data_KXD # _chem_comp.id KXD _chem_comp.name "2-azanyl-9-[(1~{R},6~{R},8~{R},9~{R},10~{S},15~{R},17~{R},18~{R})-8-[4-azanyl-5-[4-(naphthalen-1-yloxymethyl)phenyl]pyrrolo[2,3-d]pyrimidin-7-yl]-3,9,12,18-tetrakis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{6,10}]octadecan-17-yl]-3~{H}-purin-6-one" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C38 H37 N9 O14 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-06-07 _chem_comp.pdbx_modified_date 2022-10-07 _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 905.700 _chem_comp.one_letter_code ? _chem_comp.three_letter_code KXD _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 8A2K _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 KXD C10 C1 C 0 1 N N N 6.152 -32.391 -5.415 0.712 -1.344 0.910 C10 KXD 1 KXD C13 C2 C 0 1 N N R 4.869 -29.034 -4.949 -0.780 -4.365 0.545 C13 KXD 2 KXD C15 C3 C 0 1 Y N N 2.763 -30.285 -5.140 -2.769 -2.831 0.483 C15 KXD 3 KXD C16 C4 C 0 1 Y N N 1.411 -30.038 -4.942 -4.072 -2.880 0.112 C16 KXD 4 KXD C17 C5 C 0 1 Y N N 0.345 -31.166 -5.182 -5.058 -1.775 0.188 C17 KXD 5 KXD C18 C6 C 0 1 Y N N -1.012 -30.905 -5.363 -5.211 -1.055 1.372 C18 KXD 6 KXD C19 C7 C 0 1 Y N N -1.899 -31.953 -5.600 -6.130 -0.027 1.437 C19 KXD 7 KXD C20 C8 C 0 1 Y N N -1.430 -33.263 -5.652 -6.899 0.288 0.331 C20 KXD 8 KXD C21 C9 C 0 1 N N N -2.383 -34.462 -5.898 -7.901 1.411 0.408 C21 KXD 9 KXD C23 C10 C 0 1 Y N N -2.672 -33.871 -8.479 -8.044 3.754 0.040 C23 KXD 10 KXD C24 C11 C 0 1 Y N N -3.652 -33.129 -9.137 -9.358 3.680 0.410 C24 KXD 11 KXD C25 C12 C 0 1 Y N N -3.431 -32.515 -10.376 -10.160 4.817 0.432 C25 KXD 12 KXD C26 C13 C 0 1 Y N N -2.198 -32.654 -10.997 -9.662 6.035 0.084 C26 KXD 13 KXD C27 C14 C 0 1 Y N N -1.195 -33.415 -10.366 -8.316 6.154 -0.303 C27 KXD 14 KXD C28 C15 C 0 1 Y N N -1.409 -34.028 -9.140 -7.493 5.001 -0.320 C28 KXD 15 KXD C02 C16 C 0 1 N N R 5.274 -34.893 -2.815 4.296 -0.037 -0.690 C02 KXD 16 KXD C03 C17 C 0 1 N N R 5.296 -35.121 -1.389 5.146 -1.058 0.097 C03 KXD 17 KXD C04 C18 C 0 1 N N N 5.852 -33.924 -0.742 5.523 -2.246 -0.774 C04 KXD 18 KXD C08 C19 C 0 1 N N S 5.602 -30.757 -3.628 1.355 -3.501 -0.223 C08 KXD 19 KXD C09 C20 C 0 1 N N R 6.249 -30.960 -4.883 0.935 -2.847 1.102 C09 KXD 20 KXD C29 C21 C 0 1 Y N N -0.357 -34.773 -8.574 -6.148 5.120 -0.706 C29 KXD 21 KXD C30 C22 C 0 1 Y N N 0.865 -34.879 -9.231 -5.653 6.338 -1.057 C30 KXD 22 KXD C31 C23 C 0 1 Y N N 1.070 -34.266 -10.453 -6.462 7.473 -1.039 C31 KXD 23 KXD C32 C24 C 0 1 Y N N 0.038 -33.543 -11.018 -7.769 7.396 -0.667 C32 KXD 24 KXD C33 C25 C 0 1 Y N N -0.098 -33.532 -5.460 -6.751 -0.424 -0.846 C33 KXD 25 KXD C34 C26 C 0 1 Y N N 0.796 -32.476 -5.230 -5.831 -1.449 -0.925 C34 KXD 26 KXD C35 C27 C 0 1 Y N N 1.307 -28.663 -4.555 -4.315 -4.242 -0.380 C35 KXD 27 KXD C36 C28 C 0 1 Y N N 2.607 -28.188 -4.526 -3.093 -4.925 -0.261 C36 KXD 28 KXD C38 C29 C 0 1 Y N N 1.903 -26.078 -3.865 -4.103 -6.805 -1.124 C38 KXD 29 KXD C40 C30 C 0 1 Y N N 0.297 -27.720 -4.207 -5.423 -4.927 -0.897 C40 KXD 30 KXD C42 C31 C 0 1 N N R 5.379 -29.303 -3.584 0.062 -4.178 -0.727 C42 KXD 31 KXD C47 C32 C 0 1 N N R 3.048 -35.142 -2.118 5.956 1.073 0.624 C47 KXD 32 KXD C49 C33 C 0 1 Y N N 1.979 -33.010 -1.372 7.427 1.397 -1.399 C49 KXD 33 KXD C51 C34 C 0 1 Y N N -0.076 -33.532 -1.762 7.910 3.500 -1.237 C51 KXD 34 KXD C52 C35 C 0 1 Y N N 0.725 -34.592 -2.099 7.092 3.181 -0.160 C52 KXD 35 KXD C54 C36 C 0 1 N N N -1.260 -35.999 -2.828 7.231 5.431 0.575 C54 KXD 36 KXD C57 C37 C 0 1 N N N -1.592 -33.669 -1.959 8.384 4.883 -1.359 C57 KXD 37 KXD C59 C38 C 0 1 N N R 3.915 -34.534 -3.149 4.474 1.222 0.193 C59 KXD 38 KXD N14 N1 N 0 1 Y N N 3.444 -29.176 -4.888 -2.183 -4.047 0.262 N14 KXD 39 KXD N37 N2 N 0 1 Y N N 2.880 -26.908 -4.186 -3.037 -6.201 -0.644 N37 KXD 40 KXD N39 N3 N 0 1 Y N N 0.643 -26.479 -3.881 -5.269 -6.199 -1.253 N39 KXD 41 KXD N41 N4 N 0 1 N N N -1.108 -28.082 -4.186 -6.647 -4.296 -1.033 N41 KXD 42 KXD N48 N5 N 0 1 Y N N 1.972 -34.245 -1.841 6.797 1.858 -0.281 N48 KXD 43 KXD N50 N6 N 0 1 Y N N 0.730 -32.561 -1.312 8.086 2.370 -1.960 N50 KXD 44 KXD N53 N7 N 0 1 N N N 0.184 -35.864 -2.639 6.762 4.166 0.735 N53 KXD 45 KXD N55 N8 N 0 1 N N N -1.751 -37.267 -3.363 6.878 6.385 1.491 N55 KXD 46 KXD N56 N9 N 0 1 N N N -2.130 -34.899 -2.478 8.002 5.776 -0.434 N56 KXD 47 KXD O01 O1 O 0 1 N N N 5.625 -36.101 -3.568 2.947 -0.445 -0.804 O01 KXD 48 KXD O05 O2 O 0 1 N N N 4.979 -32.819 -0.955 4.379 -3.092 -0.938 O05 KXD 49 KXD O07 O3 O 0 1 N N N 6.473 -31.049 -2.481 2.353 -4.496 0.004 O07 KXD 50 KXD O11 O4 O 0 1 N N N 4.776 -32.723 -5.516 1.762 -0.630 1.556 O11 KXD 51 KXD O12 O5 O 0 1 N N N 5.516 -30.044 -5.779 -0.271 -3.475 1.539 O12 KXD 52 KXD O22 O6 O 0 1 N N N -3.064 -34.501 -7.194 -7.274 2.636 0.025 O22 KXD 53 KXD O43 O7 O 0 1 N N N 6.605 -28.605 -3.381 0.354 -5.440 -1.327 O43 KXD 54 KXD O44 O8 O 0 1 N N N 6.891 -31.477 0.069 4.238 -3.659 1.633 O44 KXD 55 KXD O45 O9 O 0 1 N N N 4.861 -30.309 -0.533 4.685 -5.445 -0.083 O45 KXD 56 KXD O46 O10 O 0 1 N N N 3.849 -35.324 -0.933 6.299 -0.318 0.524 O46 KXD 57 KXD O58 O11 O 0 1 N N N -2.312 -32.788 -1.688 9.111 5.213 -2.283 O58 KXD 58 KXD O60 O12 O 0 1 N N N 3.702 -35.116 -4.432 3.655 1.168 1.351 O60 KXD 59 KXD O62 O13 O 0 1 N N N 3.157 -34.288 -6.887 1.459 1.447 0.133 O62 KXD 60 KXD O63 O14 O 0 1 N N N 5.338 -35.098 -6.372 1.442 1.743 2.634 O63 KXD 61 KXD P06 P1 P 0 1 N N N 5.816 -31.404 -0.956 3.926 -4.194 0.145 P06 KXD 62 KXD P61 P2 P 0 1 N N N 4.215 -34.283 -5.796 2.067 0.937 1.382 P61 KXD 63 KXD H1 H1 H 0 1 N N N 6.654 -33.083 -4.723 0.687 -1.106 -0.152 H1 KXD 64 KXD H2 H2 H 0 1 N N N 6.626 -32.455 -6.405 -0.243 -1.071 1.362 H2 KXD 65 KXD H3 H3 H 0 1 N N N 5.154 -28.022 -5.273 -0.703 -5.393 0.891 H3 KXD 66 KXD H4 H4 H 0 1 N N N 3.190 -31.227 -5.449 -2.269 -1.963 0.886 H4 KXD 67 KXD H5 H5 H 0 1 N N N -1.376 -29.889 -5.320 -4.612 -1.300 2.236 H5 KXD 68 KXD H6 H6 H 0 1 N N N -2.950 -31.749 -5.743 -6.250 0.531 2.353 H6 KXD 69 KXD H7 H7 H 0 1 N N N -3.156 -34.441 -5.115 -8.733 1.202 -0.264 H7 KXD 70 KXD H8 H8 H 0 1 N N N -1.791 -35.384 -5.804 -8.272 1.497 1.430 H8 KXD 71 KXD H9 H9 H 0 1 N N N -4.621 -33.023 -8.672 -9.778 2.725 0.690 H9 KXD 72 KXD H10 H10 H 0 1 N N N -4.214 -31.938 -10.845 -11.195 4.731 0.728 H10 KXD 73 KXD H11 H11 H 0 1 N N N -2.010 -32.185 -11.951 -10.299 6.907 0.106 H11 KXD 74 KXD H12 H12 H 0 1 N N N 5.959 -34.074 -3.080 4.741 0.138 -1.675 H12 KXD 75 KXD H13 H13 H 0 1 N N N 5.894 -36.010 -1.140 4.584 -1.386 0.974 H13 KXD 76 KXD H14 H14 H 0 1 N N N 5.956 -34.106 0.338 5.856 -1.902 -1.751 H14 KXD 77 KXD H15 H15 H 0 1 N N N 6.839 -33.700 -1.173 6.325 -2.810 -0.300 H15 KXD 78 KXD H16 H16 H 0 1 N N N 4.653 -31.309 -3.560 1.695 -2.757 -0.936 H16 KXD 79 KXD H17 H17 H 0 1 N N N 7.307 -30.665 -4.827 1.716 -3.003 1.847 H17 KXD 80 KXD H18 H18 H 0 1 N N N -0.499 -35.266 -7.623 -5.510 4.249 -0.724 H18 KXD 81 KXD H19 H19 H 0 1 N N N 1.664 -35.448 -8.780 -4.619 6.427 -1.354 H19 KXD 82 KXD H20 H20 H 0 1 N N N 2.021 -34.351 -10.957 -6.044 8.428 -1.322 H20 KXD 83 KXD H21 H21 H 0 1 N N N 0.184 -33.069 -11.977 -8.384 8.284 -0.658 H21 KXD 84 KXD H22 H22 H 0 1 N N N 0.260 -34.551 -5.486 -7.354 -0.174 -1.707 H22 KXD 85 KXD H23 H23 H 0 1 N N N 1.846 -32.686 -5.089 -5.717 -2.004 -1.845 H23 KXD 86 KXD H24 H24 H 0 1 N N N 2.136 -25.061 -3.587 -4.020 -7.839 -1.425 H24 KXD 87 KXD H25 H25 H 0 1 N N N 4.628 -29.040 -2.824 -0.456 -3.526 -1.426 H25 KXD 88 KXD H26 H26 H 0 1 N N N 2.664 -36.109 -2.474 6.069 1.411 1.647 H26 KXD 89 KXD H27 H27 H 0 1 N N N 2.859 -32.454 -1.084 7.389 0.380 -1.762 H27 KXD 90 KXD H28 H28 H 0 1 N N N 3.785 -33.442 -3.173 4.326 2.125 -0.377 H28 KXD 91 KXD H29 H29 H 0 1 N N N -1.653 -27.290 -3.910 -6.746 -3.368 -0.769 H29 KXD 92 KXD H30 H30 H 0 1 N N N -1.389 -28.378 -5.099 -7.406 -4.782 -1.392 H30 KXD 93 KXD H31 H31 H 0 1 N N N 0.798 -36.618 -2.870 6.195 3.955 1.494 H31 KXD 94 KXD H32 H32 H 0 1 N N N -2.732 -37.405 -3.503 6.304 6.152 2.237 H32 KXD 95 KXD H33 H33 H 0 1 N N N -1.106 -37.997 -3.589 7.202 7.294 1.394 H33 KXD 96 KXD H34 H34 H 0 1 N N N 6.517 -36.355 -3.362 2.827 -1.279 -1.278 H34 KXD 97 KXD H35 H35 H 0 1 N N N 6.928 -28.780 -2.505 -0.429 -5.933 -1.608 H35 KXD 98 KXD H36 H36 H 0 1 N N N 6.731 -30.827 0.743 5.170 -3.456 1.791 H36 KXD 99 KXD H37 H37 H 0 1 N N N 5.100 -35.395 -7.243 0.483 1.653 2.719 H37 KXD 100 # 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 KXD C32 C31 DOUB Y N 1 KXD C32 C27 SING Y N 2 KXD C26 C25 DOUB Y N 3 KXD C26 C27 SING Y N 4 KXD C31 C30 SING Y N 5 KXD C25 C24 SING Y N 6 KXD C27 C28 DOUB Y N 7 KXD C30 C29 DOUB Y N 8 KXD C28 C29 SING Y N 9 KXD C28 C23 SING Y N 10 KXD C24 C23 DOUB Y N 11 KXD C23 O22 SING N N 12 KXD O22 C21 SING N N 13 KXD O62 P61 DOUB N N 14 KXD O63 P61 SING N N 15 KXD C21 C20 SING N N 16 KXD P61 O11 SING N N 17 KXD P61 O60 SING N N 18 KXD O12 C13 SING N N 19 KXD O12 C09 SING N N 20 KXD C20 C19 DOUB Y N 21 KXD C20 C33 SING Y N 22 KXD C19 C18 SING Y N 23 KXD O11 C10 SING N N 24 KXD C33 C34 DOUB Y N 25 KXD C10 C09 SING N N 26 KXD C18 C17 DOUB Y N 27 KXD C34 C17 SING Y N 28 KXD C17 C16 SING N N 29 KXD C15 C16 DOUB Y N 30 KXD C15 N14 SING Y N 31 KXD C13 N14 SING N N 32 KXD C13 C42 SING N N 33 KXD C16 C35 SING Y N 34 KXD N14 C36 SING Y N 35 KXD C09 C08 SING N N 36 KXD C35 C36 DOUB Y N 37 KXD C35 C40 SING Y N 38 KXD C36 N37 SING Y N 39 KXD O60 C59 SING N N 40 KXD C40 N41 SING N N 41 KXD C40 N39 DOUB Y N 42 KXD N37 C38 DOUB Y N 43 KXD N39 C38 SING Y N 44 KXD C08 C42 SING N N 45 KXD C08 O07 SING N N 46 KXD C42 O43 SING N N 47 KXD O01 C02 SING N N 48 KXD N55 C54 SING N N 49 KXD C59 C02 SING N N 50 KXD C59 C47 SING N N 51 KXD C54 N53 SING N N 52 KXD C54 N56 DOUB N N 53 KXD C02 C03 SING N N 54 KXD N53 C52 SING N N 55 KXD O07 P06 SING N N 56 KXD N56 C57 SING N N 57 KXD C47 N48 SING N N 58 KXD C47 O46 SING N N 59 KXD C52 N48 SING Y N 60 KXD C52 C51 DOUB Y N 61 KXD C57 C51 SING N N 62 KXD C57 O58 DOUB N N 63 KXD N48 C49 SING Y N 64 KXD C51 N50 SING Y N 65 KXD C03 O46 SING N N 66 KXD C03 C04 SING N N 67 KXD C49 N50 DOUB Y N 68 KXD P06 O05 SING N N 69 KXD P06 O45 DOUB N N 70 KXD P06 O44 SING N N 71 KXD O05 C04 SING N N 72 KXD C10 H1 SING N N 73 KXD C10 H2 SING N N 74 KXD C13 H3 SING N N 75 KXD C15 H4 SING N N 76 KXD C18 H5 SING N N 77 KXD C19 H6 SING N N 78 KXD C21 H7 SING N N 79 KXD C21 H8 SING N N 80 KXD C24 H9 SING N N 81 KXD C25 H10 SING N N 82 KXD C26 H11 SING N N 83 KXD C02 H12 SING N N 84 KXD C03 H13 SING N N 85 KXD C04 H14 SING N N 86 KXD C04 H15 SING N N 87 KXD C08 H16 SING N N 88 KXD C09 H17 SING N N 89 KXD C29 H18 SING N N 90 KXD C30 H19 SING N N 91 KXD C31 H20 SING N N 92 KXD C32 H21 SING N N 93 KXD C33 H22 SING N N 94 KXD C34 H23 SING N N 95 KXD C38 H24 SING N N 96 KXD C42 H25 SING N N 97 KXD C47 H26 SING N N 98 KXD C49 H27 SING N N 99 KXD C59 H28 SING N N 100 KXD N41 H29 SING N N 101 KXD N41 H30 SING N N 102 KXD N53 H31 SING N N 103 KXD N55 H32 SING N N 104 KXD N55 H33 SING N N 105 KXD O01 H34 SING N N 106 KXD O43 H35 SING N N 107 KXD O44 H36 SING N N 108 KXD O63 H37 SING N N 109 # 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 KXD InChI InChI 1.06 "InChI=1S/C38H37N9O14P2/c39-32-26-22(20-10-8-18(9-11-20)13-55-23-7-3-5-19-4-1-2-6-21(19)23)12-46(33(26)42-16-41-32)36-29(49)30-25(59-36)15-57-63(53,54)61-31-28(48)24(14-56-62(51,52)60-30)58-37(31)47-17-43-27-34(47)44-38(40)45-35(27)50/h1-12,16-17,24-25,28-31,36-37,48-49H,13-15H2,(H,51,52)(H,53,54)(H2,39,41,42)(H3,40,44,45,50)/t24-,25-,28-,29-,30-,31-,36-,37-/m1/s1" KXD InChIKey InChI 1.06 DBFLURMMWIAUJW-DANBCEJISA-N KXD SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)c2ncn([C@@H]3O[C@@H]4CO[P](O)(=O)O[C@H]5[C@@H](O)[C@@H](O[C@@H]5CO[P](O)(=O)O[C@@H]3[C@@H]4O)n6cc(c7ccc(COc8cccc9ccccc89)cc7)c%10c(N)ncnc6%10)c2N1" KXD SMILES CACTVS 3.385 "NC1=NC(=O)c2ncn([CH]3O[CH]4CO[P](O)(=O)O[CH]5[CH](O)[CH](O[CH]5CO[P](O)(=O)O[CH]3[CH]4O)n6cc(c7ccc(COc8cccc9ccccc89)cc7)c%10c(N)ncnc6%10)c2N1" KXD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc2c(c1)cccc2OCc3ccc(cc3)c4cn(c5c4c(ncn5)N)[C@H]6[C@@H]([C@H]7[C@H](O6)COP(=O)(O[C@@H]8[C@@H]([C@@H](COP(=O)(O7)O)O[C@H]8n9cnc1c9NC(=NC1=O)N)O)O)O" KXD SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc2c(c1)cccc2OCc3ccc(cc3)c4cn(c5c4c(ncn5)N)C6C(C7C(O6)COP(=O)(OC8C(C(COP(=O)(O7)O)OC8n9cnc1c9NC(=NC1=O)N)O)O)O" # _pdbx_chem_comp_identifier.comp_id KXD _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-azanyl-9-[(1~{R},6~{R},8~{R},9~{R},10~{S},15~{R},17~{R},18~{R})-8-[4-azanyl-5-[4-(naphthalen-1-yloxymethyl)phenyl]pyrrolo[2,3-d]pyrimidin-7-yl]-3,9,12,18-tetrakis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{6,10}]octadecan-17-yl]-3~{H}-purin-6-one" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site KXD "Create component" 2022-06-07 PDBE KXD "Modify descriptor" 2022-08-22 RCSB KXD "Initial release" 2022-10-12 RCSB #