data_VB5 # _chem_comp.id VB5 _chem_comp.name "4-[(4,4-dimethylpiperidin-1-yl)methyl]-~{N}-[[(3~{R})-1-[6-(methylamino)pyrimidin-4-yl]-3-oxidanyl-piperidin-3-yl]methyl]-2-oxidanyl-benzamide" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C26 H38 N6 O3" _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 482.618 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VB5 _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 7OED _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 VB5 C10 C1 C 0 1 Y N N 14.328 -23.899 -13.879 -2.074 1.660 -0.392 C10 VB5 1 VB5 C15 C2 C 0 1 N N N 13.121 -22.451 -12.216 -0.145 1.082 1.073 C15 VB5 2 VB5 C17 C3 C 0 1 N N N 11.923 -21.145 -10.433 2.166 1.295 0.331 C17 VB5 3 VB5 C20 C4 C 0 1 N N N 9.070 -20.171 -12.904 2.741 -0.564 -1.887 C20 VB5 4 VB5 C21 C5 C 0 1 N N N 9.562 -18.760 -13.301 4.244 -0.739 -1.662 C21 VB5 5 VB5 C22 C6 C 0 1 N N N 11.326 -18.934 -11.401 4.422 1.490 -0.728 C22 VB5 6 VB5 C24 C7 C 0 1 Y N N 10.034 -16.759 -11.750 5.993 -0.178 -0.191 C24 VB5 7 VB5 C26 C8 C 0 1 Y N N 10.141 -15.120 -10.103 8.127 0.613 0.168 C26 VB5 8 VB5 C28 C9 C 0 1 Y N N 9.077 -14.624 -12.122 7.780 -1.654 0.386 C28 VB5 9 VB5 C01 C10 C 0 1 N N N 20.703 -26.264 -15.814 -8.993 -1.786 0.581 C01 VB5 10 VB5 C02 C11 C 0 1 N N N 20.915 -24.998 -14.968 -8.045 -2.027 -0.595 C02 VB5 11 VB5 C03 C12 C 0 1 N N N 22.242 -25.118 -14.183 -8.432 -3.326 -1.306 C03 VB5 12 VB5 C04 C13 C 0 1 N N N 20.906 -23.804 -15.899 -8.143 -0.858 -1.579 C04 VB5 13 VB5 C05 C14 C 0 1 N N N 19.506 -23.604 -16.483 -7.698 0.429 -0.879 C05 VB5 14 VB5 C07 C15 C 0 1 N N N 17.350 -23.350 -16.258 -5.807 1.540 0.147 C07 VB5 15 VB5 C08 C16 C 0 1 Y N N 16.210 -23.105 -15.199 -4.326 1.420 0.393 C08 VB5 16 VB5 C09 C17 C 0 1 Y N N 15.315 -24.131 -14.851 -3.431 1.765 -0.607 C09 VB5 17 VB5 C11 C18 C 0 1 Y N N 16.115 -21.861 -14.589 -3.867 0.966 1.614 C11 VB5 18 VB5 C12 C19 C 0 1 Y N N 15.118 -21.628 -13.627 -2.505 0.859 1.849 C12 VB5 19 VB5 C14 C20 C 0 1 Y N N 14.233 -22.652 -13.279 -1.597 1.203 0.838 C14 VB5 20 VB5 C18 C21 C 0 1 N N R 10.749 -20.319 -11.033 2.924 1.731 -0.925 C18 VB5 21 VB5 C19 C22 C 0 1 N N N 10.221 -20.980 -12.304 2.434 0.917 -2.126 C19 VB5 22 VB5 C30 C23 C 0 1 N N N 7.613 -14.201 -14.141 7.375 -4.080 0.612 C30 VB5 23 VB5 C31 C24 C 0 1 Y N N 9.354 -15.891 -12.577 6.437 -1.470 0.072 C31 VB5 24 VB5 C34 C25 C 0 1 N N N 18.448 -24.600 -14.808 -6.205 -0.812 0.576 C34 VB5 25 VB5 C35 C26 C 0 1 N N N 19.756 -24.872 -13.967 -6.607 -2.135 -0.081 C35 VB5 26 VB5 N06 N1 N 0 1 N N N 18.522 -23.539 -15.599 -6.316 0.278 -0.407 N06 VB5 27 VB5 N16 N2 N 0 1 N N N 13.022 -21.218 -11.423 0.725 1.414 0.098 N16 VB5 28 VB5 N23 N3 N 0 1 N N N 10.359 -18.144 -12.210 4.663 0.059 -0.503 N23 VB5 29 VB5 N25 N4 N 0 1 Y N N 10.421 -16.378 -10.539 6.863 0.829 -0.133 N25 VB5 30 VB5 N27 N5 N 0 1 Y N N 9.470 -14.244 -10.910 8.586 -0.595 0.423 N27 VB5 31 VB5 N29 N6 N 0 1 N N N 8.348 -13.683 -12.985 8.272 -2.922 0.655 N29 VB5 32 VB5 O13 O1 O 0 1 N N N 15.040 -20.378 -13.030 -2.053 0.414 3.049 O13 VB5 33 VB5 O32 O2 O 0 1 N N N 9.746 -20.188 -10.081 2.691 3.121 -1.163 O32 VB5 34 VB5 O33 O3 O 0 1 N N N 12.346 -23.330 -12.031 0.267 0.684 2.145 O33 VB5 35 VB5 H1 H1 H 0 1 N N N 13.646 -24.688 -13.600 -1.380 1.926 -1.176 H1 VB5 36 VB5 H2 H2 H 0 1 N N N 11.574 -22.161 -10.195 2.412 0.259 0.562 H2 VB5 37 VB5 H3 H3 H 0 1 N N N 12.285 -20.657 -9.516 2.453 1.932 1.168 H3 VB5 38 VB5 H4 H4 H 0 1 N N N 8.264 -20.079 -12.161 2.433 -1.144 -2.758 H4 VB5 39 VB5 H5 H5 H 0 1 N N N 8.689 -20.688 -13.797 2.198 -0.911 -1.008 H5 VB5 40 VB5 H6 H6 H 0 1 N N N 10.188 -18.838 -14.202 4.464 -1.790 -1.478 H6 VB5 41 VB5 H7 H7 H 0 1 N N N 8.691 -18.123 -13.513 4.785 -0.404 -2.548 H7 VB5 42 VB5 H8 H8 H 0 1 N N N 12.250 -19.073 -11.982 4.962 1.814 -1.617 H8 VB5 43 VB5 H9 H9 H 0 1 N N N 11.554 -18.383 -10.476 4.771 2.057 0.136 H9 VB5 44 VB5 H10 H10 H 0 1 N N N 10.450 -14.812 -9.115 8.807 1.451 0.206 H10 VB5 45 VB5 H11 H11 H 0 1 N N N 20.706 -27.148 -15.159 -8.921 -2.618 1.282 H11 VB5 46 VB5 H12 H12 H 0 1 N N N 19.737 -26.198 -16.337 -8.716 -0.861 1.087 H12 VB5 47 VB5 H13 H13 H 0 1 N N N 21.514 -26.352 -16.552 -10.016 -1.708 0.214 H13 VB5 48 VB5 H14 H14 H 0 1 N N N 22.200 -25.997 -13.523 -9.455 -3.248 -1.673 H14 VB5 49 VB5 H15 H15 H 0 1 N N N 23.077 -25.230 -14.890 -7.757 -3.497 -2.144 H15 VB5 50 VB5 H16 H16 H 0 1 N N N 22.393 -24.212 -13.578 -8.360 -4.158 -0.606 H16 VB5 51 VB5 H17 H17 H 0 1 N N N 21.621 -23.975 -16.717 -7.497 -1.048 -2.436 H17 VB5 52 VB5 H18 H18 H 0 1 N N N 21.199 -22.904 -15.339 -9.174 -0.751 -1.916 H18 VB5 53 VB5 H19 H19 H 0 1 N N N 19.509 -22.665 -17.056 -7.752 1.261 -1.581 H19 VB5 54 VB5 H20 H20 H 0 1 N N N 19.298 -24.446 -17.160 -8.352 0.626 -0.031 H20 VB5 55 VB5 H21 H21 H 0 1 N N N 17.434 -22.476 -16.920 -6.316 1.755 1.087 H21 VB5 56 VB5 H22 H22 H 0 1 N N N 17.114 -24.242 -16.857 -5.994 2.348 -0.560 H22 VB5 57 VB5 H23 H23 H 0 1 N N N 15.386 -25.096 -15.330 -3.799 2.119 -1.558 H23 VB5 58 VB5 H24 H24 H 0 1 N N N 16.806 -21.074 -14.854 -4.571 0.699 2.389 H24 VB5 59 VB5 H25 H25 H 0 1 N N N 9.862 -21.991 -12.061 2.945 1.255 -3.027 H25 VB5 60 VB5 H26 H26 H 0 1 N N N 11.036 -21.047 -13.040 1.359 1.053 -2.243 H26 VB5 61 VB5 H27 H27 H 0 1 N N N 7.130 -13.368 -14.672 6.575 -3.948 1.339 H27 VB5 62 VB5 H28 H28 H 0 1 N N N 8.311 -14.713 -14.820 6.947 -4.171 -0.387 H28 VB5 63 VB5 H29 H29 H 0 1 N N N 6.846 -14.912 -13.799 7.937 -4.984 0.850 H29 VB5 64 VB5 H30 H30 H 0 1 N N N 9.045 -16.201 -13.564 5.757 -2.308 0.034 H30 VB5 65 VB5 H31 H31 H 0 1 N N N 17.613 -24.451 -14.108 -6.867 -0.609 1.418 H31 VB5 66 VB5 H32 H32 H 0 1 N N N 18.250 -25.483 -15.433 -5.177 -0.880 0.930 H32 VB5 67 VB5 H33 H33 H 0 1 N N N 19.649 -25.804 -13.393 -6.541 -2.939 0.651 H33 VB5 68 VB5 H34 H34 H 0 1 N N N 19.942 -24.036 -13.277 -5.937 -2.345 -0.915 H34 VB5 69 VB5 H36 H36 H 0 1 N N N 13.667 -20.463 -11.546 0.396 1.732 -0.757 H36 VB5 70 VB5 H37 H37 H 0 1 N N N 9.017 -13.027 -13.334 9.209 -3.043 0.873 H37 VB5 71 VB5 H38 H38 H 0 1 N N N 14.324 -20.369 -12.406 -1.935 -0.545 3.093 H38 VB5 72 VB5 H39 H39 H 0 1 N N N 10.100 -19.775 -9.302 1.761 3.347 -1.297 H39 VB5 73 # # 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 VB5 C05 C04 SING N N 1 VB5 C05 N06 SING N N 2 VB5 C07 N06 SING N N 3 VB5 C07 C08 SING N N 4 VB5 C04 C02 SING N N 5 VB5 C01 C02 SING N N 6 VB5 N06 C34 SING N N 7 VB5 C08 C09 DOUB Y N 8 VB5 C08 C11 SING Y N 9 VB5 C02 C03 SING N N 10 VB5 C02 C35 SING N N 11 VB5 C09 C10 SING Y N 12 VB5 C34 C35 SING N N 13 VB5 C11 C12 DOUB Y N 14 VB5 C30 N29 SING N N 15 VB5 C10 C14 DOUB Y N 16 VB5 C12 C14 SING Y N 17 VB5 C12 O13 SING N N 18 VB5 C21 C20 SING N N 19 VB5 C21 N23 SING N N 20 VB5 C14 C15 SING N N 21 VB5 N29 C28 SING N N 22 VB5 C20 C19 SING N N 23 VB5 C31 C28 DOUB Y N 24 VB5 C31 C24 SING Y N 25 VB5 C19 C18 SING N N 26 VB5 C15 O33 DOUB N N 27 VB5 C15 N16 SING N N 28 VB5 N23 C24 SING N N 29 VB5 N23 C22 SING N N 30 VB5 C28 N27 SING Y N 31 VB5 C24 N25 DOUB Y N 32 VB5 N16 C17 SING N N 33 VB5 C22 C18 SING N N 34 VB5 C18 C17 SING N N 35 VB5 C18 O32 SING N N 36 VB5 N27 C26 DOUB Y N 37 VB5 N25 C26 SING Y N 38 VB5 C10 H1 SING N N 39 VB5 C17 H2 SING N N 40 VB5 C17 H3 SING N N 41 VB5 C20 H4 SING N N 42 VB5 C20 H5 SING N N 43 VB5 C21 H6 SING N N 44 VB5 C21 H7 SING N N 45 VB5 C22 H8 SING N N 46 VB5 C22 H9 SING N N 47 VB5 C26 H10 SING N N 48 VB5 C01 H11 SING N N 49 VB5 C01 H12 SING N N 50 VB5 C01 H13 SING N N 51 VB5 C03 H14 SING N N 52 VB5 C03 H15 SING N N 53 VB5 C03 H16 SING N N 54 VB5 C04 H17 SING N N 55 VB5 C04 H18 SING N N 56 VB5 C05 H19 SING N N 57 VB5 C05 H20 SING N N 58 VB5 C07 H21 SING N N 59 VB5 C07 H22 SING N N 60 VB5 C09 H23 SING N N 61 VB5 C11 H24 SING N N 62 VB5 C19 H25 SING N N 63 VB5 C19 H26 SING N N 64 VB5 C30 H27 SING N N 65 VB5 C30 H28 SING N N 66 VB5 C30 H29 SING N N 67 VB5 C31 H30 SING N N 68 VB5 C34 H31 SING N N 69 VB5 C34 H32 SING N N 70 VB5 C35 H33 SING N N 71 VB5 C35 H34 SING N N 72 VB5 N16 H36 SING N N 73 VB5 N29 H37 SING N N 74 VB5 O13 H38 SING N N 75 VB5 O32 H39 SING N N 76 # # 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 VB5 InChI InChI 1.03 "InChI=1S/C26H38N6O3/c1-25(2)8-11-31(12-9-25)15-19-5-6-20(21(33)13-19)24(34)28-16-26(35)7-4-10-32(17-26)23-14-22(27-3)29-18-30-23/h5-6,13-14,18,33,35H,4,7-12,15-17H2,1-3H3,(H,28,34)(H,27,29,30)/t26-/m1/s1" VB5 InChIKey InChI 1.03 BEGALFNTKBNFJE-AREMUKBSSA-N VB5 SMILES_CANONICAL CACTVS 3.385 "CNc1cc(ncn1)N2CCC[C@@](O)(CNC(=O)c3ccc(CN4CCC(C)(C)CC4)cc3O)C2" VB5 SMILES CACTVS 3.385 "CNc1cc(ncn1)N2CCC[C](O)(CNC(=O)c3ccc(CN4CCC(C)(C)CC4)cc3O)C2" VB5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1(CCN(CC1)Cc2ccc(c(c2)O)C(=O)NC[C@@]3(CCCN(C3)c4cc(ncn4)NC)O)C" VB5 SMILES "OpenEye OEToolkits" 2.0.7 "CC1(CCN(CC1)Cc2ccc(c(c2)O)C(=O)NCC3(CCCN(C3)c4cc(ncn4)NC)O)C" # _pdbx_chem_comp_identifier.comp_id VB5 _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-[(4,4-dimethylpiperidin-1-yl)methyl]-~{N}-[[(3~{R})-1-[6-(methylamino)pyrimidin-4-yl]-3-oxidanyl-piperidin-3-yl]methyl]-2-oxidanyl-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 VB5 "Create component" 2021-05-04 PDBE VB5 "Initial release" 2021-10-20 RCSB ##