data_VBS # _chem_comp.id VBS _chem_comp.name "(3S)-3-benzyl-5-[9-ethyl-8-(2-methylpyrimidin-5-yl)-9H-purin-6-yl]-3-methyl-1,3-dihydro-2H-indol-2-one" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C28 H25 N7 O" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-07-24 _chem_comp.pdbx_modified_date 2020-12-25 _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 475.544 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VBS _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 7JIS _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # 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 VBS C1 C1 C 0 1 Y N N 36.678 14.205 33.344 2.089 1.276 -0.130 C1 VBS 1 VBS C2 C2 C 0 1 Y N N 35.759 15.145 32.839 3.050 2.236 0.246 C2 VBS 2 VBS C4 C3 C 0 1 Y N N 36.951 16.869 33.763 1.459 3.882 0.040 C4 VBS 3 VBS C6 C4 C 0 1 Y N N 37.768 14.719 34.105 0.784 1.722 -0.416 C6 VBS 4 VBS C7 C5 C 0 1 Y N N 38.830 13.869 34.728 -0.273 0.766 -0.817 C7 VBS 5 VBS C8 C6 C 0 1 Y N N 40.088 14.422 35.059 -1.597 0.976 -0.422 C8 VBS 6 VBS C11 C7 C 0 1 Y N N 39.601 11.732 35.555 -0.938 -1.235 -1.970 C11 VBS 7 VBS C12 C8 C 0 1 Y N N 38.605 12.512 35.005 0.045 -0.347 -1.596 C12 VBS 8 VBS N13 N1 N 0 1 N N N 41.963 11.699 36.453 -3.408 -1.779 -1.821 N13 VBS 9 VBS C16 C9 C 0 1 N N S 42.485 13.912 36.080 -4.059 0.022 -0.545 C16 VBS 10 VBS C17 C10 C 0 1 N N N 43.387 14.481 34.965 -4.335 -0.081 0.957 C17 VBS 11 VBS C18 C11 C 0 1 Y N N 43.664 13.597 33.762 -5.816 -0.243 1.186 C18 VBS 12 VBS C19 C12 C 0 1 Y N N 42.984 13.815 32.570 -6.617 0.872 1.344 C19 VBS 13 VBS C21 C13 C 0 1 Y N N 44.203 12.024 31.507 -8.534 -0.540 1.594 C21 VBS 14 VBS C23 C14 C 0 1 Y N N 44.636 12.603 33.804 -6.374 -1.507 1.231 C23 VBS 15 VBS C24 C15 C 0 1 N N N 42.412 14.955 37.207 -4.766 1.243 -1.136 C24 VBS 16 VBS C31 C16 C 0 1 Y N N 33.027 9.949 30.531 6.713 -2.871 0.544 C31 VBS 17 VBS C33 C17 C 0 1 Y N N 35.043 10.971 30.990 4.514 -2.205 0.501 C33 VBS 18 VBS C34 C18 C 0 1 N N N 32.294 8.789 29.905 7.714 -3.992 0.651 C34 VBS 19 VBS C35 C19 C 0 1 N N N 33.689 15.119 31.502 5.500 2.113 0.876 C35 VBS 20 VBS C36 C20 C 0 1 N N N 32.752 15.807 32.500 6.265 2.593 -0.359 C36 VBS 21 VBS N3 N2 N 0 1 Y N N 35.919 16.440 33.069 2.693 3.512 0.317 N3 VBS 22 VBS N5 N3 N 0 1 Y N N 37.852 16.044 34.246 0.524 3.024 -0.317 N5 VBS 23 VBS C9 C21 C 0 1 Y N N 41.072 13.628 35.613 -2.570 0.084 -0.799 C9 VBS 24 VBS C10 C22 C 0 1 Y N N 40.842 12.285 35.878 -2.259 -1.031 -1.571 C10 VBS 25 VBS C14 C23 C 0 1 N N N 42.965 12.571 36.612 -4.501 -1.241 -1.253 C14 VBS 26 VBS O15 O1 O 0 1 N N N 44.047 12.314 37.097 -5.629 -1.684 -1.300 O15 VBS 27 VBS C20 C24 C 0 1 Y N N 43.244 13.027 31.451 -7.976 0.724 1.549 C20 VBS 28 VBS C22 C25 C 0 1 Y N N 44.898 11.812 32.689 -7.732 -1.656 1.440 C22 VBS 29 VBS N25 N4 N 0 1 Y N N 34.804 14.444 32.161 4.215 1.544 0.464 N25 VBS 30 VBS C26 C26 C 0 1 Y N N 35.121 13.112 32.249 3.951 0.220 0.224 C26 VBS 31 VBS N27 N5 N 0 1 Y N N 36.236 12.978 32.944 2.693 0.075 -0.120 N27 VBS 32 VBS C28 C27 C 0 1 Y N N 34.361 11.997 31.653 4.933 -0.879 0.341 C28 VBS 33 VBS C29 C28 C 0 1 Y N N 32.957 11.924 31.718 6.308 -0.623 0.295 C29 VBS 34 VBS N30 N6 N 0 1 Y N N 32.335 10.896 31.153 7.151 -1.636 0.394 N30 VBS 35 VBS N32 N7 N 0 1 Y N N 34.353 9.983 30.446 5.426 -3.156 0.597 N32 VBS 36 VBS H1 H1 H 0 1 N N N 37.060 17.929 33.941 1.204 4.930 0.108 H1 VBS 37 VBS H2 H2 H 0 1 N N N 40.280 15.469 34.878 -1.854 1.836 0.178 H2 VBS 38 VBS H3 H3 H 0 1 N N N 39.419 10.683 35.738 -0.684 -2.096 -2.570 H3 VBS 39 VBS H4 H4 H 0 1 N N N 37.643 12.074 34.785 1.066 -0.511 -1.908 H4 VBS 40 VBS H5 H5 H 0 1 N N N 42.015 10.736 36.718 -3.417 -2.599 -2.338 H5 VBS 41 VBS H6 H6 H 0 1 N N N 44.357 14.729 35.421 -3.808 -0.943 1.365 H6 VBS 42 VBS H7 H7 H 0 1 N N N 42.911 15.401 34.594 -3.988 0.825 1.453 H7 VBS 43 VBS H8 H8 H 0 1 N N N 42.247 14.602 32.510 -6.181 1.860 1.309 H8 VBS 44 VBS H9 H9 H 0 1 N N N 44.406 11.415 30.639 -9.595 -0.656 1.758 H9 VBS 45 VBS H10 H10 H 0 1 N N N 45.195 12.443 34.714 -5.749 -2.378 1.103 H10 VBS 46 VBS H11 H11 H 0 1 N N N 41.773 14.575 38.018 -5.843 1.143 -0.997 H11 VBS 47 VBS H12 H12 H 0 1 N N N 43.423 15.146 37.596 -4.417 2.145 -0.632 H12 VBS 48 VBS H13 H13 H 0 1 N N N 41.987 15.890 36.814 -4.542 1.313 -2.200 H13 VBS 49 VBS H14 H14 H 0 1 N N N 36.121 10.986 30.923 3.463 -2.447 0.541 H14 VBS 50 VBS H15 H15 H 0 1 N N N 33.019 8.103 29.443 7.976 -4.146 1.698 H15 VBS 51 VBS H16 H16 H 0 1 N N N 31.725 8.254 30.680 7.280 -4.907 0.247 H16 VBS 52 VBS H17 H17 H 0 1 N N N 31.603 9.164 29.136 8.610 -3.735 0.087 H17 VBS 53 VBS H18 H18 H 0 1 N N N 34.092 15.877 30.814 6.085 1.352 1.393 H18 VBS 54 VBS H19 H19 H 0 1 N N N 33.113 14.375 30.931 5.326 2.955 1.546 H19 VBS 55 VBS H20 H20 H 0 1 N N N 31.932 16.298 31.955 7.221 3.017 -0.052 H20 VBS 56 VBS H21 H21 H 0 1 N N N 32.336 15.057 33.189 6.439 1.751 -1.029 H21 VBS 57 VBS H22 H22 H 0 1 N N N 33.315 16.559 33.072 5.680 3.354 -0.876 H22 VBS 58 VBS H23 H23 H 0 1 N N N 42.697 13.197 30.535 -8.602 1.595 1.669 H23 VBS 59 VBS H24 H24 H 0 1 N N N 45.643 11.032 32.744 -8.168 -2.643 1.476 H24 VBS 60 VBS H25 H25 H 0 1 N N N 32.392 12.695 32.221 6.674 0.385 0.173 H25 VBS 61 # # 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 VBS C34 C31 SING N N 1 VBS N32 C31 DOUB Y N 2 VBS N32 C33 SING Y N 3 VBS C31 N30 SING Y N 4 VBS C33 C28 DOUB Y N 5 VBS N30 C29 DOUB Y N 6 VBS C20 C21 DOUB Y N 7 VBS C20 C19 SING Y N 8 VBS C35 N25 SING N N 9 VBS C35 C36 SING N N 10 VBS C21 C22 SING Y N 11 VBS C28 C29 SING Y N 12 VBS C28 C26 SING N N 13 VBS N25 C26 SING Y N 14 VBS N25 C2 SING Y N 15 VBS C26 N27 DOUB Y N 16 VBS C19 C18 DOUB Y N 17 VBS C22 C23 DOUB Y N 18 VBS C2 N3 DOUB Y N 19 VBS C2 C1 SING Y N 20 VBS N27 C1 SING Y N 21 VBS N3 C4 SING Y N 22 VBS C1 C6 DOUB Y N 23 VBS C18 C23 SING Y N 24 VBS C18 C17 SING N N 25 VBS C4 N5 DOUB Y N 26 VBS C6 N5 SING Y N 27 VBS C6 C7 SING N N 28 VBS C7 C12 DOUB Y N 29 VBS C7 C8 SING Y N 30 VBS C17 C16 SING N N 31 VBS C12 C11 SING Y N 32 VBS C8 C9 DOUB Y N 33 VBS C11 C10 DOUB Y N 34 VBS C9 C10 SING Y N 35 VBS C9 C16 SING N N 36 VBS C10 N13 SING N N 37 VBS C16 C14 SING N N 38 VBS C16 C24 SING N N 39 VBS N13 C14 SING N N 40 VBS C14 O15 DOUB N N 41 VBS C4 H1 SING N N 42 VBS C8 H2 SING N N 43 VBS C11 H3 SING N N 44 VBS C12 H4 SING N N 45 VBS N13 H5 SING N N 46 VBS C17 H6 SING N N 47 VBS C17 H7 SING N N 48 VBS C19 H8 SING N N 49 VBS C21 H9 SING N N 50 VBS C23 H10 SING N N 51 VBS C24 H11 SING N N 52 VBS C24 H12 SING N N 53 VBS C24 H13 SING N N 54 VBS C33 H14 SING N N 55 VBS C34 H15 SING N N 56 VBS C34 H16 SING N N 57 VBS C34 H17 SING N N 58 VBS C35 H18 SING N N 59 VBS C35 H19 SING N N 60 VBS C36 H20 SING N N 61 VBS C36 H21 SING N N 62 VBS C36 H22 SING N N 63 VBS C20 H23 SING N N 64 VBS C22 H24 SING N N 65 VBS C29 H25 SING N N 66 # # 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 VBS SMILES ACDLabs 12.01 "c12c(ncnc1n(CC)c(n2)c3cnc(nc3)C)c5ccc6NC(C(C)(Cc4ccccc4)c6c5)=O" VBS InChI InChI 1.03 "InChI=1S/C28H25N7O/c1-4-35-25(20-14-29-17(2)30-15-20)34-24-23(31-16-32-26(24)35)19-10-11-22-21(12-19)28(3,27(36)33-22)13-18-8-6-5-7-9-18/h5-12,14-16H,4,13H2,1-3H3,(H,33,36)/t28-/m0/s1" VBS InChIKey InChI 1.03 FFRRAJYYORCXFZ-NDEPHWFRSA-N VBS SMILES_CANONICAL CACTVS 3.385 "CCn1c(nc2c1ncnc2c3ccc4NC(=O)[C@@](C)(Cc5ccccc5)c4c3)c6cnc(C)nc6" VBS SMILES CACTVS 3.385 "CCn1c(nc2c1ncnc2c3ccc4NC(=O)[C](C)(Cc5ccccc5)c4c3)c6cnc(C)nc6" VBS SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCn1c2c(c(ncn2)c3ccc4c(c3)[C@](C(=O)N4)(C)Cc5ccccc5)nc1c6cnc(nc6)C" VBS SMILES "OpenEye OEToolkits" 2.0.7 "CCn1c2c(c(ncn2)c3ccc4c(c3)C(C(=O)N4)(C)Cc5ccccc5)nc1c6cnc(nc6)C" # # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier VBS "SYSTEMATIC NAME" ACDLabs 12.01 "(3S)-3-benzyl-5-[9-ethyl-8-(2-methylpyrimidin-5-yl)-9H-purin-6-yl]-3-methyl-1,3-dihydro-2H-indol-2-one" VBS "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(3~{S})-5-[9-ethyl-8-(2-methylpyrimidin-5-yl)purin-6-yl]-3-methyl-3-(phenylmethyl)-1~{H}-indol-2-one" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site VBS "Create component" 2020-07-24 RCSB VBS "Initial release" 2020-12-30 RCSB ##