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 #