data_KY8 # _chem_comp.id KY8 _chem_comp.name "(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[3-azanylpropyl-[3-(pyrimidin-2-ylamino)propyl]amino]methyl]oxolane-3,4-diol" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H30 N10 O3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-07-04 _chem_comp.pdbx_modified_date 2020-02-28 _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 458.517 _chem_comp.one_letter_code ? _chem_comp.three_letter_code KY8 _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 6S74 _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 KY8 C02 C1 C 0 1 N N S 13.116 28.653 13.455 1.542 0.392 2.906 C02 KY8 1 KY8 C03 C2 C 0 1 N N R 13.360 27.433 13.262 2.872 0.094 2.172 C03 KY8 2 KY8 C05 C3 C 0 1 N N R 14.575 27.474 12.694 2.380 -0.579 0.866 C05 KY8 3 KY8 C07 C4 C 0 1 Y N N 16.119 25.300 11.737 4.457 -1.233 -0.424 C07 KY8 4 KY8 N12 N1 N 0 1 N N N 17.934 21.937 12.096 6.968 -0.862 -3.100 N12 KY8 5 KY8 C13 C5 C 0 1 Y N N 16.623 24.126 12.368 5.115 -0.698 -1.545 C13 KY8 6 KY8 C15 C6 C 0 1 Y N N 15.421 25.314 14.177 3.388 0.553 -1.152 C15 KY8 7 KY8 C17 C7 C 0 1 N N R 14.428 29.164 13.725 0.482 0.378 1.786 C17 KY8 8 KY8 C18 C8 C 0 1 N N N 14.709 29.283 15.145 -0.239 1.726 1.737 C18 KY8 9 KY8 C20 C9 C 0 1 N N N 15.383 31.674 14.882 -1.695 3.060 0.335 C20 KY8 10 KY8 C09 C10 C 0 1 Y N N 17.011 24.635 9.691 6.042 -2.893 -0.308 C09 KY8 11 KY8 C11 C11 C 0 1 Y N N 17.345 23.197 11.547 6.278 -1.342 -2.001 C11 KY8 12 KY8 C21 C12 C 0 1 N N N 14.480 32.933 14.602 -0.615 3.760 -0.493 C21 KY8 13 KY8 C22 C13 C 0 1 N N N 15.179 33.846 13.501 -1.128 5.126 -0.951 C22 KY8 14 KY8 C24 C14 C 0 1 N N N 15.256 30.697 17.087 -2.389 0.853 1.047 C24 KY8 15 KY8 C25 C15 C 0 1 N N N 14.308 30.533 18.186 -3.296 0.649 -0.169 C25 KY8 16 KY8 C26 C16 C 0 1 N N N 14.994 31.078 19.528 -4.483 -0.234 0.222 C26 KY8 17 KY8 C28 C17 C 0 1 Y N N 13.690 31.054 21.623 -6.496 -1.199 -0.829 C28 KY8 18 KY8 C30 C18 C 0 1 Y N N 12.428 30.846 23.744 -8.370 -2.095 -1.819 C30 KY8 19 KY8 C31 C19 C 0 1 Y N N 12.011 32.241 23.617 -8.709 -2.689 -0.613 C31 KY8 20 KY8 C32 C20 C 0 1 Y N N 12.427 33.022 22.479 -7.872 -2.503 0.475 C32 KY8 21 KY8 N06 N2 N 0 1 Y N N 15.258 26.078 12.855 3.373 -0.423 -0.200 N06 KY8 22 KY8 N08 N3 N 0 1 Y N N 16.300 25.556 10.407 4.952 -2.321 0.157 N08 KY8 23 KY8 N10 N4 N 0 1 Y N N 17.504 23.482 10.247 6.699 -2.423 -1.352 N10 KY8 24 KY8 N14 N5 N 0 1 Y N N 16.186 24.152 13.923 4.411 0.389 -1.940 N14 KY8 25 KY8 N19 N6 N 0 1 N N N 14.554 30.676 15.699 -1.250 1.701 0.671 N19 KY8 26 KY8 N23 N7 N 0 1 N N N 16.639 34.046 13.536 -0.091 5.798 -1.746 N23 KY8 27 KY8 N27 N8 N 0 1 N N N 14.406 30.473 20.756 -5.351 -0.429 -0.941 N27 KY8 28 KY8 N29 N9 N 0 1 Y N N 13.286 30.270 22.767 -7.270 -1.365 -1.892 N29 KY8 29 KY8 N33 N10 N 0 1 Y N N 13.244 32.414 21.482 -6.788 -1.757 0.336 N33 KY8 30 KY8 O01 O1 O 0 1 N N N 12.565 29.373 12.346 1.262 -0.624 3.871 O01 KY8 31 KY8 O04 O2 O 0 1 N N N 12.392 26.712 12.411 3.685 -0.801 2.934 O04 KY8 32 KY8 O16 O3 O 0 1 N N N 15.257 28.350 13.353 1.173 0.147 0.547 O16 KY8 33 KY8 H1 H1 H 0 1 N N N 12.480 28.809 14.338 1.579 1.371 3.383 H1 KY8 34 KY8 H2 H2 H 0 1 N N N 13.424 26.894 14.219 3.411 1.017 1.956 H2 KY8 35 KY8 H3 H3 H 0 1 N N N 14.513 27.709 11.621 2.163 -1.633 1.036 H3 KY8 36 KY8 H4 H4 H 0 1 N N N 18.402 21.441 11.365 6.650 -0.072 -3.565 H4 KY8 37 KY8 H5 H5 H 0 1 N N N 18.589 22.162 12.817 7.769 -1.315 -3.406 H5 KY8 38 KY8 H6 H6 H 0 1 N N N 15.021 25.612 15.135 2.659 1.344 -1.239 H6 KY8 39 KY8 H7 H7 H 0 1 N N N 14.545 30.148 13.248 -0.237 -0.421 1.966 H7 KY8 40 KY8 H8 H8 H 0 1 N N N 14.021 28.619 15.688 -0.725 1.914 2.694 H8 KY8 41 KY8 H9 H9 H 0 1 N N N 15.745 28.958 15.318 0.483 2.517 1.534 H9 KY8 42 KY8 H10 H10 H 0 1 N N N 15.691 31.215 13.931 -1.870 3.623 1.253 H10 KY8 43 KY8 H11 H11 H 0 1 N N N 16.276 31.973 15.451 -2.618 3.009 -0.241 H11 KY8 44 KY8 H12 H12 H 0 1 N N N 17.193 24.823 8.643 6.420 -3.774 0.190 H12 KY8 45 KY8 H13 H13 H 0 1 N N N 14.354 33.509 15.531 0.280 3.893 0.115 H13 KY8 46 KY8 H14 H14 H 0 1 N N N 13.495 32.605 14.237 -0.375 3.151 -1.365 H14 KY8 47 KY8 H15 H15 H 0 1 N N N 14.719 34.842 13.574 -2.023 4.993 -1.559 H15 KY8 48 KY8 H16 H16 H 0 1 N N N 14.941 33.404 12.522 -1.368 5.735 -0.079 H16 KY8 49 KY8 H17 H17 H 0 1 N N N 15.989 29.878 17.126 -2.954 1.335 1.845 H17 KY8 50 KY8 H18 H18 H 0 1 N N N 15.775 31.659 17.207 -2.024 -0.114 1.393 H18 KY8 51 KY8 H19 H19 H 0 1 N N N 13.393 31.107 17.977 -3.662 1.616 -0.515 H19 KY8 52 KY8 H20 H20 H 0 1 N N N 14.055 29.469 18.303 -2.732 0.167 -0.966 H20 KY8 53 KY8 H21 H21 H 0 1 N N N 16.068 30.840 19.497 -4.117 -1.201 0.569 H21 KY8 54 KY8 H22 H22 H 0 1 N N N 14.861 32.169 19.574 -5.047 0.248 1.020 H22 KY8 55 KY8 H23 H23 H 0 1 N N N 12.085 30.253 24.579 -8.997 -2.227 -2.688 H23 KY8 56 KY8 H24 H24 H 0 1 N N N 11.389 32.688 24.378 -9.602 -3.290 -0.526 H24 KY8 57 KY8 H25 H25 H 0 1 N N N 12.124 34.054 22.383 -8.107 -2.952 1.429 H25 KY8 58 KY8 H27 H27 H 0 1 N N N 16.913 34.641 12.780 -0.407 6.703 -2.060 H27 KY8 59 KY8 H28 H28 H 0 1 N N N 16.896 34.470 14.404 0.770 5.875 -1.226 H28 KY8 60 KY8 H30 H30 H 0 1 N N N 13.846 29.713 20.426 -5.123 -0.019 -1.790 H30 KY8 61 KY8 H31 H31 H 0 1 N N N 12.420 30.278 12.596 1.898 -0.661 4.599 H31 KY8 62 KY8 H32 H32 H 0 1 N N N 11.543 26.699 12.837 3.943 -0.458 3.800 H32 KY8 63 # # 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 KY8 C09 N10 DOUB Y N 1 KY8 C09 N08 SING Y N 2 KY8 N10 C11 SING Y N 3 KY8 N08 C07 DOUB Y N 4 KY8 C11 N12 SING N N 5 KY8 C11 C13 DOUB Y N 6 KY8 C07 C13 SING Y N 7 KY8 C07 N06 SING Y N 8 KY8 O01 C02 SING N N 9 KY8 C13 N14 SING Y N 10 KY8 O04 C03 SING N N 11 KY8 C05 N06 SING N N 12 KY8 C05 C03 SING N N 13 KY8 C05 O16 SING N N 14 KY8 N06 C15 SING Y N 15 KY8 C03 C02 SING N N 16 KY8 O16 C17 SING N N 17 KY8 C02 C17 SING N N 18 KY8 C22 N23 SING N N 19 KY8 C22 C21 SING N N 20 KY8 C17 C18 SING N N 21 KY8 N14 C15 DOUB Y N 22 KY8 C21 C20 SING N N 23 KY8 C20 N19 SING N N 24 KY8 C18 N19 SING N N 25 KY8 N19 C24 SING N N 26 KY8 C24 C25 SING N N 27 KY8 C25 C26 SING N N 28 KY8 C26 N27 SING N N 29 KY8 N27 C28 SING N N 30 KY8 N33 C28 DOUB Y N 31 KY8 N33 C32 SING Y N 32 KY8 C28 N29 SING Y N 33 KY8 C32 C31 DOUB Y N 34 KY8 N29 C30 DOUB Y N 35 KY8 C31 C30 SING Y N 36 KY8 C02 H1 SING N N 37 KY8 C03 H2 SING N N 38 KY8 C05 H3 SING N N 39 KY8 N12 H4 SING N N 40 KY8 N12 H5 SING N N 41 KY8 C15 H6 SING N N 42 KY8 C17 H7 SING N N 43 KY8 C18 H8 SING N N 44 KY8 C18 H9 SING N N 45 KY8 C20 H10 SING N N 46 KY8 C20 H11 SING N N 47 KY8 C09 H12 SING N N 48 KY8 C21 H13 SING N N 49 KY8 C21 H14 SING N N 50 KY8 C22 H15 SING N N 51 KY8 C22 H16 SING N N 52 KY8 C24 H17 SING N N 53 KY8 C24 H18 SING N N 54 KY8 C25 H19 SING N N 55 KY8 C25 H20 SING N N 56 KY8 C26 H21 SING N N 57 KY8 C26 H22 SING N N 58 KY8 C30 H23 SING N N 59 KY8 C31 H24 SING N N 60 KY8 C32 H25 SING N N 61 KY8 N23 H27 SING N N 62 KY8 N23 H28 SING N N 63 KY8 N27 H30 SING N N 64 KY8 O01 H31 SING N N 65 KY8 O04 H32 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 KY8 InChI InChI 1.03 "InChI=1S/C20H30N10O3/c21-4-1-8-29(9-3-7-25-20-23-5-2-6-24-20)10-13-15(31)16(32)19(33-13)30-12-28-14-17(22)26-11-27-18(14)30/h2,5-6,11-13,15-16,19,31-32H,1,3-4,7-10,21H2,(H2,22,26,27)(H,23,24,25)/t13-,15-,16-,19-/m1/s1" KY8 InChIKey InChI 1.03 WJNNCQSJBOESHI-NVQRDWNXSA-N KY8 SMILES_CANONICAL CACTVS 3.385 "NCCCN(CCCNc1ncccn1)C[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34" KY8 SMILES CACTVS 3.385 "NCCCN(CCCNc1ncccn1)C[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34" KY8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cnc(nc1)NCCCN(CCCN)C[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O" KY8 SMILES "OpenEye OEToolkits" 2.0.7 "c1cnc(nc1)NCCCN(CCCN)CC2C(C(C(O2)n3cnc4c3ncnc4N)O)O" # _pdbx_chem_comp_identifier.comp_id KY8 _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 "(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[3-azanylpropyl-[3-(pyrimidin-2-ylamino)propyl]amino]methyl]oxolane-3,4-diol" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site KY8 "Create component" 2019-07-04 PDBE KY8 "Initial release" 2020-03-04 RCSB ##