data_VA8 # _chem_comp.id VA8 _chem_comp.name "~{N}-[[(3~{R})-1-[6-(3~{H}-benzimidazol-4-ylmethylamino)pyrimidin-4-yl]-3-oxidanyl-piperidin-3-yl]methyl]-4-[(4,4-dimethylpiperidin-1-yl)methyl]benzamide" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C33 H42 N8 O2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-05-04 _chem_comp.pdbx_modified_date 2021-10-15 _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 582.739 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VA8 _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 7OEL _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 VA8 C10 C1 C 0 1 Y N N -43.256 31.256 24.387 -4.559 -0.357 -2.112 C10 VA8 1 VA8 C13 C2 C 0 1 Y N N -44.552 31.716 24.482 -3.885 -1.186 -1.213 C13 VA8 2 VA8 C17 C3 C 0 1 N N R -44.351 35.889 26.673 0.132 -3.411 0.446 C17 VA8 3 VA8 C20 C4 C 0 1 N N N -43.472 37.509 24.288 1.987 -1.688 1.854 C20 VA8 4 VA8 C21 C5 C 0 1 N N N -42.875 35.976 26.124 1.652 -3.565 0.357 C21 VA8 5 VA8 C01 C6 C 0 1 N N N -44.660 24.125 22.498 -10.187 3.627 -0.330 C01 VA8 6 VA8 C02 C7 C 0 1 N N N -43.262 24.746 22.880 -9.337 3.275 0.893 C02 VA8 7 VA8 C03 C8 C 0 1 N N N -42.441 23.802 23.736 -9.432 4.403 1.923 C03 VA8 8 VA8 C04 C9 C 0 1 N N N -43.521 25.936 23.706 -7.878 3.093 0.467 C04 VA8 9 VA8 C05 C10 C 0 1 N N N -43.778 27.204 22.928 -7.781 1.925 -0.517 C05 VA8 10 VA8 C07 C11 C 0 1 N N N -43.251 28.848 21.266 -8.074 -0.467 -0.743 C07 VA8 11 VA8 C08 C12 C 0 1 Y N N -43.675 29.860 22.377 -6.597 -0.718 -0.907 C08 VA8 12 VA8 C09 C13 C 0 1 Y N N -42.813 30.354 23.379 -5.911 -0.129 -1.954 C09 VA8 13 VA8 C11 C14 C 0 1 Y N N -44.975 30.355 22.445 -5.937 -1.549 -0.019 C11 VA8 14 VA8 C12 C15 C 0 1 Y N N -45.415 31.238 23.445 -4.585 -1.782 -0.163 C12 VA8 15 VA8 C14 C16 C 0 1 N N N -44.984 32.727 25.523 -2.436 -1.432 -1.374 C14 VA8 16 VA8 C16 C17 C 0 1 N N N -44.531 34.487 27.269 -0.352 -2.475 -0.663 C16 VA8 17 VA8 C18 C18 C 0 1 N N N -45.245 36.062 25.438 -0.237 -2.821 1.810 C18 VA8 18 VA8 C19 C19 C 0 1 N N N -44.956 37.345 24.708 0.477 -1.479 1.987 C19 VA8 19 VA8 C23 C20 C 0 1 Y N N -41.477 38.178 25.781 3.659 -2.335 0.328 C23 VA8 20 VA8 C25 C21 C 0 1 Y N N -40.112 39.126 27.398 5.528 -3.583 -0.179 C25 VA8 21 VA8 C27 C22 C 0 1 Y N N -40.051 40.193 25.309 5.824 -1.332 0.214 C27 VA8 22 VA8 C29 C23 C 0 1 N N N -40.130 41.551 22.971 6.108 1.084 0.640 C29 VA8 23 VA8 C30 C24 C 0 1 Y N N -41.463 42.443 22.749 7.219 2.102 0.678 C30 VA8 24 VA8 C31 C25 C 0 1 Y N N -42.136 43.048 23.877 7.708 2.645 -0.502 C31 VA8 25 VA8 C33 C26 C 0 1 Y N N -42.948 43.850 25.927 8.231 3.289 -2.548 C33 VA8 26 VA8 C35 C27 C 0 1 Y N N -43.340 43.868 23.687 8.744 3.593 -0.458 C35 VA8 27 VA8 C36 C28 C 0 1 Y N N -43.815 44.042 22.354 9.271 3.979 0.777 C36 VA8 28 VA8 C37 C29 C 0 1 Y N N -43.192 43.475 21.281 8.777 3.434 1.929 C37 VA8 29 VA8 C38 C30 C 0 1 Y N N -42.013 42.678 21.493 7.751 2.501 1.886 C38 VA8 30 VA8 C39 C31 C 0 1 Y N N -40.995 39.195 24.908 4.456 -1.199 0.433 C39 VA8 31 VA8 C42 C32 C 0 1 N N N -42.719 26.466 20.936 -9.693 0.836 0.498 C42 VA8 32 VA8 C43 C33 C 0 1 N N N -42.413 25.113 21.628 -9.847 1.971 1.513 C43 VA8 33 VA8 N06 N1 N 0 1 N N N -42.821 27.570 21.895 -8.280 0.701 0.123 N06 VA8 34 VA8 N15 N2 N 0 1 N N N -44.112 33.476 26.307 -1.788 -2.232 -0.504 N15 VA8 35 VA8 N22 N3 N 0 1 N N N -42.426 37.167 25.311 2.290 -2.254 0.532 N22 VA8 36 VA8 N24 N4 N 0 1 Y N N -41.008 38.176 27.072 4.228 -3.499 0.022 N24 VA8 37 VA8 N26 N5 N 0 1 Y N N -39.605 40.129 26.623 6.317 -2.532 -0.088 N26 VA8 38 VA8 N28 N6 N 0 1 N N N -39.597 41.201 24.382 6.661 -0.231 0.307 N28 VA8 39 VA8 N32 N7 N 0 1 Y N N -41.926 43.071 25.320 7.405 2.474 -1.837 N32 VA8 40 VA8 N34 N8 N 0 1 Y N N -43.795 44.330 24.990 9.014 3.944 -1.742 N34 VA8 41 VA8 O40 O1 O 0 1 N N N -44.684 36.762 27.670 -0.486 -4.690 0.296 O40 VA8 42 VA8 O41 O2 O 0 1 N N N -46.184 32.989 25.684 -1.829 -0.912 -2.290 O41 VA8 43 VA8 H1 H1 H 0 1 N N N -42.538 31.599 25.117 -4.023 0.107 -2.927 H1 VA8 44 VA8 H2 H2 H 0 1 N N N -43.303 36.864 23.413 2.497 -0.731 1.966 H2 VA8 45 VA8 H3 H3 H 0 1 N N N -43.324 38.561 24.002 2.328 -2.374 2.629 H3 VA8 46 VA8 H4 H4 H 0 1 N N N -42.721 35.088 25.493 1.995 -4.242 1.139 H4 VA8 47 VA8 H5 H5 H 0 1 N N N -42.210 35.924 26.999 1.920 -3.972 -0.618 H5 VA8 48 VA8 H6 H6 H 0 1 N N N -45.218 23.884 23.415 -10.121 2.822 -1.062 H6 VA8 49 VA8 H7 H7 H 0 1 N N N -45.232 24.850 21.900 -11.226 3.756 -0.025 H7 VA8 50 VA8 H8 H8 H 0 1 N N N -44.505 23.207 21.912 -9.820 4.552 -0.773 H8 VA8 51 VA8 H9 H9 H 0 1 N N N -43.016 23.524 24.631 -10.471 4.531 2.227 H9 VA8 52 VA8 H10 H10 H 0 1 N N N -42.202 22.897 23.158 -8.827 4.152 2.794 H10 VA8 53 VA8 H11 H11 H 0 1 N N N -41.508 24.300 24.040 -9.067 5.330 1.481 H11 VA8 54 VA8 H12 H12 H 0 1 N N N -44.403 25.733 24.331 -7.523 4.004 -0.013 H12 VA8 55 VA8 H13 H13 H 0 1 N N N -42.645 26.102 24.351 -7.267 2.882 1.345 H13 VA8 56 VA8 H14 H14 H 0 1 N N N -43.813 28.032 23.652 -8.382 2.144 -1.400 H14 VA8 57 VA8 H15 H15 H 0 1 N N N -44.760 27.099 22.444 -6.741 1.783 -0.811 H15 VA8 58 VA8 H16 H16 H 0 1 N N N -42.417 29.269 20.685 -8.521 -0.279 -1.720 H16 VA8 59 VA8 H17 H17 H 0 1 N N N -44.104 28.659 20.598 -8.543 -1.342 -0.292 H17 VA8 60 VA8 H18 H18 H 0 1 N N N -41.781 30.036 23.381 -6.433 0.512 -2.648 H18 VA8 61 VA8 H19 H19 H 0 1 N N N -45.681 30.044 21.690 -6.482 -2.016 0.788 H19 VA8 62 VA8 H20 H20 H 0 1 N N N -46.443 31.569 23.431 -4.071 -2.431 0.531 H20 VA8 63 VA8 H21 H21 H 0 1 N N N -45.590 34.332 27.521 0.186 -1.529 -0.601 H21 VA8 64 VA8 H22 H22 H 0 1 N N N -43.920 34.398 28.180 -0.167 -2.936 -1.634 H22 VA8 65 VA8 H23 H23 H 0 1 N N N -46.297 36.065 25.759 -1.316 -2.670 1.861 H23 VA8 66 VA8 H24 H24 H 0 1 N N N -45.073 35.218 24.754 0.072 -3.507 2.599 H24 VA8 67 VA8 H25 H25 H 0 1 N N N -45.225 38.185 25.365 0.251 -1.074 2.974 H25 VA8 68 VA8 H26 H26 H 0 1 N N N -45.578 37.375 23.801 0.137 -0.782 1.221 H26 VA8 69 VA8 H27 H27 H 0 1 N N N -39.743 39.090 28.412 5.959 -4.542 -0.425 H27 VA8 70 VA8 H28 H28 H 0 1 N N N -40.315 40.591 22.466 5.623 1.038 1.615 H28 VA8 71 VA8 H29 H29 H 0 1 N N N -39.315 42.084 22.459 5.377 1.373 -0.116 H29 VA8 72 VA8 H30 H30 H 0 1 N N N -43.035 44.033 26.988 8.236 3.378 -3.624 H30 VA8 73 VA8 H31 H31 H 0 1 N N N -44.697 44.643 22.188 10.068 4.707 0.822 H31 VA8 74 VA8 H32 H32 H 0 1 N N N -43.579 43.623 20.284 9.185 3.737 2.882 H32 VA8 75 VA8 H33 H33 H 0 1 N N N -41.530 42.239 20.632 7.371 2.079 2.805 H33 VA8 76 VA8 H34 H34 H 0 1 N N N -41.360 39.214 23.892 4.025 -0.240 0.679 H34 VA8 77 VA8 H35 H35 H 0 1 N N N -41.911 26.690 20.223 -10.042 -0.097 0.941 H35 VA8 78 VA8 H36 H36 H 0 1 N N N -43.672 26.379 20.394 -10.285 1.059 -0.390 H36 VA8 79 VA8 H37 H37 H 0 1 N N N -42.563 24.319 20.882 -9.267 1.741 2.406 H37 VA8 80 VA8 H38 H38 H 0 1 N N N -41.358 25.131 21.938 -10.898 2.081 1.779 H38 VA8 81 VA8 H40 H40 H 0 1 N N N -43.131 33.309 26.203 -2.272 -2.647 0.227 H40 VA8 82 VA8 H41 H41 H 0 1 N N N -38.632 40.984 24.234 7.614 -0.331 0.153 H41 VA8 83 VA8 H42 H42 H 0 1 N N N -41.182 42.612 25.805 6.728 1.881 -2.202 H42 VA8 84 VA8 H44 H44 H 0 1 N N N -44.111 36.626 28.415 -1.452 -4.668 0.343 H44 VA8 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 VA8 C42 C43 SING N N 1 VA8 C42 N06 SING N N 2 VA8 C07 N06 SING N N 3 VA8 C07 C08 SING N N 4 VA8 C37 C38 DOUB Y N 5 VA8 C37 C36 SING Y N 6 VA8 C38 C30 SING Y N 7 VA8 C43 C02 SING N N 8 VA8 N06 C05 SING N N 9 VA8 C36 C35 DOUB Y N 10 VA8 C08 C11 DOUB Y N 11 VA8 C08 C09 SING Y N 12 VA8 C11 C12 SING Y N 13 VA8 C01 C02 SING N N 14 VA8 C30 C29 SING N N 15 VA8 C30 C31 DOUB Y N 16 VA8 C02 C04 SING N N 17 VA8 C02 C03 SING N N 18 VA8 C05 C04 SING N N 19 VA8 C29 N28 SING N N 20 VA8 C09 C10 DOUB Y N 21 VA8 C12 C13 DOUB Y N 22 VA8 C35 C31 SING Y N 23 VA8 C35 N34 SING Y N 24 VA8 C31 N32 SING Y N 25 VA8 C20 C19 SING N N 26 VA8 C20 N22 SING N N 27 VA8 N28 C27 SING N N 28 VA8 C10 C13 SING Y N 29 VA8 C13 C14 SING N N 30 VA8 C19 C18 SING N N 31 VA8 C39 C27 DOUB Y N 32 VA8 C39 C23 SING Y N 33 VA8 N34 C33 DOUB Y N 34 VA8 C27 N26 SING Y N 35 VA8 N22 C23 SING N N 36 VA8 N22 C21 SING N N 37 VA8 N32 C33 SING Y N 38 VA8 C18 C17 SING N N 39 VA8 C14 O41 DOUB N N 40 VA8 C14 N15 SING N N 41 VA8 C23 N24 DOUB Y N 42 VA8 C21 C17 SING N N 43 VA8 N15 C16 SING N N 44 VA8 N26 C25 DOUB Y N 45 VA8 C17 C16 SING N N 46 VA8 C17 O40 SING N N 47 VA8 N24 C25 SING Y N 48 VA8 C10 H1 SING N N 49 VA8 C20 H2 SING N N 50 VA8 C20 H3 SING N N 51 VA8 C21 H4 SING N N 52 VA8 C21 H5 SING N N 53 VA8 C01 H6 SING N N 54 VA8 C01 H7 SING N N 55 VA8 C01 H8 SING N N 56 VA8 C03 H9 SING N N 57 VA8 C03 H10 SING N N 58 VA8 C03 H11 SING N N 59 VA8 C04 H12 SING N N 60 VA8 C04 H13 SING N N 61 VA8 C05 H14 SING N N 62 VA8 C05 H15 SING N N 63 VA8 C07 H16 SING N N 64 VA8 C07 H17 SING N N 65 VA8 C09 H18 SING N N 66 VA8 C11 H19 SING N N 67 VA8 C12 H20 SING N N 68 VA8 C16 H21 SING N N 69 VA8 C16 H22 SING N N 70 VA8 C18 H23 SING N N 71 VA8 C18 H24 SING N N 72 VA8 C19 H25 SING N N 73 VA8 C19 H26 SING N N 74 VA8 C25 H27 SING N N 75 VA8 C29 H28 SING N N 76 VA8 C29 H29 SING N N 77 VA8 C33 H30 SING N N 78 VA8 C36 H31 SING N N 79 VA8 C37 H32 SING N N 80 VA8 C38 H33 SING N N 81 VA8 C39 H34 SING N N 82 VA8 C42 H35 SING N N 83 VA8 C42 H36 SING N N 84 VA8 C43 H37 SING N N 85 VA8 C43 H38 SING N N 86 VA8 N15 H40 SING N N 87 VA8 N28 H41 SING N N 88 VA8 N32 H42 SING N N 89 VA8 O40 H44 SING N N 90 # # 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 VA8 InChI InChI 1.03 "InChI=1S/C33H42N8O2/c1-32(2)12-15-40(16-13-32)19-24-7-9-25(10-8-24)31(42)35-20-33(43)11-4-14-41(21-33)29-17-28(37-23-38-29)34-18-26-5-3-6-27-30(26)39-22-36-27/h3,5-10,17,22-23,43H,4,11-16,18-21H2,1-2H3,(H,35,42)(H,36,39)(H,34,37,38)/t33-/m1/s1" VA8 InChIKey InChI 1.03 IASLOXMPEUOUSU-MGBGTMOVSA-N VA8 SMILES_CANONICAL CACTVS 3.385 "CC1(C)CCN(CC1)Cc2ccc(cc2)C(=O)NC[C@]3(O)CCCN(C3)c4cc(NCc5cccc6nc[nH]c56)ncn4" VA8 SMILES CACTVS 3.385 "CC1(C)CCN(CC1)Cc2ccc(cc2)C(=O)NC[C]3(O)CCCN(C3)c4cc(NCc5cccc6nc[nH]c56)ncn4" VA8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1(CCN(CC1)Cc2ccc(cc2)C(=O)NC[C@@]3(CCCN(C3)c4cc(ncn4)NCc5cccc6c5[nH]cn6)O)C" VA8 SMILES "OpenEye OEToolkits" 2.0.7 "CC1(CCN(CC1)Cc2ccc(cc2)C(=O)NCC3(CCCN(C3)c4cc(ncn4)NCc5cccc6c5[nH]cn6)O)C" # _pdbx_chem_comp_identifier.comp_id VA8 _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 "~{N}-[[(3~{R})-1-[6-(3~{H}-benzimidazol-4-ylmethylamino)pyrimidin-4-yl]-3-oxidanyl-piperidin-3-yl]methyl]-4-[(4,4-dimethylpiperidin-1-yl)methyl]benzamide" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site VA8 "Create component" 2021-05-04 PDBE VA8 "Initial release" 2021-10-20 RCSB ##