data_DVS # _chem_comp.id DVS _chem_comp.name "5'-S-[3-(N'-benzylcarbamimidamido)propyl]-5'-thioadenosine" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C21 H28 N8 O3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-04-26 _chem_comp.pdbx_modified_date 2023-05-05 _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 472.564 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DVS _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 8G2F _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 DVS N1 N1 N 0 1 Y N N 27.172 1.098 -3.994 -8.738 2.457 0.404 N1 DVS 1 DVS C7 C1 C 0 1 N N S 20.682 -0.773 -0.682 -3.872 -2.890 -0.218 C7 DVS 2 DVS C8 C2 C 0 1 N N S 20.893 -1.903 -1.713 -2.759 -2.086 0.483 C8 DVS 3 DVS N2 N2 N 0 1 Y N N 23.338 0.372 -3.007 -5.178 0.553 0.100 N2 DVS 4 DVS C9 C3 C 0 1 N N N 19.662 -2.210 -2.545 -1.462 -2.182 -0.323 C9 DVS 5 DVS O1 O1 O 0 1 N N N 21.011 -1.221 0.631 -4.354 -3.928 0.638 O1 DVS 6 DVS C1 C4 C 0 1 Y N N 24.839 1.283 -4.340 -6.498 2.293 -0.287 C1 DVS 7 DVS C5 C5 C 0 1 N N R 22.658 -0.409 -1.975 -4.645 -0.738 0.541 C5 DVS 8 DVS C6 C6 C 0 1 N N R 21.605 0.359 -1.176 -4.985 -1.848 -0.486 C6 DVS 9 DVS N3 N3 N 0 1 Y N N 23.599 1.636 -4.853 -5.277 2.530 -0.821 N3 DVS 10 DVS C4 C7 C 0 1 Y N N 22.749 1.077 -4.025 -4.500 1.510 -0.595 C4 DVS 11 DVS C3 C8 C 0 1 Y N N 26.880 0.381 -2.901 -8.645 1.258 0.951 C3 DVS 12 DVS C2 C9 C 0 1 Y N N 24.694 0.511 -3.195 -6.450 1.022 0.311 C2 DVS 13 DVS N4 N4 N 0 1 N N N 16.288 -3.725 -5.816 4.920 -0.480 -0.196 N4 DVS 14 DVS O2 O2 O 0 1 N N N 22.186 1.034 -0.065 -6.277 -2.403 -0.228 O2 DVS 15 DVS O O3 O 0 1 N N N 21.962 -1.480 -2.596 -3.197 -0.719 0.549 O DVS 16 DVS N N5 N 0 1 Y N N 25.679 0.027 -2.428 -7.536 0.549 0.912 N DVS 17 DVS C C10 C 0 1 Y N N 26.156 1.568 -4.756 -7.704 3.011 -0.220 C DVS 18 DVS N7 N6 N 0 1 N N N 26.458 2.224 -5.880 -7.812 4.267 -0.790 N7 DVS 19 DVS S S1 S 0 1 N N N 19.056 -0.760 -3.441 -0.125 -1.358 0.584 S DVS 20 DVS C10 C11 C 0 1 N N N 17.678 -1.469 -4.392 1.305 -1.574 -0.511 C10 DVS 21 DVS C11 C12 C 0 1 N N N 18.153 -2.134 -5.668 2.536 -0.922 0.122 C11 DVS 22 DVS C12 C13 C 0 1 N N N 17.022 -2.670 -6.501 3.741 -1.104 -0.802 C12 DVS 23 DVS C13 C14 C 0 1 N N N 14.960 -3.717 -5.714 6.130 -0.517 -0.848 C13 DVS 24 DVS N6 N7 N 0 1 N N N 14.261 -4.775 -5.478 6.228 -1.107 -2.007 N6 DVS 25 DVS N5 N8 N 0 1 N N N 14.302 -2.521 -5.825 7.236 0.068 -0.279 N5 DVS 26 DVS C14 C15 C 0 1 N N N 12.854 -2.403 -5.795 8.525 0.029 -0.974 C14 DVS 27 DVS C15 C16 C 0 1 Y N N 12.283 -2.135 -4.422 9.565 0.736 -0.144 C15 DVS 28 DVS C20 C17 C 0 1 Y N N 12.983 -2.471 -3.271 9.774 2.093 -0.307 C20 DVS 29 DVS C19 C18 C 0 1 Y N N 12.400 -2.322 -2.016 10.728 2.742 0.454 C19 DVS 30 DVS C18 C19 C 0 1 Y N N 11.127 -1.822 -1.898 11.473 2.034 1.379 C18 DVS 31 DVS C17 C20 C 0 1 Y N N 10.422 -1.469 -3.035 11.264 0.677 1.542 C17 DVS 32 DVS C16 C21 C 0 1 Y N N 10.995 -1.625 -4.287 10.306 0.029 0.784 C16 DVS 33 DVS H1 H1 H 0 1 N N N 19.637 -0.433 -0.728 -3.507 -3.309 -1.156 H1 DVS 34 DVS H2 H2 H 0 1 N N N 21.194 -2.814 -1.175 -2.600 -2.474 1.489 H2 DVS 35 DVS H3 H3 H 0 1 N N N 18.866 -2.571 -1.878 -1.206 -3.230 -0.475 H3 DVS 36 DVS H4 H4 H 0 1 N N N 19.914 -2.995 -3.273 -1.598 -1.697 -1.289 H4 DVS 37 DVS H5 H5 H 0 1 N N N 20.875 -0.514 1.251 -5.075 -4.448 0.258 H5 DVS 38 DVS H6 H6 H 0 1 N N N 23.404 -0.807 -1.272 -5.033 -0.995 1.527 H6 DVS 39 DVS H7 H7 H 0 1 N N N 21.049 1.045 -1.832 -4.923 -1.467 -1.505 H7 DVS 40 DVS H8 H8 H 0 1 N N N 21.678 1.164 -4.135 -3.470 1.433 -0.912 H8 DVS 41 DVS H9 H9 H 0 1 N N N 27.728 0.043 -2.324 -9.509 0.845 1.448 H9 DVS 42 DVS H10 H10 H 0 1 N N N 16.799 -4.482 -5.408 4.847 -0.041 0.666 H10 DVS 43 DVS H11 H11 H 0 1 N N N 21.510 1.501 0.411 -6.535 -3.102 -0.845 H11 DVS 44 DVS H12 H12 H 0 1 N N N 27.452 2.266 -5.986 -7.050 4.662 -1.243 H12 DVS 45 DVS H13 H13 H 0 1 N N N 26.060 1.745 -6.662 -8.650 4.754 -0.738 H13 DVS 46 DVS H14 H14 H 0 1 N N N 16.974 -0.664 -4.651 1.492 -2.637 -0.659 H14 DVS 47 DVS H15 H15 H 0 1 N N N 17.166 -2.218 -3.770 1.099 -1.104 -1.473 H15 DVS 48 DVS H16 H16 H 0 1 N N N 18.820 -2.968 -5.403 2.349 0.141 0.270 H16 DVS 49 DVS H17 H17 H 0 1 N N N 18.709 -1.395 -6.264 2.741 -1.392 1.084 H17 DVS 50 DVS H18 H18 H 0 1 N N N 17.433 -3.075 -7.438 3.536 -0.634 -1.764 H18 DVS 51 DVS H19 H19 H 0 1 N N N 16.329 -1.847 -6.730 3.929 -2.168 -0.950 H19 DVS 52 DVS H20 H20 H 0 1 N N N 14.834 -5.589 -5.383 5.447 -1.520 -2.408 H20 DVS 53 DVS H21 H21 H 0 1 N N N 14.845 -1.688 -5.932 7.163 0.507 0.583 H21 DVS 54 DVS H22 H22 H 0 1 N N N 12.561 -1.575 -6.458 8.824 -1.008 -1.126 H22 DVS 55 DVS H23 H23 H 0 1 N N N 12.423 -3.343 -6.170 8.432 0.526 -1.940 H23 DVS 56 DVS H24 H24 H 0 1 N N N 13.990 -2.852 -3.350 9.192 2.646 -1.030 H24 DVS 57 DVS H25 H25 H 0 1 N N N 12.952 -2.601 -1.131 10.892 3.802 0.326 H25 DVS 58 DVS H26 H26 H 0 1 N N N 10.678 -1.705 -0.923 12.219 2.540 1.973 H26 DVS 59 DVS H27 H27 H 0 1 N N N 9.422 -1.071 -2.946 11.846 0.124 2.264 H27 DVS 60 DVS H28 H28 H 0 1 N N N 10.436 -1.348 -5.168 10.140 -1.030 0.914 H28 DVS 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 DVS C12 N4 SING N N 1 DVS C12 C11 SING N N 2 DVS N7 C SING N N 3 DVS N5 C14 SING N N 4 DVS N5 C13 SING N N 5 DVS N4 C13 SING N N 6 DVS C14 C15 SING N N 7 DVS C13 N6 DOUB N N 8 DVS C11 C10 SING N N 9 DVS N3 C1 SING Y N 10 DVS N3 C4 DOUB Y N 11 DVS C C1 DOUB Y N 12 DVS C N1 SING Y N 13 DVS C15 C16 DOUB Y N 14 DVS C15 C20 SING Y N 15 DVS C10 S SING N N 16 DVS C1 C2 SING Y N 17 DVS C16 C17 SING Y N 18 DVS C4 N2 SING Y N 19 DVS N1 C3 DOUB Y N 20 DVS S C9 SING N N 21 DVS C20 C19 DOUB Y N 22 DVS C2 N2 SING Y N 23 DVS C2 N DOUB Y N 24 DVS C17 C18 DOUB Y N 25 DVS N2 C5 SING N N 26 DVS C3 N SING Y N 27 DVS O C5 SING N N 28 DVS O C8 SING N N 29 DVS C9 C8 SING N N 30 DVS C19 C18 SING Y N 31 DVS C5 C6 SING N N 32 DVS C8 C7 SING N N 33 DVS C6 C7 SING N N 34 DVS C6 O2 SING N N 35 DVS C7 O1 SING N N 36 DVS C7 H1 SING N N 37 DVS C8 H2 SING N N 38 DVS C9 H3 SING N N 39 DVS C9 H4 SING N N 40 DVS O1 H5 SING N N 41 DVS C5 H6 SING N N 42 DVS C6 H7 SING N N 43 DVS C4 H8 SING N N 44 DVS C3 H9 SING N N 45 DVS N4 H10 SING N N 46 DVS O2 H11 SING N N 47 DVS N7 H12 SING N N 48 DVS N7 H13 SING N N 49 DVS C10 H14 SING N N 50 DVS C10 H15 SING N N 51 DVS C11 H16 SING N N 52 DVS C11 H17 SING N N 53 DVS C12 H18 SING N N 54 DVS C12 H19 SING N N 55 DVS N6 H20 SING N N 56 DVS N5 H21 SING N N 57 DVS C14 H22 SING N N 58 DVS C14 H23 SING N N 59 DVS C20 H24 SING N N 60 DVS C19 H25 SING N N 61 DVS C18 H26 SING N N 62 DVS C17 H27 SING N N 63 DVS C16 H28 SING N N 64 # 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 DVS SMILES ACDLabs 12.01 "N=C(NCc1ccccc1)NCCCSCC1OC(n2cnc3c(N)ncnc32)C(O)C1O" DVS InChI InChI 1.06 "InChI=1S/C21H28N8O3S/c22-18-15-19(27-11-26-18)29(12-28-15)20-17(31)16(30)14(32-20)10-33-8-4-7-24-21(23)25-9-13-5-2-1-3-6-13/h1-3,5-6,11-12,14,16-17,20,30-31H,4,7-10H2,(H2,22,26,27)(H3,23,24,25)/t14-,16-,17-,20-/m1/s1" DVS InChIKey InChI 1.06 LTPOXWXTHQVJKG-WVSUBDOOSA-N DVS SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CSCCCNC(=N)NCc4ccccc4)[C@@H](O)[C@H]3O" DVS SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CSCCCNC(=N)NCc4ccccc4)[CH](O)[CH]3O" DVS SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(/NCCCSC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)\NCc4ccccc4" DVS SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CNC(=N)NCCCSCC2C(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 DVS "SYSTEMATIC NAME" ACDLabs 12.01 "5'-S-[3-(N'-benzylcarbamimidamido)propyl]-5'-thioadenosine" DVS "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "1-[3-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]propyl]-3-(phenylmethyl)guanidine" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site DVS "Create component" 2023-04-26 RCSB DVS "Initial release" 2023-05-10 RCSB #