data_GV3 # _chem_comp.id GV3 _chem_comp.name "5'-S-[3-(N'-phenylcarbamimidamido)propyl]-5'-thioadenosine" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H26 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 2023-05-01 _chem_comp.pdbx_modified_date 2024-04-19 _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 458.537 _chem_comp.one_letter_code ? _chem_comp.three_letter_code GV3 _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 8SHB _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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 GV3 N1 N1 N 0 1 Y N N N N N 27.158 0.971 -3.981 -7.970 2.269 0.223 N1 GV3 1 GV3 C7 C1 C 0 1 N N S N N N 20.735 -0.797 -0.488 -2.953 -2.973 0.171 C7 GV3 2 GV3 C8 C2 C 0 1 N N S N N N 20.976 -1.963 -1.456 -1.829 -2.032 0.646 C8 GV3 3 GV3 N2 N2 N 0 1 Y N N N N N 23.374 0.261 -2.840 -4.366 0.438 -0.005 N2 GV3 4 GV3 C9 C3 C 0 1 N N N N N N 19.790 -2.354 -2.315 -0.584 -2.229 -0.221 C9 GV3 5 GV3 O1 O1 O 0 1 N N N N N N 21.014 -1.252 0.829 -3.338 -3.862 1.222 O1 GV3 6 GV3 C1 C4 C 0 1 Y N N N N N 24.819 1.142 -4.244 -5.775 2.049 -0.586 C1 GV3 7 GV3 C5 C5 C 0 1 N N R N N N 22.714 -0.486 -1.782 -3.757 -0.745 0.609 C5 GV3 8 GV3 C6 C6 C 0 1 N N R N N N 21.677 0.310 -0.995 -4.120 -2.023 -0.190 C6 GV3 9 GV3 N3 N3 N 0 1 Y N N N N N 23.561 1.451 -4.737 -4.601 2.224 -1.238 N3 GV3 10 GV3 C4 C7 C 0 1 Y N N N N N 22.745 0.915 -3.866 -3.772 1.279 -0.898 C4 GV3 11 GV3 C3 C8 C 0 1 Y N N N N N 26.911 0.284 -2.864 -7.795 1.185 0.956 C3 GV3 12 GV3 C2 C9 C 0 1 Y N N N N N 24.720 0.411 -3.073 -5.639 0.901 0.212 C2 GV3 13 GV3 N4 N4 N 0 1 N N N N N N 16.263 -3.990 -5.666 5.723 -0.361 -0.834 N4 GV3 14 GV3 O2 O2 O 0 1 N N N N N N 22.291 0.997 0.089 -5.370 -2.559 0.248 O2 GV3 15 GV3 O O3 O 0 1 N N N N N N 21.998 -1.550 -2.379 -2.313 -0.685 0.512 O GV3 16 GV3 N N5 N 0 1 Y N N N N N 25.734 -0.045 -2.327 -6.665 0.509 0.960 N GV3 17 GV3 C C10 C 0 1 Y N N N N N 26.114 1.431 -4.708 -7.001 2.736 -0.557 C GV3 18 GV3 N7 N6 N 0 1 N N N N N N 26.367 2.128 -5.829 -7.194 3.873 -1.322 N7 GV3 19 GV3 S S1 S 0 1 N N N N N N 18.991 -1.007 -3.224 0.777 -1.227 0.437 S GV3 20 GV3 C10 C11 C 0 1 N N N N N N 17.600 -1.952 -3.912 2.140 -1.588 -0.705 C10 GV3 21 GV3 C11 C12 C 0 1 N N N N N N 17.456 -1.759 -5.391 3.383 -0.805 -0.279 C11 GV3 22 GV3 C12 C13 C 0 1 N N N N N N 17.086 -2.947 -6.269 4.532 -1.110 -1.242 C12 GV3 23 GV3 C13 C14 C 0 1 N N N N N N 15.003 -3.850 -5.218 6.889 -0.476 -1.554 C13 GV3 24 GV3 N6 N7 N 0 1 N N N N N N 14.310 -4.866 -4.811 6.934 -1.252 -2.600 N6 GV3 25 GV3 N5 N8 N 0 1 N N N N N N 14.398 -2.608 -5.287 8.007 0.229 -1.171 N5 GV3 26 GV3 C14 C15 C 0 1 Y N N N N N 13.121 -2.293 -4.778 7.998 0.963 0.019 C14 GV3 27 GV3 C19 C16 C 0 1 Y N N N N N 12.112 -1.724 -5.544 7.404 0.435 1.158 C19 GV3 28 GV3 C18 C17 C 0 1 Y N N N N N 10.889 -1.421 -4.966 7.396 1.163 2.332 C18 GV3 29 GV3 C17 C18 C 0 1 Y N N N N N 10.665 -1.674 -3.631 7.978 2.417 2.374 C17 GV3 30 GV3 C16 C19 C 0 1 Y N N N N N 11.662 -2.246 -2.866 8.570 2.945 1.241 C16 GV3 31 GV3 C15 C20 C 0 1 Y N N N N N 12.887 -2.562 -3.434 8.586 2.220 0.066 C15 GV3 32 GV3 H1 H1 H 0 1 N N N N N N 19.692 -0.458 -0.576 -2.634 -3.536 -0.706 H1 GV3 33 GV3 H2 H2 H 0 1 N N N N N N 21.312 -2.840 -0.883 -1.589 -2.237 1.689 H2 GV3 34 GV3 H3 H3 H 0 1 N N N N N N 19.035 -2.811 -1.659 -0.298 -3.281 -0.212 H3 GV3 35 GV3 H4 H4 H 0 1 N N N N N N 20.136 -3.097 -3.049 -0.801 -1.920 -1.244 H4 GV3 36 GV3 H5 H5 H 0 1 N N N N N N 20.871 -0.544 1.446 -4.062 -4.458 0.987 H5 GV3 37 GV3 H6 H6 H 0 1 N N N N N N 23.465 -0.878 -1.081 -4.070 -0.840 1.648 H6 GV3 38 GV3 H7 H7 H 0 1 N N N N N N 21.133 0.996 -1.661 -4.139 -1.820 -1.260 H7 GV3 39 GV3 H8 H8 H 0 1 N N N N N N 21.670 0.982 -3.949 -2.763 1.177 -1.269 H8 GV3 40 GV3 H9 H9 H 0 1 N N N N N N 27.782 -0.051 -2.320 -8.609 0.839 1.576 H9 GV3 41 GV3 H10 H10 H 0 1 N N N N N N 16.676 -4.896 -5.577 5.690 0.217 -0.055 H10 GV3 42 GV3 H11 H11 H 0 1 N N N N N N 21.633 1.487 0.568 -5.641 -3.360 -0.222 H11 GV3 43 GV3 H12 H12 H 0 1 N N N N N N 27.356 2.203 -5.960 -6.478 4.204 -1.887 H12 GV3 44 GV3 H13 H13 H 0 1 N N N N N N 25.962 1.657 -6.613 -8.044 4.339 -1.293 H13 GV3 45 GV3 H14 H14 H 0 1 N N N N N N 16.672 -1.624 -3.421 2.358 -2.656 -0.683 H14 GV3 46 GV3 H15 H15 H 0 1 N N N N N N 17.764 -3.021 -3.709 1.855 -1.295 -1.715 H15 GV3 47 GV3 H16 H16 H 0 1 N N N N N N 18.419 -1.377 -5.759 3.165 0.263 -0.300 H16 GV3 48 GV3 H17 H17 H 0 1 N N N N N N 16.678 -0.996 -5.540 3.668 -1.098 0.732 H17 GV3 49 GV3 H18 H18 H 0 1 N N N N N N 18.023 -3.416 -6.603 4.247 -0.817 -2.252 H18 GV3 50 GV3 H19 H19 H 0 1 N N N N N N 16.540 -2.557 -7.141 4.751 -2.178 -1.220 H19 GV3 51 GV3 H20 H20 H 0 1 N N N N N N 13.370 -4.612 -4.584 7.731 -1.276 -3.153 H20 GV3 52 GV3 H21 H21 H 0 1 N N N N N N 14.908 -1.873 -5.734 8.803 0.215 -1.727 H21 GV3 53 GV3 H22 H22 H 0 1 N N N N N N 12.280 -1.517 -6.591 6.949 -0.544 1.126 H22 GV3 54 GV3 H23 H23 H 0 1 N N N N N N 10.106 -0.983 -5.567 6.935 0.753 3.218 H23 GV3 55 GV3 H24 H24 H 0 1 N N N N N N 9.713 -1.426 -3.184 7.970 2.984 3.293 H24 GV3 56 GV3 H25 H25 H 0 1 N N N N N N 11.487 -2.448 -1.820 9.024 3.925 1.277 H25 GV3 57 GV3 H26 H26 H 0 1 N N N N N N 13.660 -3.017 -2.832 9.053 2.632 -0.817 H26 GV3 58 # 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 GV3 C12 N4 SING N N 1 GV3 C12 C11 SING N N 2 GV3 N7 C SING N N 3 GV3 N4 C13 SING N N 4 GV3 C19 C18 DOUB Y N 5 GV3 C19 C14 SING Y N 6 GV3 C11 C10 SING N N 7 GV3 N5 C13 SING N N 8 GV3 N5 C14 SING N N 9 GV3 C13 N6 DOUB N N 10 GV3 C18 C17 SING Y N 11 GV3 C14 C15 DOUB Y N 12 GV3 N3 C1 SING Y N 13 GV3 N3 C4 DOUB Y N 14 GV3 C C1 DOUB Y N 15 GV3 C N1 SING Y N 16 GV3 C1 C2 SING Y N 17 GV3 N1 C3 DOUB Y N 18 GV3 C10 S SING N N 19 GV3 C4 N2 SING Y N 20 GV3 C17 C16 DOUB Y N 21 GV3 C15 C16 SING Y N 22 GV3 S C9 SING N N 23 GV3 C2 N2 SING Y N 24 GV3 C2 N DOUB Y N 25 GV3 C3 N SING Y N 26 GV3 N2 C5 SING N N 27 GV3 O C5 SING N N 28 GV3 O C8 SING N N 29 GV3 C9 C8 SING N N 30 GV3 C5 C6 SING N N 31 GV3 C8 C7 SING N N 32 GV3 C6 C7 SING N N 33 GV3 C6 O2 SING N N 34 GV3 C7 O1 SING N N 35 GV3 C7 H1 SING N N 36 GV3 C8 H2 SING N N 37 GV3 C9 H3 SING N N 38 GV3 C9 H4 SING N N 39 GV3 O1 H5 SING N N 40 GV3 C5 H6 SING N N 41 GV3 C6 H7 SING N N 42 GV3 C4 H8 SING N N 43 GV3 C3 H9 SING N N 44 GV3 N4 H10 SING N N 45 GV3 O2 H11 SING N N 46 GV3 N7 H12 SING N N 47 GV3 N7 H13 SING N N 48 GV3 C10 H14 SING N N 49 GV3 C10 H15 SING N N 50 GV3 C11 H16 SING N N 51 GV3 C11 H17 SING N N 52 GV3 C12 H18 SING N N 53 GV3 C12 H19 SING N N 54 GV3 N6 H20 SING N N 55 GV3 N5 H21 SING N N 56 GV3 C19 H22 SING N N 57 GV3 C18 H23 SING N N 58 GV3 C17 H24 SING N N 59 GV3 C16 H25 SING N N 60 GV3 C15 H26 SING N N 61 # 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 GV3 SMILES ACDLabs 12.01 "N=C(Nc1ccccc1)NCCCSCC1OC(n2cnc3c(N)ncnc32)C(O)C1O" GV3 InChI InChI 1.06 "InChI=1S/C20H26N8O3S/c21-17-14-18(25-10-24-17)28(11-26-14)19-16(30)15(29)13(31-19)9-32-8-4-7-23-20(22)27-12-5-2-1-3-6-12/h1-3,5-6,10-11,13,15-16,19,29-30H,4,7-9H2,(H2,21,24,25)(H3,22,23,27)/t13-,15-,16-,19-/m1/s1" GV3 InChIKey InChI 1.06 PAOYFGCZLHEXFB-NVQRDWNXSA-N GV3 SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CSCCCNC(=N)Nc4ccccc4)[C@@H](O)[C@H]3O" GV3 SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CSCCCNC(=N)Nc4ccccc4)[CH](O)[CH]3O" GV3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(\NCCCSC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)/Nc4ccccc4" GV3 SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)NC(=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 GV3 "SYSTEMATIC NAME" ACDLabs 12.01 "5'-S-[3-(N'-phenylcarbamimidamido)propyl]-5'-thioadenosine" GV3 "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-phenyl-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 GV3 "Create component" 2023-05-01 RCSB GV3 "Initial release" 2024-04-24 RCSB #