data_VAT # _chem_comp.id VAT _chem_comp.name "4-(2-azaspiro[3.4]octan-2-ylmethyl)-~{N}-[[(3~{R})-3-oxidanyl-1-[6-[(phenylmethyl)amino]pyrimidin-4-yl]piperidin-3-yl]methyl]benzamide" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C32 H40 N6 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 540.699 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VAT _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 7OEF _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 VAT C10 C1 C 0 1 N N N -43.028 28.772 21.007 7.376 -0.833 0.465 C10 VAT 1 VAT C13 C2 C 0 1 N N N -42.569 26.369 21.060 9.043 0.495 -0.705 C13 VAT 2 VAT C15 C3 C 0 1 N N N -44.237 24.840 22.308 10.234 2.478 0.458 C15 VAT 3 VAT C17 C4 C 0 1 N N N -42.563 24.162 24.002 9.962 3.698 -1.640 C17 VAT 4 VAT C20 C5 C 0 1 Y N N -45.366 31.190 22.969 3.939 -0.627 2.009 C20 VAT 5 VAT C22 C6 C 0 1 N N N -45.349 35.912 25.637 -0.714 -2.348 -1.928 C22 VAT 6 VAT C24 C7 C 0 1 N N N -43.823 37.522 24.247 -2.849 -1.065 -1.740 C24 VAT 7 VAT C02 C8 C 0 1 N N R -44.167 35.616 26.573 -1.069 -3.056 -0.617 C02 VAT 8 VAT C03 C9 C 0 1 N N N -44.332 34.169 27.101 -0.470 -2.283 0.559 C03 VAT 9 VAT C05 C10 C 0 1 N N N -44.919 32.646 25.171 1.714 -1.467 1.270 C05 VAT 10 VAT C06 C11 C 0 1 Y N N -44.464 31.599 24.023 3.168 -1.304 1.063 C06 VAT 11 VAT C07 C12 C 0 1 Y N N -43.135 31.129 24.061 3.777 -1.827 -0.079 C07 VAT 12 VAT C08 C13 C 0 1 Y N N -42.690 30.224 23.050 5.135 -1.671 -0.266 C08 VAT 13 VAT C09 C14 C 0 1 Y N N -43.579 29.786 22.006 5.893 -0.999 0.675 C09 VAT 14 VAT C12 C15 C 0 1 N N N -43.502 27.182 22.777 7.826 1.549 0.660 C12 VAT 15 VAT C14 C16 C 0 1 N N N -43.028 25.797 22.394 8.983 1.957 -0.255 C14 VAT 16 VAT C16 C17 C 0 1 N N N -43.781 23.682 23.161 10.602 3.809 -0.234 C16 VAT 17 VAT C18 C18 C 0 1 N N N -41.865 25.238 23.208 8.625 2.966 -1.354 C18 VAT 18 VAT C19 C19 C 0 1 Y N N -44.925 30.258 21.936 5.296 -0.478 1.810 C19 VAT 19 VAT C23 C20 C 0 1 N N N -45.212 37.283 24.974 -1.334 -0.947 -1.926 C23 VAT 20 VAT C25 C21 C 0 1 N N N -42.832 35.770 25.720 -2.591 -3.112 -0.469 C25 VAT 21 VAT C27 C22 C 0 1 Y N N -41.583 38.172 25.701 -4.497 -1.757 -0.209 C27 VAT 22 VAT C29 C23 C 0 1 Y N N -40.303 39.014 27.535 -6.429 -2.921 0.261 C29 VAT 23 VAT C31 C24 C 0 1 Y N N -39.989 40.092 25.368 -6.577 -0.627 0.108 C31 VAT 24 VAT C33 C25 C 0 1 N N N -39.635 41.636 23.110 -6.701 1.835 -0.053 C33 VAT 25 VAT C34 C26 C 0 1 Y N N -41.147 42.317 22.756 -7.736 2.924 0.065 C34 VAT 26 VAT C35 C27 C 0 1 Y N N -41.574 42.385 21.377 -7.984 3.511 1.292 C35 VAT 27 VAT C36 C28 C 0 1 Y N N -42.853 42.953 21.021 -8.934 4.510 1.400 C36 VAT 28 VAT C37 C29 C 0 1 Y N N -43.717 43.466 22.055 -9.634 4.922 0.282 C37 VAT 29 VAT C38 C30 C 0 1 Y N N -43.303 43.406 23.441 -9.386 4.335 -0.945 C38 VAT 30 VAT C39 C31 C 0 1 Y N N -42.023 42.834 23.795 -8.433 3.339 -1.054 C39 VAT 31 VAT C40 C32 C 0 1 Y N N -40.987 39.140 24.816 -5.213 -0.565 -0.161 C40 VAT 32 VAT N04 N1 N 0 1 N N N -43.979 33.208 26.054 0.972 -2.121 0.355 N04 VAT 33 VAT N11 N2 N 0 1 N N N -42.437 27.703 21.790 7.630 0.413 -0.271 N11 VAT 34 VAT N26 N3 N 0 1 N N N -42.611 37.145 25.109 -3.136 -1.749 -0.472 N26 VAT 35 VAT N28 N4 N 0 1 Y N N -41.221 38.134 27.042 -5.137 -2.905 0.005 N28 VAT 36 VAT N30 N5 N 0 1 Y N N -39.690 39.980 26.743 -7.142 -1.815 0.316 N30 VAT 37 VAT N32 N6 N 0 1 N N N -39.322 41.136 24.521 -7.336 0.532 0.167 N32 VAT 38 VAT O01 O1 O 0 1 N N N -44.237 36.438 27.686 -0.541 -4.383 -0.634 O01 VAT 39 VAT O21 O2 O 0 1 N N N -46.111 32.963 25.299 1.186 -1.011 2.266 O21 VAT 40 VAT H1 H1 H 0 1 N N N -43.840 28.378 20.378 7.878 -0.793 1.431 H1 VAT 41 VAT H2 H2 H 0 1 N N N -42.265 29.243 20.369 7.758 -1.677 -0.109 H2 VAT 42 VAT H3 H3 H 0 1 N N N -41.624 25.954 20.678 9.181 0.371 -1.780 H3 VAT 43 VAT H4 H4 H 0 1 N N N -43.326 26.350 20.263 9.722 -0.120 -0.114 H4 VAT 44 VAT H5 H5 H 0 1 N N N -45.145 25.305 22.718 10.020 2.650 1.513 H5 VAT 45 VAT H6 H6 H 0 1 N N N -44.423 24.524 21.271 11.050 1.763 0.353 H6 VAT 46 VAT H7 H7 H 0 1 N N N -42.907 24.568 24.965 9.778 4.687 -2.060 H7 VAT 47 VAT H8 H8 H 0 1 N N N -41.876 23.322 24.183 10.591 3.106 -2.305 H8 VAT 48 VAT H9 H9 H 0 1 N N N -46.374 31.577 22.946 3.474 -0.217 2.893 H9 VAT 49 VAT H10 H10 H 0 1 N N N -45.387 35.139 24.855 0.369 -2.266 -2.016 H10 VAT 50 VAT H11 H11 H 0 1 N N N -46.281 35.889 26.221 -1.108 -2.919 -2.768 H11 VAT 51 VAT H12 H12 H 0 1 N N N -43.801 36.915 23.330 -3.291 -0.069 -1.724 H12 VAT 52 VAT H13 H13 H 0 1 N N N -43.746 38.587 23.984 -3.272 -1.638 -2.565 H13 VAT 53 VAT H14 H14 H 0 1 N N N -43.672 34.021 27.968 -0.939 -1.301 0.626 H14 VAT 54 VAT H15 H15 H 0 1 N N N -45.377 34.009 27.404 -0.646 -2.833 1.484 H15 VAT 55 VAT H16 H16 H 0 1 N N N -42.463 31.449 24.844 3.186 -2.352 -0.815 H16 VAT 56 VAT H17 H17 H 0 1 N N N -41.672 29.863 23.069 5.607 -2.075 -1.150 H17 VAT 57 VAT H18 H18 H 0 1 N N N -44.542 27.410 22.501 8.139 1.249 1.660 H18 VAT 58 VAT H19 H19 H 0 1 N N N -43.334 27.456 23.829 6.999 2.260 0.667 H19 VAT 59 VAT H20 H20 H 0 1 N N N -44.596 23.366 23.829 10.179 4.652 0.312 H20 VAT 60 VAT H21 H21 H 0 1 N N N -43.484 22.839 22.520 11.684 3.911 -0.314 H21 VAT 61 VAT H22 H22 H 0 1 N N N -41.426 26.004 23.864 7.873 3.669 -0.997 H22 VAT 62 VAT H23 H23 H 0 1 N N N -41.082 24.818 22.559 8.273 2.449 -2.247 H23 VAT 63 VAT H24 H24 H 0 1 N N N -45.591 29.938 21.149 5.894 0.046 2.541 H24 VAT 64 VAT H25 H25 H 0 1 N N N -46.013 37.386 24.228 -0.911 -0.363 -1.108 H25 VAT 65 VAT H26 H26 H 0 1 N N N -45.332 38.054 25.749 -1.121 -0.454 -2.874 H26 VAT 66 VAT H27 H27 H 0 1 N N N -41.979 35.549 26.379 -3.016 -3.675 -1.300 H27 VAT 67 VAT H28 H28 H 0 1 N N N -42.864 35.035 24.902 -2.847 -3.603 0.470 H28 VAT 68 VAT H29 H29 H 0 1 N N N -40.042 38.959 28.581 -6.918 -3.869 0.431 H29 VAT 69 VAT H30 H30 H 0 1 N N N -38.881 42.401 22.872 -6.260 1.860 -1.049 H30 VAT 70 VAT H31 H31 H 0 1 N N N -39.511 40.776 22.436 -5.923 1.990 0.694 H31 VAT 71 VAT H32 H32 H 0 1 N N N -40.926 42.005 20.601 -7.437 3.189 2.165 H32 VAT 72 VAT H33 H33 H 0 1 N N N -43.161 42.993 19.986 -9.128 4.969 2.358 H33 VAT 73 VAT H34 H34 H 0 1 N N N -44.673 43.895 21.795 -10.377 5.702 0.367 H34 VAT 74 VAT H35 H35 H 0 1 N N N -43.953 43.790 24.214 -9.933 4.657 -1.818 H35 VAT 75 VAT H36 H36 H 0 1 N N N -41.718 42.791 24.830 -8.236 2.884 -2.013 H36 VAT 76 VAT H37 H37 H 0 1 N N N -41.260 39.173 23.772 -4.723 0.383 -0.326 H37 VAT 77 VAT H38 H38 H 0 1 N N N -43.021 32.937 25.962 1.392 -2.485 -0.440 H38 VAT 78 VAT H40 H40 H 0 1 N N N -39.365 41.962 25.082 -8.286 0.481 0.354 H40 VAT 79 VAT H41 H41 H 0 1 N N N -43.505 36.253 28.263 0.421 -4.423 -0.728 H41 VAT 80 # # 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 VAT C10 C09 SING N N 1 VAT C10 N11 SING N N 2 VAT C13 C14 SING N N 3 VAT C13 N11 SING N N 4 VAT C15 C14 SING N N 5 VAT C15 C16 SING N N 6 VAT C17 C16 SING N N 7 VAT C17 C18 SING N N 8 VAT C20 C06 DOUB Y N 9 VAT C20 C19 SING Y N 10 VAT C22 C02 SING N N 11 VAT C22 C23 SING N N 12 VAT C24 C23 SING N N 13 VAT C24 N26 SING N N 14 VAT C02 C03 SING N N 15 VAT C02 C25 SING N N 16 VAT C02 O01 SING N N 17 VAT C03 N04 SING N N 18 VAT C05 C06 SING N N 19 VAT C05 N04 SING N N 20 VAT C05 O21 DOUB N N 21 VAT C06 C07 SING Y N 22 VAT C07 C08 DOUB Y N 23 VAT C08 C09 SING Y N 24 VAT C09 C19 DOUB Y N 25 VAT C12 C14 SING N N 26 VAT C12 N11 SING N N 27 VAT C14 C18 SING N N 28 VAT C25 N26 SING N N 29 VAT C27 C40 DOUB Y N 30 VAT C27 N26 SING N N 31 VAT C27 N28 SING Y N 32 VAT C29 N28 DOUB Y N 33 VAT C29 N30 SING Y N 34 VAT C31 C40 SING Y N 35 VAT C31 N30 DOUB Y N 36 VAT C31 N32 SING N N 37 VAT C33 N32 SING N N 38 VAT C34 C35 DOUB Y N 39 VAT C34 C39 SING Y N 40 VAT C35 C36 SING Y N 41 VAT C36 C37 DOUB Y N 42 VAT C37 C38 SING Y N 43 VAT C38 C39 DOUB Y N 44 VAT C33 C34 SING N N 45 VAT C10 H1 SING N N 46 VAT C10 H2 SING N N 47 VAT C13 H3 SING N N 48 VAT C13 H4 SING N N 49 VAT C15 H5 SING N N 50 VAT C15 H6 SING N N 51 VAT C17 H7 SING N N 52 VAT C17 H8 SING N N 53 VAT C20 H9 SING N N 54 VAT C22 H10 SING N N 55 VAT C22 H11 SING N N 56 VAT C24 H12 SING N N 57 VAT C24 H13 SING N N 58 VAT C03 H14 SING N N 59 VAT C03 H15 SING N N 60 VAT C07 H16 SING N N 61 VAT C08 H17 SING N N 62 VAT C12 H18 SING N N 63 VAT C12 H19 SING N N 64 VAT C16 H20 SING N N 65 VAT C16 H21 SING N N 66 VAT C18 H22 SING N N 67 VAT C18 H23 SING N N 68 VAT C19 H24 SING N N 69 VAT C23 H25 SING N N 70 VAT C23 H26 SING N N 71 VAT C25 H27 SING N N 72 VAT C25 H28 SING N N 73 VAT C29 H29 SING N N 74 VAT C33 H30 SING N N 75 VAT C33 H31 SING N N 76 VAT C35 H32 SING N N 77 VAT C36 H33 SING N N 78 VAT C37 H34 SING N N 79 VAT C38 H35 SING N N 80 VAT C39 H36 SING N N 81 VAT C40 H37 SING N N 82 VAT N04 H38 SING N N 83 VAT N32 H40 SING N N 84 VAT O01 H41 SING N N 85 # # 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 VAT InChI InChI 1.03 "InChI=1S/C32H40N6O2/c39-30(27-11-9-26(10-12-27)19-37-21-31(22-37)13-4-5-14-31)34-20-32(40)15-6-16-38(23-32)29-17-28(35-24-36-29)33-18-25-7-2-1-3-8-25/h1-3,7-12,17,24,40H,4-6,13-16,18-23H2,(H,34,39)(H,33,35,36)/t32-/m1/s1" VAT InChIKey InChI 1.03 SVCYBAWPGFFEQO-JGCGQSQUSA-N VAT SMILES_CANONICAL CACTVS 3.385 "O[C@]1(CCCN(C1)c2cc(NCc3ccccc3)ncn2)CNC(=O)c4ccc(CN5CC6(CCCC6)C5)cc4" VAT SMILES CACTVS 3.385 "O[C]1(CCCN(C1)c2cc(NCc3ccccc3)ncn2)CNC(=O)c4ccc(CN5CC6(CCCC6)C5)cc4" VAT SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CNc2cc(ncn2)N3CCC[C@](C3)(CNC(=O)c4ccc(cc4)CN5CC6(C5)CCCC6)O" VAT SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CNc2cc(ncn2)N3CCCC(C3)(CNC(=O)c4ccc(cc4)CN5CC6(C5)CCCC6)O" # _pdbx_chem_comp_identifier.comp_id VAT _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 "4-(2-azaspiro[3.4]octan-2-ylmethyl)-~{N}-[[(3~{R})-3-oxidanyl-1-[6-[(phenylmethyl)amino]pyrimidin-4-yl]piperidin-3-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 VAT "Create component" 2021-05-04 PDBE VAT "Initial release" 2021-10-20 RCSB ##