data_YHI # _chem_comp.id YHI _chem_comp.name "benzyl (1R,2S,5S)-2-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}carbamoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-3-carboxylate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C23 H31 N3 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-03-08 _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 429.509 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YHI _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 7LYI _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 YHI C10 C1 C 0 1 Y N N N N N -5.099 -23.860 -23.141 7.699 1.840 0.921 C10 YHI 1 YHI C15 C2 C 0 1 N N R N N N -11.890 -28.471 -23.012 -0.205 -2.832 -0.378 C15 YHI 2 YHI C17 C3 C 0 1 N N N N N N -14.194 -27.465 -22.503 1.956 -2.711 -1.853 C17 YHI 3 YHI C21 C4 C 0 1 N N S N N N -7.903 -29.094 -20.115 -3.519 -0.256 1.282 C21 YHI 4 YHI C22 C5 C 0 1 N N N N N N -7.291 -28.139 -19.042 -4.769 0.246 0.556 C22 YHI 5 YHI C24 C6 C 0 1 N N N N N N -6.072 -26.357 -20.457 -3.929 2.629 0.497 C24 YHI 6 YHI C01 C7 C 0 1 N N S N N N -12.122 -27.621 -24.252 0.970 -3.169 0.564 C01 YHI 7 YHI C02 C8 C 0 1 N N N N N N -11.247 -26.410 -24.104 1.542 -1.805 1.007 C02 YHI 8 YHI N03 N1 N 0 1 N N N N N N -10.942 -26.308 -22.665 1.124 -0.862 -0.056 N03 YHI 9 YHI C04 C9 C 0 1 N N N N N N -10.407 -25.256 -22.144 1.837 0.148 -0.593 C04 YHI 10 YHI O05 O1 O 0 1 N N N N N N -10.297 -24.126 -22.950 3.089 0.391 -0.163 O05 YHI 11 YHI C06 C10 C 0 1 N N N N N N -9.303 -23.119 -22.611 3.798 1.494 -0.787 C06 YHI 12 YHI C07 C11 C 0 1 Y N N N N N -7.827 -23.476 -22.782 5.174 1.613 -0.182 C07 YHI 13 YHI C08 C12 C 0 1 Y N N N N N -6.841 -22.546 -22.289 6.234 0.921 -0.736 C08 YHI 14 YHI C09 C13 C 0 1 Y N N N N N -5.513 -22.745 -22.442 7.496 1.030 -0.181 C09 YHI 15 YHI C11 C14 C 0 1 Y N N N N N -5.968 -24.812 -23.670 6.639 2.535 1.472 C11 YHI 16 YHI C12 C15 C 0 1 Y N N N N N -7.334 -24.597 -23.534 5.376 2.422 0.920 C12 YHI 17 YHI O13 O2 O 0 1 N N N N N N -9.998 -25.185 -21.019 1.350 0.839 -1.466 O13 YHI 18 YHI C14 C16 C 0 1 N N S N N N -11.029 -27.661 -22.114 -0.250 -1.289 -0.421 C14 YHI 19 YHI C16 C17 C 0 1 N N N N N N -13.337 -28.364 -23.496 1.022 -3.534 -0.963 C16 YHI 20 YHI C18 C18 C 0 1 N N N N N N -14.004 -29.462 -24.034 0.885 -5.010 -1.340 C18 YHI 21 YHI C19 C19 C 0 1 N N N N N N -9.551 -28.160 -21.837 -1.240 -0.764 0.586 C19 YHI 22 YHI N20 N2 N 0 1 N N N N N N -9.237 -28.657 -20.495 -2.557 -0.766 0.302 N20 YHI 23 YHI C23 C20 C 0 1 N N S N N N -7.126 -26.653 -19.344 -4.396 1.422 -0.349 C23 YHI 24 YHI C25 C21 C 0 1 N N N N N N -5.160 -25.291 -19.973 -4.503 3.817 -0.307 C25 YHI 25 YHI N26 N3 N 0 1 N N N N N N -5.535 -25.095 -18.491 -5.654 3.276 -1.039 N26 YHI 26 YHI C27 C22 C 0 1 N N N N N N -6.683 -25.835 -18.144 -5.616 1.933 -1.083 C27 YHI 27 YHI O28 O3 O 0 1 N N N N N N -7.214 -25.823 -17.054 -6.440 1.232 -1.633 O28 YHI 28 YHI C29 C23 C 0 1 N N N N N N -8.028 -30.456 -19.676 -3.906 -1.377 2.249 C29 YHI 29 YHI O30 O4 O 0 1 N N N N N N -6.614 -30.844 -19.427 -4.601 -2.402 1.536 O30 YHI 30 YHI O31 O5 O 0 1 N N N N N N -8.630 -28.129 -22.667 -0.851 -0.340 1.654 O31 YHI 31 YHI H1 H1 H 0 1 N N N N N N -4.039 -24.003 -23.287 8.684 1.925 1.354 H1 YHI 32 YHI H2 H2 H 0 1 N N N N N N -11.446 -29.447 -23.257 -1.155 -3.364 -0.325 H2 YHI 33 YHI H3 H3 H 0 1 N N N N N N -14.989 -28.075 -22.049 2.782 -3.337 -2.190 H3 YHI 34 YHI H4 H4 H 0 1 N N N N N N -13.541 -27.067 -21.713 1.403 -2.343 -2.718 H4 YHI 35 YHI H5 H5 H 0 1 N N N N N N -14.645 -26.631 -23.061 2.347 -1.866 -1.286 H5 YHI 36 YHI H6 H6 H 0 1 N N N N N N -7.251 -29.059 -21.000 -3.069 0.566 1.839 H6 YHI 37 YHI H7 H7 H 0 1 N N N N N N -7.931 -28.212 -18.151 -5.186 -0.560 -0.048 H7 YHI 38 YHI H8 H8 H 0 1 N N N N N N -6.289 -28.528 -18.806 -5.509 0.571 1.288 H8 YHI 39 YHI H9 H9 H 0 1 N N N N N N -6.583 -26.021 -21.371 -4.358 2.592 1.498 H9 YHI 40 YHI H10 H10 H 0 1 N N N N N N -5.495 -27.268 -20.673 -2.841 2.677 0.541 H10 YHI 41 YHI H11 H11 H 0 1 N N N N N N -11.860 -28.184 -25.160 0.934 -3.967 1.306 H11 YHI 42 YHI H12 H12 H 0 1 N N N N N N -10.321 -26.534 -24.684 1.119 -1.509 1.966 H12 YHI 43 YHI H13 H13 H 0 1 N N N N N N -11.778 -25.510 -24.448 2.629 -1.851 1.067 H13 YHI 44 YHI H14 H14 H 0 1 N N N N N N -9.501 -22.240 -23.241 3.887 1.310 -1.857 H14 YHI 45 YHI H15 H15 H 0 1 N N N N N N -9.454 -22.854 -21.554 3.247 2.420 -0.621 H15 YHI 46 YHI H16 H16 H 0 1 N N N N N N -7.177 -21.656 -21.778 6.078 0.295 -1.602 H16 YHI 47 YHI H17 H17 H 0 1 N N N N N N -4.796 -22.051 -22.029 8.323 0.483 -0.609 H17 YHI 48 YHI H18 H18 H 0 1 N N N N N N -5.591 -25.691 -24.171 6.797 3.168 2.333 H18 YHI 49 YHI H19 H19 H 0 1 N N N N N N -8.032 -25.279 -23.998 4.548 2.965 1.351 H19 YHI 50 YHI H20 H20 H 0 1 N N N N N N -11.529 -27.599 -21.136 -0.508 -0.945 -1.423 H20 YHI 51 YHI H21 H21 H 0 1 N N N N N N -14.789 -29.792 -23.338 0.614 -5.588 -0.456 H21 YHI 52 YHI H22 H22 H 0 1 N N N N N N -14.460 -29.179 -24.994 0.109 -5.121 -2.098 H22 YHI 53 YHI H23 H23 H 0 1 N N N N N N -13.289 -30.282 -24.195 1.833 -5.374 -1.735 H23 YHI 54 YHI H24 H24 H 0 1 N N N N N N -9.968 -28.697 -19.814 -2.869 -1.106 -0.552 H24 YHI 55 YHI H25 H25 H 0 1 N N N N N N -8.095 -26.263 -19.688 -3.619 1.127 -1.055 H25 YHI 56 YHI H26 H26 H 0 1 N N N N N N -4.110 -25.606 -20.069 -4.825 4.609 0.369 H26 YHI 57 YHI H27 H27 H 0 1 N N N N N N -8.627 -30.524 -18.756 -3.006 -1.794 2.700 H27 YHI 58 YHI H28 H28 H 0 1 N N N N N N -8.482 -31.085 -20.456 -4.552 -0.976 3.030 H28 YHI 59 YHI H29 H29 H 0 1 N N N N N N -6.580 -31.745 -19.127 -4.877 -3.147 2.087 H29 YHI 60 YHI H30 H30 H 0 1 N N N N N N -5.317 -24.361 -20.539 -3.756 4.196 -1.005 H30 YHI 61 YHI H31 H31 H 0 1 N N N N N N -5.027 -24.515 -17.855 -6.351 3.817 -1.440 H31 YHI 62 # 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 YHI C01 C02 SING N N 1 YHI C01 C16 SING N N 2 YHI C01 C15 SING N N 3 YHI C02 N03 SING N N 4 YHI C18 C16 SING N N 5 YHI C11 C12 DOUB Y N 6 YHI C11 C10 SING Y N 7 YHI C12 C07 SING Y N 8 YHI C16 C15 SING N N 9 YHI C16 C17 SING N N 10 YHI C10 C09 DOUB Y N 11 YHI C15 C14 SING N N 12 YHI O05 C06 SING N N 13 YHI O05 C04 SING N N 14 YHI C07 C06 SING N N 15 YHI C07 C08 DOUB Y N 16 YHI O31 C19 DOUB N N 17 YHI N03 C04 SING N N 18 YHI N03 C14 SING N N 19 YHI C09 C08 SING Y N 20 YHI C04 O13 DOUB N N 21 YHI C14 C19 SING N N 22 YHI C19 N20 SING N N 23 YHI N20 C21 SING N N 24 YHI C24 C25 SING N N 25 YHI C24 C23 SING N N 26 YHI C21 C29 SING N N 27 YHI C21 C22 SING N N 28 YHI C25 N26 SING N N 29 YHI C29 O30 SING N N 30 YHI C23 C22 SING N N 31 YHI C23 C27 SING N N 32 YHI N26 C27 SING N N 33 YHI C27 O28 DOUB N N 34 YHI C10 H1 SING N N 35 YHI C15 H2 SING N N 36 YHI C17 H3 SING N N 37 YHI C17 H4 SING N N 38 YHI C17 H5 SING N N 39 YHI C21 H6 SING N N 40 YHI C22 H7 SING N N 41 YHI C22 H8 SING N N 42 YHI C24 H9 SING N N 43 YHI C24 H10 SING N N 44 YHI C01 H11 SING N N 45 YHI C02 H12 SING N N 46 YHI C02 H13 SING N N 47 YHI C06 H14 SING N N 48 YHI C06 H15 SING N N 49 YHI C08 H16 SING N N 50 YHI C09 H17 SING N N 51 YHI C11 H18 SING N N 52 YHI C12 H19 SING N N 53 YHI C14 H20 SING N N 54 YHI C18 H21 SING N N 55 YHI C18 H22 SING N N 56 YHI C18 H23 SING N N 57 YHI N20 H24 SING N N 58 YHI C23 H25 SING N N 59 YHI C25 H26 SING N N 60 YHI C29 H27 SING N N 61 YHI C29 H28 SING N N 62 YHI O30 H29 SING N N 63 YHI C25 H30 SING N N 64 YHI N26 H31 SING N N 65 # 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 YHI SMILES ACDLabs 12.01 "O=C1NCCC1CC(CO)NC(=O)C1C2C(CN1C(=O)OCc1ccccc1)C2(C)C" YHI InChI InChI 1.03 "InChI=1S/C23H31N3O5/c1-23(2)17-11-26(22(30)31-13-14-6-4-3-5-7-14)19(18(17)23)21(29)25-16(12-27)10-15-8-9-24-20(15)28/h3-7,15-19,27H,8-13H2,1-2H3,(H,24,28)(H,25,29)/t15-,16-,17-,18-,19-/m0/s1" YHI InChIKey InChI 1.03 KXNVRILCTPCDNL-VMXHOPILSA-N YHI SMILES_CANONICAL CACTVS 3.385 "CC1(C)[C@H]2CN([C@@H]([C@@H]12)C(=O)N[C@H](CO)C[C@@H]3CCNC3=O)C(=O)OCc4ccccc4" YHI SMILES CACTVS 3.385 "CC1(C)[CH]2CN([CH]([CH]12)C(=O)N[CH](CO)C[CH]3CCNC3=O)C(=O)OCc4ccccc4" YHI SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)OCc3ccccc3)C(=O)N[C@@H](C[C@@H]4CCNC4=O)CO)C" YHI SMILES "OpenEye OEToolkits" 2.0.7 "CC1(C2C1C(N(C2)C(=O)OCc3ccccc3)C(=O)NC(CC4CCNC4=O)CO)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 YHI "SYSTEMATIC NAME" ACDLabs 12.01 "benzyl (1R,2S,5S)-2-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}carbamoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-3-carboxylate" YHI "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(phenylmethyl) (1~{R},2~{S},5~{S})-6,6-dimethyl-2-[[(2~{S})-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]carbamoyl]-3-azabicyclo[3.1.0]hexane-3-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 YHI "Create component" 2021-03-08 RCSB YHI "Initial release" 2021-03-17 RCSB YHI "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id YHI _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 C29 _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 ? #