data_V9R # _chem_comp.id V9R _chem_comp.name "~{tert}-butyl ~{N}-[1-[(2~{R})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{S})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C31 H41 N5 O7" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "(R,S,S)-13b; 13b-H; ketoamide inhibitor 13b (bound)" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-02-28 _chem_comp.pdbx_modified_date 2023-08-13 _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 595.687 _chem_comp.one_letter_code ? _chem_comp.three_letter_code V9R _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 8A4Q _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.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 V9R O26 O1 O 0 1 N N N -7.566 -22.658 -3.888 5.966 -0.486 -0.221 O26 V9R 1 V9R C24 C1 C 0 1 N N N -6.956 -23.407 -3.125 5.902 -1.579 0.308 C24 V9R 2 V9R O25 O2 O 0 1 N N N -5.587 -23.183 -2.702 6.848 -2.504 0.058 O25 V9R 3 V9R C27 C2 C 0 1 N N N -4.692 -22.107 -3.019 7.914 -2.127 -0.852 C27 V9R 4 V9R C31 C3 C 0 1 N N N -3.417 -22.338 -2.197 7.319 -1.770 -2.215 C31 V9R 5 V9R C32 C4 C 0 1 N N N -5.316 -20.797 -2.575 8.662 -0.917 -0.289 C32 V9R 6 V9R C33 C5 C 0 1 N N N -4.441 -22.121 -4.517 8.886 -3.298 -1.011 C33 V9R 7 V9R N23 N1 N 0 1 N N N -7.439 -24.542 -2.632 4.887 -1.862 1.148 N23 V9R 8 V9R C19 C6 C 0 1 N N N -8.603 -25.101 -2.981 3.961 -0.866 1.491 C19 V9R 9 V9R C21 C7 C 0 1 N N N -8.883 -26.370 -2.304 3.204 -0.219 0.490 C21 V9R 10 V9R O22 O3 O 0 1 N N N -8.012 -26.790 -1.492 3.352 -0.526 -0.682 O22 V9R 11 V9R C18 C8 C 0 1 N N N -9.540 -24.631 -3.902 3.778 -0.513 2.799 C18 V9R 12 V9R C17 C9 C 0 1 N N N -10.714 -25.325 -4.155 2.846 0.486 3.115 C17 V9R 13 V9R C16 C10 C 0 1 N N N -10.985 -26.510 -3.495 2.140 1.089 2.131 C16 V9R 14 V9R N15 N2 N 0 1 N N N -10.114 -27.012 -2.599 2.318 0.736 0.830 N15 V9R 15 V9R C20 C11 C 0 1 N N R -10.378 -28.291 -1.915 1.539 1.406 -0.215 C20 V9R 16 V9R C22 C12 C 0 1 N N N -10.796 -29.396 -2.895 1.718 2.921 -0.091 C22 V9R 17 V9R C29 C13 C 0 1 N N N -9.618 -29.636 -3.851 3.176 3.287 -0.375 C29 V9R 18 V9R C34 C14 C 0 1 N N N -9.721 -28.930 -5.206 3.586 4.749 -0.188 C34 V9R 19 V9R C30 C15 C 0 1 N N N -9.870 -30.454 -5.124 3.460 4.163 -1.597 C30 V9R 20 V9R C36 C16 C 0 1 N N N -11.308 -28.114 -0.734 0.082 1.058 -0.057 C36 V9R 21 V9R O37 O4 O 0 1 N N N -12.224 -27.289 -0.693 -0.315 0.562 0.976 O37 V9R 22 V9R N38 N3 N 0 1 N N N -10.894 -28.942 0.240 -0.781 1.297 -1.064 N38 V9R 23 V9R C40 C17 C 0 1 N N S -11.267 -29.063 1.625 -2.214 1.061 -0.873 C40 V9R 24 V9R C42 C18 C 0 1 N N N -11.783 -27.884 2.467 -2.851 2.292 -0.224 C42 V9R 25 V9R C45 C19 C 0 1 N N S -11.263 -26.448 2.309 -4.229 1.922 0.329 C45 V9R 26 V9R C47 C20 C 0 1 N N N -11.036 -25.777 3.643 -4.097 0.919 1.453 C47 V9R 27 V9R O48 O5 O 0 1 N N N -11.684 -26.008 4.653 -3.884 -0.266 1.305 O48 V9R 28 V9R N49 N4 N 0 1 N N N -10.066 -24.862 3.529 -4.247 1.531 2.640 N49 V9R 29 V9R C51 C21 C 0 1 N N N -9.440 -24.858 2.207 -4.482 2.970 2.471 C51 V9R 30 V9R C54 C22 C 0 1 N N N -9.974 -26.131 1.533 -4.894 3.150 0.993 C54 V9R 31 V9R C57 C23 C 0 1 N N S -12.093 -30.351 1.827 -2.874 0.800 -2.228 C57 V9R 32 V9R O40 O6 O 0 1 N N N -11.110 -31.227 2.399 -2.827 1.990 -3.018 O40 V9R 33 V9R C35 C24 C 0 1 N N N -12.790 -31.058 0.665 -4.310 0.393 -2.018 C35 V9R 34 V9R O41 O7 O 0 1 N N N -12.472 -32.211 0.382 -5.207 1.111 -2.406 O41 V9R 35 V9R N36 N5 N 0 1 N N N -13.779 -30.396 0.043 -4.597 -0.769 -1.398 N36 V9R 36 V9R C13 C25 C 0 1 N N N -14.619 -31.006 -0.999 -5.992 -1.165 -1.194 C13 V9R 37 V9R C14 C26 C 0 1 Y N N -14.380 -30.434 -2.376 -6.039 -2.494 -0.484 C14 V9R 38 V9R C28 C27 C 0 1 Y N N -14.137 -31.283 -3.462 -6.066 -2.539 0.897 C28 V9R 39 V9R C26 C28 C 0 1 Y N N -13.919 -30.707 -4.719 -6.108 -3.757 1.548 C26 V9R 40 V9R C25 C29 C 0 1 Y N N -13.970 -29.310 -4.893 -6.123 -4.931 0.818 C25 V9R 41 V9R C23 C30 C 0 1 Y N N -14.235 -28.475 -3.810 -6.097 -4.886 -0.563 C23 V9R 42 V9R C15 C31 C 0 1 Y N N -14.446 -29.044 -2.545 -6.060 -3.667 -1.214 C15 V9R 43 V9R H1 H1 H 0 1 N N N -3.662 -22.317 -1.125 6.627 -0.936 -2.102 H1 V9R 44 V9R H2 H2 H 0 1 N N N -2.987 -23.317 -2.455 8.120 -1.487 -2.899 H2 V9R 45 V9R H3 H3 H 0 1 N N N -2.687 -21.546 -2.422 6.787 -2.632 -2.617 H3 V9R 46 V9R H4 H4 H 0 1 N N N -5.484 -20.820 -1.488 9.086 -1.171 0.683 H4 V9R 47 V9R H5 H5 H 0 1 N N N -4.640 -19.966 -2.824 9.463 -0.634 -0.972 H5 V9R 48 V9R H6 H6 H 0 1 N N N -6.277 -20.655 -3.092 7.969 -0.083 -0.176 H6 V9R 49 V9R H7 H7 H 0 1 N N N -3.756 -21.302 -4.782 8.354 -4.161 -1.412 H7 V9R 50 V9R H8 H8 H 0 1 N N N -3.991 -23.083 -4.804 9.687 -3.016 -1.694 H8 V9R 51 V9R H9 H9 H 0 1 N N N -5.394 -21.988 -5.050 9.311 -3.553 -0.039 H9 V9R 52 V9R H10 H10 H 0 1 N N N -9.347 -23.708 -4.429 4.344 -0.998 3.581 H10 V9R 53 V9R H12 H12 H 0 1 N N N -11.422 -24.937 -4.873 2.691 0.774 4.144 H12 V9R 54 V9R H13 H13 H 0 1 N N N -11.904 -27.038 -3.700 1.424 1.857 2.382 H13 V9R 55 V9R H14 H14 H 0 1 N N N -9.416 -28.618 -1.493 1.887 1.078 -1.194 H14 V9R 56 V9R H15 H15 H 0 1 N N N -11.682 -29.078 -3.464 1.071 3.423 -0.810 H15 V9R 57 V9R H16 H16 H 0 1 N N N -11.026 -30.320 -2.344 1.454 3.237 0.918 H16 V9R 58 V9R H17 H17 H 0 1 N N N -8.617 -29.710 -3.400 3.911 2.522 -0.122 H17 V9R 59 V9R H18 H18 H 0 1 N N N -8.824 -28.489 -5.666 2.817 5.450 0.136 H18 V9R 60 V9R H19 H19 H 0 1 N N N -10.596 -28.304 -5.434 4.591 4.946 0.186 H19 V9R 61 V9R H20 H20 H 0 1 N N N -10.852 -30.921 -5.293 4.381 3.975 -2.148 H20 V9R 62 V9R H21 H21 H 0 1 N N N -9.080 -31.106 -5.524 2.608 4.478 -2.199 H21 V9R 63 V9R H22 H22 H 0 1 N N N -10.196 -29.596 -0.052 -0.453 1.625 -1.916 H22 V9R 64 V9R H23 H23 H 0 1 N N N -10.318 -29.311 2.122 -2.357 0.195 -0.226 H23 V9R 65 V9R H24 H24 H 0 1 N N N -12.867 -27.835 2.286 -2.216 2.644 0.589 H24 V9R 66 V9R H25 H25 H 0 1 N N N -11.599 -28.158 3.516 -2.958 3.081 -0.969 H25 V9R 67 V9R H26 H26 H 0 1 N N N -12.066 -25.885 1.810 -4.863 1.525 -0.464 H26 V9R 68 V9R H27 H27 H 0 1 N N N -9.797 -24.246 4.270 -4.207 1.081 3.498 H27 V9R 69 V9R H28 H28 H 0 1 N N N -8.344 -24.893 2.294 -5.285 3.302 3.129 H28 V9R 70 V9R H29 H29 H 0 1 N N N -9.734 -23.963 1.639 -3.569 3.528 2.680 H29 V9R 71 V9R H30 H30 H 0 1 N N N -10.192 -25.949 0.470 -4.492 4.078 0.586 H30 V9R 72 V9R H31 H31 H 0 1 N N N -9.250 -26.955 1.623 -5.978 3.114 0.883 H31 V9R 73 V9R H32 H32 H 0 1 N N N -12.857 -30.134 2.588 -2.341 0.001 -2.743 H32 V9R 74 V9R H33 H33 H 0 1 N N N -11.114 -32.055 1.933 -3.283 2.745 -2.620 H33 V9R 75 V9R H34 H34 H 0 1 N N N -13.952 -29.445 0.300 -3.879 -1.343 -1.088 H34 V9R 76 V9R H35 H35 H 0 1 N N N -15.674 -30.846 -0.734 -6.499 -0.412 -0.590 H35 V9R 77 V9R H36 H36 H 0 1 N N N -14.408 -32.085 -1.029 -6.491 -1.251 -2.159 H36 V9R 78 V9R H37 H37 H 0 1 N N N -14.118 -32.355 -3.333 -6.053 -1.622 1.468 H37 V9R 79 V9R H38 H38 H 0 1 N N N -13.709 -31.342 -5.567 -6.128 -3.792 2.628 H38 V9R 80 V9R H39 H39 H 0 1 N N N -13.803 -28.884 -5.871 -6.155 -5.883 1.327 H39 V9R 81 V9R H40 H40 H 0 1 N N N -14.277 -27.404 -3.942 -6.108 -5.803 -1.133 H40 V9R 82 V9R H41 H41 H 0 1 N N N -14.660 -28.409 -1.698 -6.040 -3.632 -2.294 H41 V9R 83 V9R H42 H42 H 0 1 N N N -6.888 -25.016 -1.945 4.796 -2.755 1.515 H42 V9R 84 # 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 V9R C34 C30 SING N N 1 V9R C34 C29 SING N N 2 V9R C30 C29 SING N N 3 V9R C25 C26 DOUB Y N 4 V9R C25 C23 SING Y N 5 V9R C26 C28 SING Y N 6 V9R C33 C27 SING N N 7 V9R C17 C18 SING N N 8 V9R C17 C16 DOUB N N 9 V9R C18 C19 DOUB N N 10 V9R O26 C24 DOUB N N 11 V9R C29 C22 SING N N 12 V9R C23 C15 DOUB Y N 13 V9R C16 N15 SING N N 14 V9R C28 C14 DOUB Y N 15 V9R C24 O25 SING N N 16 V9R C24 N23 SING N N 17 V9R C27 O25 SING N N 18 V9R C27 C32 SING N N 19 V9R C27 C31 SING N N 20 V9R C19 N23 SING N N 21 V9R C19 C21 SING N N 22 V9R C22 C20 SING N N 23 V9R N15 C21 SING N N 24 V9R N15 C20 SING N N 25 V9R C15 C14 SING Y N 26 V9R C14 C13 SING N N 27 V9R C21 O22 DOUB N N 28 V9R C20 C36 SING N N 29 V9R C13 N36 SING N N 30 V9R C36 O37 DOUB N N 31 V9R C36 N38 SING N N 32 V9R N36 C35 SING N N 33 V9R N38 C40 SING N N 34 V9R O41 C35 DOUB N N 35 V9R C35 C57 SING N N 36 V9R C54 C51 SING N N 37 V9R C54 C45 SING N N 38 V9R C40 C57 SING N N 39 V9R C40 C42 SING N N 40 V9R C57 O40 SING N N 41 V9R C51 N49 SING N N 42 V9R C45 C42 SING N N 43 V9R C45 C47 SING N N 44 V9R N49 C47 SING N N 45 V9R C47 O48 DOUB N N 46 V9R C31 H1 SING N N 47 V9R C31 H2 SING N N 48 V9R C31 H3 SING N N 49 V9R C32 H4 SING N N 50 V9R C32 H5 SING N N 51 V9R C32 H6 SING N N 52 V9R C33 H7 SING N N 53 V9R C33 H8 SING N N 54 V9R C33 H9 SING N N 55 V9R C18 H10 SING N N 56 V9R C17 H12 SING N N 57 V9R C16 H13 SING N N 58 V9R C20 H14 SING N N 59 V9R C22 H15 SING N N 60 V9R C22 H16 SING N N 61 V9R C29 H17 SING N N 62 V9R C34 H18 SING N N 63 V9R C34 H19 SING N N 64 V9R C30 H20 SING N N 65 V9R C30 H21 SING N N 66 V9R N38 H22 SING N N 67 V9R C40 H23 SING N N 68 V9R C42 H24 SING N N 69 V9R C42 H25 SING N N 70 V9R C45 H26 SING N N 71 V9R N49 H27 SING N N 72 V9R C51 H28 SING N N 73 V9R C51 H29 SING N N 74 V9R C54 H30 SING N N 75 V9R C54 H31 SING N N 76 V9R C57 H32 SING N N 77 V9R O40 H33 SING N N 78 V9R N36 H34 SING N N 79 V9R C13 H35 SING N N 80 V9R C13 H36 SING N N 81 V9R C28 H37 SING N N 82 V9R C26 H38 SING N N 83 V9R C25 H39 SING N N 84 V9R C23 H40 SING N N 85 V9R C15 H41 SING N N 86 V9R N23 H42 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 V9R InChI InChI 1.06 "InChI=1S/C31H41N5O7/c1-31(2,3)43-30(42)35-22-10-7-15-36(29(22)41)24(16-19-11-12-19)27(39)34-23(17-21-13-14-32-26(21)38)25(37)28(40)33-18-20-8-5-4-6-9-20/h4-10,15,19,21,23-25,37H,11-14,16-18H2,1-3H3,(H,32,38)(H,33,40)(H,34,39)(H,35,42)/t21-,23-,24+,25-/m0/s1" V9R InChIKey InChI 1.06 FRACPXUHUTXLCX-CGBRIMPHSA-N V9R SMILES_CANONICAL CACTVS 3.385 "CC(C)(C)OC(=O)NC1=CC=CN([C@H](CC2CC2)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@H](O)C(=O)NCc4ccccc4)C1=O" V9R SMILES CACTVS 3.385 "CC(C)(C)OC(=O)NC1=CC=CN([CH](CC2CC2)C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)C(=O)NCc4ccccc4)C1=O" V9R SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)(C)OC(=O)NC1=CC=CN(C1=O)[C@H](CC2CC2)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@@H](C(=O)NCc4ccccc4)O" V9R SMILES "OpenEye OEToolkits" 2.0.7 "CC(C)(C)OC(=O)NC1=CC=CN(C1=O)C(CC2CC2)C(=O)NC(CC3CCNC3=O)C(C(=O)NCc4ccccc4)O" # _pdbx_chem_comp_identifier.comp_id V9R _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 "~{tert}-butyl ~{N}-[1-[(2~{R})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{S})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate" # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 V9R "(R,S,S)-13b" AUTHOR ? 2 V9R 13b-H AUTHOR ? 3 V9R "ketoamide inhibitor 13b (bound)" AUTHOR ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site V9R "Create component" 2023-02-28 PDBE V9R "Initial release" 2023-03-08 RCSB V9R "Modify aromatic_flag" 2023-08-13 PDBE V9R "Modify descriptor" 2023-08-13 PDBE V9R "Modify name" 2023-08-13 PDBE #