data_VB8 # _chem_comp.id VB8 _chem_comp.name "4-[(4,4-dimethylpiperidin-1-yl)methyl]-2-methylsulfanyl-~{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 "C33 H44 N6 O2 S" _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 588.806 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VB8 _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 7OEM _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 VB8 C10 C1 C 0 1 Y N N -45.710 30.712 23.736 -3.568 1.845 -0.394 C10 VB8 1 VB8 C15 C2 C 0 1 Y N N -44.785 31.332 24.549 -2.980 1.302 0.751 C15 VB8 2 VB8 C20 C3 C 0 1 N N N -45.083 36.044 25.702 0.958 2.429 -2.129 C20 VB8 3 VB8 C21 C4 C 0 1 N N N -44.798 37.312 25.049 1.586 1.032 -2.143 C21 VB8 4 VB8 C22 C5 C 0 1 N N N -43.310 37.396 24.603 3.095 1.155 -1.920 C22 VB8 5 VB8 C01 C6 C 0 1 N N N -42.697 23.323 23.798 -8.720 -4.164 -2.252 C01 VB8 6 VB8 C02 C7 C 0 1 N N N -43.175 24.582 23.032 -8.611 -2.950 -1.327 C02 VB8 7 VB8 C03 C8 C 0 1 N N N -44.326 24.147 22.067 -9.568 -3.120 -0.145 C03 VB8 8 VB8 C04 C9 C 0 1 N N N -43.702 25.553 23.934 -7.175 -2.830 -0.809 C04 VB8 9 VB8 C05 C10 C 0 1 N N N -44.095 26.817 23.141 -7.057 -1.580 0.067 C05 VB8 10 VB8 C07 C11 C 0 1 N N N -43.434 28.381 21.670 -7.179 0.838 0.046 C07 VB8 11 VB8 C08 C12 C 0 1 Y N N -43.942 29.442 22.667 -5.702 0.998 0.298 C08 VB8 12 VB8 C09 C13 C 0 1 Y N N -45.306 29.768 22.797 -4.919 1.691 -0.613 C09 VB8 13 VB8 C11 C14 C 0 1 Y N N -43.013 30.058 23.468 -5.136 0.447 1.429 C11 VB8 14 VB8 C12 C15 C 0 1 Y N N -43.453 30.984 24.406 -3.775 0.596 1.669 C12 VB8 15 VB8 C14 C16 C 0 1 N N N -41.821 33.252 24.408 -4.457 -0.901 3.933 C14 VB8 16 VB8 C16 C17 C 0 1 N N N -45.198 32.397 25.636 -1.536 1.468 0.993 C16 VB8 17 VB8 C18 C18 C 0 1 N N N -44.551 34.292 27.314 0.658 2.310 0.350 C18 VB8 18 VB8 C19 C19 C 0 1 N N R -44.242 35.732 26.826 1.279 3.111 -0.797 C19 VB8 19 VB8 C23 C20 C 0 1 N N N -42.713 35.911 26.546 2.797 3.173 -0.613 C23 VB8 20 VB8 C25 C21 C 0 1 Y N N -41.375 38.163 26.201 4.704 1.823 -0.338 C25 VB8 21 VB8 C27 C22 C 0 1 Y N N -39.971 38.971 27.815 6.620 2.988 0.195 C27 VB8 22 VB8 C29 C23 C 0 1 Y N N -39.954 40.028 25.757 6.781 0.696 0.013 C29 VB8 23 VB8 C31 C24 C 0 1 N N N -39.825 41.183 23.451 6.922 -1.761 -0.190 C31 VB8 24 VB8 C32 C25 C 0 1 Y N N -41.037 42.088 23.160 7.959 -2.847 -0.064 C32 VB8 25 VB8 C33 C26 C 0 1 Y N N -41.314 42.393 21.832 8.696 -3.231 -1.169 C33 VB8 26 VB8 C34 C27 C 0 1 Y N N -42.407 43.211 21.498 9.646 -4.228 -1.054 C34 VB8 27 VB8 C35 C28 C 0 1 Y N N -43.220 43.712 22.512 9.861 -4.841 0.166 C35 VB8 28 VB8 C36 C29 C 0 1 Y N N -42.948 43.416 23.836 9.125 -4.456 1.271 C36 VB8 29 VB8 C37 C30 C 0 1 Y N N -41.845 42.593 24.172 8.178 -3.456 1.158 C37 VB8 30 VB8 C38 C31 C 0 1 Y N N -40.929 39.140 25.302 5.425 0.633 -0.292 C38 VB8 31 VB8 C41 C32 C 0 1 N N N -42.357 26.448 21.568 -8.804 -0.465 -1.189 C41 VB8 32 VB8 C42 C33 C 0 1 N N N -42.049 25.136 22.317 -8.974 -1.681 -2.102 C42 VB8 33 VB8 N06 N1 N 0 1 N N N -43.017 27.417 22.385 -7.413 -0.393 -0.721 N06 VB8 34 VB8 N17 N2 N 0 1 N N N -44.175 33.271 26.266 -0.778 2.145 0.109 N17 VB8 35 VB8 N24 N3 N 0 1 N N N -42.391 37.192 25.780 3.350 1.813 -0.632 N24 VB8 36 VB8 N26 N4 N 0 1 Y N N -40.899 38.099 27.424 5.333 2.970 -0.090 N26 VB8 37 VB8 N28 N5 N 0 1 Y N N -39.514 39.914 26.994 7.337 1.884 0.248 N28 VB8 38 VB8 N30 N6 N 0 1 N N N -39.427 41.093 24.884 7.544 -0.460 0.071 N30 VB8 39 VB8 O39 O1 O 0 1 N N N -44.538 36.571 27.940 0.743 4.436 -0.798 O39 VB8 40 VB8 O40 O2 O 0 1 N N N -46.323 32.481 26.001 -1.029 0.993 1.991 O40 VB8 41 VB8 S13 S1 S 0 1 N N N -42.296 31.822 25.437 -3.048 -0.107 3.112 S13 VB8 42 VB8 H1 H1 H 0 1 N N N -46.757 30.961 23.829 -2.964 2.389 -1.105 H1 VB8 43 VB8 H2 H2 H 0 1 N N N -46.125 36.069 26.053 1.367 3.020 -2.949 H2 VB8 44 VB8 H3 H3 H 0 1 N N N -44.966 35.243 24.957 -0.122 2.345 -2.245 H3 VB8 45 VB8 H4 H4 H 0 1 N N N -45.008 38.132 25.751 1.149 0.429 -1.347 H4 VB8 46 VB8 H5 H5 H 0 1 N N N -45.444 37.412 24.164 1.397 0.558 -3.105 H5 VB8 47 VB8 H6 H6 H 0 1 N N N -43.113 36.617 23.852 3.543 0.161 -1.915 H6 VB8 48 VB8 H7 H7 H 0 1 N N N -43.120 38.386 24.163 3.534 1.746 -2.723 H7 VB8 49 VB8 H8 H8 H 0 1 N N N -41.885 23.599 24.487 -8.456 -5.066 -1.701 H8 VB8 50 VB8 H9 H9 H 0 1 N N N -43.536 22.902 24.371 -9.743 -4.249 -2.620 H9 VB8 51 VB8 H10 H10 H 0 1 N N N -42.331 22.574 23.080 -8.040 -4.041 -3.095 H10 VB8 52 VB8 H11 H11 H 0 1 N N N -45.160 23.733 22.653 -9.306 -4.023 0.407 H11 VB8 53 VB8 H12 H12 H 0 1 N N N -44.677 25.020 21.498 -9.489 -2.255 0.514 H12 VB8 54 VB8 H13 H13 H 0 1 N N N -43.951 23.382 21.371 -10.590 -3.204 -0.514 H13 VB8 55 VB8 H14 H14 H 0 1 N N N -44.590 25.144 24.439 -6.925 -3.712 -0.220 H14 VB8 56 VB8 H15 H15 H 0 1 N N N -42.940 25.811 24.684 -6.489 -2.750 -1.653 H15 VB8 57 VB8 H16 H16 H 0 1 N N N -44.471 27.565 23.854 -7.732 -1.668 0.918 H16 VB8 58 VB8 H17 H17 H 0 1 N N N -44.896 26.545 22.438 -6.032 -1.483 0.425 H17 VB8 59 VB8 H18 H18 H 0 1 N N N -42.615 28.788 21.058 -7.706 0.778 0.998 H18 VB8 60 VB8 H19 H19 H 0 1 N N N -44.251 28.048 21.014 -7.546 1.694 -0.520 H19 VB8 61 VB8 H20 H20 H 0 1 N N N -46.039 29.285 22.168 -5.372 2.112 -1.499 H20 VB8 62 VB8 H21 H21 H 0 1 N N N -41.962 29.828 23.371 -5.751 -0.098 2.129 H21 VB8 63 VB8 H22 H22 H 0 1 N N N -41.087 33.867 24.950 -5.211 -0.149 4.168 H22 VB8 64 VB8 H23 H23 H 0 1 N N N -41.376 32.895 23.467 -4.887 -1.653 3.272 H23 VB8 65 VB8 H24 H24 H 0 1 N N N -42.713 33.856 24.186 -4.120 -1.377 4.854 H24 VB8 66 VB8 H25 H25 H 0 1 N N N -45.627 34.208 27.528 1.132 1.330 0.407 H25 VB8 67 VB8 H26 H26 H 0 1 N N N -43.978 34.093 28.232 0.810 2.842 1.289 H26 VB8 68 VB8 H27 H27 H 0 1 N N N -42.362 35.052 25.955 3.237 3.756 -1.422 H27 VB8 69 VB8 H28 H28 H 0 1 N N N -42.181 35.935 27.509 3.028 3.645 0.342 H28 VB8 70 VB8 H29 H29 H 0 1 N N N -39.581 38.912 28.820 7.100 3.935 0.391 H29 VB8 71 VB8 H30 H30 H 0 1 N N N -40.067 40.169 23.101 6.507 -1.770 -1.197 H30 VB8 72 VB8 H31 H31 H 0 1 N N N -38.967 41.572 22.884 6.125 -1.934 0.533 H31 VB8 73 VB8 H32 H32 H 0 1 N N N -40.683 41.998 21.050 8.528 -2.752 -2.123 H32 VB8 74 VB8 H33 H33 H 0 1 N N N -42.615 43.449 20.465 10.221 -4.528 -1.918 H33 VB8 75 VB8 H34 H34 H 0 1 N N N -44.067 44.335 22.264 10.604 -5.620 0.256 H34 VB8 76 VB8 H35 H35 H 0 1 N N N -43.579 43.814 24.617 9.293 -4.935 2.225 H35 VB8 77 VB8 H36 H36 H 0 1 N N N -41.634 42.360 25.205 7.606 -3.153 2.022 H36 VB8 78 VB8 H37 H37 H 0 1 N N N -41.323 39.203 24.299 4.945 -0.314 -0.488 H37 VB8 79 VB8 H38 H38 H 0 1 N N N -41.410 26.878 21.211 -9.047 0.442 -1.743 H38 VB8 80 VB8 H39 H39 H 0 1 N N N -43.003 26.217 20.708 -9.471 -0.558 -0.332 H39 VB8 81 VB8 H40 H40 H 0 1 N N N -41.707 24.392 21.582 -8.316 -1.582 -2.966 H40 VB8 82 VB8 H41 H41 H 0 1 N N N -41.244 25.333 23.041 -10.009 -1.742 -2.437 H41 VB8 83 VB8 H43 H43 H 0 1 N N N -43.218 33.182 25.991 -1.182 2.524 -0.687 H43 VB8 84 VB8 H44 H44 H 0 1 N N N -38.431 41.003 24.897 8.488 -0.408 0.285 H44 VB8 85 VB8 H45 H45 H 0 1 N N N -43.970 36.345 28.667 -0.216 4.472 -0.913 H45 VB8 86 # # 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 VB8 C34 C33 DOUB Y N 1 VB8 C34 C35 SING Y N 2 VB8 C41 C42 SING N N 3 VB8 C41 N06 SING N N 4 VB8 C07 N06 SING N N 5 VB8 C07 C08 SING N N 6 VB8 C33 C32 SING Y N 7 VB8 C03 C02 SING N N 8 VB8 C42 C02 SING N N 9 VB8 N06 C05 SING N N 10 VB8 C35 C36 DOUB Y N 11 VB8 C08 C09 DOUB Y N 12 VB8 C08 C11 SING Y N 13 VB8 C09 C10 SING Y N 14 VB8 C02 C01 SING N N 15 VB8 C02 C04 SING N N 16 VB8 C05 C04 SING N N 17 VB8 C32 C31 SING N N 18 VB8 C32 C37 DOUB Y N 19 VB8 C31 N30 SING N N 20 VB8 C11 C12 DOUB Y N 21 VB8 C10 C15 DOUB Y N 22 VB8 C36 C37 SING Y N 23 VB8 C12 C15 SING Y N 24 VB8 C12 S13 SING N N 25 VB8 C14 S13 SING N N 26 VB8 C15 C16 SING N N 27 VB8 C22 C21 SING N N 28 VB8 C22 N24 SING N N 29 VB8 N30 C29 SING N N 30 VB8 C21 C20 SING N N 31 VB8 C38 C29 DOUB Y N 32 VB8 C38 C25 SING Y N 33 VB8 C16 O40 DOUB N N 34 VB8 C16 N17 SING N N 35 VB8 C20 C19 SING N N 36 VB8 C29 N28 SING Y N 37 VB8 N24 C25 SING N N 38 VB8 N24 C23 SING N N 39 VB8 C25 N26 DOUB Y N 40 VB8 N17 C18 SING N N 41 VB8 C23 C19 SING N N 42 VB8 C19 C18 SING N N 43 VB8 C19 O39 SING N N 44 VB8 N28 C27 DOUB Y N 45 VB8 N26 C27 SING Y N 46 VB8 C10 H1 SING N N 47 VB8 C20 H2 SING N N 48 VB8 C20 H3 SING N N 49 VB8 C21 H4 SING N N 50 VB8 C21 H5 SING N N 51 VB8 C22 H6 SING N N 52 VB8 C22 H7 SING N N 53 VB8 C01 H8 SING N N 54 VB8 C01 H9 SING N N 55 VB8 C01 H10 SING N N 56 VB8 C03 H11 SING N N 57 VB8 C03 H12 SING N N 58 VB8 C03 H13 SING N N 59 VB8 C04 H14 SING N N 60 VB8 C04 H15 SING N N 61 VB8 C05 H16 SING N N 62 VB8 C05 H17 SING N N 63 VB8 C07 H18 SING N N 64 VB8 C07 H19 SING N N 65 VB8 C09 H20 SING N N 66 VB8 C11 H21 SING N N 67 VB8 C14 H22 SING N N 68 VB8 C14 H23 SING N N 69 VB8 C14 H24 SING N N 70 VB8 C18 H25 SING N N 71 VB8 C18 H26 SING N N 72 VB8 C23 H27 SING N N 73 VB8 C23 H28 SING N N 74 VB8 C27 H29 SING N N 75 VB8 C31 H30 SING N N 76 VB8 C31 H31 SING N N 77 VB8 C33 H32 SING N N 78 VB8 C34 H33 SING N N 79 VB8 C35 H34 SING N N 80 VB8 C36 H35 SING N N 81 VB8 C37 H36 SING N N 82 VB8 C38 H37 SING N N 83 VB8 C41 H38 SING N N 84 VB8 C41 H39 SING N N 85 VB8 C42 H40 SING N N 86 VB8 C42 H41 SING N N 87 VB8 N17 H43 SING N N 88 VB8 N30 H44 SING N N 89 VB8 O39 H45 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 VB8 InChI InChI 1.03 "InChI=1S/C33H44N6O2S/c1-32(2)13-16-38(17-14-32)21-26-10-11-27(28(18-26)42-3)31(40)35-22-33(41)12-7-15-39(23-33)30-19-29(36-24-37-30)34-20-25-8-5-4-6-9-25/h4-6,8-11,18-19,24,41H,7,12-17,20-23H2,1-3H3,(H,35,40)(H,34,36,37)/t33-/m1/s1" VB8 InChIKey InChI 1.03 CGGPQJWTZLKAFY-MGBGTMOVSA-N VB8 SMILES_CANONICAL CACTVS 3.385 "CSc1cc(CN2CCC(C)(C)CC2)ccc1C(=O)NC[C@]3(O)CCCN(C3)c4cc(NCc5ccccc5)ncn4" VB8 SMILES CACTVS 3.385 "CSc1cc(CN2CCC(C)(C)CC2)ccc1C(=O)NC[C]3(O)CCCN(C3)c4cc(NCc5ccccc5)ncn4" VB8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1(CCN(CC1)Cc2ccc(c(c2)SC)C(=O)NC[C@@]3(CCCN(C3)c4cc(ncn4)NCc5ccccc5)O)C" VB8 SMILES "OpenEye OEToolkits" 2.0.7 "CC1(CCN(CC1)Cc2ccc(c(c2)SC)C(=O)NCC3(CCCN(C3)c4cc(ncn4)NCc5ccccc5)O)C" # _pdbx_chem_comp_identifier.comp_id VB8 _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]-2-methylsulfanyl-~{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 VB8 "Create component" 2021-05-04 PDBE VB8 "Initial release" 2021-10-20 RCSB ##