data_VDP # _chem_comp.id VDP _chem_comp.name "(3R,5S)-5-[(2R)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[(2Z)-2-[(3S,5R)-2-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]propyl]-3-methyl-3-oxidanyl-1-(4-phenylbutyl)pyrrolidin-2-one" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C37 H53 N O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-02-11 _chem_comp.pdbx_modified_date 2016-12-02 _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 575.821 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ? _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 4XWQ _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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 VDP O3 O1 O 0 1 N N N -9.324 18.089 -29.127 4.950 3.998 0.669 O3 VDP 1 VDP C25 C1 C 0 1 N N N -9.517 19.235 -28.753 3.923 3.611 0.153 C25 VDP 2 VDP C26 C2 C 0 1 N N R -8.955 19.763 -27.467 2.599 4.340 0.204 C26 VDP 3 VDP O4 O2 O 0 1 N N N -9.360 18.879 -26.440 2.335 4.805 1.529 O4 VDP 4 VDP C24 C3 C 0 1 N N N -7.438 19.904 -27.521 2.593 5.508 -0.785 C24 VDP 5 VDP C27 C4 C 0 1 N N N -9.600 21.119 -27.304 1.561 3.273 -0.213 C27 VDP 6 VDP C23 C5 C 0 1 N N S -10.236 21.468 -28.657 2.426 2.301 -1.046 C23 VDP 7 VDP N28 N1 N 0 1 N N N -10.196 20.186 -29.380 3.798 2.474 -0.553 N28 VDP 8 VDP C28 C6 C 0 1 N N N -10.780 20.160 -30.725 4.889 1.526 -0.794 C28 VDP 9 VDP C29 C7 C 0 1 N N N -9.559 19.931 -31.626 4.933 0.499 0.339 C29 VDP 10 VDP C30 C8 C 0 1 N N N -9.119 21.228 -32.296 6.140 -0.421 0.146 C30 VDP 11 VDP C31 C9 C 0 1 N N N -7.619 21.523 -32.262 6.253 -1.370 1.341 C31 VDP 12 VDP C32 C10 C 0 1 Y N N -7.446 23.033 -32.089 7.442 -2.277 1.151 C32 VDP 13 VDP C33 C11 C 0 1 Y N N -7.550 23.633 -30.821 8.683 -1.899 1.628 C33 VDP 14 VDP C34 C12 C 0 1 Y N N -7.397 25.020 -30.669 9.773 -2.731 1.454 C34 VDP 15 VDP C35 C13 C 0 1 Y N N -7.140 25.839 -31.777 9.622 -3.941 0.802 C35 VDP 16 VDP C36 C14 C 0 1 Y N N -7.051 25.252 -33.043 8.381 -4.319 0.325 C36 VDP 17 VDP C37 C15 C 0 1 Y N N -7.205 23.858 -33.192 7.290 -3.489 0.504 C37 VDP 18 VDP C22 C16 C 0 1 N N N -11.672 21.943 -28.439 1.960 0.860 -0.832 C22 VDP 19 VDP C20 C17 C 0 1 N N R -11.613 23.382 -27.940 0.553 0.688 -1.410 C20 VDP 20 VDP C21 C18 C 0 1 N N N -10.541 24.211 -28.638 0.600 0.872 -2.928 C21 VDP 21 VDP C16 C19 C 0 1 N N R -12.944 23.976 -27.474 0.035 -0.713 -1.081 C16 VDP 22 VDP C11 C20 C 0 1 N N R -12.973 25.361 -26.817 -1.364 -0.905 -1.646 C11 VDP 23 VDP C18 C21 C 0 1 N N N -11.898 25.414 -25.726 -2.112 0.429 -1.607 C18 VDP 24 VDP C9 C22 C 0 1 N N S -14.377 25.406 -26.188 -2.022 -1.890 -0.639 C9 VDP 25 VDP C15 C23 C 0 1 N N N -14.533 24.010 -25.565 -1.610 -1.270 0.698 C15 VDP 26 VDP C17 C24 C 0 1 N N N -13.555 23.106 -26.359 -0.124 -0.883 0.453 C17 VDP 27 VDP C12 C25 C 0 1 N N N -12.816 26.557 -27.743 -1.503 -1.502 -3.027 C12 VDP 28 VDP C13 C26 C 0 1 N N N -13.042 27.888 -26.982 -2.997 -1.481 -3.393 C13 VDP 29 VDP C14 C27 C 0 1 N N N -14.288 27.958 -26.081 -3.837 -2.272 -2.392 C14 VDP 30 VDP C8 C28 C 0 1 N N N -14.437 26.649 -25.326 -3.486 -1.877 -0.964 C8 VDP 31 VDP C7 C29 C 0 1 N N N -14.542 26.639 -23.977 -4.414 -1.544 -0.067 C7 VDP 32 VDP C6 C30 C 0 1 N N N -14.526 27.887 -23.218 -5.830 -1.550 -0.441 C6 VDP 33 VDP C5 C31 C 0 1 N N N -14.334 28.045 -21.879 -6.769 -1.213 0.467 C5 VDP 34 VDP C4 C32 C 0 1 N N N -14.365 29.481 -21.381 -8.245 -1.206 0.119 C4 VDP 35 VDP C3 C33 C 0 1 N N R -14.735 29.635 -19.904 -8.858 0.098 0.641 C3 VDP 36 VDP O2 O3 O 0 1 N N N -16.144 29.482 -19.767 -10.261 0.105 0.370 O2 VDP 37 VDP C2 C34 C 0 1 N N N -14.110 28.565 -19.028 -8.630 0.209 2.149 C2 VDP 38 VDP C1 C35 C 0 1 N N S -14.669 27.235 -19.499 -7.134 0.361 2.439 C1 VDP 39 VDP O1 O4 O 0 1 N N N -14.242 26.253 -18.565 -6.647 1.564 1.840 O1 VDP 40 VDP C10 C36 C 0 1 N N N -14.126 26.989 -20.872 -6.410 -0.838 1.850 C10 VDP 41 VDP C19 C37 C 0 1 N N N -13.432 25.890 -21.084 -5.496 -1.517 2.543 C19 VDP 42 VDP H1 H1 H 0 1 N N N -9.595 18.040 -26.818 2.988 5.433 1.864 H1 VDP 43 VDP H2 H2 H 0 1 N N N -7.071 20.293 -26.560 2.776 5.133 -1.792 H2 VDP 44 VDP H3 H3 H 0 1 N N N -6.985 18.921 -27.715 1.623 6.006 -0.753 H3 VDP 45 VDP H4 H4 H 0 1 N N N -7.163 20.600 -28.327 3.374 6.218 -0.514 H4 VDP 46 VDP H5 H5 H 0 1 N N N -8.842 21.870 -27.036 1.145 2.772 0.661 H5 VDP 47 VDP H6 H6 H 0 1 N N N -10.371 21.081 -26.521 0.772 3.713 -0.821 H6 VDP 48 VDP H7 H7 H 0 1 N N N -9.646 22.240 -29.173 2.373 2.561 -2.104 H7 VDP 49 VDP H8 H8 H 0 1 N N N -11.272 21.115 -30.961 4.722 1.014 -1.742 H8 VDP 50 VDP H9 H9 H 0 1 N N N -11.505 19.339 -30.825 5.835 2.065 -0.834 H9 VDP 51 VDP H10 H10 H 0 1 N N N -9.818 19.196 -32.402 5.020 1.016 1.294 H10 VDP 52 VDP H11 H11 H 0 1 N N N -8.730 19.543 -31.016 4.018 -0.094 0.328 H11 VDP 53 VDP H12 H12 H 0 1 N N N -9.637 22.059 -31.795 6.011 -1.002 -0.768 H12 VDP 54 VDP H13 H13 H 0 1 N N N -9.430 21.185 -33.350 7.046 0.179 0.071 H13 VDP 55 VDP H14 H14 H 0 1 N N N -7.152 20.993 -31.419 6.381 -0.790 2.255 H14 VDP 56 VDP H15 H15 H 0 1 N N N -7.152 21.198 -33.203 5.347 -1.970 1.416 H15 VDP 57 VDP H16 H16 H 0 1 N N N -7.750 23.020 -29.955 8.801 -0.954 2.136 H16 VDP 58 VDP H17 H17 H 0 1 N N N -7.478 25.461 -29.687 10.743 -2.435 1.826 H17 VDP 59 VDP H18 H18 H 0 1 N N N -7.013 26.905 -31.655 10.474 -4.590 0.665 H18 VDP 60 VDP H19 H19 H 0 1 N N N -6.864 25.868 -33.910 8.264 -5.264 -0.184 H19 VDP 61 VDP H20 H20 H 0 1 N N N -7.135 23.419 -34.177 6.320 -3.785 0.132 H20 VDP 62 VDP H21 H21 H 0 1 N N N -12.230 21.897 -29.386 2.645 0.178 -1.336 H21 VDP 63 VDP H22 H22 H 0 1 N N N -12.168 21.307 -27.691 1.944 0.638 0.235 H22 VDP 64 VDP H23 H23 H 0 1 N N N -11.126 23.225 -26.966 -0.112 1.433 -0.974 H23 VDP 65 VDP H24 H24 H 0 1 N N N -10.549 25.235 -28.236 1.016 1.851 -3.163 H24 VDP 66 VDP H25 H25 H 0 1 N N N -9.555 23.756 -28.464 1.225 0.095 -3.369 H25 VDP 67 VDP H26 H26 H 0 1 N N N -10.746 24.240 -29.718 -0.410 0.799 -3.333 H26 VDP 68 VDP H27 H27 H 0 1 N N N -13.639 23.982 -28.327 0.711 -1.470 -1.479 H27 VDP 69 VDP H28 H28 H 0 1 N N N -12.012 24.549 -25.056 -1.667 1.116 -2.328 H28 VDP 70 VDP H29 H29 H 0 1 N N N -10.902 25.389 -26.192 -3.159 0.266 -1.860 H29 VDP 71 VDP H30 H30 H 0 1 N N N -12.009 26.343 -25.147 -2.042 0.856 -0.607 H30 VDP 72 VDP H31 H31 H 0 1 N N N -15.114 25.506 -26.998 -1.605 -2.892 -0.745 H31 VDP 73 VDP H32 H32 H 0 1 N N N -15.567 23.651 -25.674 -2.209 -0.386 0.915 H32 VDP 74 VDP H33 H33 H 0 1 N N N -14.263 24.030 -24.499 -1.694 -1.999 1.504 H33 VDP 75 VDP H34 H34 H 0 1 N N N -14.098 22.256 -26.798 0.533 -1.674 0.812 H34 VDP 76 VDP H35 H35 H 0 1 N N N -12.762 22.732 -25.695 0.107 0.055 0.959 H35 VDP 77 VDP H36 H36 H 0 1 N N N -13.552 26.480 -28.557 -0.938 -0.909 -3.746 H36 VDP 78 VDP H37 H37 H 0 1 N N N -11.800 26.553 -28.165 -1.138 -2.529 -3.025 H37 VDP 79 VDP H38 H38 H 0 1 N N N -12.160 28.065 -26.348 -3.344 -0.447 -3.409 H38 VDP 80 VDP H39 H39 H 0 1 N N N -13.124 28.691 -27.729 -3.126 -1.913 -4.385 H39 VDP 81 VDP H40 H40 H 0 1 N N N -14.177 28.785 -25.364 -4.893 -2.069 -2.571 H40 VDP 82 VDP H41 H41 H 0 1 N N N -15.181 28.128 -26.701 -3.648 -3.336 -2.527 H41 VDP 83 VDP H42 H42 H 0 1 N N N -14.639 25.698 -23.456 -4.122 -1.270 0.936 H42 VDP 84 VDP H43 H43 H 0 1 N N N -14.685 28.792 -23.786 -6.123 -1.824 -1.444 H43 VDP 85 VDP H44 H44 H 0 1 N N N -13.367 29.918 -21.532 -8.367 -1.262 -0.963 H44 VDP 86 VDP H45 H45 H 0 1 N N N -15.103 30.036 -21.979 -8.736 -2.057 0.589 H45 VDP 87 VDP H46 H46 H 0 1 N N N -14.415 30.627 -19.552 -8.388 0.945 0.141 H46 VDP 88 VDP H47 H47 H 0 1 N N N -16.386 29.576 -18.853 -10.480 0.042 -0.569 H47 VDP 89 VDP H48 H48 H 0 1 N N N -13.016 28.577 -19.138 -9.164 1.079 2.533 H48 VDP 90 VDP H49 H49 H 0 1 N N N -14.375 28.736 -17.974 -9.004 -0.690 2.639 H49 VDP 91 VDP H50 H50 H 0 1 N N N -15.767 27.290 -19.537 -6.970 0.395 3.516 H50 VDP 92 VDP H51 H51 H 0 1 N N N -14.609 26.447 -17.710 -5.704 1.722 1.985 H51 VDP 93 VDP H52 H52 H 0 1 N N N -13.266 25.192 -20.277 -4.998 -2.364 2.094 H52 VDP 94 VDP H53 H53 H 0 1 N N N -13.028 25.687 -22.065 -5.253 -1.221 3.553 H53 VDP 95 # 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 VDP C37 C36 DOUB Y N 1 VDP C37 C32 SING Y N 2 VDP C36 C35 SING Y N 3 VDP C30 C31 SING N N 4 VDP C30 C29 SING N N 5 VDP C31 C32 SING N N 6 VDP C32 C33 DOUB Y N 7 VDP C35 C34 DOUB Y N 8 VDP C29 C28 SING N N 9 VDP C33 C34 SING Y N 10 VDP C28 N28 SING N N 11 VDP N28 C25 SING N N 12 VDP N28 C23 SING N N 13 VDP O3 C25 DOUB N N 14 VDP C25 C26 SING N N 15 VDP C23 C22 SING N N 16 VDP C23 C27 SING N N 17 VDP C21 C20 SING N N 18 VDP C22 C20 SING N N 19 VDP C20 C16 SING N N 20 VDP C12 C13 SING N N 21 VDP C12 C11 SING N N 22 VDP C24 C26 SING N N 23 VDP C16 C11 SING N N 24 VDP C16 C17 SING N N 25 VDP C26 C27 SING N N 26 VDP C26 O4 SING N N 27 VDP C13 C14 SING N N 28 VDP C11 C9 SING N N 29 VDP C11 C18 SING N N 30 VDP C17 C15 SING N N 31 VDP C9 C15 SING N N 32 VDP C9 C8 SING N N 33 VDP C14 C8 SING N N 34 VDP C8 C7 DOUB N E 35 VDP C7 C6 SING N N 36 VDP C6 C5 DOUB N Z 37 VDP C5 C4 SING N N 38 VDP C5 C10 SING N N 39 VDP C4 C3 SING N N 40 VDP C19 C10 DOUB N N 41 VDP C10 C1 SING N N 42 VDP C3 O2 SING N N 43 VDP C3 C2 SING N N 44 VDP C1 C2 SING N N 45 VDP C1 O1 SING N N 46 VDP O4 H1 SING N N 47 VDP C24 H2 SING N N 48 VDP C24 H3 SING N N 49 VDP C24 H4 SING N N 50 VDP C27 H5 SING N N 51 VDP C27 H6 SING N N 52 VDP C23 H7 SING N N 53 VDP C28 H8 SING N N 54 VDP C28 H9 SING N N 55 VDP C29 H10 SING N N 56 VDP C29 H11 SING N N 57 VDP C30 H12 SING N N 58 VDP C30 H13 SING N N 59 VDP C31 H14 SING N N 60 VDP C31 H15 SING N N 61 VDP C33 H16 SING N N 62 VDP C34 H17 SING N N 63 VDP C35 H18 SING N N 64 VDP C36 H19 SING N N 65 VDP C37 H20 SING N N 66 VDP C22 H21 SING N N 67 VDP C22 H22 SING N N 68 VDP C20 H23 SING N N 69 VDP C21 H24 SING N N 70 VDP C21 H25 SING N N 71 VDP C21 H26 SING N N 72 VDP C16 H27 SING N N 73 VDP C18 H28 SING N N 74 VDP C18 H29 SING N N 75 VDP C18 H30 SING N N 76 VDP C9 H31 SING N N 77 VDP C15 H32 SING N N 78 VDP C15 H33 SING N N 79 VDP C17 H34 SING N N 80 VDP C17 H35 SING N N 81 VDP C12 H36 SING N N 82 VDP C12 H37 SING N N 83 VDP C13 H38 SING N N 84 VDP C13 H39 SING N N 85 VDP C14 H40 SING N N 86 VDP C14 H41 SING N N 87 VDP C7 H42 SING N N 88 VDP C6 H43 SING N N 89 VDP C4 H44 SING N N 90 VDP C4 H45 SING N N 91 VDP C3 H46 SING N N 92 VDP O2 H47 SING N N 93 VDP C2 H48 SING N N 94 VDP C2 H49 SING N N 95 VDP C1 H50 SING N N 96 VDP O1 H51 SING N N 97 VDP C19 H52 SING N N 98 VDP C19 H53 SING N N 99 # 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 VDP SMILES ACDLabs 12.01 "O=C2N(CCCCc1ccccc1)C(CC2(O)C)CC(C)C5CCC4C(=C\C=C3/C(=C)C(O)CC(O)C3)\CCCC45C" VDP InChI InChI 1.03 ;InChI=1S/C37H53NO4/c1-25(21-30-24-37(4,42)35(41)38(30)20-9-8-13-27-11-6-5-7-12-27)32-17-18-33-28(14-10-19-36(32,33)3)15-16-29-22-31(39)23-34(40)26(29)2/h5-7,11-12,15-16,25,30-34,39-40,42H,2,8-10,13-14,17-24H2,1,3-4H3/b28-15+,29-16-/t25-,30+,31-,32-,33+,34+,36-,37-/m1/s1 ; VDP InChIKey InChI 1.03 IVUJLUOFPHOBPG-HEMHZJQPSA-N VDP SMILES_CANONICAL CACTVS 3.385 "C[C@H](C[C@H]1C[C@@](C)(O)C(=O)N1CCCCc2ccccc2)[C@H]3CC[C@H]4\C(CCC[C@]34C)=C\C=C5\C[C@@H](O)C[C@H](O)C5=C" VDP SMILES CACTVS 3.385 "C[CH](C[CH]1C[C](C)(O)C(=O)N1CCCCc2ccccc2)[CH]3CC[CH]4C(CCC[C]34C)=CC=C5C[CH](O)C[CH](O)C5=C" VDP SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "C[C@H](C[C@H]1C[C@@](C(=O)N1CCCCc2ccccc2)(C)O)[C@H]3CC[C@@H]\4[C@@]3(CCC/C4=C\C=C/5\C[C@H](C[C@@H](C5=C)O)O)C" VDP SMILES "OpenEye OEToolkits" 1.9.2 "CC(CC1CC(C(=O)N1CCCCc2ccccc2)(C)O)C3CCC4C3(CCCC4=CC=C5CC(CC(C5=C)O)O)C" # 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 VDP "SYSTEMATIC NAME" ACDLabs 12.01 "(3R,5S)-5-{(2R)-2-[(1R,3aS,4E,7aR)-4-{(2Z)-2-[(3S,5R)-3,5-dihydroxy-2-methylidenecyclohexylidene]ethylidene}-7a-methyloctahydro-1H-inden-1-yl]propyl}-3-hydroxy-3-methyl-1-(4-phenylbutyl)pyrrolidin-2-one (non-preferred name)" VDP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "(3R,5S)-5-[(2R)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[(2Z)-2-[(3S,5R)-2-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]propyl]-3-methyl-3-oxidanyl-1-(4-phenylbutyl)pyrrolidin-2-one" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site VDP "Create component" 2015-02-11 PDBJ VDP "Initial release" 2016-12-07 RCSB #