data_Y4D # _chem_comp.id Y4D _chem_comp.name "(1R,2S)-2-((S)-2-(((((1R,3s,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 2021-02-03 _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 Y4D _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 7LKU _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 Y4D N11 N1 N 0 1 N N N N N N 10.370 20.433 27.010 2.837 -0.115 0.473 N11 Y4D 1 Y4D C12 C1 C 0 1 N N N N N N 10.833 21.720 27.258 1.542 0.050 0.806 C12 Y4D 2 Y4D C14 C2 C 0 1 N N N N N N 13.305 21.998 27.787 0.661 0.741 -1.406 C14 Y4D 3 Y4D C15 C3 C 0 1 N N N N N N 14.702 22.497 27.360 -0.357 0.403 -2.498 C15 Y4D 4 Y4D C16 C4 C 0 1 N N N N N N 15.159 21.841 26.041 -0.242 1.421 -3.634 C16 Y4D 5 Y4D O20 O1 O 0 1 N N N N N N 10.789 25.505 25.547 -3.149 -0.335 0.447 O20 Y4D 6 Y4D C23 C5 C 0 1 N N N N N N 7.005 26.505 25.087 -6.732 -1.465 0.079 C23 Y4D 7 Y4D C24 C6 C 0 1 N N R N N N 5.735 26.705 25.966 -8.025 -1.066 0.788 C24 Y4D 8 Y4D C25 C7 C 0 1 N N N N N N 5.950 26.189 27.392 -7.734 0.014 1.831 C25 Y4D 9 Y4D C26 C8 C 0 1 N N S N N N 7.152 26.893 28.027 -7.133 1.237 1.136 C26 Y4D 10 Y4D C27 C9 C 0 1 N N N N N N 8.450 26.699 27.189 -5.835 0.847 0.429 C27 Y4D 11 Y4D C28 C10 C 0 1 N N N N N N 6.798 28.388 28.206 -8.133 1.785 0.117 C28 Y4D 12 Y4D C29 C11 C 0 1 N N N N N N 6.188 29.081 26.953 -8.459 0.712 -0.922 C29 Y4D 13 Y4D C02 C12 C 0 1 N N N N N N 6.802 21.066 24.469 3.810 -2.575 0.146 C02 Y4D 14 Y4D C04 C13 C 0 1 N N N N N N 5.799 22.735 25.773 5.876 -3.285 -0.643 C04 Y4D 15 Y4D C05 C14 C 0 1 N N N N N N 6.962 22.071 26.598 6.072 -3.015 0.865 C05 Y4D 16 Y4D C06 C15 C 0 1 N N S N N N 7.746 21.155 25.661 4.818 -2.175 1.201 C06 Y4D 17 Y4D C07 C16 C 0 1 N N N N N N 8.030 19.784 26.378 5.132 -0.681 1.101 C07 Y4D 18 Y4D C08 C17 C 0 1 N N S N N N 9.114 19.853 27.477 3.886 0.128 1.467 C08 Y4D 19 Y4D C09 C18 C 0 1 N N R N N N 9.323 18.442 28.041 4.233 1.618 1.488 C09 Y4D 20 Y4D C13 C19 C 0 1 N N S N N N 12.192 22.226 26.693 0.463 -0.200 -0.216 C13 Y4D 21 Y4D C17 C20 C 0 1 N N N N N N 15.754 22.305 28.481 -0.077 -1.000 -3.040 C17 Y4D 22 Y4D C19 C21 C 0 1 N N N N N N 11.041 24.135 25.579 -1.944 -0.562 -0.109 C19 Y4D 23 Y4D C21 C22 C 0 1 N N N N N N 9.560 25.993 24.954 -4.285 -1.024 -0.140 C21 Y4D 24 Y4D C22 C23 C 0 1 N N S N N N 8.233 25.937 25.852 -5.561 -0.645 0.619 C22 Y4D 25 Y4D C30 C24 C 0 1 N N N N N N 5.306 28.191 26.029 -9.029 -0.527 -0.234 C30 Y4D 26 Y4D N03 N2 N 0 1 N N N N N N 5.720 21.947 24.543 4.429 -3.200 -0.871 N03 Y4D 27 Y4D N18 N3 N 0 1 N N N N N N 12.116 23.629 26.310 -0.849 0.046 0.388 N18 Y4D 28 Y4D O01 O2 O 0 1 N N N N N N 6.942 20.303 23.517 2.617 -2.368 0.212 O01 Y4D 29 Y4D O10 O3 O 0 1 N N N N N N 10.145 18.540 29.179 3.102 2.364 1.942 O10 Y4D 30 Y4D O31 O4 O 0 1 N N N N N N 10.291 23.378 24.975 -1.844 -1.314 -1.058 O31 Y4D 31 Y4D O32 O5 O 0 1 N N N N N N 10.164 22.523 27.933 1.244 0.399 1.929 O32 Y4D 32 Y4D H1 H1 H 0 1 N N N N N N 10.957 19.844 26.455 3.075 -0.398 -0.424 H1 Y4D 33 Y4D H2 H2 H 0 1 N N N N N N 13.009 22.533 28.701 1.670 0.620 -1.801 H2 Y4D 34 Y4D H3 H3 H 0 1 N N N N N N 13.370 20.920 27.998 0.518 1.772 -1.083 H3 Y4D 35 Y4D H4 H4 H 0 1 N N N N N N 14.619 23.578 27.175 -1.363 0.438 -2.079 H4 Y4D 36 Y4D H5 H5 H 0 1 N N N N N N 16.155 22.219 25.769 0.763 1.387 -4.053 H5 Y4D 37 Y4D H6 H6 H 0 1 N N N N N N 15.204 20.750 26.171 -0.968 1.181 -4.412 H6 Y4D 38 Y4D H7 H7 H 0 1 N N N N N N 14.443 22.086 25.243 -0.442 2.421 -3.248 H7 Y4D 39 Y4D H8 H8 H 0 1 N N N N N N 7.286 27.480 24.661 -6.538 -2.526 0.254 H8 Y4D 40 Y4D H9 H9 H 0 1 N N N N N N 6.754 25.808 24.274 -6.832 -1.297 -0.993 H9 Y4D 41 Y4D H10 H10 H 0 1 N N N N N N 4.914 26.131 25.511 -8.451 -1.940 1.284 H10 Y4D 42 Y4D H11 H11 H 0 1 N N N N N N 5.051 26.391 27.992 -8.667 0.301 2.322 H11 Y4D 43 Y4D H12 H12 H 0 1 N N N N N N 6.136 25.105 27.363 -7.041 -0.368 2.577 H12 Y4D 44 Y4D H13 H13 H 0 1 N N N N N N 7.321 26.459 29.023 -6.921 2.007 1.882 H13 Y4D 45 Y4D H14 H14 H 0 1 N N N N N N 9.172 26.133 27.796 -5.914 1.072 -0.634 H14 Y4D 46 Y4D H15 H15 H 0 1 N N N N N N 8.864 27.692 26.958 -5.008 1.422 0.852 H15 Y4D 47 Y4D H16 H16 H 0 1 N N N N N N 7.719 28.925 28.477 -9.048 2.083 0.631 H16 Y4D 48 Y4D H17 H17 H 0 1 N N N N N N 6.071 28.469 29.027 -7.702 2.654 -0.382 H17 Y4D 49 Y4D H18 H18 H 0 1 N N N N N N 7.020 29.470 26.348 -9.199 1.105 -1.624 H18 Y4D 50 Y4D H19 H19 H 0 1 N N N N N N 5.567 29.918 27.303 -7.558 0.447 -1.474 H19 Y4D 51 Y4D H20 H20 H 0 1 N N N N N N 6.035 23.785 25.546 6.396 -2.530 -1.232 H20 Y4D 52 Y4D H21 H21 H 0 1 N N N N N N 4.851 22.683 26.328 6.241 -4.280 -0.898 H21 Y4D 53 Y4D H22 H22 H 0 1 N N N N N N 6.542 21.484 27.428 6.080 -3.947 1.431 H22 Y4D 54 Y4D H23 H23 H 0 1 N N N N N N 7.626 22.850 26.999 6.984 -2.445 1.044 H23 Y4D 55 Y4D H24 H24 H 0 1 N N N N N N 8.695 21.627 25.367 4.447 -2.420 2.196 H24 Y4D 56 Y4D H25 H25 H 0 1 N N N N N N 7.094 19.436 26.839 5.941 -0.433 1.788 H25 Y4D 57 Y4D H26 H26 H 0 1 N N N N N N 8.356 19.059 25.618 5.435 -0.440 0.082 H26 Y4D 58 Y4D H27 H27 H 0 1 N N N N N N 8.720 20.481 28.290 3.531 -0.177 2.451 H27 Y4D 59 Y4D S1 S1 S 0 1 N Y N N N N 9.774 17.808 27.306 4.682 2.159 -0.184 S1 Y4D 60 Y4D H29 H29 H 0 1 N N N N N N 8.333 18.095 28.373 5.073 1.786 2.162 H29 Y4D 61 Y4D H30 H30 H 0 1 N N N N N N 12.449 21.617 25.814 0.518 -1.234 -0.557 H30 Y4D 62 Y4D H31 H31 H 0 1 N N N N N N 15.397 22.784 29.405 0.929 -1.034 -3.458 H31 Y4D 63 Y4D H32 H32 H 0 1 N N N N N N 15.907 21.230 28.660 -0.159 -1.725 -2.230 H32 Y4D 64 Y4D H33 H33 H 0 1 N N N N N N 16.705 22.764 28.174 -0.803 -1.240 -3.817 H33 Y4D 65 Y4D H34 H34 H 0 1 N N N N N N 9.724 27.044 24.673 -4.385 -0.733 -1.186 H34 Y4D 66 Y4D H35 H35 H 0 1 N N N N N N 9.371 25.397 24.049 -4.130 -2.101 -0.076 H35 Y4D 67 Y4D H36 H36 H 0 1 N N N N N N 8.034 24.881 26.087 -5.420 -0.860 1.679 H36 Y4D 68 Y4D H37 H37 H 0 1 N N N N N N 5.350 28.604 25.011 -9.233 -1.296 -0.980 H37 Y4D 69 Y4D H38 H38 H 0 1 N N N N N N 4.271 28.234 26.398 -9.958 -0.266 0.275 H38 Y4D 70 Y4D H39 H39 H 0 1 N N N N N N 4.998 22.027 23.856 3.977 -3.549 -1.655 H39 Y4D 71 Y4D H40 H40 H 0 1 N N N N N N 12.855 24.247 26.579 -0.928 0.647 1.146 H40 Y4D 72 Y4D H41 H41 H 0 1 N N N N N N 10.286 17.674 29.544 2.316 2.262 1.389 H41 Y4D 73 Y4D O2 O6 O 0 1 N Y N N N N ? ? ? 5.914 1.573 -0.583 O2 Y4D 74 Y4D O1 O7 O 0 1 N Y N N N N ? ? ? 3.547 2.131 -1.039 O1 Y4D 75 Y4D O3 O8 O 0 1 N Y N N N N ? ? ? 5.002 3.639 -0.032 O3 Y4D 76 Y4D H45 H45 H 0 1 N Y N N N N ? ? ? 5.262 4.072 -0.856 H45 Y4D 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 Y4D O01 C02 DOUB N N 1 Y4D C02 N03 SING N N 2 Y4D C02 C06 SING N N 3 Y4D N03 C04 SING N N 4 Y4D C21 O20 SING N N 5 Y4D C21 C22 SING N N 6 Y4D O31 C19 DOUB N N 7 Y4D C23 C22 SING N N 8 Y4D C23 C24 SING N N 9 Y4D O20 C19 SING N N 10 Y4D C19 N18 SING N N 11 Y4D C06 C07 SING N N 12 Y4D C06 C05 SING N N 13 Y4D C04 C05 SING N N 14 Y4D C22 C27 SING N N 15 Y4D C24 C30 SING N N 16 Y4D C24 C25 SING N N 17 Y4D C30 C29 SING N N 18 Y4D C16 C15 SING N N 19 Y4D N18 C13 SING N N 20 Y4D C07 C08 SING N N 21 Y4D C13 C12 SING N N 22 Y4D C13 C14 SING N N 23 Y4D C29 C28 SING N N 24 Y4D N11 C12 SING N N 25 Y4D N11 C08 SING N N 26 Y4D C27 C26 SING N N 27 Y4D C12 O32 DOUB N N 28 Y4D C15 C14 SING N N 29 Y4D C15 C17 SING N N 30 Y4D C25 C26 SING N N 31 Y4D C08 C09 SING N N 32 Y4D C26 C28 SING N N 33 Y4D C09 O10 SING N N 34 Y4D N11 H1 SING N N 35 Y4D C14 H2 SING N N 36 Y4D C14 H3 SING N N 37 Y4D C15 H4 SING N N 38 Y4D C16 H5 SING N N 39 Y4D C16 H6 SING N N 40 Y4D C16 H7 SING N N 41 Y4D C23 H8 SING N N 42 Y4D C23 H9 SING N N 43 Y4D C24 H10 SING N N 44 Y4D C25 H11 SING N N 45 Y4D C25 H12 SING N N 46 Y4D C26 H13 SING N N 47 Y4D C27 H14 SING N N 48 Y4D C27 H15 SING N N 49 Y4D C28 H16 SING N N 50 Y4D C28 H17 SING N N 51 Y4D C29 H18 SING N N 52 Y4D C29 H19 SING N N 53 Y4D C04 H20 SING N N 54 Y4D C04 H21 SING N N 55 Y4D C05 H22 SING N N 56 Y4D C05 H23 SING N N 57 Y4D C06 H24 SING N N 58 Y4D C07 H25 SING N N 59 Y4D C07 H26 SING N N 60 Y4D C08 H27 SING N N 61 Y4D C09 S1 SING N N 62 Y4D C09 H29 SING N N 63 Y4D C13 H30 SING N N 64 Y4D C17 H31 SING N N 65 Y4D C17 H32 SING N N 66 Y4D C17 H33 SING N N 67 Y4D C21 H34 SING N N 68 Y4D C21 H35 SING N N 69 Y4D C22 H36 SING N N 70 Y4D C30 H37 SING N N 71 Y4D C30 H38 SING N N 72 Y4D N03 H39 SING N N 73 Y4D N18 H40 SING N N 74 Y4D O10 H41 SING N N 75 Y4D S1 O2 DOUB N N 76 Y4D S1 O1 DOUB N N 77 Y4D S1 O3 SING N N 78 Y4D O3 H45 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 Y4D 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" Y4D InChIKey InChI 1.03 PGYROSRJIVXTOE-ZDCSSWJMSA-N Y4D 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" Y4D 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" Y4D SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)[C@H](O)S(=O)(=O)O)NC(=O)OCC2C[C@@H]3CCC[C@@H](C3)C2" Y4D 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 Y4D _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 "(1~{R},2~{S})-2-[[(2~{S})-2-[[(1~{S},5~{R})-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 Y4D "Create component" 2021-02-03 RCSB Y4D "Other modification" 2021-02-04 RCSB Y4D "Other modification" 2021-02-08 RCSB Y4D "Modify name" 2021-02-09 RCSB Y4D "Initial release" 2021-02-17 RCSB Y4D "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id Y4D _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 ? #