data_A1D88 # _chem_comp.id A1D88 _chem_comp.name "S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] (E)-but-2-enethioate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C25 H40 N7 O17 P3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "crotonoyl-CoA ; crotonyl-coenzyme A " _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2024-06-12 _chem_comp.pdbx_modified_date 2025-04-25 _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 835.608 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1D88 _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 8ZRY _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBC _chem_comp.pdbx_pcm ? # 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_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_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 A1D88 P23 P1 P 0 1 N N N N N N 115.743 77.450 75.451 -0.893 -3.457 -1.694 P23 A1D88 1 A1D88 P27 P2 P 0 1 N N N N N N 117.186 75.621 77.234 -3.702 -2.523 -1.551 P27 A1D88 2 A1D88 P49 P3 P 0 1 N N N N N N 120.648 71.652 79.883 -9.002 -1.816 2.018 P49 A1D88 3 A1D88 C01 C1 C 0 1 N N N N N N 114.617 85.135 93.010 17.593 4.913 -0.440 C01 A1D88 4 A1D88 C02 C2 C 0 1 N N N N N N 114.876 84.293 91.774 16.399 4.051 -0.761 C02 A1D88 5 A1D88 C03 C3 C 0 1 N N N N N N 113.872 83.865 91.094 15.566 3.682 0.208 C03 A1D88 6 A1D88 C04 C4 C 0 1 N N N N N N 114.177 83.043 89.871 14.401 2.840 -0.105 C04 A1D88 7 A1D88 O05 O1 O 0 1 N N N N N N 114.903 83.440 89.053 14.199 2.482 -1.251 O05 A1D88 8 A1D88 S06 S1 S 0 1 N N N N N N 113.399 81.419 89.607 13.297 2.351 1.178 S06 A1D88 9 A1D88 C07 C5 C 0 1 N N N N N N 113.846 80.857 87.935 12.114 1.372 0.219 C07 A1D88 10 A1D88 C08 C6 C 0 1 N N N N N N 113.105 81.759 86.958 11.030 0.827 1.150 C08 A1D88 11 A1D88 N09 N1 N 0 1 N N N N N N 113.727 81.725 85.667 10.073 0.035 0.374 N09 A1D88 12 A1D88 C10 C7 C 0 1 N N N N N N 113.119 80.834 84.697 9.024 -0.548 0.989 C10 A1D88 13 A1D88 O11 O2 O 0 1 N N N N N N 112.151 80.195 84.962 8.873 -0.416 2.185 O11 A1D88 14 A1D88 C12 C8 C 0 1 N N N N N N 113.734 80.764 83.295 8.040 -1.363 0.191 C12 A1D88 15 A1D88 C13 C9 C 0 1 N N N N N N 114.157 79.323 83.103 6.955 -1.908 1.122 C13 A1D88 16 A1D88 N14 N2 N 0 1 N N N N N N 114.748 79.068 81.787 5.998 -2.700 0.346 N14 A1D88 17 A1D88 C15 C10 C 0 1 N N N N N N 113.904 78.825 80.649 4.950 -3.282 0.961 C15 A1D88 18 A1D88 O16 O3 O 0 1 N N N N N N 112.745 78.848 80.772 4.849 -3.229 2.169 O16 A1D88 19 A1D88 C17 C11 C 0 1 N N R N N N 114.512 78.544 79.252 3.902 -4.000 0.149 C17 A1D88 20 A1D88 C18 C12 C 0 1 N N N N N N 114.786 79.834 78.388 2.612 -3.178 0.142 C18 A1D88 21 A1D88 C19 C13 C 0 1 N N N N N N 113.443 80.456 78.027 2.032 -3.128 1.556 C19 A1D88 22 A1D88 C20 C14 C 0 1 N N N N N N 115.652 80.891 79.147 2.914 -1.757 -0.337 C20 A1D88 23 A1D88 C21 C15 C 0 1 N N N N N N 115.498 79.471 77.073 1.598 -3.829 -0.802 C21 A1D88 24 A1D88 O22 O4 O 0 1 N N N N N N 114.920 78.306 76.579 0.393 -3.062 -0.808 O22 A1D88 25 A1D88 O24 O5 O 0 1 N N N N N N 116.214 78.377 74.362 -1.301 -4.845 -1.380 O24 A1D88 26 A1D88 O25 O6 O 0 1 N N N N N N 114.879 76.371 74.903 -0.523 -3.347 -3.257 O25 A1D88 27 A1D88 O26 O7 O 0 1 N N N N N N 117.065 76.772 76.089 -2.105 -2.453 -1.357 O26 A1D88 28 A1D88 O28 O8 O 0 1 N N N N N N 117.748 74.402 76.567 -4.194 -3.850 -1.119 O28 A1D88 29 A1D88 O29 O9 O 0 1 N N N N N N 115.947 75.255 77.948 -4.065 -2.295 -3.103 O29 A1D88 30 A1D88 O30 O10 O 0 1 N N N N N N 118.375 76.166 78.190 -4.401 -1.376 -0.663 O30 A1D88 31 A1D88 C31 C16 C 0 1 N N N N N N 119.635 75.809 77.769 -5.819 -1.243 -0.539 C31 A1D88 32 A1D88 C32 C17 C 0 1 N N R N N N 120.339 75.279 79.024 -6.142 -0.058 0.373 C32 A1D88 33 A1D88 C33 C18 C 0 1 N N S N N N 119.531 74.062 79.612 -7.664 0.029 0.622 C33 A1D88 34 A1D88 C34 C19 C 0 1 N N R N N N 118.747 74.689 80.746 -7.955 1.546 0.644 C34 A1D88 35 A1D88 C35 C20 C 0 1 N N R N N N 119.621 75.564 81.256 -6.575 2.197 0.405 C35 A1D88 36 A1D88 O36 O11 O 0 1 N N N N N N 120.239 76.224 79.919 -5.804 1.185 -0.280 O36 A1D88 37 A1D88 N37 N3 N 0 1 Y N N N N N 118.874 76.592 82.004 -6.711 3.389 -0.435 N37 A1D88 38 A1D88 C38 C21 C 0 1 Y N N N N N 118.102 77.537 81.481 -6.563 3.444 -1.789 C38 A1D88 39 A1D88 N39 N4 N 0 1 Y N N N N N 117.583 78.259 82.444 -6.754 4.661 -2.208 N39 A1D88 40 A1D88 C40 C22 C 0 1 Y N N N N N 118.017 77.774 83.598 -7.036 5.462 -1.153 C40 A1D88 41 A1D88 C41 C23 C 0 1 Y N N N N N 117.816 78.082 84.948 -7.324 6.829 -0.999 C41 A1D88 42 A1D88 N42 N5 N 0 1 Y N N N N N 118.423 77.347 85.818 -7.560 7.293 0.223 N42 A1D88 43 A1D88 C43 C24 C 0 1 Y N N N N N 119.200 76.326 85.503 -7.526 6.496 1.276 C43 A1D88 44 A1D88 N44 N6 N 0 1 Y N N N N N 119.429 75.995 84.254 -7.260 5.210 1.180 N44 A1D88 45 A1D88 C45 C25 C 0 1 Y N N N N N 118.845 76.695 83.308 -7.018 4.655 -0.004 C45 A1D88 46 A1D88 N46 N7 N 0 1 N N N N N N 116.986 79.175 85.408 -7.361 7.673 -2.096 N46 A1D88 47 A1D88 O47 O12 O 0 1 N N N N N N 118.302 73.735 81.631 -8.480 1.937 1.914 O47 A1D88 48 A1D88 O48 O13 O 0 1 N N N N N N 120.467 73.230 80.245 -8.000 -0.563 1.879 O48 A1D88 49 A1D88 O50 O14 O 0 1 N N N N N N 119.344 70.921 79.988 -9.047 -2.300 3.553 O50 A1D88 50 A1D88 O51 O15 O 0 1 N N N N N N 121.640 71.109 80.855 -10.479 -1.376 1.551 O51 A1D88 51 A1D88 O52 O16 O 0 1 N N N N N N 121.150 71.531 78.476 -8.526 -2.926 1.164 O52 A1D88 52 A1D88 O53 O17 O 0 1 N N N N N N 115.655 77.792 79.458 4.370 -4.164 -1.192 O53 A1D88 53 A1D88 H1 H1 H 0 1 N N N N N N 115.576 85.416 93.470 18.154 5.111 -1.353 H1 A1D88 54 A1D88 H2 H2 H 0 1 N N N N N N 114.066 86.044 92.726 17.255 5.856 -0.009 H2 A1D88 55 A1D88 H3 H3 H 0 1 N N N N N N 114.021 84.555 93.730 18.233 4.396 0.275 H3 A1D88 56 A1D88 H4 H4 H 0 1 N N N N N N 115.886 84.058 91.471 16.220 3.733 -1.777 H4 A1D88 57 A1D88 H5 H5 H 0 1 N N N N N N 112.856 84.085 91.387 15.745 3.999 1.224 H5 A1D88 58 A1D88 H6 H6 H 0 1 N N N N N N 113.539 79.810 87.792 11.656 2.001 -0.544 H6 A1D88 59 A1D88 H7 H7 H 0 1 N N N N N N 114.932 80.945 87.783 12.634 0.542 -0.260 H7 A1D88 60 A1D88 H8 H8 H 0 1 N N N N N N 113.118 82.791 87.338 11.488 0.197 1.913 H8 A1D88 61 A1D88 H9 H9 H 0 1 N N N N N N 112.064 81.415 86.867 10.511 1.657 1.629 H9 A1D88 62 A1D88 H10 H10 H 0 1 N N N N N N 114.529 82.280 85.449 10.193 -0.071 -0.583 H10 A1D88 63 A1D88 H11 H11 H 0 1 N N N N N N 114.605 81.432 83.225 7.581 -0.733 -0.572 H11 A1D88 64 A1D88 H12 H12 H 0 1 N N N N N N 112.991 81.050 82.536 8.559 -2.193 -0.288 H12 A1D88 65 A1D88 H13 H13 H 0 1 N N N N N N 113.272 78.680 83.220 7.414 -2.537 1.885 H13 A1D88 66 A1D88 H14 H14 H 0 1 N N N N N N 114.899 79.070 83.875 6.436 -1.077 1.601 H14 A1D88 67 A1D88 H15 H15 H 0 1 N N N N N N 115.742 79.063 81.680 6.119 -2.805 -0.611 H15 A1D88 68 A1D88 H16 H16 H 0 1 N N N N N N 113.779 77.941 78.697 3.708 -4.978 0.589 H16 A1D88 69 A1D88 H17 H17 H 0 1 N N N N N N 112.905 80.729 78.947 1.073 -2.609 1.538 H17 A1D88 70 A1D88 H18 H18 H 0 1 N N N N N N 113.608 81.357 77.418 1.889 -4.143 1.927 H18 A1D88 71 A1D88 H19 H19 H 0 1 N N N N N N 112.846 79.731 77.454 2.720 -2.595 2.212 H19 A1D88 72 A1D88 H20 H20 H 0 1 N N N N N N 115.157 81.162 80.091 3.327 -1.793 -1.345 H20 A1D88 73 A1D88 H21 H21 H 0 1 N N N N N N 116.644 80.466 79.362 1.994 -1.172 -0.342 H21 A1D88 74 A1D88 H22 H22 H 0 1 N N N N N N 115.766 81.789 78.522 3.636 -1.293 0.335 H22 A1D88 75 A1D88 H23 H23 H 0 1 N N N N N N 116.569 79.305 77.262 2.011 -3.865 -1.810 H23 A1D88 76 A1D88 H24 H24 H 0 1 N N N N N N 115.376 80.286 76.345 1.383 -4.842 -0.461 H24 A1D88 77 A1D88 H25 H25 H 0 1 N N N N N N 114.793 76.480 73.963 -0.247 -2.463 -3.534 H25 A1D88 78 A1D88 H26 H26 H 0 1 N N N N N N 115.775 74.328 77.830 -3.771 -1.443 -3.455 H26 A1D88 79 A1D88 H27 H27 H 0 1 N N N N N N 119.578 75.026 76.998 -6.255 -1.074 -1.523 H27 A1D88 80 A1D88 H28 H28 H 0 1 N N N N N N 120.169 76.682 77.366 -6.233 -2.156 -0.109 H28 A1D88 81 A1D88 H29 H29 H 0 1 N N N N N N 121.370 74.974 78.793 -5.607 -0.150 1.318 H29 A1D88 82 A1D88 H30 H30 H 0 1 N N N N N N 118.897 73.573 78.858 -8.212 -0.456 -0.186 H30 A1D88 83 A1D88 H31 H31 H 0 1 N N N N N N 117.888 75.219 80.309 -8.647 1.814 -0.155 H31 A1D88 84 A1D88 H32 H32 H 0 1 N N N N N N 120.421 75.111 81.860 -6.107 2.454 1.355 H32 A1D88 85 A1D88 H33 H33 H 0 1 N N N N N N 117.929 77.688 80.426 -6.323 2.601 -2.420 H33 A1D88 86 A1D88 H34 H34 H 0 1 N N N N N N 119.658 75.749 86.293 -7.723 6.914 2.251 H34 A1D88 87 A1D88 H35 H35 H 0 1 N N N N N N 117.002 79.208 86.407 -7.187 7.322 -2.984 H35 A1D88 88 A1D88 H36 H36 H 0 1 N N N N N N 117.336 80.037 85.040 -7.561 8.615 -1.977 H36 A1D88 89 A1D88 H37 H37 H 0 1 N N N N N N 117.815 74.154 82.331 -8.681 2.881 1.983 H37 A1D88 90 A1D88 H38 H38 H 0 1 N N N N N N 119.123 70.544 79.145 -9.632 -3.053 3.711 H38 A1D88 91 A1D88 H39 H39 H 0 1 N N N N N N 122.402 70.790 80.386 -10.855 -0.650 2.068 H39 A1D88 92 A1D88 H40 H40 H 0 1 N N N N N N 115.442 77.028 79.981 4.563 -3.333 -1.646 H40 A1D88 93 # 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 A1D88 O24 P23 DOUB N N 1 A1D88 O25 P23 SING N N 2 A1D88 P23 O26 SING N N 3 A1D88 P23 O22 SING N N 4 A1D88 O26 P27 SING N N 5 A1D88 O28 P27 DOUB N N 6 A1D88 O22 C21 SING N N 7 A1D88 C21 C18 SING N N 8 A1D88 P27 O29 SING N N 9 A1D88 P27 O30 SING N N 10 A1D88 C31 O30 SING N N 11 A1D88 C31 C32 SING N N 12 A1D88 C19 C18 SING N N 13 A1D88 C18 C20 SING N N 14 A1D88 C18 C17 SING N N 15 A1D88 O52 P49 DOUB N N 16 A1D88 C32 C33 SING N N 17 A1D88 C32 O36 SING N N 18 A1D88 C17 O53 SING N N 19 A1D88 C17 C15 SING N N 20 A1D88 C33 O48 SING N N 21 A1D88 C33 C34 SING N N 22 A1D88 P49 O50 SING N N 23 A1D88 P49 O48 SING N N 24 A1D88 P49 O51 SING N N 25 A1D88 O36 C35 SING N N 26 A1D88 C15 O16 DOUB N N 27 A1D88 C15 N14 SING N N 28 A1D88 C34 C35 SING N N 29 A1D88 C34 O47 SING N N 30 A1D88 C35 N37 SING N N 31 A1D88 C38 N37 SING Y N 32 A1D88 C38 N39 DOUB Y N 33 A1D88 N14 C13 SING N N 34 A1D88 N37 C45 SING Y N 35 A1D88 N39 C40 SING Y N 36 A1D88 C13 C12 SING N N 37 A1D88 C12 C10 SING N N 38 A1D88 C45 C40 DOUB Y N 39 A1D88 C45 N44 SING Y N 40 A1D88 C40 C41 SING Y N 41 A1D88 N44 C43 DOUB Y N 42 A1D88 C10 O11 DOUB N N 43 A1D88 C10 N09 SING N N 44 A1D88 C41 N46 SING N N 45 A1D88 C41 N42 DOUB Y N 46 A1D88 C43 N42 SING Y N 47 A1D88 N09 C08 SING N N 48 A1D88 C08 C07 SING N N 49 A1D88 C07 S06 SING N N 50 A1D88 O05 C04 DOUB N N 51 A1D88 S06 C04 SING N N 52 A1D88 C04 C03 SING N N 53 A1D88 C03 C02 DOUB N E 54 A1D88 C02 C01 SING N N 55 A1D88 C01 H1 SING N N 56 A1D88 C01 H2 SING N N 57 A1D88 C01 H3 SING N N 58 A1D88 C02 H4 SING N N 59 A1D88 C03 H5 SING N N 60 A1D88 C07 H6 SING N N 61 A1D88 C07 H7 SING N N 62 A1D88 C08 H8 SING N N 63 A1D88 C08 H9 SING N N 64 A1D88 N09 H10 SING N N 65 A1D88 C12 H11 SING N N 66 A1D88 C12 H12 SING N N 67 A1D88 C13 H13 SING N N 68 A1D88 C13 H14 SING N N 69 A1D88 N14 H15 SING N N 70 A1D88 C17 H16 SING N N 71 A1D88 C19 H17 SING N N 72 A1D88 C19 H18 SING N N 73 A1D88 C19 H19 SING N N 74 A1D88 C20 H20 SING N N 75 A1D88 C20 H21 SING N N 76 A1D88 C20 H22 SING N N 77 A1D88 C21 H23 SING N N 78 A1D88 C21 H24 SING N N 79 A1D88 O25 H25 SING N N 80 A1D88 O29 H26 SING N N 81 A1D88 C31 H27 SING N N 82 A1D88 C31 H28 SING N N 83 A1D88 C32 H29 SING N N 84 A1D88 C33 H30 SING N N 85 A1D88 C34 H31 SING N N 86 A1D88 C35 H32 SING N N 87 A1D88 C38 H33 SING N N 88 A1D88 C43 H34 SING N N 89 A1D88 N46 H35 SING N N 90 A1D88 N46 H36 SING N N 91 A1D88 O47 H37 SING N N 92 A1D88 O50 H38 SING N N 93 A1D88 O51 H39 SING N N 94 A1D88 O53 H40 SING N N 95 # 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 A1D88 InChI InChI 1.06 "InChI=1S/C25H40N7O17P3S/c1-4-5-16(34)53-9-8-27-15(33)6-7-28-23(37)20(36)25(2,3)11-46-52(43,44)49-51(41,42)45-10-14-19(48-50(38,39)40)18(35)24(47-14)32-13-31-17-21(26)29-12-30-22(17)32/h4-5,12-14,18-20,24,35-36H,6-11H2,1-3H3,(H,27,33)(H,28,37)(H,41,42)(H,43,44)(H2,26,29,30)(H2,38,39,40)/b5-4+/t14-,18-,19-,20+,24-/m1/s1" A1D88 InChIKey InChI 1.06 KFWWCMJSYSSPSK-PAXLJYGASA-N A1D88 SMILES_CANONICAL CACTVS 3.385 "C/C=C/C(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23" A1D88 SMILES CACTVS 3.385 "CC=CC(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23" A1D88 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C/C=C/C(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O" A1D88 SMILES "OpenEye OEToolkits" 2.0.7 "CC=CC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O" # _pdbx_chem_comp_identifier.comp_id A1D88 _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 "~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] (~{E})-but-2-enethioate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1D88 "Create component" 2024-06-12 PDBC A1D88 "Initial release" 2025-04-30 RCSB # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 A1D88 "crotonoyl-CoA " PUBCHEM ? 2 A1D88 "crotonyl-coenzyme A " PUBCHEM ? #