data_Y3C
# 
_chem_comp.id                                    Y3C 
_chem_comp.name                                  "(2~{S})-5-azanyl-5-oxidanylidene-2-[[(2~{S})-2-(3-oxidanylidene-1~{H}-isoindol-2-yl)-3-phenyl-propanoyl]amino]pentanoic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C22 H23 N3 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-11-16 
_chem_comp.pdbx_modified_date                    2024-01-12 
_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                        409.435 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y3C 
_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        8R5C 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
# 
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 
Y3C N1  N1  N 0 1 N N N N N N 10.685 -7.545  27.980 1.452  0.340  -0.244 N1  Y3C 1  
Y3C N3  N2  N 0 1 N N N N N N 11.048 -2.884  22.517 -5.703 0.508  -3.494 N3  Y3C 2  
Y3C C4  C1  C 0 1 Y N N N N N 9.966  -10.954 28.868 1.375  -3.636 -0.354 C4  Y3C 3  
Y3C C5  C2  C 0 1 Y N N N N N 10.741 -11.927 29.494 2.366  -4.448 -0.875 C5  Y3C 4  
Y3C C6  C3  C 0 1 Y N N N N N 11.845 -12.418 28.862 3.696  -4.143 -0.655 C6  Y3C 5  
Y3C C7  C4  C 0 1 N N N N N N 9.517  -9.442  26.938 0.635  -1.632 0.950  C7  Y3C 6  
Y3C C8  C5  C 0 1 N N S N N N 10.284 -8.152  26.728 0.291  -0.535 -0.059 C8  Y3C 7  
Y3C C10 C6  C 0 1 N N N N N N 9.799  -7.328  29.107 2.149  0.579  -1.512 C10 Y3C 8  
Y3C C13 C7  C 0 1 N N N N N N 11.868 -6.881  28.106 2.050  1.061  0.721  C13 Y3C 9  
Y3C C15 C8  C 0 1 Y N N N N N 11.335 -5.205  31.847 5.147  3.007  -1.396 C15 Y3C 10 
Y3C C17 C9  C 0 1 Y N N N N N 12.814 -5.415  29.968 4.098  2.705  0.738  C17 Y3C 11 
Y3C C20 C10 C 0 1 N N N N N N 7.916  -6.078  23.538 -3.460 0.307  2.289  C20 Y3C 12 
Y3C C21 C11 C 0 1 N N N N N N 10.023 -4.852  21.568 -4.368 0.618  -1.415 C21 Y3C 13 
Y3C C22 C12 C 0 1 N N N N N N 11.213 -3.915  21.719 -5.614 0.246  -2.175 C22 Y3C 14 
Y3C C1  C13 C 0 1 Y N N N N N 12.239 -11.934 27.649 4.036  -3.026 0.087  C1  Y3C 15 
Y3C C2  C14 C 0 1 Y N N N N N 11.477 -10.962 27.027 3.045  -2.214 0.607  C2  Y3C 16 
Y3C C3  C15 C 0 1 Y N N N N N 10.335 -10.489 27.636 1.715  -2.517 0.382  C3  Y3C 17 
Y3C C9  C16 C 0 1 N N N N N N 9.488  -7.150  25.894 -0.872 0.274  0.455  C9  Y3C 18 
Y3C C11 C17 C 0 1 Y N N N N N 10.653 -6.505  30.007 3.263  1.548  -1.206 C11 Y3C 19 
Y3C C12 C18 C 0 1 Y N N N N N 11.842 -6.227  29.383 3.181  1.825  0.161  C12 Y3C 20 
Y3C C14 C19 C 0 1 Y N N N N N 10.352 -5.952  31.236 4.239  2.136  -1.976 C14 Y3C 21 
Y3C C16 C20 C 0 1 Y N N N N N 12.532 -4.935  31.219 5.074  3.288  -0.043 C16 Y3C 22 
Y3C O1  O1  O 0 1 N N N N N N 12.768 -6.889  27.267 1.707  1.080  1.887  O1  Y3C 23 
Y3C O2  O2  O 0 1 N N N N N N 8.497  -6.603  26.341 -0.676 1.346  0.987  O2  Y3C 24 
Y3C N2  N3  N 0 1 N N N N N N 9.992  -6.880  24.708 -2.129 -0.194 0.324  N2  Y3C 25 
Y3C C18 C21 C 0 1 N N S N N N 9.425  -5.935  23.776 -3.259 0.593  0.823  C18 Y3C 26 
Y3C C19 C22 C 0 1 N N N N N N 10.189 -6.037  22.481 -4.525 0.214  0.052  C19 Y3C 27 
Y3C O3  O3  O 0 1 N N N N N N 7.227  -5.031  23.397 -4.446 0.920  2.963  O3  Y3C 28 
Y3C O4  O4  O 0 1 N N N N N N 7.476  -7.253  23.379 -2.734 -0.473 2.858  O4  Y3C 29 
Y3C O5  O5  O 0 1 N N N N N N 12.216 -4.054  21.040 -6.538 -0.291 -1.600 O5  Y3C 30 
Y3C H1  H1  H 0 1 N N N N N N 11.758 -2.183  22.581 -4.965 0.937  -3.954 H1  Y3C 31 
Y3C H2  H2  H 0 1 N N N N N N 10.213 -2.801  23.060 -6.506 0.268  -3.984 H2  Y3C 32 
Y3C H3  H3  H 0 1 N N N N N N 9.080  -10.570 29.352 0.336  -3.875 -0.526 H3  Y3C 33 
Y3C H4  H4  H 0 1 N N N N N N 10.469 -12.290 30.474 2.101  -5.320 -1.454 H4  Y3C 34 
Y3C H5  H5  H 0 1 N N N N N N 12.418 -13.205 29.330 4.470  -4.777 -1.061 H5  Y3C 35 
Y3C H6  H6  H 0 1 N N N N N N 8.625  -9.228  27.546 0.987  -1.177 1.875  H6  Y3C 36 
Y3C H7  H7  H 0 1 N N N N N N 9.207  -9.832  25.957 -0.254 -2.230 1.154  H7  Y3C 37 
Y3C H8  H8  H 0 1 N N N N N N 11.193 -8.399  26.160 0.024  -0.990 -1.013 H8  Y3C 38 
Y3C H9  H9  H 0 1 N N N N N N 8.892  -6.783  28.805 2.559  -0.355 -1.896 H9  Y3C 39 
Y3C H10 H10 H 0 1 N N N N N N 9.514  -8.278  29.582 1.463  1.015  -2.240 H10 Y3C 40 
Y3C H11 H11 H 0 1 N N N N N N 11.164 -4.822  32.842 5.913  3.468  -2.001 H11 Y3C 41 
Y3C H12 H12 H 0 1 N N N N N N 13.738 -5.178  29.462 4.045  2.927  1.794  H12 Y3C 42 
Y3C H13 H13 H 0 1 N N N N N N 9.100  -4.315  21.831 -3.511 0.100  -1.845 H13 Y3C 43 
Y3C H14 H14 H 0 1 N N N N N N 9.961  -5.199  20.526 -4.211 1.695  -1.481 H14 Y3C 44 
Y3C H15 H15 H 0 1 N N N N N N 13.137 -12.306 27.179 5.075  -2.788 0.259  H15 Y3C 45 
Y3C H16 H16 H 0 1 N N N N N N 11.777 -10.574 26.065 3.310  -1.340 1.182  H16 Y3C 46 
Y3C H17 H17 H 0 1 N N N N N N 9.387  -6.099  31.698 4.298  1.918  -3.032 H17 Y3C 47 
Y3C H18 H18 H 0 1 N N N N N N 13.267 -4.329  31.727 5.785  3.967  0.403  H18 Y3C 48 
Y3C H19 H19 H 0 1 N N N N N N 10.824 -7.362  24.434 -2.285 -1.051 -0.102 H19 Y3C 49 
Y3C H20 H20 H 0 1 N N N N N N 9.592  -4.923  24.174 -3.053 1.654  0.685  H20 Y3C 50 
Y3C H21 H21 H 0 1 N N N N N N 9.843  -6.934  21.947 -5.381 0.733  0.482  H21 Y3C 51 
Y3C H22 H22 H 0 1 N N N N N N 11.258 -6.141  22.719 -4.682 -0.863 0.117  H22 Y3C 52 
Y3C H23 H23 H 0 1 N N N N N N 6.339  -5.266  23.156 -4.536 0.705  3.902  H23 Y3C 53 
# 
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 
Y3C O5  C22 DOUB N N 1  
Y3C C21 C22 SING N N 2  
Y3C C21 C19 SING N N 3  
Y3C C22 N3  SING N N 4  
Y3C C19 C18 SING N N 5  
Y3C O4  C20 DOUB N N 6  
Y3C O3  C20 SING N N 7  
Y3C C20 C18 SING N N 8  
Y3C C18 N2  SING N N 9  
Y3C N2  C9  SING N N 10 
Y3C C9  O2  DOUB N N 11 
Y3C C9  C8  SING N N 12 
Y3C C8  C7  SING N N 13 
Y3C C8  N1  SING N N 14 
Y3C C7  C3  SING N N 15 
Y3C C2  C3  DOUB Y N 16 
Y3C C2  C1  SING Y N 17 
Y3C O1  C13 DOUB N N 18 
Y3C C3  C4  SING Y N 19 
Y3C C1  C6  DOUB Y N 20 
Y3C N1  C13 SING N N 21 
Y3C N1  C10 SING N N 22 
Y3C C13 C12 SING N N 23 
Y3C C6  C5  SING Y N 24 
Y3C C4  C5  DOUB Y N 25 
Y3C C10 C11 SING N N 26 
Y3C C12 C17 DOUB Y N 27 
Y3C C12 C11 SING Y N 28 
Y3C C17 C16 SING Y N 29 
Y3C C11 C14 DOUB Y N 30 
Y3C C16 C15 DOUB Y N 31 
Y3C C14 C15 SING Y N 32 
Y3C N3  H1  SING N N 33 
Y3C N3  H2  SING N N 34 
Y3C C4  H3  SING N N 35 
Y3C C5  H4  SING N N 36 
Y3C C6  H5  SING N N 37 
Y3C C7  H6  SING N N 38 
Y3C C7  H7  SING N N 39 
Y3C C8  H8  SING N N 40 
Y3C C10 H9  SING N N 41 
Y3C C10 H10 SING N N 42 
Y3C C15 H11 SING N N 43 
Y3C C17 H12 SING N N 44 
Y3C C21 H13 SING N N 45 
Y3C C21 H14 SING N N 46 
Y3C C1  H15 SING N N 47 
Y3C C2  H16 SING N N 48 
Y3C C14 H17 SING N N 49 
Y3C C16 H18 SING N N 50 
Y3C N2  H19 SING N N 51 
Y3C C18 H20 SING N N 52 
Y3C C19 H21 SING N N 53 
Y3C C19 H22 SING N N 54 
Y3C O3  H23 SING N N 55 
# 
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 
Y3C InChI            InChI                1.06  "InChI=1S/C22H23N3O5/c23-19(26)11-10-17(22(29)30)24-20(27)18(12-14-6-2-1-3-7-14)25-13-15-8-4-5-9-16(15)21(25)28/h1-9,17-18H,10-13H2,(H2,23,26)(H,24,27)(H,29,30)/t17-,18-/m0/s1" 
Y3C InChIKey         InChI                1.06  HSTLLKBRGCBKBS-ROUUACIJSA-N                                                                                                                                                      
Y3C SMILES_CANONICAL CACTVS               3.385 "NC(=O)CC[C@H](NC(=O)[C@H](Cc1ccccc1)N2Cc3ccccc3C2=O)C(O)=O"                                                                                                                     
Y3C SMILES           CACTVS               3.385 "NC(=O)CC[CH](NC(=O)[CH](Cc1ccccc1)N2Cc3ccccc3C2=O)C(O)=O"                                                                                                                       
Y3C SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)C[C@@H](C(=O)N[C@@H](CCC(=O)N)C(=O)O)N2Cc3ccccc3C2=O"                                                                                                                 
Y3C SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CC(C(=O)NC(CCC(=O)N)C(=O)O)N2Cc3ccccc3C2=O"                                                                                                                           
# 
_pdbx_chem_comp_identifier.comp_id           Y3C 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "(2~{S})-5-azanyl-5-oxidanylidene-2-[[(2~{S})-2-(3-oxidanylidene-1~{H}-isoindol-2-yl)-3-phenyl-propanoyl]amino]pentanoic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
Y3C "Create component" 2023-11-16 PDBE 
Y3C "Initial release"  2024-01-17 RCSB 
# 
