data_VYJ # _chem_comp.id VYJ _chem_comp.name "11-cyclopentyl-2-({2-ethoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C36 H46 N8 O3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-09-21 _chem_comp.pdbx_modified_date 2021-06-25 _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 638.802 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VYJ _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 7K6G _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 VYJ C13 C1 C 0 1 N N N -8.378 -37.975 -28.170 6.287 0.814 1.103 C13 VYJ 1 VYJ C15 C2 C 0 1 N N N -9.809 -40.010 -27.798 7.094 1.596 -1.043 C15 VYJ 2 VYJ C20 C3 C 0 1 N N N -9.128 -43.720 -28.578 10.014 3.816 -1.897 C20 VYJ 3 VYJ C21 C4 C 0 1 N N N -7.324 -37.357 -29.119 6.882 -0.567 0.820 C21 VYJ 4 VYJ C22 C5 C 0 1 N N N -7.093 -35.868 -28.796 6.077 -1.630 1.574 C22 VYJ 5 VYJ C24 C6 C 0 1 Y N N -4.993 -33.554 -24.928 1.928 -3.150 -0.550 C24 VYJ 6 VYJ C26 C7 C 0 1 Y N N -2.545 -35.742 -21.338 -2.230 -0.902 0.065 C26 VYJ 7 VYJ C28 C8 C 0 1 Y N N -1.208 -36.410 -19.514 -2.105 1.310 0.700 C28 VYJ 8 VYJ C01 C9 C 0 1 N N N -3.664 -30.276 -22.551 0.028 -5.253 -3.674 C01 VYJ 9 VYJ C02 C10 C 0 1 N N N -4.217 -31.302 -23.545 0.851 -4.557 -2.588 C02 VYJ 10 VYJ C04 C11 C 0 1 Y N N -4.326 -33.661 -23.700 0.571 -3.038 -0.780 C04 VYJ 11 VYJ C05 C12 C 0 1 Y N N -3.909 -34.908 -23.220 -0.208 -2.211 0.032 C05 VYJ 12 VYJ C06 C13 C 0 1 Y N N -4.156 -36.060 -23.985 0.381 -1.501 1.072 C06 VYJ 13 VYJ C07 C14 C 0 1 Y N N -4.803 -35.952 -25.204 1.734 -1.610 1.306 C07 VYJ 14 VYJ C08 C15 C 0 1 Y N N -5.236 -34.701 -25.708 2.517 -2.440 0.500 C08 VYJ 15 VYJ C09 C16 C 0 1 N N N -5.897 -34.726 -26.975 3.967 -2.558 0.749 C09 VYJ 16 VYJ C11 C17 C 0 1 N N N -7.752 -36.256 -26.399 4.012 -0.187 1.357 C11 VYJ 17 VYJ C12 C18 C 0 1 N N N -7.955 -37.762 -26.695 4.840 0.860 0.605 C12 VYJ 18 VYJ C16 C19 C 0 1 N N N -10.067 -41.454 -28.264 7.858 2.725 -1.737 C16 VYJ 19 VYJ C18 C20 C 0 1 N N N -7.591 -41.764 -28.659 9.207 3.034 0.248 C18 VYJ 20 VYJ C19 C21 C 0 1 N N N -7.362 -40.290 -28.264 8.443 1.904 0.943 C19 VYJ 21 VYJ C29 C22 C 0 1 Y N N -1.041 -37.692 -20.061 -3.485 1.410 0.598 C29 VYJ 22 VYJ C31 C23 C 0 1 N N N -0.677 -39.906 -19.196 -5.160 3.150 0.317 C31 VYJ 23 VYJ C32 C24 C 0 1 Y N N -1.795 -40.507 -19.849 -5.861 2.587 -0.842 C32 VYJ 24 VYJ C33 C25 C 0 1 Y N N -2.213 -40.162 -21.177 -6.096 1.219 -0.946 C33 VYJ 25 VYJ C35 C26 C 0 1 Y N N -1.667 -37.956 -21.304 -4.201 0.287 0.183 C35 VYJ 26 VYJ C37 C27 C 0 1 N N N -1.591 -39.221 -23.407 -6.466 -0.510 0.793 C37 VYJ 27 VYJ C38 C28 C 0 1 N N N -0.634 -38.199 -24.078 -6.123 -1.991 0.560 C38 VYJ 28 VYJ C39 C29 C 0 1 N N N -0.373 -38.705 -25.512 -5.716 -2.570 1.931 C39 VYJ 29 VYJ C40 C30 C 0 1 N N N -0.276 -40.224 -25.320 -6.399 -1.633 2.957 C40 VYJ 30 VYJ C41 C31 C 0 1 N N N -1.209 -40.546 -24.126 -6.256 -0.239 2.297 C41 VYJ 31 VYJ C42 C32 C 0 1 Y N N -3.344 -40.824 -21.732 -6.805 0.719 -2.029 C42 VYJ 32 VYJ C43 C33 C 0 1 Y N N -4.040 -41.816 -21.021 -7.252 1.573 -3.018 C43 VYJ 33 VYJ C44 C34 C 0 1 Y N N -3.625 -42.150 -19.726 -6.996 2.932 -2.935 C44 VYJ 34 VYJ C45 C35 C 0 1 Y N N -2.518 -41.511 -19.147 -6.310 3.434 -1.861 C45 VYJ 35 VYJ C47 C36 C 0 1 N N N 1.012 -38.170 -18.831 -3.588 3.331 2.089 C47 VYJ 36 VYJ N10 N1 N 0 1 N N N -6.966 -35.524 -27.387 4.660 -1.497 1.210 N10 VYJ 37 VYJ N14 N2 N 0 1 N N N -8.577 -39.430 -28.417 7.077 1.838 0.407 N14 VYJ 38 VYJ N17 N3 N 0 1 N N N -8.869 -42.329 -28.123 9.225 2.791 -1.201 N17 VYJ 39 VYJ N25 N4 N 0 1 N N N -3.289 -34.837 -22.014 -1.578 -2.098 -0.200 N25 VYJ 40 VYJ N27 N5 N 0 1 Y N N -1.941 -35.485 -20.163 -1.518 0.155 0.422 N27 VYJ 41 VYJ N30 N6 N 0 1 N N N -0.262 -38.614 -19.401 -4.122 2.605 0.934 N30 VYJ 42 VYJ N34 N7 N 0 1 N N N -1.585 -39.180 -21.935 -5.576 0.342 0.001 N34 VYJ 43 VYJ N36 N8 N 0 1 Y N N -2.411 -36.979 -21.888 -3.549 -0.847 -0.052 N36 VYJ 44 VYJ O03 O1 O 0 1 N N N -4.070 -32.579 -22.898 -0.006 -3.731 -1.797 O03 VYJ 45 VYJ O23 O2 O 0 1 N N N -5.404 -33.941 -27.831 4.536 -3.611 0.539 O23 VYJ 46 VYJ O46 O3 O 0 1 N N N -0.022 -40.602 -18.390 -5.567 4.211 0.750 O46 VYJ 47 VYJ H1 H1 H 0 1 N N N -9.333 -37.453 -28.331 6.308 1.006 2.175 H1 VYJ 48 VYJ H2 H2 H 0 1 N N N -9.692 -40.006 -26.704 6.071 1.564 -1.418 H2 VYJ 49 VYJ H3 H3 H 0 1 N N N -10.672 -39.388 -28.077 7.586 0.645 -1.246 H3 VYJ 50 VYJ H4 H4 H 0 1 N N N -10.078 -44.075 -28.151 9.541 4.789 -1.769 H4 VYJ 51 VYJ H5 H5 H 0 1 N N N -9.189 -43.741 -29.676 11.021 3.843 -1.481 H5 VYJ 52 VYJ H6 H6 H 0 1 N N N -8.309 -44.374 -28.244 10.067 3.574 -2.959 H6 VYJ 53 VYJ H7 H7 H 0 1 N N N -7.677 -37.449 -30.157 6.838 -0.770 -0.250 H7 VYJ 54 VYJ H8 H8 H 0 1 N N N -6.375 -37.901 -29.005 7.919 -0.592 1.153 H8 VYJ 55 VYJ H9 H9 H 0 1 N N N -6.167 -35.555 -29.302 6.433 -2.623 1.299 H9 VYJ 56 VYJ H10 H10 H 0 1 N N N -7.943 -35.301 -29.204 6.193 -1.482 2.648 H10 VYJ 57 VYJ H11 H11 H 0 1 N N N -5.322 -32.587 -25.278 2.531 -3.789 -1.178 H11 VYJ 58 VYJ H12 H12 H 0 1 N N N -0.747 -36.164 -18.569 -1.516 2.164 1.001 H12 VYJ 59 VYJ H13 H13 H 0 1 N N N -3.744 -29.267 -22.982 0.682 -5.883 -4.277 H13 VYJ 60 VYJ H14 H14 H 0 1 N N N -4.242 -30.323 -21.616 -0.742 -5.869 -3.209 H14 VYJ 61 VYJ H15 H15 H 0 1 N N N -2.608 -30.502 -22.341 -0.442 -4.503 -4.310 H15 VYJ 62 VYJ H16 H16 H 0 1 N N N -3.643 -31.277 -24.483 1.321 -5.307 -1.952 H16 VYJ 63 VYJ H17 H17 H 0 1 N N N -5.277 -31.099 -23.758 1.620 -3.942 -3.053 H17 VYJ 64 VYJ H18 H18 H 0 1 N N N -3.842 -37.028 -23.623 -0.224 -0.862 1.698 H18 VYJ 65 VYJ H19 H19 H 0 1 N N N -4.982 -36.844 -25.786 2.189 -1.057 2.114 H19 VYJ 66 VYJ H20 H20 H 0 1 N N N -7.244 -36.167 -25.427 3.960 0.079 2.413 H20 VYJ 67 VYJ H21 H21 H 0 1 N N N -8.744 -35.785 -26.339 3.006 -0.225 0.940 H21 VYJ 68 VYJ H22 H22 H 0 1 N N N -8.739 -38.158 -26.033 4.425 1.851 0.785 H22 VYJ 69 VYJ H23 H23 H 0 1 N N N -7.012 -38.298 -26.508 4.816 0.644 -0.463 H23 VYJ 70 VYJ H24 H24 H 0 1 N N N -10.365 -41.434 -29.323 7.897 2.532 -2.809 H24 VYJ 71 VYJ H25 H25 H 0 1 N N N -10.884 -41.877 -27.661 7.350 3.673 -1.557 H25 VYJ 72 VYJ H26 H26 H 0 1 N N N -7.613 -41.832 -29.757 8.715 3.985 0.452 H26 VYJ 73 VYJ H27 H27 H 0 1 N N N -6.754 -42.363 -28.271 10.230 3.067 0.624 H27 VYJ 74 VYJ H28 H28 H 0 1 N N N -7.044 -40.258 -27.211 8.951 0.957 0.762 H28 VYJ 75 VYJ H29 H29 H 0 1 N N N -6.564 -39.880 -28.900 8.404 2.097 2.015 H29 VYJ 76 VYJ H30 H30 H 0 1 N N N -2.607 -38.965 -23.741 -7.504 -0.319 0.521 H30 VYJ 77 VYJ H31 H31 H 0 1 N N N 0.312 -38.142 -23.519 -6.996 -2.520 0.176 H31 VYJ 78 VYJ H32 H32 H 0 1 N N N -1.103 -37.204 -24.107 -5.295 -2.077 -0.144 H32 VYJ 79 VYJ H33 H33 H 0 1 N N N 0.566 -38.295 -25.913 -6.085 -3.590 2.039 H33 VYJ 80 VYJ H34 H34 H 0 1 N N N -1.204 -38.442 -26.183 -4.633 -2.541 2.050 H34 VYJ 81 VYJ H35 H35 H 0 1 N N N -0.614 -40.749 -26.226 -7.450 -1.896 3.080 H35 VYJ 82 VYJ H36 H36 H 0 1 N N N 0.759 -40.518 -25.090 -5.878 -1.664 3.914 H36 VYJ 83 VYJ H37 H37 H 0 1 N N N -2.120 -41.042 -24.493 -5.260 0.167 2.476 H37 VYJ 84 VYJ H38 H38 H 0 1 N N N -0.689 -41.211 -23.421 -7.019 0.442 2.674 H38 VYJ 85 VYJ H39 H39 H 0 1 N N N -3.676 -40.557 -22.725 -7.008 -0.340 -2.098 H39 VYJ 86 VYJ H40 H40 H 0 1 N N N -4.886 -42.316 -21.469 -7.803 1.180 -3.860 H40 VYJ 87 VYJ H41 H41 H 0 1 N N N -4.161 -42.905 -19.169 -7.338 3.591 -3.719 H41 VYJ 88 VYJ H42 H42 H 0 1 N N N -2.209 -41.787 -18.150 -6.117 4.495 -1.804 H42 VYJ 89 VYJ H43 H43 H 0 1 N N N 1.511 -39.019 -18.341 -2.817 4.026 1.756 H43 VYJ 90 VYJ H44 H44 H 0 1 N N N 1.656 -37.780 -19.633 -4.392 3.886 2.573 H44 VYJ 91 VYJ H45 H45 H 0 1 N N N 0.826 -37.377 -18.091 -3.157 2.623 2.797 H45 VYJ 92 VYJ H48 H48 H 0 1 N N N -3.402 -33.962 -21.543 -2.075 -2.855 -0.547 H48 VYJ 93 # # 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 VYJ C21 C22 SING N N 1 VYJ C21 C13 SING N N 2 VYJ C22 N10 SING N N 3 VYJ C18 C19 SING N N 4 VYJ C18 N17 SING N N 5 VYJ C20 N17 SING N N 6 VYJ N14 C19 SING N N 7 VYJ N14 C13 SING N N 8 VYJ N14 C15 SING N N 9 VYJ C16 N17 SING N N 10 VYJ C16 C15 SING N N 11 VYJ C13 C12 SING N N 12 VYJ O23 C09 DOUB N N 13 VYJ N10 C09 SING N N 14 VYJ N10 C11 SING N N 15 VYJ C09 C08 SING N N 16 VYJ C12 C11 SING N N 17 VYJ C08 C07 DOUB Y N 18 VYJ C08 C24 SING Y N 19 VYJ C39 C40 SING N N 20 VYJ C39 C38 SING N N 21 VYJ C40 C41 SING N N 22 VYJ C07 C06 SING Y N 23 VYJ C24 C04 DOUB Y N 24 VYJ C41 C37 SING N N 25 VYJ C38 C37 SING N N 26 VYJ C06 C05 DOUB Y N 27 VYJ C04 C05 SING Y N 28 VYJ C04 O03 SING N N 29 VYJ C02 O03 SING N N 30 VYJ C02 C01 SING N N 31 VYJ C37 N34 SING N N 32 VYJ C05 N25 SING N N 33 VYJ N25 C26 SING N N 34 VYJ N34 C35 SING N N 35 VYJ N34 C33 SING N N 36 VYJ N36 C26 DOUB Y N 37 VYJ N36 C35 SING Y N 38 VYJ C42 C33 DOUB Y N 39 VYJ C42 C43 SING Y N 40 VYJ C26 N27 SING Y N 41 VYJ C35 C29 DOUB Y N 42 VYJ C33 C32 SING Y N 43 VYJ C43 C44 DOUB Y N 44 VYJ N27 C28 DOUB Y N 45 VYJ C29 C28 SING Y N 46 VYJ C29 N30 SING N N 47 VYJ C32 C31 SING N N 48 VYJ C32 C45 DOUB Y N 49 VYJ C44 C45 SING Y N 50 VYJ N30 C31 SING N N 51 VYJ N30 C47 SING N N 52 VYJ C31 O46 DOUB N N 53 VYJ C13 H1 SING N N 54 VYJ C15 H2 SING N N 55 VYJ C15 H3 SING N N 56 VYJ C20 H4 SING N N 57 VYJ C20 H5 SING N N 58 VYJ C20 H6 SING N N 59 VYJ C21 H7 SING N N 60 VYJ C21 H8 SING N N 61 VYJ C22 H9 SING N N 62 VYJ C22 H10 SING N N 63 VYJ C24 H11 SING N N 64 VYJ C28 H12 SING N N 65 VYJ C01 H13 SING N N 66 VYJ C01 H14 SING N N 67 VYJ C01 H15 SING N N 68 VYJ C02 H16 SING N N 69 VYJ C02 H17 SING N N 70 VYJ C06 H18 SING N N 71 VYJ C07 H19 SING N N 72 VYJ C11 H20 SING N N 73 VYJ C11 H21 SING N N 74 VYJ C12 H22 SING N N 75 VYJ C12 H23 SING N N 76 VYJ C16 H24 SING N N 77 VYJ C16 H25 SING N N 78 VYJ C18 H26 SING N N 79 VYJ C18 H27 SING N N 80 VYJ C19 H28 SING N N 81 VYJ C19 H29 SING N N 82 VYJ C37 H30 SING N N 83 VYJ C38 H31 SING N N 84 VYJ C38 H32 SING N N 85 VYJ C39 H33 SING N N 86 VYJ C39 H34 SING N N 87 VYJ C40 H35 SING N N 88 VYJ C40 H36 SING N N 89 VYJ C41 H37 SING N N 90 VYJ C41 H38 SING N N 91 VYJ C42 H39 SING N N 92 VYJ C43 H40 SING N N 93 VYJ C44 H41 SING N N 94 VYJ C45 H42 SING N N 95 VYJ C47 H43 SING N N 96 VYJ C47 H44 SING N N 97 VYJ C47 H45 SING N N 98 VYJ N25 H48 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 VYJ SMILES ACDLabs 12.01 "C1(CCN(CC1)C(c6cc(c(Nc4ncc3N(C(=O)c2ccccc2N(c3n4)C5CCCC5)C)cc6)OCC)=O)N7CCN(C)CC7" VYJ InChI InChI 1.03 "InChI=1S/C36H46N8O3/c1-4-47-32-23-25(34(45)43-17-15-26(16-18-43)42-21-19-40(2)20-22-42)13-14-29(32)38-36-37-24-31-33(39-36)44(27-9-5-6-10-27)30-12-8-7-11-28(30)35(46)41(31)3/h7-8,11-14,23-24,26-27H,4-6,9-10,15-22H2,1-3H3,(H,37,38,39)" VYJ InChIKey InChI 1.03 XVBGRTMNFNMINE-UHFFFAOYSA-N VYJ SMILES_CANONICAL CACTVS 3.385 "CCOc1cc(ccc1Nc2ncc3N(C)C(=O)c4ccccc4N(C5CCCC5)c3n2)C(=O)N6CCC(CC6)N7CCN(C)CC7" VYJ SMILES CACTVS 3.385 "CCOc1cc(ccc1Nc2ncc3N(C)C(=O)c4ccccc4N(C5CCCC5)c3n2)C(=O)N6CCC(CC6)N7CCN(C)CC7" VYJ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCOc1cc(ccc1Nc2ncc3c(n2)N(c4ccccc4C(=O)N3C)C5CCCC5)C(=O)N6CCC(CC6)N7CCN(CC7)C" VYJ SMILES "OpenEye OEToolkits" 2.0.7 "CCOc1cc(ccc1Nc2ncc3c(n2)N(c4ccccc4C(=O)N3C)C5CCCC5)C(=O)N6CCC(CC6)N7CCN(CC7)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 VYJ "SYSTEMATIC NAME" ACDLabs 12.01 "11-cyclopentyl-2-({2-ethoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one" VYJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "11-cyclopentyl-2-[[2-ethoxy-4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]carbonyl-phenyl]amino]-5-methyl-pyrimido[4,5-b][1,4]benzodiazepin-6-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 VYJ "Create component" 2020-09-21 RCSB VYJ "Initial release" 2021-06-30 RCSB ##