data_YDD # _chem_comp.id YDD _chem_comp.name "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5S)-3,4-bis(oxidanyl)-5-tetradecoxy-oxolan-2-yl]methyl hydrogen phosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C29 H51 N5 O14 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-11-08 _chem_comp.pdbx_modified_date 2021-03-26 _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 755.688 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YDD _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 6L71 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # 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 YDD N N1 N 0 1 Y N N -19.661 14.929 -3.503 -2.926 -5.457 0.670 N YDD 1 YDD C C1 C 0 1 N N N -11.807 25.962 -15.113 15.421 -3.432 -0.474 C YDD 2 YDD O O1 O 0 1 N N N -13.226 13.557 -16.198 0.994 6.175 1.125 O YDD 3 YDD C1 C2 C 0 1 N N N -13.072 26.072 -15.934 14.193 -2.886 -1.205 C1 YDD 4 YDD C10 C3 C 0 1 N N N -13.150 16.721 -17.959 5.076 3.470 0.714 C10 YDD 5 YDD C11 C4 C 0 1 N N N -11.849 16.092 -17.552 3.848 4.016 -0.017 C11 YDD 6 YDD C12 C5 C 0 1 N N N -11.924 14.643 -17.970 3.007 4.850 0.952 C12 YDD 7 YDD C13 C6 C 0 1 N N N -11.932 13.768 -16.751 1.779 5.396 0.221 C13 YDD 8 YDD C14 C7 C 0 1 N N S -13.436 13.992 -14.857 -0.183 6.735 0.540 C14 YDD 9 YDD C15 C8 C 0 1 N N R -14.204 12.652 -13.108 -2.332 5.939 1.061 C15 YDD 10 YDD C16 C9 C 0 1 N N N -15.371 12.493 -12.160 -3.571 5.530 0.263 C16 YDD 11 YDD C17 C10 C 0 1 N N N -17.941 13.027 -6.913 -4.005 -1.906 -2.244 C17 YDD 12 YDD C18 C11 C 0 1 N N R -18.174 12.481 -5.521 -2.903 -2.880 -1.823 C18 YDD 13 YDD C19 C12 C 0 1 N N R -19.372 13.516 -3.808 -2.395 -4.606 -0.398 C19 YDD 14 YDD C2 C13 C 0 1 N N N -14.012 24.919 -15.613 13.352 -2.052 -0.236 C2 YDD 15 YDD C20 C14 C 0 1 N N R -20.391 12.764 -4.648 -2.573 -5.293 -1.770 C20 YDD 16 YDD C21 C15 C 0 1 N N S -19.521 11.786 -5.418 -2.914 -4.130 -2.730 C21 YDD 17 YDD C22 C16 C 0 1 Y N N -20.127 15.883 -4.323 -4.186 -5.408 1.189 C22 YDD 18 YDD C23 C17 C 0 1 Y N N -19.739 16.804 -2.394 -3.154 -6.987 2.259 C23 YDD 19 YDD C24 C18 C 0 1 Y N N -19.571 17.580 -1.263 -2.717 -8.040 3.081 C24 YDD 20 YDD C25 C19 C 0 1 Y N N -18.756 15.715 -0.098 -0.655 -7.943 2.048 C25 YDD 21 YDD C26 C20 C 0 1 Y N N -19.395 15.469 -2.322 -2.249 -6.452 1.328 C26 YDD 22 YDD C27 C21 C 0 1 N N S -13.124 13.581 -12.572 -2.342 7.466 1.325 C27 YDD 23 YDD C28 C22 C 0 1 N N R -12.326 13.717 -13.846 -0.826 7.743 1.516 C28 YDD 24 YDD C3 C23 C 0 1 N N N -14.859 24.543 -16.824 12.124 -1.505 -0.967 C3 YDD 25 YDD C4 C24 C 0 1 N N N -15.502 23.182 -16.602 11.283 -0.671 0.001 C4 YDD 26 YDD C5 C25 C 0 1 N N N -15.191 22.257 -17.767 10.055 -0.125 -0.729 C5 YDD 27 YDD C6 C26 C 0 1 N N N -15.521 20.823 -17.392 9.214 0.709 0.239 C6 YDD 28 YDD C7 C27 C 0 1 N N N -14.681 19.868 -18.215 7.986 1.255 -0.492 C7 YDD 29 YDD C8 C28 C 0 1 N N N -14.732 18.498 -17.570 7.145 2.089 0.477 C8 YDD 30 YDD C9 C29 C 0 1 N N N -13.355 17.995 -17.183 5.917 2.636 -0.254 C9 YDD 31 YDD N1 N2 N 0 1 Y N N -20.193 17.047 -3.638 -4.319 -6.309 2.118 N1 YDD 32 YDD N2 N3 N 0 1 N N N -19.890 18.889 -1.283 -3.564 -8.606 4.017 N2 YDD 33 YDD N3 N4 N 0 1 Y N N -19.079 17.016 -0.146 -1.470 -8.479 2.938 N3 YDD 34 YDD N4 N5 N 0 1 Y N N -18.905 14.942 -1.171 -1.021 -6.957 1.258 N4 YDD 35 YDD O1 O2 O 0 1 N N N -14.561 13.260 -14.349 -1.142 5.700 0.292 O1 YDD 36 YDD O10 O3 O 0 1 N N N -21.331 12.065 -3.831 -1.359 -5.932 -2.171 O10 YDD 37 YDD O11 O4 O 0 1 N N N -19.359 10.555 -4.706 -1.923 -4.017 -3.752 O11 YDD 38 YDD O12 O5 O 0 1 N N N -12.352 13.077 -11.493 -3.076 7.779 2.510 O12 YDD 39 YDD O13 O6 O 0 1 N N N -11.658 12.467 -14.007 -0.426 7.473 2.862 O13 YDD 40 YDD O2 O7 O 0 1 N N N -14.912 11.776 -11.016 -3.603 4.108 0.130 O2 YDD 41 YDD O3 O8 O 0 1 N N N -14.973 11.276 -8.460 -6.169 3.533 0.120 O3 YDD 42 YDD O4 O9 O 0 1 N N N -14.079 13.514 -9.334 -4.887 3.862 -2.029 O4 YDD 43 YDD O5 O10 O 0 1 N N N -16.507 13.126 -9.571 -4.421 1.757 -0.717 O5 YDD 44 YDD O6 O11 O 0 1 N N N -19.054 13.053 -9.841 -6.394 0.095 -1.222 O6 YDD 45 YDD O7 O12 O 0 1 N N N -17.637 10.946 -10.143 -4.909 0.971 -3.066 O7 YDD 46 YDD O8 O13 O 0 1 N N N -17.879 11.916 -7.797 -3.904 -0.708 -1.472 O8 YDD 47 YDD O9 O14 O 0 1 N N N -18.177 13.553 -4.584 -3.159 -3.385 -0.494 O9 YDD 48 YDD P P1 P 0 1 N N N -15.071 12.440 -9.561 -4.773 3.326 -0.654 P YDD 49 YDD P1 P2 P 0 1 N N N -17.789 12.201 -9.368 -4.907 0.538 -1.650 P1 YDD 50 YDD H9 H1 H 0 1 N N N -11.138 26.801 -15.355 16.018 -2.602 -0.096 H9 YDD 51 YDD H10 H2 H 0 1 N N N -12.061 25.993 -14.043 15.100 -4.057 0.360 H10 YDD 52 YDD H11 H3 H 0 1 N N N -11.302 25.012 -15.343 16.020 -4.026 -1.164 H11 YDD 53 YDD H12 H4 H 0 1 N N N -12.814 26.043 -17.003 14.514 -2.261 -2.038 H12 YDD 54 YDD H13 H5 H 0 1 N N N -13.573 27.024 -15.703 13.596 -3.716 -1.582 H13 YDD 55 YDD H30 H6 H 0 1 N N N -13.127 16.947 -19.035 5.674 4.300 1.092 H30 YDD 56 YDD H31 H7 H 0 1 N N N -13.976 16.026 -17.747 4.755 2.845 1.548 H31 YDD 57 YDD H33 H8 H 0 1 N N N -11.715 16.167 -16.463 4.169 4.641 -0.850 H33 YDD 58 YDD H32 H9 H 0 1 N N N -11.010 16.591 -18.060 3.251 3.186 -0.394 H32 YDD 59 YDD H34 H10 H 0 1 N N N -12.845 14.476 -18.547 2.686 4.225 1.785 H34 YDD 60 YDD H35 H11 H 0 1 N N N -11.051 14.396 -18.593 3.605 5.680 1.329 H35 YDD 61 YDD H131 H12 H 0 0 N N N -11.509 12.790 -17.025 1.182 4.566 -0.157 H131 YDD 62 YDD H132 H13 H 0 0 N N N -11.300 14.239 -15.983 2.101 6.021 -0.613 H132 YDD 63 YDD H H14 H 0 1 N N N -13.659 15.069 -14.845 0.071 7.235 -0.395 H YDD 64 YDD H1 H15 H 0 1 N N N -13.758 11.663 -13.290 -2.292 5.393 2.003 H1 YDD 65 YDD H36 H16 H 0 1 N N N -15.743 13.483 -11.856 -4.467 5.867 0.785 H36 YDD 66 YDD H37 H17 H 0 1 N N N -16.179 11.933 -12.653 -3.534 5.986 -0.726 H37 YDD 67 YDD H40 H18 H 0 1 N N N -16.994 13.587 -6.944 -3.894 -1.667 -3.302 H40 YDD 68 YDD H41 H19 H 0 1 N N N -18.769 13.691 -7.201 -4.979 -2.365 -2.076 H41 YDD 69 YDD H2 H20 H 0 1 N N N -17.379 11.761 -5.278 -1.929 -2.391 -1.864 H2 YDD 70 YDD H3 H21 H 0 1 N N N -19.202 12.964 -2.872 -1.343 -4.385 -0.218 H3 YDD 71 YDD H15 H22 H 0 1 N N N -14.677 25.217 -14.789 13.031 -2.677 0.597 H15 YDD 72 YDD H14 H23 H 0 1 N N N -13.417 24.046 -15.307 13.949 -1.222 0.141 H14 YDD 73 YDD H4 H24 H 0 1 N N N -20.894 13.453 -5.342 -3.389 -6.013 -1.734 H4 YDD 74 YDD H5 H25 H 0 1 N N N -19.938 11.618 -6.422 -3.901 -4.274 -3.170 H5 YDD 75 YDD H44 H26 H 0 1 N N N -20.403 15.744 -5.358 -4.959 -4.723 0.874 H44 YDD 76 YDD H47 H27 H 0 1 N N N -18.372 15.292 0.818 0.350 -8.330 1.965 H47 YDD 77 YDD H6 H28 H 0 1 N N N -13.573 14.551 -12.313 -2.736 8.011 0.467 H6 YDD 78 YDD H7 H29 H 0 1 N N N -11.627 14.564 -13.789 -0.580 8.767 1.235 H7 YDD 79 YDD H16 H30 H 0 1 N N N -14.220 24.503 -17.718 12.445 -0.881 -1.800 H16 YDD 80 YDD H17 H31 H 0 1 N N N -15.645 25.299 -16.969 11.527 -2.336 -1.344 H17 YDD 81 YDD H18 H32 H 0 1 N N N -16.592 23.305 -16.517 10.962 -1.296 0.835 H18 YDD 82 YDD H19 H33 H 0 1 N N N -15.109 22.742 -15.674 11.880 0.159 0.379 H19 YDD 83 YDD H21 H34 H 0 1 N N N -14.122 22.332 -18.017 10.376 0.500 -1.563 H21 YDD 84 YDD H20 H35 H 0 1 N N N -15.793 22.554 -18.639 9.458 -0.955 -1.107 H20 YDD 85 YDD H22 H36 H 0 1 N N N -16.587 20.631 -17.586 8.893 0.084 1.072 H22 YDD 86 YDD H23 H37 H 0 1 N N N -15.309 20.667 -16.324 9.811 1.539 0.616 H23 YDD 87 YDD H25 H38 H 0 1 N N N -13.641 20.224 -18.247 8.307 1.880 -1.325 H25 YDD 88 YDD H24 H39 H 0 1 N N N -15.081 19.811 -19.238 7.389 0.425 -0.869 H24 YDD 89 YDD H27 H40 H 0 1 N N N -15.355 18.555 -16.665 6.824 1.465 1.310 H27 YDD 90 YDD H26 H41 H 0 1 N N N -15.181 17.789 -18.280 7.742 2.920 0.854 H26 YDD 91 YDD H29 H42 H 0 1 N N N -13.310 17.796 -16.102 5.320 1.805 -0.632 H29 YDD 92 YDD H28 H43 H 0 1 N N N -12.587 18.735 -17.452 6.238 3.260 -1.088 H28 YDD 93 YDD H46 H44 H 0 1 N N N -19.700 19.293 -0.388 -4.471 -8.278 4.112 H46 YDD 94 YDD H45 H45 H 0 1 N N N -19.345 19.354 -1.981 -3.250 -9.333 4.578 H45 YDD 95 YDD H42 H46 H 0 1 N N N -21.866 12.691 -3.357 -1.415 -6.379 -3.027 H42 YDD 96 YDD H43 H47 H 0 1 N N N -20.198 10.115 -4.638 -1.886 -4.776 -4.351 H43 YDD 97 YDD H48 H48 H 0 1 N N N -12.840 13.170 -10.683 -3.110 8.724 2.715 H48 YDD 98 YDD H49 H49 H 0 1 N N N -10.987 12.378 -13.341 0.527 7.547 3.011 H49 YDD 99 YDD H38 H50 H 0 1 N N N -14.282 11.482 -7.841 -6.167 3.204 1.030 H38 YDD 100 YDD H39 H51 H 0 1 N N N -19.496 12.599 -10.549 -6.468 -0.201 -0.305 H39 YDD 101 # # 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 YDD C7 C8 SING N N 1 YDD C7 C6 SING N N 2 YDD C12 C11 SING N N 3 YDD C12 C13 SING N N 4 YDD C10 C11 SING N N 5 YDD C10 C9 SING N N 6 YDD C5 C6 SING N N 7 YDD C5 C4 SING N N 8 YDD C8 C9 SING N N 9 YDD C3 C4 SING N N 10 YDD C3 C2 SING N N 11 YDD C13 O SING N N 12 YDD O C14 SING N N 13 YDD C1 C2 SING N N 14 YDD C1 C SING N N 15 YDD C14 O1 SING N N 16 YDD C14 C28 SING N N 17 YDD O1 C15 SING N N 18 YDD O13 C28 SING N N 19 YDD C28 C27 SING N N 20 YDD C15 C27 SING N N 21 YDD C15 C16 SING N N 22 YDD C27 O12 SING N N 23 YDD C16 O2 SING N N 24 YDD O2 P SING N N 25 YDD O7 P1 DOUB N N 26 YDD O6 P1 SING N N 27 YDD O5 P SING N N 28 YDD O5 P1 SING N N 29 YDD P O4 DOUB N N 30 YDD P O3 SING N N 31 YDD P1 O8 SING N N 32 YDD O8 C17 SING N N 33 YDD C17 C18 SING N N 34 YDD C18 C21 SING N N 35 YDD C18 O9 SING N N 36 YDD C21 O11 SING N N 37 YDD C21 C20 SING N N 38 YDD C20 O10 SING N N 39 YDD C20 C19 SING N N 40 YDD O9 C19 SING N N 41 YDD C22 N1 DOUB Y N 42 YDD C22 N SING Y N 43 YDD C19 N SING N N 44 YDD N1 C23 SING Y N 45 YDD N C26 SING Y N 46 YDD C23 C26 DOUB Y N 47 YDD C23 C24 SING Y N 48 YDD C26 N4 SING Y N 49 YDD N2 C24 SING N N 50 YDD C24 N3 DOUB Y N 51 YDD N4 C25 DOUB Y N 52 YDD N3 C25 SING Y N 53 YDD C H9 SING N N 54 YDD C H10 SING N N 55 YDD C H11 SING N N 56 YDD C1 H12 SING N N 57 YDD C1 H13 SING N N 58 YDD C10 H30 SING N N 59 YDD C10 H31 SING N N 60 YDD C11 H33 SING N N 61 YDD C11 H32 SING N N 62 YDD C12 H34 SING N N 63 YDD C12 H35 SING N N 64 YDD C13 H131 SING N N 65 YDD C13 H132 SING N N 66 YDD C14 H SING N N 67 YDD C15 H1 SING N N 68 YDD C16 H36 SING N N 69 YDD C16 H37 SING N N 70 YDD C17 H40 SING N N 71 YDD C17 H41 SING N N 72 YDD C18 H2 SING N N 73 YDD C19 H3 SING N N 74 YDD C2 H15 SING N N 75 YDD C2 H14 SING N N 76 YDD C20 H4 SING N N 77 YDD C21 H5 SING N N 78 YDD C22 H44 SING N N 79 YDD C25 H47 SING N N 80 YDD C27 H6 SING N N 81 YDD C28 H7 SING N N 82 YDD C3 H16 SING N N 83 YDD C3 H17 SING N N 84 YDD C4 H18 SING N N 85 YDD C4 H19 SING N N 86 YDD C5 H21 SING N N 87 YDD C5 H20 SING N N 88 YDD C6 H22 SING N N 89 YDD C6 H23 SING N N 90 YDD C7 H25 SING N N 91 YDD C7 H24 SING N N 92 YDD C8 H27 SING N N 93 YDD C8 H26 SING N N 94 YDD C9 H29 SING N N 95 YDD C9 H28 SING N N 96 YDD N2 H46 SING N N 97 YDD N2 H45 SING N N 98 YDD O10 H42 SING N N 99 YDD O11 H43 SING N N 100 YDD O12 H48 SING N N 101 YDD O13 H49 SING N N 102 YDD O3 H38 SING N N 103 YDD O6 H39 SING N N 104 # # 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 YDD InChI InChI 1.03 "InChI=1S/C29H51N5O14P2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-43-29-25(38)23(36)20(47-29)16-45-50(41,42)48-49(39,40)44-15-19-22(35)24(37)28(46-19)34-18-33-21-26(30)31-17-32-27(21)34/h17-20,22-25,28-29,35-38H,2-16H2,1H3,(H,39,40)(H,41,42)(H2,30,31,32)/t19-,20-,22-,23-,24-,25-,28-,29+/m1/s1" YDD InChIKey InChI 1.03 XDVQERDQBQWVRC-UHUMEYFMSA-N YDD SMILES_CANONICAL CACTVS 3.385 "CCCCCCCCCCCCCCO[C@H]1O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34)[C@@H](O)[C@H]1O" YDD SMILES CACTVS 3.385 "CCCCCCCCCCCCCCO[CH]1O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34)[CH](O)[CH]1O" YDD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCCCCCCCCCCCCCO[C@@H]1[C@@H]([C@@H]([C@H](O1)COP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)O)O" YDD SMILES "OpenEye OEToolkits" 2.0.7 "CCCCCCCCCCCCCCOC1C(C(C(O1)COP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)O)O" # _pdbx_chem_comp_identifier.comp_id YDD _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~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{S})-3,4-bis(oxidanyl)-5-tetradecoxy-oxolan-2-yl]methyl hydrogen phosphate" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YDD "Create component" 2019-11-08 PDBJ YDD "Initial release" 2021-03-31 RCSB ##