data_YVU # _chem_comp.id YVU _chem_comp.name "5'-S-[2-(benzylcarbamamido)ethyl]-5'-thioadenosine" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H25 N7 O4 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-02-24 _chem_comp.pdbx_modified_date 2023-04-21 _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 459.522 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YVU _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 8G2G _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 YVU N1 N1 N 0 1 Y N N 18.778 19.658 38.055 -8.521 1.918 0.174 N1 YVU 1 YVU C7 C1 C 0 1 N N N 16.010 12.033 39.098 -0.762 -1.876 -0.398 C7 YVU 2 YVU C8 C2 C 0 1 N N N 17.198 9.732 40.198 1.921 -1.047 0.026 C8 YVU 3 YVU N2 N2 N 0 1 Y N N 18.320 17.935 39.679 -7.205 0.033 0.415 N2 YVU 4 YVU C9 C3 C 0 1 N N N 17.702 9.955 41.613 2.969 -0.488 0.990 C9 YVU 5 YVU O1 O1 O 0 1 N N N 18.485 7.417 42.614 5.234 0.440 2.121 O1 YVU 6 YVU C1 C4 C 0 1 Y N N 18.950 19.018 39.215 -8.377 0.631 0.434 C1 YVU 7 YVU C5 C5 C 0 1 N N R 16.657 15.325 39.921 -4.168 -0.916 0.235 C5 YVU 8 YVU C6 C6 C 0 1 N N S 16.582 13.016 40.101 -2.164 -2.075 0.179 C6 YVU 9 YVU N3 N3 N 0 1 Y N N 16.150 17.299 36.908 -4.948 2.535 -0.413 N3 YVU 10 YVU C4 C7 C 0 1 Y N N 15.878 16.332 37.750 -4.106 1.548 -0.306 C4 YVU 11 YVU C3 C8 C 0 1 Y N N 17.124 18.041 37.560 -6.201 2.088 -0.157 C3 YVU 12 YVU O3 O2 O 0 1 N N N 14.974 15.909 41.640 -5.485 -2.447 -1.161 O3 YVU 13 YVU C2 C9 C 0 1 Y N N 17.424 17.480 38.793 -6.101 0.715 0.127 C2 YVU 14 YVU N4 N4 N 0 1 Y N N 16.626 16.363 38.899 -4.768 0.404 0.026 N4 YVU 15 YVU C10 C10 C 0 1 N N N 19.343 8.228 42.286 5.328 0.120 0.951 C10 YVU 16 YVU N6 N5 N 0 1 N N N 20.653 7.930 42.375 6.508 0.242 0.312 N6 YVU 17 YVU C11 C11 C 0 1 N N N 21.072 6.647 42.912 7.678 0.759 1.025 C11 YVU 18 YVU C12 C12 C 0 1 Y N N 20.993 5.486 41.954 8.860 0.795 0.091 C12 YVU 19 YVU C17 C13 C 0 1 Y N N 20.830 5.686 40.586 9.692 -0.304 -0.013 C17 YVU 20 YVU C16 C14 C 0 1 Y N N 20.901 4.619 39.704 10.773 -0.273 -0.874 C16 YVU 21 YVU C15 C15 C 0 1 Y N N 21.126 3.341 40.175 11.023 0.857 -1.630 C15 YVU 22 YVU C14 C16 C 0 1 Y N N 21.286 3.132 41.532 10.191 1.956 -1.526 C14 YVU 23 YVU C13 C17 C 0 1 Y N N 21.197 4.193 42.416 9.110 1.925 -0.664 C13 YVU 24 YVU N5 N6 N 0 1 N N N 19.058 9.454 41.795 4.251 -0.356 0.295 N5 YVU 25 YVU S S1 S 0 1 N N N 15.573 10.481 39.874 0.333 -1.211 0.887 S YVU 26 YVU O O3 O 0 1 N N N 17.035 14.119 39.290 -2.751 -0.799 0.487 O YVU 27 YVU C18 C18 C 0 1 N N S 15.551 13.581 41.086 -3.070 -2.756 -0.865 C18 YVU 28 YVU O2 O4 O 0 1 N N N 15.988 13.524 42.441 -3.557 -4.003 -0.368 O2 YVU 29 YVU C19 C19 C 0 1 N N R 15.317 15.016 40.583 -4.237 -1.758 -1.064 C19 YVU 30 YVU C C20 C 0 1 Y N N 17.836 19.206 37.199 -7.475 2.681 -0.124 C YVU 31 YVU N N7 N 0 1 N N N 17.577 19.930 36.108 -7.635 4.029 -0.396 N YVU 32 YVU H1 H1 H 0 1 N N N 16.760 11.843 38.317 -0.373 -2.833 -0.746 H1 YVU 33 YVU H2 H2 H 0 1 N N N 15.109 12.471 38.643 -0.808 -1.178 -1.233 H2 YVU 34 YVU H3 H3 H 0 1 N N N 17.122 8.649 40.023 1.807 -0.369 -0.820 H3 YVU 35 YVU H4 H4 H 0 1 N N N 17.926 10.166 39.497 2.242 -2.025 -0.333 H4 YVU 36 YVU H5 H5 H 0 1 N N N 17.690 11.034 41.828 2.647 0.490 1.349 H5 YVU 37 YVU H6 H6 H 0 1 N N N 17.034 9.434 42.314 3.082 -1.166 1.836 H6 YVU 38 YVU H7 H7 H 0 1 N N N 19.703 19.434 39.868 -9.254 0.048 0.672 H7 YVU 39 YVU H8 H8 H 0 1 N N N 17.384 15.594 40.701 -4.663 -1.435 1.056 H8 YVU 40 YVU H9 H9 H 0 1 N N N 17.416 12.556 40.652 -2.111 -2.688 1.079 H9 YVU 41 YVU H10 H10 H 0 1 N N N 15.130 15.577 37.556 -3.039 1.625 -0.458 H10 YVU 42 YVU H11 H11 H 0 1 N N N 14.133 15.660 42.005 -5.576 -2.988 -1.957 H11 YVU 43 YVU H12 H12 H 0 1 N N N 21.338 8.592 42.071 6.582 -0.013 -0.621 H12 YVU 44 YVU H13 H13 H 0 1 N N N 20.433 6.417 43.777 7.468 1.767 1.385 H13 YVU 45 YVU H14 H14 H 0 1 N N N 22.117 6.743 43.243 7.903 0.111 1.872 H14 YVU 46 YVU H15 H15 H 0 1 N N N 20.647 6.681 40.209 9.497 -1.187 0.577 H15 YVU 47 YVU H16 H16 H 0 1 N N N 20.780 4.788 38.644 11.424 -1.132 -0.955 H16 YVU 48 YVU H17 H17 H 0 1 N N N 21.177 2.510 39.488 11.869 0.882 -2.301 H17 YVU 49 YVU H18 H18 H 0 1 N N N 21.481 2.137 41.904 10.386 2.839 -2.116 H18 YVU 50 YVU H19 H19 H 0 1 N N N 21.287 4.013 43.477 8.458 2.783 -0.586 H19 YVU 51 YVU H20 H20 H 0 1 N N N 19.820 10.051 41.543 4.326 -0.611 -0.638 H20 YVU 52 YVU H21 H21 H 0 1 N N N 14.614 13.016 40.971 -2.529 -2.904 -1.800 H21 YVU 53 YVU H22 H22 H 0 1 N N N 15.315 13.885 43.007 -4.133 -4.475 -0.985 H22 YVU 54 YVU H23 H23 H 0 1 N N N 14.529 15.003 39.816 -4.069 -1.134 -1.942 H23 YVU 55 YVU H24 H24 H 0 1 N N N 18.160 20.742 36.100 -6.864 4.575 -0.613 H24 YVU 56 YVU H25 H25 H 0 1 N N N 17.760 19.381 35.293 -8.519 4.426 -0.370 H25 YVU 57 # 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 YVU N C SING N N 1 YVU N3 C3 SING Y N 2 YVU N3 C4 DOUB Y N 3 YVU C C3 SING Y N 4 YVU C N1 DOUB Y N 5 YVU C3 C2 DOUB Y N 6 YVU C4 N4 SING Y N 7 YVU N1 C1 SING Y N 8 YVU C2 N4 SING Y N 9 YVU C2 N2 SING Y N 10 YVU N4 C5 SING N N 11 YVU C7 S SING N N 12 YVU C7 C6 SING N N 13 YVU C1 N2 DOUB Y N 14 YVU O C5 SING N N 15 YVU O C6 SING N N 16 YVU C16 C15 DOUB Y N 17 YVU C16 C17 SING Y N 18 YVU S C8 SING N N 19 YVU C5 C19 SING N N 20 YVU C6 C18 SING N N 21 YVU C15 C14 SING Y N 22 YVU C8 C9 SING N N 23 YVU C19 C18 SING N N 24 YVU C19 O3 SING N N 25 YVU C17 C12 DOUB Y N 26 YVU C18 O2 SING N N 27 YVU C14 C13 DOUB Y N 28 YVU C9 N5 SING N N 29 YVU N5 C10 SING N N 30 YVU C12 C13 SING Y N 31 YVU C12 C11 SING N N 32 YVU C10 N6 SING N N 33 YVU C10 O1 DOUB N N 34 YVU N6 C11 SING N N 35 YVU C7 H1 SING N N 36 YVU C7 H2 SING N N 37 YVU C8 H3 SING N N 38 YVU C8 H4 SING N N 39 YVU C9 H5 SING N N 40 YVU C9 H6 SING N N 41 YVU C1 H7 SING N N 42 YVU C5 H8 SING N N 43 YVU C6 H9 SING N N 44 YVU C4 H10 SING N N 45 YVU O3 H11 SING N N 46 YVU N6 H12 SING N N 47 YVU C11 H13 SING N N 48 YVU C11 H14 SING N N 49 YVU C17 H15 SING N N 50 YVU C16 H16 SING N N 51 YVU C15 H17 SING N N 52 YVU C14 H18 SING N N 53 YVU C13 H19 SING N N 54 YVU N5 H20 SING N N 55 YVU C18 H21 SING N N 56 YVU O2 H22 SING N N 57 YVU C19 H23 SING N N 58 YVU N H24 SING N N 59 YVU N H25 SING N N 60 # 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 YVU SMILES ACDLabs 12.01 "Nc1ncnc2c1ncn2C1OC(CSCCNC(=O)NCc2ccccc2)C(O)C1O" YVU InChI InChI 1.06 "InChI=1S/C20H25N7O4S/c21-17-14-18(25-10-24-17)27(11-26-14)19-16(29)15(28)13(31-19)9-32-7-6-22-20(30)23-8-12-4-2-1-3-5-12/h1-5,10-11,13,15-16,19,28-29H,6-9H2,(H2,21,24,25)(H2,22,23,30)/t13-,15-,16-,19-/m1/s1" YVU InChIKey InChI 1.06 UTFOOFWJWOBJJY-NVQRDWNXSA-N YVU SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CSCCNC(=O)NCc4ccccc4)[C@@H](O)[C@H]3O" YVU SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CSCCNC(=O)NCc4ccccc4)[CH](O)[CH]3O" YVU SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CNC(=O)NCCSC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O" YVU SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CNC(=O)NCCSCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O" # 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 YVU "SYSTEMATIC NAME" ACDLabs 12.01 "5'-S-[2-(benzylcarbamamido)ethyl]-5'-thioadenosine" YVU "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "1-[2-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]ethyl]-3-(phenylmethyl)urea" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YVU "Create component" 2023-02-24 RCSB YVU "Initial release" 2023-04-26 RCSB #