data_MK1 # _chem_comp.id MK1 _chem_comp.name ;N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C36 H47 N5 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms INDINAVIR _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2020-06-17 _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 613.789 _chem_comp.one_letter_code ? _chem_comp.three_letter_code MK1 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1HSG _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # 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 MK1 N1 N1 N 0 1 N N N 9.280 23.763 3.004 0.011 0.044 5.540 N1 MK1 1 MK1 C1 C1 C 0 1 N N N 9.498 23.983 4.459 1.228 -0.429 4.871 C1 MK1 2 MK1 C2 C2 C 0 1 N N S 10.591 24.905 4.962 1.387 0.283 3.527 C2 MK1 3 MK1 C3 C3 C 0 1 N N N 10.591 24.864 6.466 2.675 -0.151 2.878 C3 MK1 4 MK1 O1 O1 O 0 1 N N N 10.937 23.849 7.057 2.654 -0.693 1.793 O1 MK1 5 MK1 N2 N2 N 0 1 N N N 10.193 25.953 7.094 3.851 0.060 3.502 N2 MK1 6 MK1 C4 C4 C 0 1 N N N 10.145 26.250 8.490 5.103 -0.362 2.871 C4 MK1 7 MK1 C5 C5 C 0 1 N N N 9.379 27.577 8.641 6.279 -0.006 3.782 C5 MK1 8 MK1 C6 C6 C 0 1 N N N 11.398 26.347 9.074 5.264 0.352 1.528 C6 MK1 9 MK1 C7 C7 C 0 1 N N N 9.364 25.283 9.268 5.073 -1.875 2.643 C7 MK1 10 MK1 N3 N3 N 0 1 N N N 11.819 24.282 4.355 0.259 -0.056 2.652 N3 MK1 11 MK1 C8 C8 C 0 1 N N N 11.753 23.776 2.961 -0.957 0.418 3.321 C8 MK1 12 MK1 C9 C9 C 0 1 N N N 10.440 23.182 2.493 -1.116 -0.294 4.664 C9 MK1 13 MK1 C10 C10 C 0 1 N N N 13.083 24.963 4.552 0.413 0.750 1.434 C10 MK1 14 MK1 C11 C11 C 0 1 N N S 14.203 24.064 5.078 -0.560 0.250 0.365 C11 MK1 15 MK1 O2 O2 O 0 1 N N N 15.242 24.884 4.634 -1.901 0.511 0.783 O2 MK1 16 MK1 C12 C12 C 0 1 N N N 14.440 23.761 6.569 -0.286 0.977 -0.953 C12 MK1 17 MK1 C13 C13 C 0 1 N N R 15.573 22.821 7.005 -1.135 0.355 -2.063 C13 MK1 18 MK1 C14 C14 C 0 1 N N N 15.644 22.664 8.534 -2.611 0.677 -1.818 C14 MK1 19 MK1 C15 C15 C 0 1 Y N N 16.733 21.750 8.961 -3.450 0.033 -2.892 C15 MK1 20 MK1 C16 C16 C 0 1 Y N N 18.058 21.916 8.553 -3.835 -1.288 -2.769 C16 MK1 21 MK1 C17 C17 C 0 1 Y N N 19.037 21.016 8.947 -4.605 -1.878 -3.753 C17 MK1 22 MK1 C18 C18 C 0 1 Y N N 18.673 19.939 9.758 -4.991 -1.146 -4.860 C18 MK1 23 MK1 C19 C19 C 0 1 Y N N 17.347 19.773 10.176 -4.607 0.175 -4.983 C19 MK1 24 MK1 C20 C20 C 0 1 Y N N 16.374 20.687 9.772 -3.841 0.767 -3.996 C20 MK1 25 MK1 C21 C21 C 0 1 N N N 15.447 21.440 6.373 -0.712 0.920 -3.395 C21 MK1 26 MK1 O3 O3 O 0 1 N N N 14.367 20.831 6.397 -0.436 2.097 -3.495 O3 MK1 27 MK1 N4 N4 N 0 1 N N N 16.583 20.913 5.924 -0.640 0.117 -4.475 N4 MK1 28 MK1 C22 C22 C 0 1 N N S 16.692 19.500 5.604 -0.121 0.638 -5.742 C22 MK1 29 MK1 C23 C23 C 0 1 N N R 18.067 18.945 5.936 -0.719 -0.145 -6.929 C23 MK1 30 MK1 O4 O4 O 0 1 N N N 19.061 19.938 5.729 -1.078 -1.470 -6.534 O4 MK1 31 MK1 C24 C24 C 0 1 N N N 18.226 17.726 5.057 0.451 -0.167 -7.935 C24 MK1 32 MK1 C25 C25 C 0 1 Y N N 17.476 17.904 3.760 1.702 -0.050 -7.090 C25 MK1 33 MK1 C26 C26 C 0 1 Y N N 17.500 17.363 2.496 3.023 -0.327 -7.399 C26 MK1 34 MK1 C27 C27 C 0 1 Y N N 16.613 17.872 1.541 4.012 -0.143 -6.453 C27 MK1 35 MK1 C28 C28 C 0 1 Y N N 15.722 18.906 1.865 3.683 0.320 -5.193 C28 MK1 36 MK1 C29 C29 C 0 1 Y N N 15.683 19.479 3.129 2.366 0.597 -4.882 C29 MK1 37 MK1 C30 C30 C 0 1 Y N N 16.504 19.061 4.128 1.373 0.414 -5.829 C30 MK1 38 MK1 C31 C31 C 0 1 N N N 8.033 23.100 2.604 -0.142 -0.762 6.758 C31 MK1 39 MK1 C32 C32 C 0 1 Y N N 6.666 23.739 2.876 -1.380 -0.324 7.498 C32 MK1 40 MK1 C33 C33 C 0 1 Y N N 6.158 24.808 2.124 -1.308 0.670 8.454 C33 MK1 41 MK1 N5 N5 N 0 1 Y N N 4.911 25.430 2.300 -2.388 1.062 9.102 N5 MK1 42 MK1 C34 C34 C 0 1 Y N N 4.207 24.839 3.348 -3.568 0.519 8.875 C34 MK1 43 MK1 C35 C35 C 0 1 Y N N 4.654 23.774 4.136 -3.716 -0.485 7.937 C35 MK1 44 MK1 C36 C36 C 0 1 Y N N 5.905 23.211 3.897 -2.604 -0.919 7.232 C36 MK1 45 MK1 H11A 1H1 H 0 0 N N N 8.532 24.318 4.904 1.155 -1.504 4.704 H11A MK1 46 MK1 H12 2H1 H 0 1 N N N 9.639 22.987 4.940 2.094 -0.217 5.499 H12 MK1 47 MK1 H2 H2 H 0 1 N N N 10.493 25.982 4.690 1.409 1.361 3.689 H2 MK1 48 MK1 HN2 HN2 H 0 1 N N N 9.884 26.651 6.417 3.867 0.494 4.370 HN2 MK1 49 MK1 H51 1H5 H 0 1 N N N 9.341 27.808 9.731 7.211 -0.321 3.312 H51 MK1 50 MK1 H52 2H5 H 0 1 N N N 9.811 28.404 8.031 6.300 1.071 3.944 H52 MK1 51 MK1 H53 3H5 H 0 1 N N N 8.372 27.558 8.161 6.165 -0.515 4.739 H53 MK1 52 MK1 H61 1H6 H 0 1 N N N 11.360 26.578 10.164 5.285 1.430 1.690 H61 MK1 53 MK1 H62 2H6 H 0 1 N N N 11.994 25.424 8.886 6.195 0.037 1.058 H62 MK1 54 MK1 H63 3H6 H 0 1 N N N 12.030 27.089 8.533 4.425 0.098 0.878 H63 MK1 55 MK1 H71 1H7 H 0 1 N N N 9.326 25.514 10.358 4.959 -2.384 3.600 H71 MK1 56 MK1 H72 2H7 H 0 1 N N N 8.335 25.180 8.850 4.235 -2.128 1.994 H72 MK1 57 MK1 H73 3H7 H 0 1 N N N 9.737 24.246 9.097 6.005 -2.190 2.173 H73 MK1 58 MK1 H81 1H8 H 0 1 N N N 12.061 24.586 2.259 -1.823 0.207 2.693 H81 MK1 59 MK1 H82 2H8 H 0 1 N N N 12.571 23.035 2.798 -0.885 1.493 3.488 H82 MK1 60 MK1 H91 1H9 H 0 1 N N N 10.430 22.085 2.693 -1.139 -1.372 4.502 H91 MK1 61 MK1 H92 2H9 H 0 1 N N N 10.402 23.184 1.378 -2.048 0.020 5.134 H92 MK1 62 MK1 H101 1H10 H 0 0 N N N 13.401 25.474 3.613 0.199 1.794 1.660 H101 MK1 63 MK1 H102 2H10 H 0 0 N N N 12.949 25.849 5.215 1.435 0.660 1.065 H102 MK1 64 MK1 H11 H11 H 0 1 N N N 14.024 23.013 4.749 -0.425 -0.821 0.223 H11 MK1 65 MK1 HO2 HO2 H 0 1 N N N 15.937 24.325 4.960 -1.977 1.468 0.896 HO2 MK1 66 MK1 H121 1H12 H 0 0 N N N 14.564 24.730 7.106 -0.542 2.031 -0.847 H121 MK1 67 MK1 H122 2H12 H 0 0 N N N 13.485 23.382 7.003 0.769 0.883 -1.207 H122 MK1 68 MK1 H13 H13 H 0 1 N N N 16.513 23.301 6.646 -0.995 -0.725 -2.066 H13 MK1 69 MK1 H141 1H14 H 0 0 N N N 15.732 23.655 9.035 -2.909 0.292 -0.843 H141 MK1 70 MK1 H142 2H14 H 0 0 N N N 14.661 22.340 8.950 -2.756 1.757 -1.842 H142 MK1 71 MK1 H16 H16 H 0 1 N N N 18.334 22.769 7.911 -3.533 -1.860 -1.904 H16 MK1 72 MK1 H17 H17 H 0 1 N N N 20.082 21.153 8.622 -4.904 -2.911 -3.657 H17 MK1 73 MK1 H18 H18 H 0 1 N N N 19.440 19.211 10.071 -5.592 -1.608 -5.630 H18 MK1 74 MK1 H19 H19 H 0 1 N N N 17.069 18.923 10.822 -4.909 0.747 -5.848 H19 MK1 75 MK1 H20 H20 H 0 1 N N N 15.325 20.569 10.092 -3.541 1.800 -4.092 H20 MK1 76 MK1 HN4 HN4 H 0 1 N N N 17.351 21.576 5.827 -0.932 -0.805 -4.414 HN4 MK1 77 MK1 H22 H22 H 0 1 N N N 15.845 19.112 6.216 -0.350 1.700 -5.836 H22 MK1 78 MK1 H23 H23 H 0 1 N N N 18.179 18.653 7.006 -1.578 0.379 -7.347 H23 MK1 79 MK1 HO4 HO4 H 0 1 N N N 19.920 19.591 5.936 -1.377 -1.928 -7.331 HO4 MK1 80 MK1 H241 1H24 H 0 0 N N N 19.299 17.478 4.883 0.456 -1.105 -8.490 H241 MK1 81 MK1 H242 2H24 H 0 0 N N N 17.922 16.792 5.585 0.377 0.677 -8.620 H242 MK1 82 MK1 H26 H26 H 0 1 N N N 18.205 16.549 2.256 3.281 -0.689 -8.384 H26 MK1 83 MK1 H27 H27 H 0 1 N N N 16.616 17.453 0.520 5.041 -0.360 -6.697 H27 MK1 84 MK1 H28 H28 H 0 1 N N N 15.025 19.282 1.096 4.454 0.464 -4.451 H28 MK1 85 MK1 H29 H29 H 0 1 N N N 14.974 20.295 3.347 2.109 0.959 -3.898 H29 MK1 86 MK1 H311 1H31 H 0 0 N N N 8.097 22.876 1.513 -0.233 -1.814 6.488 H311 MK1 87 MK1 H312 2H31 H 0 0 N N N 8.029 22.077 3.049 0.730 -0.625 7.397 H312 MK1 88 MK1 H33 H33 H 0 1 N N N 6.801 25.196 1.316 -0.359 1.138 8.667 H33 MK1 89 MK1 H34 H34 H 0 1 N N N 3.208 25.250 3.573 -4.430 0.864 9.428 H34 MK1 90 MK1 H35 H35 H 0 1 N N N 4.019 23.377 4.946 -4.685 -0.925 7.755 H35 MK1 91 MK1 H36 H36 H 0 1 N N N 6.283 22.368 4.500 -2.689 -1.702 6.493 H36 MK1 92 # # 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 MK1 N1 C1 SING N N 1 MK1 N1 C9 SING N N 2 MK1 N1 C31 SING N N 3 MK1 C1 C2 SING N N 4 MK1 C1 H11A SING N N 5 MK1 C1 H12 SING N N 6 MK1 C2 C3 SING N N 7 MK1 C2 N3 SING N N 8 MK1 C2 H2 SING N N 9 MK1 C3 O1 DOUB N N 10 MK1 C3 N2 SING N N 11 MK1 N2 C4 SING N N 12 MK1 N2 HN2 SING N N 13 MK1 C4 C5 SING N N 14 MK1 C4 C6 SING N N 15 MK1 C4 C7 SING N N 16 MK1 C5 H51 SING N N 17 MK1 C5 H52 SING N N 18 MK1 C5 H53 SING N N 19 MK1 C6 H61 SING N N 20 MK1 C6 H62 SING N N 21 MK1 C6 H63 SING N N 22 MK1 C7 H71 SING N N 23 MK1 C7 H72 SING N N 24 MK1 C7 H73 SING N N 25 MK1 N3 C8 SING N N 26 MK1 N3 C10 SING N N 27 MK1 C8 C9 SING N N 28 MK1 C8 H81 SING N N 29 MK1 C8 H82 SING N N 30 MK1 C9 H91 SING N N 31 MK1 C9 H92 SING N N 32 MK1 C10 C11 SING N N 33 MK1 C10 H101 SING N N 34 MK1 C10 H102 SING N N 35 MK1 C11 O2 SING N N 36 MK1 C11 C12 SING N N 37 MK1 C11 H11 SING N N 38 MK1 O2 HO2 SING N N 39 MK1 C12 C13 SING N N 40 MK1 C12 H121 SING N N 41 MK1 C12 H122 SING N N 42 MK1 C13 C14 SING N N 43 MK1 C13 C21 SING N N 44 MK1 C13 H13 SING N N 45 MK1 C14 C15 SING N N 46 MK1 C14 H141 SING N N 47 MK1 C14 H142 SING N N 48 MK1 C15 C16 DOUB Y N 49 MK1 C15 C20 SING Y N 50 MK1 C16 C17 SING Y N 51 MK1 C16 H16 SING N N 52 MK1 C17 C18 DOUB Y N 53 MK1 C17 H17 SING N N 54 MK1 C18 C19 SING Y N 55 MK1 C18 H18 SING N N 56 MK1 C19 C20 DOUB Y N 57 MK1 C19 H19 SING N N 58 MK1 C20 H20 SING N N 59 MK1 C21 O3 DOUB N N 60 MK1 C21 N4 SING N N 61 MK1 N4 C22 SING N N 62 MK1 N4 HN4 SING N N 63 MK1 C22 C23 SING N N 64 MK1 C22 C30 SING N N 65 MK1 C22 H22 SING N N 66 MK1 C23 O4 SING N N 67 MK1 C23 C24 SING N N 68 MK1 C23 H23 SING N N 69 MK1 O4 HO4 SING N N 70 MK1 C24 C25 SING N N 71 MK1 C24 H241 SING N N 72 MK1 C24 H242 SING N N 73 MK1 C25 C26 DOUB Y N 74 MK1 C25 C30 SING Y N 75 MK1 C26 C27 SING Y N 76 MK1 C26 H26 SING N N 77 MK1 C27 C28 DOUB Y N 78 MK1 C27 H27 SING N N 79 MK1 C28 C29 SING Y N 80 MK1 C28 H28 SING N N 81 MK1 C29 C30 DOUB Y N 82 MK1 C29 H29 SING N N 83 MK1 C31 C32 SING N N 84 MK1 C31 H311 SING N N 85 MK1 C31 H312 SING N N 86 MK1 C32 C33 SING Y N 87 MK1 C32 C36 DOUB Y N 88 MK1 C33 N5 DOUB Y N 89 MK1 C33 H33 SING N N 90 MK1 N5 C34 SING Y N 91 MK1 C34 C35 DOUB Y N 92 MK1 C34 H34 SING N N 93 MK1 C35 C36 SING Y N 94 MK1 C35 H35 SING N N 95 MK1 C36 H36 SING N N 96 # # 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 MK1 SMILES ACDLabs 10.04 "O=C(NC2c1ccccc1CC2O)C(Cc3ccccc3)CC(O)CN5C(C(=O)NC(C)(C)C)CN(Cc4cnccc4)CC5" MK1 SMILES_CANONICAL CACTVS 3.341 "CC(C)(C)NC(=O)[C@@H]1CN(CCN1C[C@@H](O)C[C@@H](Cc2ccccc2)C(=O)N[C@@H]3[C@H](O)Cc4ccccc34)Cc5cccnc5" MK1 SMILES CACTVS 3.341 "CC(C)(C)NC(=O)[CH]1CN(CCN1C[CH](O)C[CH](Cc2ccccc2)C(=O)N[CH]3[CH](O)Cc4ccccc34)Cc5cccnc5" MK1 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC(C)(C)NC(=O)[C@@H]1C[N@@](CC[N@]1C[C@H](C[C@@H](Cc2ccccc2)C(=O)N[C@H]3c4ccccc4C[C@H]3O)O)Cc5cccnc5" MK1 SMILES "OpenEye OEToolkits" 1.5.0 "CC(C)(C)NC(=O)C1CN(CCN1CC(CC(Cc2ccccc2)C(=O)NC3c4ccccc4CC3O)O)Cc5cccnc5" MK1 InChI InChI 1.03 "InChI=1S/C36H47N5O4/c1-36(2,3)39-35(45)31-24-40(22-26-12-9-15-37-21-26)16-17-41(31)23-29(42)19-28(18-25-10-5-4-6-11-25)34(44)38-33-30-14-8-7-13-27(30)20-32(33)43/h4-15,21,28-29,31-33,42-43H,16-20,22-24H2,1-3H3,(H,38,44)(H,39,45)/t28-,29+,31+,32-,33+/m1/s1" MK1 InChIKey InChI 1.03 CBVCZFGXHXORBI-PXQQMZJSSA-N # # 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 MK1 "SYSTEMATIC NAME" ACDLabs 10.04 "(2S)-1-[(2S,4R)-4-benzyl-2-hydroxy-5-{[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]amino}-5-oxopentyl]-N-tert-butyl-4-(pyridin-3-ylmethyl)piperazine-2-carboxamide (non-preferred name)" MK1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(1S,2S,4R)-N-tert-butyl-1-[(2S,4R)-2-hydroxy-5-[[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]amino]-5-oxo-4-(phenylmethyl)pentyl]-4-(pyridin-3-ylmethyl)piperazine-2-carboxamide" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site MK1 "Create component" 1999-07-08 RCSB MK1 "Modify descriptor" 2011-06-04 RCSB MK1 "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id MK1 _pdbx_chem_comp_synonyms.name INDINAVIR _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##