data_XF8 # _chem_comp.id XF8 _chem_comp.name "(2-methyl-2-phenylsulfanyl-propyl) ~{N}-[(2~{S})-1-[[(2~{S},3~{S})-3-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-4-(cyclopropylamino)-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C28 H42 N4 O9 S2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-11-14 _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 642.784 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XF8 _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 8F45 _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 XF8 C02 C1 C 0 1 N N N N N N 11.070 24.373 25.994 2.113 0.078 0.934 C02 XF8 1 XF8 C04 C2 C 0 1 N N S N N N 11.716 22.355 27.127 -0.316 0.191 1.090 C04 XF8 2 XF8 C05 C3 C 0 1 N N N N N N 12.783 21.919 28.150 -0.604 1.587 1.645 C05 XF8 3 XF8 C06 C4 C 0 1 N N N N N N 14.203 22.138 27.611 0.489 1.975 2.643 C06 XF8 4 XF8 C07 C5 C 0 1 N N N N N N 15.256 22.126 28.780 0.271 3.418 3.103 C07 XF8 5 XF8 C08 C6 C 0 1 N N N N N N 14.494 21.117 26.528 0.431 1.040 3.852 C08 XF8 6 XF8 C09 C7 C 0 1 N N N N N N 10.384 21.858 27.660 -1.455 -0.242 0.203 C09 XF8 7 XF8 C11 C8 C 0 1 N N S N N N 8.635 20.167 27.870 -3.827 -0.644 -0.182 C11 XF8 8 XF8 C12 C9 C 0 1 N N N N N N 7.588 19.925 26.748 -4.244 -2.105 0.003 C12 XF8 9 XF8 C13 C10 C 0 1 N N S N N N 7.054 21.230 26.157 -3.122 -3.021 -0.488 C13 XF8 10 XF8 C14 C11 C 0 1 N N N N N N 6.016 21.061 25.094 -2.063 -3.181 0.580 C14 XF8 11 XF8 C16 C12 C 0 1 N N N N N N 5.187 22.807 26.346 -2.451 -5.312 -0.257 C16 XF8 12 XF8 C17 C13 C 0 1 N N N N N N 6.296 22.098 27.161 -3.654 -4.455 -0.713 C17 XF8 13 XF8 C19 C14 C 0 1 N N S N N N 9.106 18.885 28.552 -5.006 0.270 0.160 C19 XF8 14 XF8 C21 C15 C 0 1 N N N N N N 8.115 18.423 29.607 -4.557 1.708 0.110 C21 XF8 15 XF8 C23 C16 C 0 1 N N N N N N 7.493 18.125 32.033 -3.633 3.619 -1.085 C23 XF8 16 XF8 C24 C17 C 0 1 N N N N N N 6.581 19.231 32.691 -3.648 4.317 -2.447 C24 XF8 17 XF8 C25 C18 C 0 1 N N N N N N 7.787 18.701 33.490 -2.317 3.924 -1.803 C25 XF8 18 XF8 C29 C19 C 0 1 N N N N N N 11.003 26.220 24.475 4.495 -0.061 0.954 C29 XF8 19 XF8 C30 C20 C 0 1 N N N N N N 12.283 27.094 24.111 5.674 -0.010 -0.020 C30 XF8 20 XF8 C31 C21 C 0 1 N N N N N N 12.658 28.047 25.228 5.539 -1.138 -1.044 C31 XF8 21 XF8 C32 C22 C 0 1 N N N N N N 13.453 26.203 23.602 5.680 1.338 -0.744 C32 XF8 22 XF8 C34 C23 C 0 1 Y N N N N N 10.296 29.262 23.025 8.450 -0.113 -0.365 C34 XF8 23 XF8 C35 C24 C 0 1 Y N N N N N 8.980 28.736 22.936 8.069 0.050 -1.692 C35 XF8 24 XF8 C36 C25 C 0 1 Y N N N N N 7.858 29.562 23.224 9.031 0.131 -2.679 C36 XF8 25 XF8 C37 C26 C 0 1 Y N N N N N 8.039 30.916 23.604 10.372 0.049 -2.349 C37 XF8 26 XF8 C38 C27 C 0 1 Y N N N N N 9.353 31.438 23.704 10.754 -0.112 -1.030 C38 XF8 27 XF8 C39 C28 C 0 1 Y N N N N N 10.478 30.614 23.415 9.798 -0.194 -0.037 C39 XF8 28 XF8 N03 N1 N 0 1 N N N N N N 11.686 23.773 27.006 0.925 0.220 0.313 N03 XF8 29 XF8 N10 N2 N 0 1 N N N N N N 9.842 20.679 27.327 -2.701 -0.342 0.705 N10 XF8 30 XF8 N15 N3 N 0 1 N N N N N N 4.944 21.947 25.167 -1.710 -4.474 0.692 N15 XF8 31 XF8 N22 N4 N 0 1 N N N N N N 8.399 18.519 30.963 -4.069 2.222 -1.036 N22 XF8 32 XF8 O01 O1 O 0 1 N N N N N N 10.433 23.697 25.136 2.154 -0.076 2.139 O01 XF8 33 XF8 O18 O2 O 0 1 N N N N N N 6.141 20.201 24.194 -1.599 -2.275 1.240 O18 XF8 34 XF8 O20 O3 O 0 1 N N N N N N 10.244 19.353 29.329 -5.480 -0.036 1.473 O20 XF8 35 XF8 O26 O4 O 0 1 N N N N N N 6.971 18.030 29.234 -4.636 2.403 1.101 O26 XF8 36 XF8 O27 O5 O 0 1 N N N N N N 9.757 22.631 28.446 -1.249 -0.500 -0.965 O27 XF8 37 XF8 O28 O6 O 0 1 N N N N N N 11.102 25.710 25.794 3.253 0.099 0.219 O28 XF8 38 XF8 S33 S1 S 0 1 N N N N N N 11.800 28.169 22.638 7.226 -0.209 0.899 S33 XF8 39 XF8 H1 H1 H 0 1 N N N N N N 11.926 21.881 26.157 -0.212 -0.513 1.916 H1 XF8 40 XF8 H2 H2 H 0 1 N N N N N N 12.656 22.507 29.071 -0.621 2.307 0.826 H2 XF8 41 XF8 H3 H3 H 0 1 N N N N N N 12.647 20.851 28.375 -1.571 1.587 2.148 H3 XF8 42 XF8 H4 H4 H 0 1 N N N N N N 14.236 23.137 27.152 1.464 1.890 2.164 H4 XF8 43 XF8 H5 H5 H 0 1 N N N N N N 14.985 22.887 29.526 -0.705 3.503 3.582 H5 XF8 44 XF8 H6 H6 H 0 1 N N N N N N 15.265 21.134 29.255 1.049 3.694 3.814 H6 XF8 45 XF8 H7 H7 H 0 1 N N N N N N 16.255 22.348 28.376 0.312 4.084 2.241 H7 XF8 46 XF8 H8 H8 H 0 1 N N N N N N 15.512 21.273 26.141 0.586 0.012 3.524 H8 XF8 47 XF8 H9 H9 H 0 1 N N N N N N 14.413 20.104 26.948 1.210 1.316 4.563 H9 XF8 48 XF8 H10 H10 H 0 1 N N N N N N 13.768 21.234 25.710 -0.545 1.125 4.331 H10 XF8 49 XF8 H11 H11 H 0 1 N N N N N N 8.213 20.852 28.620 -3.528 -0.479 -1.217 H11 XF8 50 XF8 H12 H12 H 0 1 N N N N N N 6.745 19.357 27.168 -4.435 -2.297 1.059 H12 XF8 51 XF8 H13 H13 H 0 1 N N N N N N 8.060 19.341 25.945 -5.149 -2.299 -0.572 H13 XF8 52 XF8 H14 H14 H 0 1 N N N N N N 7.898 21.808 25.752 -2.684 -2.628 -1.406 H14 XF8 53 XF8 H15 H15 H 0 1 N N N N N N 5.523 23.806 26.030 -2.800 -6.220 0.234 H15 XF8 54 XF8 H16 H16 H 0 1 N N N N N N 4.271 22.902 26.947 -1.822 -5.564 -1.111 H16 XF8 55 XF8 H17 H17 H 0 1 N N N N N N 5.852 21.473 27.950 -4.528 -4.649 -0.092 H17 XF8 56 XF8 H18 H18 H 0 1 N N N N N N 6.971 22.838 27.615 -3.879 -4.628 -1.765 H18 XF8 57 XF8 H20 H20 H 0 1 N N N N N N 7.067 17.111 32.003 -3.880 4.220 -0.209 H20 XF8 58 XF8 H21 H21 H 0 1 N N N N N N 6.597 20.257 32.296 -3.983 3.736 -3.306 H21 XF8 59 XF8 H22 H22 H 0 1 N N N N N N 5.560 18.977 33.011 -3.905 5.376 -2.467 H22 XF8 60 XF8 H23 H23 H 0 1 N N N N N N 7.624 18.067 34.374 -1.698 4.726 -1.400 H23 XF8 61 XF8 H24 H24 H 0 1 N N N N N N 8.661 19.348 33.659 -1.775 3.085 -2.239 H24 XF8 62 XF8 H25 H25 H 0 1 N N N N N N 10.103 26.848 24.397 4.491 -1.021 1.470 H25 XF8 63 XF8 H26 H26 H 0 1 N N N N N N 10.926 25.381 23.768 4.591 0.743 1.684 H26 XF8 64 XF8 H27 H27 H 0 1 N N N N N N 12.950 27.472 26.119 4.735 -0.902 -1.741 H27 XF8 65 XF8 H28 H28 H 0 1 N N N N N N 13.500 28.677 24.905 6.475 -1.247 -1.591 H28 XF8 66 XF8 H29 H29 H 0 1 N N N N N N 11.795 28.685 25.471 5.309 -2.071 -0.528 H29 XF8 67 XF8 H30 H30 H 0 1 N N N N N N 13.791 25.542 24.414 5.743 2.143 -0.012 H30 XF8 68 XF8 H31 H31 H 0 1 N N N N N N 13.108 25.594 22.754 6.539 1.387 -1.413 H31 XF8 69 XF8 H32 H32 H 0 1 N N N N N N 14.287 26.843 23.278 4.762 1.444 -1.322 H32 XF8 70 XF8 H33 H33 H 0 1 N N N N N N 8.830 27.706 22.649 7.023 0.112 -1.951 H33 XF8 71 XF8 H34 H34 H 0 1 N N N N N N 6.860 29.154 23.153 8.737 0.257 -3.711 H34 XF8 72 XF8 H35 H35 H 0 1 N N N N N N 7.185 31.543 23.815 11.122 0.112 -3.123 H35 XF8 73 XF8 H36 H36 H 0 1 N N N N N N 9.502 32.466 24.001 11.802 -0.176 -0.776 H36 XF8 74 XF8 H37 H37 H 0 1 N N N N N N 11.475 31.021 23.493 10.097 -0.320 0.993 H37 XF8 75 XF8 H38 H38 H 0 1 N N N N N N 12.140 24.331 27.700 0.892 0.343 -0.649 H38 XF8 76 XF8 H39 H39 H 0 1 N N N N N N 10.321 20.121 26.649 -2.853 -0.213 1.655 H39 XF8 77 XF8 H40 H40 H 0 1 N N N N N N 4.163 21.993 24.544 -1.051 -4.809 1.320 H40 XF8 78 XF8 H41 H41 H 0 1 N N N N N N 9.292 18.886 31.224 -4.006 1.666 -1.829 H41 XF8 79 XF8 H42 H42 H 0 1 N N N N N N 10.624 18.624 29.805 -4.817 0.081 2.168 H42 XF8 80 XF8 S1 S2 S 0 1 N Y N N N N ? ? ? -6.340 0.010 -1.041 S1 XF8 81 XF8 O3 O7 O 0 1 N Y N N N N ? ? ? -5.704 0.318 -2.388 O3 XF8 82 XF8 O2 O8 O 0 1 N Y N N N N ? ? ? -6.679 -1.368 -1.120 O2 XF8 83 XF8 O1 O9 O 0 1 N Y N N N N ? ? ? -7.345 1.004 -0.892 O1 XF8 84 XF8 H19 H19 H 0 1 N N N N N N ? ? ? -6.306 0.221 -3.139 H19 XF8 85 # 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 XF8 S33 C34 SING N N 1 XF8 S33 C30 SING N N 2 XF8 C35 C34 DOUB Y N 3 XF8 C35 C36 SING Y N 4 XF8 C34 C39 SING Y N 5 XF8 C36 C37 DOUB Y N 6 XF8 C39 C38 DOUB Y N 7 XF8 C32 C30 SING N N 8 XF8 C37 C38 SING Y N 9 XF8 C30 C29 SING N N 10 XF8 C30 C31 SING N N 11 XF8 O18 C14 DOUB N N 12 XF8 C29 O28 SING N N 13 XF8 C14 N15 SING N N 14 XF8 C14 C13 SING N N 15 XF8 O01 C02 DOUB N N 16 XF8 N15 C16 SING N N 17 XF8 O28 C02 SING N N 18 XF8 C02 N03 SING N N 19 XF8 C13 C12 SING N N 20 XF8 C13 C17 SING N N 21 XF8 C16 C17 SING N N 22 XF8 C08 C06 SING N N 23 XF8 C12 C11 SING N N 24 XF8 N03 C04 SING N N 25 XF8 C04 C09 SING N N 26 XF8 C04 C05 SING N N 27 XF8 N10 C09 SING N N 28 XF8 N10 C11 SING N N 29 XF8 C06 C05 SING N N 30 XF8 C06 C07 SING N N 31 XF8 C09 O27 DOUB N N 32 XF8 C11 C19 SING N N 33 XF8 C19 O20 SING N N 34 XF8 C19 C21 SING N N 35 XF8 O26 C21 DOUB N N 36 XF8 C21 N22 SING N N 37 XF8 N22 C23 SING N N 38 XF8 C23 C24 SING N N 39 XF8 C23 C25 SING N N 40 XF8 C24 C25 SING N N 41 XF8 C04 H1 SING N N 42 XF8 C05 H2 SING N N 43 XF8 C05 H3 SING N N 44 XF8 C06 H4 SING N N 45 XF8 C07 H5 SING N N 46 XF8 C07 H6 SING N N 47 XF8 C07 H7 SING N N 48 XF8 C08 H8 SING N N 49 XF8 C08 H9 SING N N 50 XF8 C08 H10 SING N N 51 XF8 C11 H11 SING N N 52 XF8 C12 H12 SING N N 53 XF8 C12 H13 SING N N 54 XF8 C13 H14 SING N N 55 XF8 C16 H15 SING N N 56 XF8 C16 H16 SING N N 57 XF8 C17 H17 SING N N 58 XF8 C17 H18 SING N N 59 XF8 C23 H20 SING N N 60 XF8 C24 H21 SING N N 61 XF8 C24 H22 SING N N 62 XF8 C25 H23 SING N N 63 XF8 C25 H24 SING N N 64 XF8 C29 H25 SING N N 65 XF8 C29 H26 SING N N 66 XF8 C31 H27 SING N N 67 XF8 C31 H28 SING N N 68 XF8 C31 H29 SING N N 69 XF8 C32 H30 SING N N 70 XF8 C32 H31 SING N N 71 XF8 C32 H32 SING N N 72 XF8 C35 H33 SING N N 73 XF8 C36 H34 SING N N 74 XF8 C37 H35 SING N N 75 XF8 C38 H36 SING N N 76 XF8 C39 H37 SING N N 77 XF8 N03 H38 SING N N 78 XF8 N10 H39 SING N N 79 XF8 N15 H40 SING N N 80 XF8 N22 H41 SING N N 81 XF8 O20 H42 SING N N 82 XF8 C19 S1 SING N N 83 XF8 S1 O3 SING N N 84 XF8 S1 O2 DOUB N N 85 XF8 S1 O1 DOUB N N 86 XF8 O3 H19 SING N N 87 # 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 XF8 SMILES ACDLabs 12.01 "CC(C)CC(NC(=O)OCC(C)(C)Sc1ccccc1)C(=O)NC(CC1CCNC1=O)C(O)(C(=O)NC1CC1)S(=O)(=O)O" XF8 InChI InChI 1.06 "InChI=1S/C28H42N4O9S2/c1-17(2)14-21(31-26(36)41-16-27(3,4)42-20-8-6-5-7-9-20)24(34)32-22(15-18-12-13-29-23(18)33)28(37,43(38,39)40)25(35)30-19-10-11-19/h5-9,17-19,21-22,37H,10-16H2,1-4H3,(H,29,33)(H,30,35)(H,31,36)(H,32,34)(H,38,39,40)/t18-,21-,22-,28-/m0/s1" XF8 InChIKey InChI 1.06 MVHBODFTFWPKCE-ZYAAQSTJSA-N XF8 SMILES_CANONICAL CACTVS 3.385 "CC(C)C[C@H](NC(=O)OCC(C)(C)Sc1ccccc1)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@@](O)(C(=O)NC3CC3)[S](O)(=O)=O" XF8 SMILES CACTVS 3.385 "CC(C)C[CH](NC(=O)OCC(C)(C)Sc1ccccc1)C(=O)N[CH](C[CH]2CCNC2=O)[C](O)(C(=O)NC3CC3)[S](O)(=O)=O" XF8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)[C@](C(=O)NC2CC2)(O)S(=O)(=O)O)NC(=O)OCC(C)(C)Sc3ccccc3" XF8 SMILES "OpenEye OEToolkits" 2.0.7 "CC(C)CC(C(=O)NC(CC1CCNC1=O)C(C(=O)NC2CC2)(O)S(=O)(=O)O)NC(=O)OCC(C)(C)Sc3ccccc3" # 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 XF8 "SYSTEMATIC NAME" ACDLabs 12.01 "(2S,3S)-1-(cyclopropylamino)-2-hydroxy-3-[(N-{[2-methyl-2-(phenylsulfanyl)propoxy]carbonyl}-L-leucyl)amino]-1-oxo-4-[(3S)-2-oxopyrrolidin-3-yl]butane-2-sulfonic acid" XF8 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S},3~{S})-1-(cyclopropylamino)-3-[[(2~{S})-4-methyl-2-[(2-methyl-2-phenylsulfanyl-propoxy)carbonylamino]pentanoyl]amino]-2-oxidanyl-1-oxidanylidene-4-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]butane-2-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 XF8 "Create component" 2022-11-14 RCSB XF8 "Initial release" 2022-11-23 RCSB XF8 "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id XF8 _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 C19 _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 ? #