data_VB2 # _chem_comp.id VB2 _chem_comp.name "4-[(4,4-dimethylpiperidin-1-yl)methyl]-~{N}-[[(3~{S})-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 VB2 _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 7OEE _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 VB2 C10 C1 C 0 1 Y N N -45.104 31.249 22.099 -2.205 -1.217 -0.731 C10 VB2 1 VB2 C15 C2 C 0 1 N N N -44.967 33.298 23.514 -0.149 -1.447 0.654 C15 VB2 2 VB2 C17 C3 C 0 1 N N N -44.951 35.746 24.070 2.086 -1.143 -0.269 C17 VB2 3 VB2 C20 C4 C 0 1 N N N -43.827 35.263 27.721 2.687 1.629 -1.083 C20 VB2 4 VB2 C21 C5 C 0 1 N N N -42.492 36.058 27.651 4.210 1.588 -0.949 C21 VB2 5 VB2 C22 C6 C 0 1 N N N -42.885 36.540 25.177 4.250 -0.779 -1.469 C22 VB2 6 VB2 C24 C7 C 0 1 Y N N -41.279 37.928 26.474 5.990 0.221 -0.239 C24 VB2 7 VB2 C26 C8 C 0 1 Y N N -39.785 39.159 27.756 8.066 -0.707 -0.612 C26 VB2 8 VB2 C28 C9 C 0 1 Y N N -40.180 39.778 25.565 7.935 1.051 0.871 C28 VB2 9 VB2 C01 C10 C 0 1 N N N -43.633 24.039 22.682 -8.591 1.802 -1.549 C01 VB2 10 VB2 C02 C11 C 0 1 N N N -42.618 25.016 23.294 -7.975 2.145 -0.191 C02 VB2 11 VB2 C03 C12 C 0 1 N N N -41.932 24.369 24.503 -8.444 3.534 0.247 C03 VB2 12 VB2 C04 C13 C 0 1 N N N -43.398 26.235 23.710 -6.448 2.132 -0.303 C04 VB2 13 VB2 C05 C14 C 0 1 N N N -43.627 27.136 22.524 -5.981 0.725 -0.684 C05 VB2 14 VB2 C07 C15 C 0 1 N N N -42.714 28.482 21.091 -5.874 -1.569 0.079 C07 VB2 15 VB2 C08 C16 C 0 1 Y N N -43.274 29.754 21.740 -4.376 -1.537 0.234 C08 VB2 16 VB2 C09 C17 C 0 1 Y N N -44.589 30.111 21.502 -3.577 -1.249 -0.861 C09 VB2 17 VB2 C11 C18 C 0 1 Y N N -42.479 30.563 22.551 -3.807 -1.795 1.465 C11 VB2 18 VB2 C12 C19 C 0 1 Y N N -42.993 31.710 23.141 -2.429 -1.761 1.615 C12 VB2 19 VB2 C14 C20 C 0 1 Y N N -44.319 32.055 22.903 -1.617 -1.475 0.509 C14 VB2 20 VB2 C18 C21 C 0 1 N N S -44.308 36.098 25.414 2.725 -0.808 -1.618 C18 VB2 21 VB2 C19 C22 C 0 1 N N N -44.347 34.880 26.331 2.237 0.565 -2.088 C19 VB2 22 VB2 C30 C23 C 0 1 N N N -40.892 41.379 23.709 7.761 2.938 2.456 C30 VB2 23 VB2 C31 C24 C 0 1 Y N N -41.061 38.750 25.412 6.563 1.123 0.652 C31 VB2 24 VB2 C34 C25 C 0 1 N N N -41.964 26.495 21.308 -7.887 -0.272 0.432 C34 VB2 25 VB2 C35 C26 C 0 1 N N N -41.532 25.353 22.264 -8.411 1.105 0.845 C35 VB2 26 VB2 N06 N1 N 0 1 N N N -42.496 27.515 21.962 -6.422 -0.231 0.339 N06 VB2 27 VB2 N16 N2 N 0 1 N N N -44.297 34.589 23.467 0.628 -1.171 -0.412 N16 VB2 28 VB2 N23 N3 N 0 1 N N N -42.206 36.806 26.410 4.628 0.255 -0.496 N23 VB2 29 VB2 N25 N4 N 0 1 Y N N -40.648 38.136 27.625 6.770 -0.672 -0.846 N25 VB2 30 VB2 N27 N5 N 0 1 Y N N -39.555 39.960 26.707 8.645 0.129 0.225 N27 VB2 31 VB2 N29 N6 N 0 1 N N N -39.863 40.713 24.494 8.553 1.927 1.750 N29 VB2 32 VB2 O13 O1 O 0 1 N N N -42.183 32.504 23.971 -1.868 -2.013 2.825 O13 VB2 33 VB2 O32 O2 O 0 1 N N N -44.984 37.183 25.995 2.359 -1.801 -2.579 O32 VB2 34 VB2 O33 O3 O 0 1 N N N -46.036 33.211 24.041 0.360 -1.672 1.735 O33 VB2 35 VB2 H1 H1 H 0 1 N N N -46.138 31.512 21.934 -1.586 -0.996 -1.588 H1 VB2 36 VB2 H2 H2 H 0 1 N N N -44.859 36.606 23.391 2.437 -2.119 0.068 H2 VB2 37 VB2 H3 H3 H 0 1 N N N -46.015 35.516 24.229 2.365 -0.385 0.463 H3 VB2 38 VB2 H4 H4 H 0 1 N N N -44.583 35.884 28.223 2.231 1.429 -0.113 H4 VB2 39 VB2 H5 H5 H 0 1 N N N -43.662 34.344 28.303 2.378 2.614 -1.433 H5 VB2 40 VB2 H6 H6 H 0 1 N N N -41.673 35.339 27.798 4.666 1.802 -1.916 H6 VB2 41 VB2 H7 H7 H 0 1 N N N -42.497 36.783 28.478 4.532 2.335 -0.224 H7 VB2 42 VB2 H8 H8 H 0 1 N N N -42.349 35.745 24.638 4.599 -1.751 -1.120 H8 VB2 43 VB2 H9 H9 H 0 1 N N N -42.892 37.456 24.568 4.705 -0.553 -2.433 H9 VB2 44 VB2 H10 H10 H 0 1 N N N -39.283 39.333 28.696 8.670 -1.444 -1.120 H10 VB2 45 VB2 H11 H11 H 0 1 N N N -44.408 23.802 23.425 -8.258 0.811 -1.859 H11 VB2 46 VB2 H12 H12 H 0 1 N N N -44.100 24.501 21.800 -9.678 1.811 -1.468 H12 VB2 47 VB2 H13 H13 H 0 1 N N N -43.117 23.115 22.382 -8.275 2.539 -2.287 H13 VB2 48 VB2 H14 H14 H 0 1 N N N -42.687 24.115 25.261 -9.531 3.541 0.329 H14 VB2 49 VB2 H15 H15 H 0 1 N N N -41.412 23.454 24.183 -8.006 3.777 1.215 H15 VB2 50 VB2 H16 H16 H 0 1 N N N -41.204 25.074 24.932 -8.131 4.272 -0.491 H16 VB2 51 VB2 H17 H17 H 0 1 N N N -42.833 26.783 24.479 -6.134 2.840 -1.070 H17 VB2 52 VB2 H18 H18 H 0 1 N N N -44.369 25.922 24.121 -6.011 2.415 0.654 H18 VB2 53 VB2 H19 H19 H 0 1 N N N -44.174 28.030 22.858 -6.408 0.449 -1.648 H19 VB2 54 VB2 H20 H20 H 0 1 N N N -44.229 26.595 21.779 -4.893 0.710 -0.750 H20 VB2 55 VB2 H21 H21 H 0 1 N N N -43.435 28.124 20.342 -6.129 -1.875 -0.936 H21 VB2 56 VB2 H22 H22 H 0 1 N N N -41.763 28.730 20.596 -6.298 -2.280 0.790 H22 VB2 57 VB2 H23 H23 H 0 1 N N N -45.209 29.507 20.856 -4.031 -1.049 -1.820 H23 VB2 58 VB2 H24 H24 H 0 1 N N N -41.447 30.293 22.723 -4.436 -2.018 2.314 H24 VB2 59 VB2 H25 H25 H 0 1 N N N -45.382 34.518 26.415 1.149 0.562 -2.154 H25 VB2 60 VB2 H26 H26 H 0 1 N N N -43.714 34.085 25.910 2.661 0.787 -3.067 H26 VB2 61 VB2 H27 H27 H 0 1 N N N -40.418 42.034 22.963 7.276 3.591 1.730 H27 VB2 62 VB2 H28 H28 H 0 1 N N N -41.507 40.625 23.196 7.003 2.445 3.065 H28 VB2 63 VB2 H29 H29 H 0 1 N N N -41.528 41.981 24.374 8.415 3.529 3.097 H29 VB2 64 VB2 H30 H30 H 0 1 N N N -41.572 38.592 24.474 5.958 1.859 1.160 H30 VB2 65 VB2 H31 H31 H 0 1 N N N -42.707 26.102 20.598 -8.184 -1.012 1.175 H31 VB2 66 VB2 H32 H32 H 0 1 N N N -41.081 26.849 20.756 -8.305 -0.543 -0.538 H32 VB2 67 VB2 H33 H33 H 0 1 N N N -41.318 24.454 21.668 -8.005 1.372 1.821 H33 VB2 68 VB2 H34 H34 H 0 1 N N N -40.622 25.664 22.798 -9.500 1.079 0.899 H34 VB2 69 VB2 H36 H36 H 0 1 N N N -43.403 34.682 23.029 0.223 -0.991 -1.275 H36 VB2 70 VB2 H37 H37 H 0 1 N N N -39.299 40.207 23.841 9.510 1.871 1.897 H37 VB2 71 VB2 H38 H38 H 0 1 N N N -42.685 33.244 24.290 -1.663 -2.946 2.976 H38 VB2 72 VB2 H39 H39 H 0 1 N N N -44.582 37.398 26.828 1.406 -1.874 -2.725 H39 VB2 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 VB2 C07 C08 SING N N 1 VB2 C07 N06 SING N N 2 VB2 C34 N06 SING N N 3 VB2 C34 C35 SING N N 4 VB2 C09 C08 DOUB Y N 5 VB2 C09 C10 SING Y N 6 VB2 C08 C11 SING Y N 7 VB2 N06 C05 SING N N 8 VB2 C10 C14 DOUB Y N 9 VB2 C35 C02 SING N N 10 VB2 C05 C04 SING N N 11 VB2 C11 C12 DOUB Y N 12 VB2 C01 C02 SING N N 13 VB2 C14 C12 SING Y N 14 VB2 C14 C15 SING N N 15 VB2 C12 O13 SING N N 16 VB2 C02 C04 SING N N 17 VB2 C02 C03 SING N N 18 VB2 N16 C15 SING N N 19 VB2 N16 C17 SING N N 20 VB2 C15 O33 DOUB N N 21 VB2 C30 N29 SING N N 22 VB2 C17 C18 SING N N 23 VB2 N29 C28 SING N N 24 VB2 C22 C18 SING N N 25 VB2 C22 N23 SING N N 26 VB2 C31 C28 DOUB Y N 27 VB2 C31 C24 SING Y N 28 VB2 C18 O32 SING N N 29 VB2 C18 C19 SING N N 30 VB2 C28 N27 SING Y N 31 VB2 C19 C20 SING N N 32 VB2 N23 C24 SING N N 33 VB2 N23 C21 SING N N 34 VB2 C24 N25 DOUB Y N 35 VB2 N27 C26 DOUB Y N 36 VB2 N25 C26 SING Y N 37 VB2 C21 C20 SING N N 38 VB2 C10 H1 SING N N 39 VB2 C17 H2 SING N N 40 VB2 C17 H3 SING N N 41 VB2 C20 H4 SING N N 42 VB2 C20 H5 SING N N 43 VB2 C21 H6 SING N N 44 VB2 C21 H7 SING N N 45 VB2 C22 H8 SING N N 46 VB2 C22 H9 SING N N 47 VB2 C26 H10 SING N N 48 VB2 C01 H11 SING N N 49 VB2 C01 H12 SING N N 50 VB2 C01 H13 SING N N 51 VB2 C03 H14 SING N N 52 VB2 C03 H15 SING N N 53 VB2 C03 H16 SING N N 54 VB2 C04 H17 SING N N 55 VB2 C04 H18 SING N N 56 VB2 C05 H19 SING N N 57 VB2 C05 H20 SING N N 58 VB2 C07 H21 SING N N 59 VB2 C07 H22 SING N N 60 VB2 C09 H23 SING N N 61 VB2 C11 H24 SING N N 62 VB2 C19 H25 SING N N 63 VB2 C19 H26 SING N N 64 VB2 C30 H27 SING N N 65 VB2 C30 H28 SING N N 66 VB2 C30 H29 SING N N 67 VB2 C31 H30 SING N N 68 VB2 C34 H31 SING N N 69 VB2 C34 H32 SING N N 70 VB2 C35 H33 SING N N 71 VB2 C35 H34 SING N N 72 VB2 N16 H36 SING N N 73 VB2 N29 H37 SING N N 74 VB2 O13 H38 SING N N 75 VB2 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 VB2 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-/m0/s1" VB2 InChIKey InChI 1.03 BEGALFNTKBNFJE-SANMLTNESA-N VB2 SMILES_CANONICAL CACTVS 3.385 "CNc1cc(ncn1)N2CCC[C@](O)(CNC(=O)c3ccc(CN4CCC(C)(C)CC4)cc3O)C2" VB2 SMILES CACTVS 3.385 "CNc1cc(ncn1)N2CCC[C](O)(CNC(=O)c3ccc(CN4CCC(C)(C)CC4)cc3O)C2" VB2 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" VB2 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 VB2 _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~{S})-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 VB2 "Create component" 2021-05-04 PDBE VB2 "Initial release" 2021-10-20 RCSB ##