SING N N 65 
Y3B C37 H63 SING N N 66 
Y3B C37 H64 SING N N 67 
Y3B C37 H62 SING N N 68 
Y3B C38 H67 SING N N 69 
Y3B C38 H65 SING N N 70 
Y3B C38 H66 SING N N 71 
# 
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 
Y3B SMILES           ACDLabs              12.01 "CC(C)(C)C(=O)Nc1cc(C#N)ccc1COC(=O)N1CC2CN(CC2C1)C(=O)c1cc2nn[NH]c2cc1"                                                                                                                        
Y3B InChI            InChI                1.06  "InChI=1S/C27H29N7O4/c1-27(2,3)25(36)29-22-8-16(10-28)4-5-18(22)15-38-26(37)34-13-19-11-33(12-20(19)14-34)24(35)17-6-7-21-23(9-17)31-32-30-21/h4-9,19-20H,11-15H2,1-3H3,(H,29,36)(H,30,31,32)" 
Y3B InChIKey         InChI                1.06  KVEPWXPZENHUEG-UHFFFAOYSA-N                                                                                                                                                                    
Y3B SMILES_CANONICAL CACTVS               3.385 "CC(C)(C)C(=O)Nc1cc(ccc1COC(=O)N2C[C@@H]3CN(C[C@H]3C2)C(=O)c4ccc5[nH]nnc5c4)C#N"                                                                                                               
Y3B SMILES           CACTVS               3.385 "CC(C)(C)C(=O)Nc1cc(ccc1COC(=O)N2C[CH]3CN(C[CH]3C2)C(=O)c4ccc5[nH]nnc5c4)C#N"                                                                                                                  
Y3B SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)(C)C(=O)Nc1cc(ccc1COC(=O)N2C[C@@H]3CN(C[C@H]3C2)C(=O)c4ccc5c(c4)nn[nH]5)C#N"                                                                                                             
Y3B SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)(C)C(=O)Nc1cc(ccc1COC(=O)N2CC3CN(CC3C2)C(=O)c4ccc5c(c4)nn[nH]5)C#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 
Y3B "SYSTEMATIC NAME" ACDLabs              12.01 "[4-cyano-2-(2,2-dimethylpropanamido)phenyl]methyl (3aR,6aS)-5-(1H-benzotriazole-5-carbonyl)hexahydropyrrolo[3,4-c]pyrrole-2(1H)-carboxylate"                                     
Y3B "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[4-cyano-2-(2,2-dimethylpropanoylamino)phenyl]methyl (3~{a}~{S},6~{a}~{S})-2-(1~{H}-benzotriazol-5-ylcarbonyl)-1,3,3~{a},4,6,6~{a}-hexahydropyrrolo[3,4-c]pyrrole-5-carboxylate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
Y3B "Create component" 2023-06-09 RCSB 
Y3B "Initial release"  2024-12-18 RCSB 
# 
