data_Y8Y # _chem_comp.id Y8Y _chem_comp.name "(1R,2S)-2-((S)-2-(((((1R,3r,5S)-bicyclo[3.3.1]nonan-3-yl)methoxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C24 H41 N3 O8 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-02-10 _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 531.663 _chem_comp.one_letter_code ? _chem_comp.three_letter_code Y8Y _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 7LKR _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 Y8Y N11 N1 N 0 1 N N N N N N -18.801 -5.735 4.871 -2.651 -0.266 0.556 N11 Y8Y 1 Y8Y C12 C1 C 0 1 N N N N N N -19.563 -6.103 3.769 -1.465 0.103 0.031 C12 Y8Y 2 Y8Y C14 C2 C 0 1 N N N N N N -21.834 -7.296 4.072 -0.699 2.093 1.296 C14 Y8Y 3 Y8Y C15 C3 C 0 1 N N N N N N -23.384 -7.198 4.098 -2.007 2.142 2.089 C15 Y8Y 4 Y8Y C16 C4 C 0 1 N N N N N N -23.877 -5.936 4.825 -1.813 1.443 3.436 C16 Y8Y 5 Y8Y O20 O1 O 0 1 N N N N N N -21.146 -4.102 0.481 3.221 0.314 0.277 O20 Y8Y 6 Y8Y C23 C5 C 0 1 N N N N N N -21.288 -3.405 -2.719 6.860 -0.229 1.066 C23 Y8Y 7 Y8Y C24 C6 C 0 1 N N S N N N -22.140 -3.064 -3.965 8.177 -0.101 0.313 C24 Y8Y 8 Y8Y C25 C7 C 0 1 N N N N N N -22.110 -1.584 -4.263 8.267 1.270 -0.356 C25 Y8Y 9 Y8Y C26 C8 C 0 1 N N R N N N -22.521 -0.808 -3.034 7.129 1.378 -1.371 C26 Y8Y 10 Y8Y C27 C9 C 0 1 N N N N N N -21.617 -1.106 -1.817 5.783 1.272 -0.672 C27 Y8Y 11 Y8Y C28 C10 C 0 1 N N N N N N -23.986 -1.150 -2.708 7.298 0.320 -2.453 C28 Y8Y 12 Y8Y C29 C11 C 0 1 N N N N N N -24.349 -2.654 -2.757 7.380 -1.089 -1.885 C29 Y8Y 13 Y8Y C02 C12 C 0 1 N N N N N N -16.239 -2.240 3.702 -5.121 2.306 -1.867 C02 Y8Y 14 Y8Y C04 C13 C 0 1 N N N N N N -15.132 -3.241 1.885 -6.918 2.193 -0.399 C04 Y8Y 15 Y8Y C05 C14 C 0 1 N N N N N N -16.178 -4.261 2.474 -6.047 0.953 -0.095 C05 Y8Y 16 Y8Y C06 C15 C 0 1 N N S N N N -16.847 -3.642 3.702 -4.715 1.326 -0.788 C06 Y8Y 17 Y8Y C07 C16 C 0 1 N N N N N N -16.569 -4.512 4.985 -4.068 0.086 -1.407 C07 Y8Y 18 Y8Y C08 C17 C 0 1 N N S N N N -17.353 -5.867 5.009 -3.667 -0.888 -0.297 C08 Y8Y 19 Y8Y C09 C18 C 0 1 N N R N N N -17.021 -6.624 6.319 -3.099 -2.165 -0.919 C09 Y8Y 20 Y8Y C13 C19 C 0 1 N N S N N N -21.126 -5.929 3.727 -0.380 0.643 0.927 C13 Y8Y 21 Y8Y C17 C20 C 0 1 N N N N N N -24.074 -8.452 4.673 -2.407 3.600 2.324 C17 Y8Y 22 Y8Y C19 C21 C 0 1 N N N N N N -21.017 -4.296 1.834 2.050 0.470 0.924 C19 Y8Y 23 Y8Y C21 C22 C 0 1 N N N N N N -20.707 -2.969 -0.204 4.414 0.192 1.095 C21 Y8Y 24 Y8Y C22 C23 C 0 1 N N R N N N -21.620 -2.612 -1.420 5.647 0.021 0.183 C22 Y8Y 25 Y8Y C30 C24 C 0 1 N N N N N N -23.585 -3.513 -3.761 8.349 -1.205 -0.720 C30 Y8Y 26 Y8Y N03 N2 N 0 1 N N N N N N -15.306 -2.021 2.681 -6.358 2.774 -1.626 N03 Y8Y 27 Y8Y N18 N3 N 0 1 N N N N N N -21.590 -5.432 2.420 0.904 0.590 0.225 N18 Y8Y 28 Y8Y O01 O2 O 0 1 N N N N N N -16.533 -1.347 4.492 -4.428 2.627 -2.809 O01 Y8Y 29 Y8Y O10 O3 O 0 1 N N N N N N -17.585 -7.906 6.234 -4.076 -2.750 -1.781 O10 Y8Y 30 Y8Y O31 O4 O 0 1 N N N N N N -20.398 -3.485 2.504 2.027 0.504 2.138 O31 Y8Y 31 Y8Y O32 O5 O 0 1 N N N N N N -19.006 -6.574 2.774 -1.271 0.000 -1.162 O32 Y8Y 32 Y8Y H1 H1 H 0 1 N N N N N N -19.293 -5.340 5.647 -2.829 -0.123 1.498 H1 Y8Y 33 Y8Y H2 H2 H 0 1 N N N N N N -21.544 -8.040 3.315 -0.803 2.686 0.387 H2 Y8Y 34 Y8Y H3 H3 H 0 1 N N N N N N -21.489 -7.627 5.062 0.109 2.500 1.904 H3 Y8Y 35 Y8Y H4 H4 H 0 1 N N N N N N -23.711 -7.109 3.051 -2.792 1.636 1.527 H4 Y8Y 36 Y8Y H5 H5 H 0 1 N N N N N N -24.977 -5.913 4.816 -1.483 0.417 3.269 H5 Y8Y 37 Y8Y H6 H6 H 0 1 N N N N N N -23.519 -5.949 5.865 -1.061 1.976 4.017 H6 Y8Y 38 Y8Y H7 H7 H 0 1 N N N N N N -23.488 -5.043 4.314 -2.757 1.437 3.982 H7 Y8Y 39 Y8Y H8 H8 H 0 1 N N N N N N -21.423 -4.475 -2.503 6.790 -1.236 1.496 H8 Y8Y 40 Y8Y H9 H9 H 0 1 N N N N N N -20.235 -3.212 -2.970 6.853 0.486 1.898 H9 Y8Y 41 Y8Y H10 H10 H 0 1 N N N N N N -21.724 -3.607 -4.827 9.001 -0.177 1.041 H10 Y8Y 42 Y8Y H11 H11 H 0 1 N N N N N N -21.091 -1.291 -4.557 8.165 2.052 0.395 H11 Y8Y 43 Y8Y H12 H12 H 0 1 N N N N N N -22.807 -1.362 -5.085 9.224 1.369 -0.865 H12 Y8Y 44 Y8Y H13 H13 H 0 1 N N N N N N -22.457 0.267 -3.257 7.195 2.371 -1.847 H13 Y8Y 45 Y8Y H14 H14 H 0 1 N N N N N N -20.587 -0.809 -2.063 5.637 2.156 -0.038 H14 Y8Y 46 Y8Y H15 H15 H 0 1 N N N N N N -21.974 -0.516 -0.960 4.986 1.277 -1.427 H15 Y8Y 47 Y8Y H16 H16 H 0 1 N N N N N N -24.202 -0.783 -1.694 6.453 0.380 -3.148 H16 Y8Y 48 Y8Y H17 H17 H 0 1 N N N N N N -24.625 -0.624 -3.432 8.211 0.533 -3.022 H17 Y8Y 49 Y8Y H18 H18 H 0 1 N N N N N N -25.419 -2.730 -3.000 6.396 -1.459 -1.616 H18 Y8Y 50 Y8Y H19 H19 H 0 1 N N N N N N -24.169 -3.073 -1.756 7.743 -1.755 -2.693 H19 Y8Y 51 Y8Y H20 H20 H 0 1 N N N N N N -14.109 -3.630 1.992 -7.953 1.896 -0.562 H20 Y8Y 52 Y8Y H21 H21 H 0 1 N N N N N N -16.941 -4.486 1.714 -5.907 0.828 0.979 H21 Y8Y 53 Y8Y H22 H22 H 0 1 N N N N N N -15.664 -5.189 2.764 -6.478 0.055 -0.537 H22 Y8Y 54 Y8Y H23 H23 H 0 1 N N N N N N -17.933 -3.576 3.539 -4.036 1.799 -0.079 H23 Y8Y 55 Y8Y H24 H24 H 0 1 N N N N N N -15.492 -4.733 5.028 -4.778 -0.399 -2.076 H24 Y8Y 56 Y8Y H25 H25 H 0 1 N N N N N N -16.859 -3.927 5.870 -3.181 0.381 -1.968 H25 Y8Y 57 Y8Y H26 H26 H 0 1 N N N N N N -16.977 -6.475 4.173 -4.543 -1.135 0.304 H26 Y8Y 58 Y8Y S1 S1 S 0 1 N Y N N N N -17.411 -6.098 7.165 -2.670 -3.339 0.395 S1 Y8Y 59 Y8Y H28 H28 H 0 1 N N N N N N -15.927 -6.738 6.336 -2.205 -1.922 -1.494 H28 Y8Y 60 Y8Y H29 H29 H 0 1 N N N N N N -21.404 -5.203 4.505 -0.324 0.041 1.833 H29 Y8Y 61 Y8Y H30 H30 H 0 1 N N N N N N -25.165 -8.310 4.659 -2.546 4.098 1.364 H30 Y8Y 62 Y8Y H31 H31 H 0 1 N N N N N N -23.811 -9.328 4.062 -3.339 3.634 2.889 H31 Y8Y 63 Y8Y H32 H32 H 0 1 N N N N N N -23.738 -8.613 5.708 -1.623 4.106 2.886 H32 Y8Y 64 Y8Y H33 H33 H 0 1 N N N N N N -19.687 -3.153 -0.571 4.533 1.090 1.701 H33 Y8Y 65 Y8Y H34 H34 H 0 1 N N N N N N -20.698 -2.117 0.492 4.321 -0.677 1.746 H34 Y8Y 66 Y8Y H35 H35 H 0 1 N N N N N N -22.651 -2.871 -1.137 5.454 -0.848 -0.446 H35 Y8Y 67 Y8Y H36 H36 H 0 1 N N N N N N -24.105 -3.465 -4.729 9.377 -1.177 -1.104 H36 Y8Y 68 Y8Y H37 H37 H 0 1 N N N N N N -23.580 -4.552 -3.399 8.210 -2.178 -0.232 H37 Y8Y 69 Y8Y H38 H38 H 0 1 N N N N N N -22.326 -5.913 1.944 0.930 0.640 -0.744 H38 Y8Y 70 Y8Y H39 H39 H 0 1 N N N N N N -17.394 -8.390 7.029 -4.352 -2.177 -2.509 H39 Y8Y 71 Y8Y O1 O6 O 0 1 N Y N N N N ? ? ? -3.778 -3.543 1.263 O1 Y8Y 72 Y8Y O2 O7 O 0 1 N Y N N N N ? ? ? -1.944 -4.439 -0.136 O2 Y8Y 73 Y8Y O3 O8 O 0 1 N Y N N N N ? ? ? -1.654 -2.598 1.252 O3 Y8Y 74 Y8Y H27 H27 H 0 1 N N N N N N -15.340 -3.043 0.823 -6.854 2.909 0.420 H27 Y8Y 75 Y8Y H40 H40 H 0 1 N N N N N N -14.828 -1.158 2.518 -6.822 3.411 -2.191 H40 Y8Y 76 Y8Y H41 H41 H 0 1 N Y N N N N ? ? ? -1.328 -3.108 2.006 H41 Y8Y 77 # 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 Y8Y C25 C24 SING N N 1 Y8Y C25 C26 SING N N 2 Y8Y C24 C30 SING N N 3 Y8Y C24 C23 SING N N 4 Y8Y C30 C29 SING N N 5 Y8Y C26 C28 SING N N 6 Y8Y C26 C27 SING N N 7 Y8Y C29 C28 SING N N 8 Y8Y C23 C22 SING N N 9 Y8Y C27 C22 SING N N 10 Y8Y C22 C21 SING N N 11 Y8Y C21 O20 SING N N 12 Y8Y O20 C19 SING N N 13 Y8Y C19 N18 SING N N 14 Y8Y C19 O31 DOUB N N 15 Y8Y C04 C05 SING N N 16 Y8Y C04 N03 SING N N 17 Y8Y N18 C13 SING N N 18 Y8Y C05 C06 SING N N 19 Y8Y N03 C02 SING N N 20 Y8Y O32 C12 DOUB N N 21 Y8Y C06 C02 SING N N 22 Y8Y C06 C07 SING N N 23 Y8Y C02 O01 DOUB N N 24 Y8Y C13 C12 SING N N 25 Y8Y C13 C14 SING N N 26 Y8Y C12 N11 SING N N 27 Y8Y C14 C15 SING N N 28 Y8Y C15 C17 SING N N 29 Y8Y C15 C16 SING N N 30 Y8Y N11 C08 SING N N 31 Y8Y C07 C08 SING N N 32 Y8Y C08 C09 SING N N 33 Y8Y O10 C09 SING N N 34 Y8Y N11 H1 SING N N 35 Y8Y C14 H2 SING N N 36 Y8Y C14 H3 SING N N 37 Y8Y C15 H4 SING N N 38 Y8Y C16 H5 SING N N 39 Y8Y C16 H6 SING N N 40 Y8Y C16 H7 SING N N 41 Y8Y C23 H8 SING N N 42 Y8Y C23 H9 SING N N 43 Y8Y C24 H10 SING N N 44 Y8Y C25 H11 SING N N 45 Y8Y C25 H12 SING N N 46 Y8Y C26 H13 SING N N 47 Y8Y C27 H14 SING N N 48 Y8Y C27 H15 SING N N 49 Y8Y C28 H16 SING N N 50 Y8Y C28 H17 SING N N 51 Y8Y C29 H18 SING N N 52 Y8Y C29 H19 SING N N 53 Y8Y C04 H20 SING N N 54 Y8Y C05 H21 SING N N 55 Y8Y C05 H22 SING N N 56 Y8Y C06 H23 SING N N 57 Y8Y C07 H24 SING N N 58 Y8Y C07 H25 SING N N 59 Y8Y C08 H26 SING N N 60 Y8Y C09 S1 SING N N 61 Y8Y C09 H28 SING N N 62 Y8Y C13 H29 SING N N 63 Y8Y C17 H30 SING N N 64 Y8Y C17 H31 SING N N 65 Y8Y C17 H32 SING N N 66 Y8Y C21 H33 SING N N 67 Y8Y C21 H34 SING N N 68 Y8Y C22 H35 SING N N 69 Y8Y C30 H36 SING N N 70 Y8Y C30 H37 SING N N 71 Y8Y N18 H38 SING N N 72 Y8Y O10 H39 SING N N 73 Y8Y S1 O1 DOUB N N 74 Y8Y S1 O2 DOUB N N 75 Y8Y S1 O3 SING N N 76 Y8Y C04 H27 SING N N 77 Y8Y N03 H40 SING N N 78 Y8Y O3 H41 SING N N 79 # 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 Y8Y InChI InChI 1.03 "InChI=1S/C24H41N3O8S/c1-14(2)8-19(27-24(31)35-13-17-10-15-4-3-5-16(9-15)11-17)22(29)26-20(23(30)36(32,33)34)12-18-6-7-25-21(18)28/h14-20,23,30H,3-13H2,1-2H3,(H,25,28)(H,26,29)(H,27,31)(H,32,33,34)/t15-,16+,17+,18-,19-,20-,23+/m0/s1" Y8Y InChIKey InChI 1.03 PGYROSRJIVXTOE-REFFYEJJSA-N Y8Y SMILES_CANONICAL CACTVS 3.385 "CC(C)C[C@H](NC(=O)OC[C@H]1C[C@@H]2CCC[C@@H](C2)C1)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@H](O)[S](O)(=O)=O" Y8Y SMILES CACTVS 3.385 "CC(C)C[CH](NC(=O)OC[CH]1C[CH]2CCC[CH](C2)C1)C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)[S](O)(=O)=O" Y8Y SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OCC2C[C@@H]3CCC[C@@H](C3)C2" Y8Y SMILES "OpenEye OEToolkits" 2.0.7 "CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OCC2CC3CCCC(C3)C2" # _pdbx_chem_comp_identifier.comp_id Y8Y _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})-2-[[(2~{S})-2-[[(1~{R},5~{S})-3-bicyclo[3.3.1]nonanyl]methoxycarbonylamino]-4-methyl-pentanoyl]amino]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propane-1-sulfonic 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 Y8Y "Create component" 2021-02-10 RCSB Y8Y "Initial release" 2021-02-17 RCSB Y8Y "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id Y8Y _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 C09 _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 ? #