data_VK9 # _chem_comp.id VK9 _chem_comp.name "~{N}-[3-[2-(6-aminopurin-9-yl)ethanoylamino]propyl]-5-[(3~{R})-1,2-dithiolan-3-yl]pentanamide" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H27 N7 O2 S2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-03-09 _chem_comp.pdbx_modified_date 2023-06-02 _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 437.583 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VK9 _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 8CRL _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 VK9 C4 C1 C 0 1 N N N 16.651 -13.154 1.472 -6.425 -0.619 0.168 C4 VK9 1 VK9 C5 C2 C 0 1 N N N 17.242 -12.410 2.687 -7.572 -0.502 -0.838 C5 VK9 2 VK9 C6 C3 C 0 1 N N R 18.601 -11.762 2.359 -8.909 -0.581 -0.099 C6 VK9 3 VK9 C7 C4 C 0 1 N N N 19.396 -12.625 1.364 -10.054 -0.617 -1.113 C7 VK9 4 VK9 C8 C5 C 0 1 N N N 20.590 -11.810 1.102 -11.380 -0.056 -0.561 C8 VK9 5 VK9 C13 C6 C 0 1 N N N 14.875 -11.718 -3.780 -0.188 -0.586 -0.314 C13 VK9 6 VK9 C15 C7 C 0 1 N N N 13.044 -11.544 -5.452 2.296 -0.624 -0.047 C15 VK9 7 VK9 C17 C8 C 0 1 N N N 13.477 -9.119 -5.511 4.672 -0.692 0.490 C17 VK9 8 VK9 C21 C9 C 0 1 Y N N 16.542 -7.173 -5.391 7.830 -1.788 0.344 C21 VK9 9 VK9 C24 C10 C 0 1 Y N N 15.190 -7.340 -3.758 7.748 0.414 0.420 C24 VK9 10 VK9 S8 S1 S 0 1 N N N 21.420 -11.835 2.667 -10.900 1.561 0.179 S8 VK9 11 VK9 S6 S2 S 0 1 N N N 19.707 -11.636 3.760 -9.105 0.891 0.972 S6 VK9 12 VK9 C3 C11 C 0 1 N N N 15.738 -12.259 0.629 -5.088 -0.541 -0.572 C3 VK9 13 VK9 C2 C12 C 0 1 N N N 14.836 -13.145 -0.247 -3.941 -0.657 0.435 C2 VK9 14 VK9 C1 C13 C 0 1 N N N 14.396 -12.370 -1.490 -2.624 -0.580 -0.294 C1 VK9 15 VK9 O2 O1 O 0 1 N N N 13.354 -11.725 -1.487 -2.604 -0.445 -1.499 O2 VK9 16 VK9 N2 N1 N 0 1 N N N 15.181 -12.469 -2.567 -1.468 -0.661 0.394 N2 VK9 17 VK9 C14 C14 C 0 1 N N N 13.918 -12.497 -4.665 0.959 -0.702 0.692 C14 VK9 18 VK9 N16 N2 N 0 1 N N N 13.823 -10.366 -5.876 3.394 -0.736 0.916 N16 VK9 19 VK9 O18 O2 O 0 1 N N N 12.503 -8.859 -4.803 4.913 -0.561 -0.691 O18 VK9 20 VK9 C19 C15 C 0 1 N N N 14.369 -7.994 -6.055 5.802 -0.807 1.481 C19 VK9 21 VK9 N20 N3 N 0 1 Y N N 15.321 -7.520 -5.056 7.082 -0.732 0.773 N20 VK9 22 VK9 N22 N4 N 0 1 Y N N 17.162 -6.782 -4.299 8.907 -1.359 -0.247 N22 VK9 23 VK9 C23 C16 C 0 1 Y N N 16.338 -6.885 -3.290 8.919 -0.004 -0.235 C23 VK9 24 VK9 N28 N5 N 0 1 Y N N 14.164 -7.540 -2.942 7.520 1.715 0.565 N28 VK9 25 VK9 C27 C17 C 0 1 Y N N 14.305 -7.271 -1.595 8.375 2.603 0.103 C27 VK9 26 VK9 N26 N6 N 0 1 Y N N 15.505 -6.799 -1.134 9.488 2.257 -0.519 N26 VK9 27 VK9 C25 C18 C 0 1 Y N N 16.486 -6.624 -2.005 9.802 0.980 -0.711 C25 VK9 28 VK9 N29 N7 N 0 1 N N N 17.648 -6.173 -1.607 10.970 0.628 -1.363 N29 VK9 29 VK9 H1 H1 H 0 1 N N N 16.068 -14.014 1.833 -6.490 0.196 0.889 H1 VK9 30 VK9 H2 H2 H 0 1 N N N 17.477 -13.511 0.840 -6.496 -1.573 0.691 H2 VK9 31 VK9 H3 H3 H 0 1 N N N 16.539 -11.623 2.999 -7.501 0.451 -1.361 H3 VK9 32 VK9 H4 H4 H 0 1 N N N 17.379 -13.126 3.510 -7.507 -1.317 -1.559 H4 VK9 33 VK9 H5 H5 H 0 1 N N N 18.457 -10.748 1.959 -8.936 -1.483 0.512 H5 VK9 34 VK9 H6 H6 H 0 1 N N N 18.822 -12.794 0.441 -9.765 -0.034 -1.987 H6 VK9 35 VK9 H7 H7 H 0 1 N N N 19.668 -13.593 1.810 -10.216 -1.650 -1.421 H7 VK9 36 VK9 H8 H8 H 0 1 N N N 21.213 -12.259 0.314 -12.099 0.090 -1.367 H8 VK9 37 VK9 H9 H9 H 0 1 N N N 20.316 -10.784 0.813 -11.788 -0.720 0.202 H9 VK9 38 VK9 H10 H10 H 0 1 N N N 15.807 -11.530 -4.333 -0.123 -1.401 -1.035 H10 VK9 39 VK9 H11 H11 H 0 1 N N N 14.412 -10.759 -3.504 -0.117 0.368 -0.836 H11 VK9 40 VK9 H12 H12 H 0 1 N N N 12.205 -11.216 -4.821 2.361 -1.439 -0.768 H12 VK9 41 VK9 H13 H13 H 0 1 N N N 12.654 -12.060 -6.342 2.367 0.330 -0.570 H13 VK9 42 VK9 H14 H14 H 0 1 N N N 16.962 -7.203 -6.385 7.569 -2.827 0.479 H14 VK9 43 VK9 H15 H15 H 0 1 N N N 16.350 -11.608 -0.013 -5.023 -1.356 -1.293 H15 VK9 44 VK9 H16 H16 H 0 1 N N N 15.115 -11.640 1.291 -5.017 0.413 -1.094 H16 VK9 45 VK9 H17 H17 H 0 1 N N N 13.948 -13.445 0.329 -4.006 0.158 1.155 H17 VK9 46 VK9 H18 H18 H 0 1 N N N 15.394 -14.042 -0.555 -4.012 -1.611 0.957 H18 VK9 47 VK9 H19 H19 H 0 1 N N N 15.985 -13.063 -2.541 -1.484 -0.769 1.358 H19 VK9 48 VK9 H20 H20 H 0 1 N N N 13.283 -13.139 -4.037 0.894 0.113 1.413 H20 VK9 49 VK9 H21 H21 H 0 1 N N N 14.495 -13.122 -5.363 0.888 -1.656 1.215 H21 VK9 50 VK9 H22 H22 H 0 1 N N N 14.631 -10.498 -6.451 3.202 -0.841 1.861 H22 VK9 51 VK9 H23 H23 H 0 1 N N N 14.926 -8.372 -6.925 5.737 0.008 2.202 H23 VK9 52 VK9 H24 H24 H 0 1 N N N 13.731 -7.153 -6.365 5.731 -1.761 2.004 H24 VK9 53 VK9 H25 H25 H 0 1 N N N 13.481 -7.430 -0.915 8.159 3.652 0.238 H25 VK9 54 VK9 H26 H26 H 0 1 N N N 17.624 -6.013 -0.620 11.188 -0.307 -1.496 H26 VK9 55 VK9 H27 H27 H 0 1 N N N 18.357 -6.846 -1.818 11.571 1.317 -1.687 H27 VK9 56 # 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 VK9 C19 C17 SING N N 1 VK9 C19 N20 SING N N 2 VK9 N16 C17 SING N N 3 VK9 N16 C15 SING N N 4 VK9 C17 O18 DOUB N N 5 VK9 C15 C14 SING N N 6 VK9 C21 N20 SING Y N 7 VK9 C21 N22 DOUB Y N 8 VK9 N20 C24 SING Y N 9 VK9 C14 C13 SING N N 10 VK9 N22 C23 SING Y N 11 VK9 C13 N2 SING N N 12 VK9 C24 C23 DOUB Y N 13 VK9 C24 N28 SING Y N 14 VK9 C23 C25 SING Y N 15 VK9 N28 C27 DOUB Y N 16 VK9 N2 C1 SING N N 17 VK9 C25 N29 SING N N 18 VK9 C25 N26 DOUB Y N 19 VK9 C27 N26 SING Y N 20 VK9 C1 O2 DOUB N N 21 VK9 C1 C2 SING N N 22 VK9 C2 C3 SING N N 23 VK9 C3 C4 SING N N 24 VK9 C8 C7 SING N N 25 VK9 C8 S8 SING N N 26 VK9 C7 C6 SING N N 27 VK9 C4 C5 SING N N 28 VK9 C6 C5 SING N N 29 VK9 C6 S6 SING N N 30 VK9 S8 S6 SING N N 31 VK9 C4 H1 SING N N 32 VK9 C4 H2 SING N N 33 VK9 C5 H3 SING N N 34 VK9 C5 H4 SING N N 35 VK9 C6 H5 SING N N 36 VK9 C7 H6 SING N N 37 VK9 C7 H7 SING N N 38 VK9 C8 H8 SING N N 39 VK9 C8 H9 SING N N 40 VK9 C13 H10 SING N N 41 VK9 C13 H11 SING N N 42 VK9 C15 H12 SING N N 43 VK9 C15 H13 SING N N 44 VK9 C21 H14 SING N N 45 VK9 C3 H15 SING N N 46 VK9 C3 H16 SING N N 47 VK9 C2 H17 SING N N 48 VK9 C2 H18 SING N N 49 VK9 N2 H19 SING N N 50 VK9 C14 H20 SING N N 51 VK9 C14 H21 SING N N 52 VK9 N16 H22 SING N N 53 VK9 C19 H23 SING N N 54 VK9 C19 H24 SING N N 55 VK9 C27 H25 SING N N 56 VK9 N29 H26 SING N N 57 VK9 N29 H27 SING N N 58 # 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 VK9 InChI InChI 1.06 "InChI=1S/C18H27N7O2S2/c19-17-16-18(23-11-22-17)25(12-24-16)10-15(27)21-8-3-7-20-14(26)5-2-1-4-13-6-9-28-29-13/h11-13H,1-10H2,(H,20,26)(H,21,27)(H2,19,22,23)/t13-/m1/s1" VK9 InChIKey InChI 1.06 AIPYQGISPXYWAZ-CYBMUJFWSA-N VK9 SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(CC(=O)NCCCNC(=O)CCCC[C@@H]3CCSS3)cnc12" VK9 SMILES CACTVS 3.385 "Nc1ncnc2n(CC(=O)NCCCNC(=O)CCCC[CH]3CCSS3)cnc12" VK9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)CC(=O)NCCCNC(=O)CCCC[C@@H]3CCSS3)N" VK9 SMILES "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)CC(=O)NCCCNC(=O)CCCCC3CCSS3)N" # _pdbx_chem_comp_identifier.comp_id VK9 _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 "~{N}-[3-[2-(6-aminopurin-9-yl)ethanoylamino]propyl]-5-[(3~{R})-1,2-dithiolan-3-yl]pentanamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site VK9 "Create component" 2023-03-09 PDBE VK9 "Initial release" 2023-06-07 RCSB #