data_H5L # _chem_comp.id H5L _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)-3-[3,4-bis(oxidanyl)phenyl]prop-2-enethioate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C30 H42 N7 O19 P3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms Caffeoyl-CoA _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-11-13 _chem_comp.pdbx_modified_date 2021-09-10 _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 929.676 _chem_comp.one_letter_code ? _chem_comp.three_letter_code H5L _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 7DEX _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 H5L N1A N1 N 0 1 Y N N 10.167 -26.652 -51.647 -7.572 7.559 2.643 N1A H5L 1 H5L C2A C1 C 0 1 Y N N 8.885 -27.213 -51.518 -8.222 6.478 3.033 C2A H5L 2 H5L N3A N2 N 0 1 Y N N 8.573 -27.906 -50.331 -8.089 5.316 2.428 N3A H5L 3 H5L C4A C2 C 0 1 Y N N 9.509 -28.024 -49.347 -7.280 5.187 1.382 C4A H5L 4 H5L C5A C3 C 0 1 Y N N 10.719 -27.472 -49.515 -6.565 6.308 0.928 C5A H5L 5 H5L C6A C4 C 0 1 Y N N 11.045 -26.805 -50.631 -6.741 7.526 1.607 C6A H5L 6 H5L N6A N3 N 0 1 N N N 12.277 -26.301 -50.689 -6.064 8.665 1.206 N6A H5L 7 H5L N7A N4 N 0 1 Y N N 11.446 -27.725 -48.414 -5.827 5.908 -0.135 N7A H5L 8 H5L C8A C5 C 0 1 Y N N 10.687 -28.425 -47.576 -6.037 4.643 -0.357 C8A H5L 9 H5L N9A N5 N 0 1 Y N N 9.489 -28.624 -48.142 -6.926 4.153 0.552 N9A H5L 10 H5L C1B C6 C 0 1 N N R 8.430 -29.392 -47.345 -7.415 2.773 0.630 C1B H5L 11 H5L C2B C7 C 0 1 N N R 8.176 -30.878 -47.700 -8.713 2.616 -0.192 C2B H5L 12 H5L O2B O1 O 0 1 N N N 7.389 -31.006 -48.911 -9.858 2.686 0.661 O2B H5L 13 H5L C3B C8 C 0 1 N N S 7.484 -31.387 -46.360 -8.592 1.210 -0.820 C3B H5L 14 H5L O3B O2 O 0 1 N N N 6.130 -32.050 -46.491 -9.657 0.368 -0.374 O3B H5L 15 H5L P3B P1 P 0 1 N N N 4.588 -31.423 -46.253 -10.699 -0.335 -1.380 P3B H5L 16 H5L O7A O3 O 0 1 N N N 3.633 -32.702 -45.951 -9.919 -1.396 -2.306 O7A H5L 17 H5L O8A O4 O 0 1 N N N 4.525 -30.613 -44.849 -11.835 -1.097 -0.531 O8A H5L 18 H5L O9A O5 O 0 1 N N N 4.077 -30.646 -47.412 -11.330 0.695 -2.236 O9A H5L 19 H5L C4B C9 C 0 1 N N R 7.551 -30.112 -45.468 -7.234 0.684 -0.304 C4B H5L 20 H5L O4B O6 O 0 1 N N N 8.780 -29.509 -45.936 -6.474 1.871 0.009 O4B H5L 21 H5L C5B C10 C 0 1 N N N 7.612 -30.374 -43.948 -6.529 -0.129 -1.391 C5B H5L 22 H5L O5B O7 O 0 1 N N N 8.305 -29.253 -43.344 -5.334 -0.702 -0.858 O5B H5L 23 H5L P1A P2 P 0 1 N N N 8.200 -28.856 -41.765 -4.340 -1.624 -1.727 P1A H5L 24 H5L O1A O8 O 0 1 N N N 6.804 -29.509 -41.244 -5.099 -2.750 -2.315 O1A H5L 25 H5L O2A O9 O 0 1 N N N 9.373 -29.310 -40.968 -3.686 -0.744 -2.906 O2A H5L 26 H5L O3A O10 O 0 1 N N N 8.021 -27.225 -41.644 -3.174 -2.200 -0.777 O3A H5L 27 H5L P2A P3 P 0 1 N N N 6.757 -26.370 -42.224 -2.087 -3.377 -0.930 P2A H5L 28 H5L O4A O11 O 0 1 N N N 5.458 -27.344 -42.375 -0.851 -2.855 -1.819 O4A H5L 29 H5L O5A O12 O 0 1 N N N 7.064 -25.590 -43.439 -2.713 -4.544 -1.592 O5A H5L 30 H5L O6A O13 O 0 1 N N N 6.370 -25.346 -41.072 -1.555 -3.809 0.527 O6A H5L 31 H5L CBP C11 C 0 1 N N N 7.231 -24.471 -39.045 -0.358 -5.036 2.231 CBP H5L 32 H5L CCP C12 C 0 1 N N N 7.372 -24.477 -40.553 -0.659 -4.902 0.736 CCP H5L 33 H5L CDP C13 C 0 1 N N N 5.811 -24.928 -38.676 0.285 -3.744 2.740 CDP H5L 34 H5L CEP C14 C 0 1 N N N 7.457 -23.044 -38.552 -1.661 -5.292 2.992 CEP H5L 35 H5L CAP C15 C 0 1 N N R 8.262 -25.434 -38.408 0.602 -6.206 2.454 CAP H5L 36 H5L OAP O14 O 0 1 N N N 9.498 -25.370 -39.132 -0.048 -7.429 2.103 OAP H5L 37 H5L C9P C16 C 0 1 N N N 8.478 -25.109 -36.903 1.826 -6.023 1.595 C9P H5L 38 H5L O9P O15 O 0 1 N N N 9.525 -24.607 -36.480 2.034 -6.776 0.668 O9P H5L 39 H5L N8P N6 N 0 1 N N N 7.409 -25.423 -36.123 2.690 -5.022 1.857 N8P H5L 40 H5L C7P C17 C 0 1 N N N 7.314 -25.187 -34.682 3.828 -4.784 0.966 C7P H5L 41 H5L C6P C18 C 0 1 N N N 6.411 -23.961 -34.413 4.644 -3.599 1.486 C6P H5L 42 H5L C5P C19 C 0 1 N N N 6.457 -23.643 -32.909 5.815 -3.354 0.569 C5P H5L 43 H5L O5P O16 O 0 1 N N N 7.424 -23.984 -32.227 5.979 -4.058 -0.405 O5P H5L 44 H5L N4P N7 N 0 1 N N N 5.386 -23.010 -32.384 6.679 -2.354 0.831 N4P H5L 45 H5L C3P C20 C 0 1 N N N 5.366 -22.726 -30.932 7.816 -2.115 -0.060 C3P H5L 46 H5L C2P C21 C 0 1 N N N 4.587 -21.466 -30.535 8.633 -0.931 0.460 C2P H5L 47 H5L S1P S1 S 0 1 N N N 4.334 -21.352 -28.717 10.039 -0.637 -0.641 S1P H5L 48 H5L C1 C22 C 0 1 Y N N 0.515 -23.599 -22.922 16.086 4.150 -1.350 C1 H5L 49 H5L C2 C23 C 0 1 Y N N 1.882 -23.362 -22.815 15.499 3.067 -1.990 C2 H5L 50 H5L C3 C24 C 0 1 Y N N 2.574 -22.889 -23.928 14.357 2.494 -1.475 C3 H5L 51 H5L C4 C25 C 0 1 Y N N 1.911 -22.647 -25.147 13.785 3.005 -0.304 C4 H5L 52 H5L C5 C26 C 0 1 Y N N 0.544 -22.895 -25.251 14.377 4.097 0.340 C5 H5L 53 H5L C6 C27 C 0 1 Y N N -0.150 -23.365 -24.140 15.525 4.661 -0.180 C6 H5L 54 H5L C7 C28 C 0 1 N N N 2.616 -22.194 -26.264 12.565 2.396 0.247 C7 H5L 55 H5L C8 C29 C 0 1 N N N 1.778 -21.828 -27.505 11.996 1.344 -0.376 C8 H5L 56 H5L C9 C30 C 0 1 N N N 2.541 -21.371 -28.779 10.782 0.738 0.172 C9 H5L 57 H5L O10 O17 O 0 1 N N N 1.926 -21.040 -29.799 10.286 1.184 1.191 O10 H5L 58 H5L O12 O18 O 0 1 N N N -0.246 -24.055 -21.884 17.212 4.710 -1.862 O12 H5L 59 H5L O13 O19 O 0 1 N N N -1.494 -23.615 -24.179 16.103 5.723 0.443 O13 H5L 60 H5L H1 H1 H 0 1 N N N 8.156 -27.115 -52.309 -8.888 6.549 3.881 H1 H5L 61 H5L H2 H2 H 0 1 N N N 12.404 -25.829 -51.562 -6.194 9.499 1.682 H2 H5L 62 H5L H3 H3 H 0 1 N N N 12.408 -25.654 -49.938 -5.460 8.628 0.447 H3 H5L 63 H5L H4 H4 H 0 1 N N N 10.987 -28.776 -46.600 -5.576 4.067 -1.145 H4 H5L 64 H5L H5 H5 H 0 1 N N N 7.475 -28.854 -47.436 -7.584 2.490 1.668 H5 H5L 65 H5L H6 H6 H 0 1 N N N 9.142 -31.392 -47.813 -8.768 3.378 -0.969 H6 H5L 66 H5L H7 H7 H 0 1 N N N 7.250 -31.926 -49.103 -9.949 3.528 1.128 H7 H5L 67 H5L H8 H8 H 0 1 N N N 8.169 -32.124 -45.915 -8.587 1.277 -1.908 H8 H5L 68 H5L H9 H9 H 0 1 N N N 2.918 -32.718 -46.576 -9.480 -2.102 -1.811 H9 H5L 69 H5L H10 H10 H 0 1 N N N 4.161 -29.748 -44.998 -12.498 -1.544 -1.073 H10 H5L 70 H5L H11 H11 H 0 1 N N N 6.689 -29.466 -45.693 -7.378 0.077 0.590 H11 H5L 71 H5L H12 H12 H 0 1 N N N 6.594 -30.452 -43.538 -7.190 -0.924 -1.737 H12 H5L 72 H5L H13 H13 H 0 1 N N N 8.160 -31.307 -43.749 -6.278 0.523 -2.227 H13 H5L 73 H5L H14 H14 H 0 1 N N N 9.083 -29.909 -40.290 -3.172 0.013 -2.593 H14 H5L 74 H5L H15 H15 H 0 1 N N N 5.093 -27.253 -43.247 -0.393 -2.090 -1.445 H15 H5L 75 H5L H16 H16 H 0 1 N N N 8.370 -24.843 -40.836 -1.117 -5.822 0.374 H16 H5L 76 H5L H17 H17 H 0 1 N N N 7.229 -23.460 -40.948 0.269 -4.719 0.194 H17 H5L 77 H5L H18 H18 H 0 1 N N N 5.698 -24.927 -37.582 0.602 -3.879 3.774 H18 H5L 78 H5L H19 H19 H 0 1 N N N 5.077 -24.240 -39.121 1.150 -3.501 2.123 H19 H5L 79 H5L H20 H20 H 0 1 N N N 5.641 -25.944 -39.061 -0.440 -2.932 2.686 H20 H5L 80 H5L H21 H21 H 0 1 N N N 7.359 -23.014 -37.457 -2.367 -4.488 2.784 H21 H5L 81 H5L H22 H22 H 0 1 N N N 8.466 -22.712 -38.839 -2.087 -6.243 2.672 H22 H5L 82 H5L H23 H23 H 0 1 N N N 6.709 -22.377 -39.005 -1.455 -5.327 4.062 H23 H5L 83 H5L H24 H24 H 0 1 N N N 7.855 -26.454 -38.475 0.896 -6.239 3.503 H24 H5L 84 H5L H25 H25 H 0 1 N N N 10.186 -25.055 -38.558 -0.338 -7.470 1.181 H25 H5L 85 H5L H26 H26 H 0 1 N N N 6.624 -25.850 -36.571 2.559 -4.460 2.637 H26 H5L 86 H5L H27 H27 H 0 1 N N N 6.882 -26.073 -34.194 4.457 -5.673 0.934 H27 H5L 87 H5L H28 H28 H 0 1 N N N 8.318 -24.998 -34.276 3.463 -4.561 -0.037 H28 H5L 88 H5L H29 H29 H 0 1 N N N 6.778 -23.097 -34.987 4.015 -2.710 1.518 H29 H5L 89 H5L H30 H30 H 0 1 N N N 5.377 -24.188 -34.713 5.009 -3.822 2.489 H30 H5L 90 H5L H31 H31 H 0 1 N N N 4.620 -22.738 -32.966 6.547 -1.791 1.611 H31 H5L 91 H5L H32 H32 H 0 1 N N N 4.909 -23.586 -30.421 8.446 -3.005 -0.092 H32 H5L 92 H5L H33 H33 H 0 1 N N N 6.405 -22.607 -30.592 7.451 -1.892 -1.063 H33 H5L 93 H5L H34 H34 H 0 1 N N N 5.148 -20.582 -30.871 8.004 -0.042 0.492 H34 H5L 94 H5L H35 H35 H 0 1 N N N 3.604 -21.486 -31.029 8.998 -1.154 1.463 H35 H5L 95 H5L H36 H36 H 0 1 N N N 2.399 -23.542 -21.884 15.939 2.672 -2.893 H36 H5L 96 H5L H37 H37 H 0 1 N N N 3.636 -22.705 -23.855 13.902 1.652 -1.975 H37 H5L 97 H5L H38 H38 H 0 1 N N N 0.028 -22.724 -26.184 13.939 4.495 1.244 H38 H5L 98 H5L H39 H39 H 0 1 N N N 3.692 -22.105 -26.259 12.125 2.792 1.151 H39 H5L 99 H5L H40 H40 H 0 1 N N N 0.700 -21.887 -27.489 12.436 0.948 -1.280 H40 H5L 100 H5L H41 H41 H 0 1 N N N 0.303 -24.177 -21.118 17.045 5.424 -2.492 H41 H5L 101 H5L H42 H42 H 0 1 N N N -1.783 -23.927 -23.330 16.761 5.478 1.108 H42 H5L 102 # # 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 H5L N1A C2A DOUB Y N 1 H5L N1A C6A SING Y N 2 H5L C2A N3A SING Y N 3 H5L N6A C6A SING N N 4 H5L C6A C5A DOUB Y N 5 H5L N3A C4A DOUB Y N 6 H5L C5A C4A SING Y N 7 H5L C5A N7A SING Y N 8 H5L C4A N9A SING Y N 9 H5L O2B C2B SING N N 10 H5L N7A C8A DOUB Y N 11 H5L N9A C8A SING Y N 12 H5L N9A C1B SING N N 13 H5L C2B C1B SING N N 14 H5L C2B C3B SING N N 15 H5L O9A P3B DOUB N N 16 H5L C1B O4B SING N N 17 H5L O3B C3B SING N N 18 H5L O3B P3B SING N N 19 H5L C3B C4B SING N N 20 H5L P3B O7A SING N N 21 H5L P3B O8A SING N N 22 H5L O4B C4B SING N N 23 H5L C4B C5B SING N N 24 H5L C5B O5B SING N N 25 H5L O5A P2A DOUB N N 26 H5L O5B P1A SING N N 27 H5L O4A P2A SING N N 28 H5L P2A O3A SING N N 29 H5L P2A O6A SING N N 30 H5L P1A O3A SING N N 31 H5L P1A O1A DOUB N N 32 H5L P1A O2A SING N N 33 H5L O6A CCP SING N N 34 H5L CCP CBP SING N N 35 H5L OAP CAP SING N N 36 H5L CBP CDP SING N N 37 H5L CBP CEP SING N N 38 H5L CBP CAP SING N N 39 H5L CAP C9P SING N N 40 H5L C9P O9P DOUB N N 41 H5L C9P N8P SING N N 42 H5L N8P C7P SING N N 43 H5L C7P C6P SING N N 44 H5L C6P C5P SING N N 45 H5L C5P N4P SING N N 46 H5L C5P O5P DOUB N N 47 H5L N4P C3P SING N N 48 H5L C3P C2P SING N N 49 H5L C2P S1P SING N N 50 H5L O10 C9 DOUB N N 51 H5L C9 S1P SING N N 52 H5L C9 C8 SING N N 53 H5L C8 C7 DOUB N E 54 H5L C7 C4 SING N N 55 H5L C5 C4 DOUB Y N 56 H5L C5 C6 SING Y N 57 H5L C4 C3 SING Y N 58 H5L O13 C6 SING N N 59 H5L C6 C1 DOUB Y N 60 H5L C3 C2 DOUB Y N 61 H5L C1 C2 SING Y N 62 H5L C1 O12 SING N N 63 H5L C2A H1 SING N N 64 H5L N6A H2 SING N N 65 H5L N6A H3 SING N N 66 H5L C8A H4 SING N N 67 H5L C1B H5 SING N N 68 H5L C2B H6 SING N N 69 H5L O2B H7 SING N N 70 H5L C3B H8 SING N N 71 H5L O7A H9 SING N N 72 H5L O8A H10 SING N N 73 H5L C4B H11 SING N N 74 H5L C5B H12 SING N N 75 H5L C5B H13 SING N N 76 H5L O2A H14 SING N N 77 H5L O4A H15 SING N N 78 H5L CCP H16 SING N N 79 H5L CCP H17 SING N N 80 H5L CDP H18 SING N N 81 H5L CDP H19 SING N N 82 H5L CDP H20 SING N N 83 H5L CEP H21 SING N N 84 H5L CEP H22 SING N N 85 H5L CEP H23 SING N N 86 H5L CAP H24 SING N N 87 H5L OAP H25 SING N N 88 H5L N8P H26 SING N N 89 H5L C7P H27 SING N N 90 H5L C7P H28 SING N N 91 H5L C6P H29 SING N N 92 H5L C6P H30 SING N N 93 H5L N4P H31 SING N N 94 H5L C3P H32 SING N N 95 H5L C3P H33 SING N N 96 H5L C2P H34 SING N N 97 H5L C2P H35 SING N N 98 H5L C2 H36 SING N N 99 H5L C3 H37 SING N N 100 H5L C5 H38 SING N N 101 H5L C7 H39 SING N N 102 H5L C8 H40 SING N N 103 H5L O12 H41 SING N N 104 H5L O13 H42 SING N N 105 # # 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 H5L InChI InChI 1.03 "InChI=1S/C30H42N7O19P3S/c1-30(2,25(43)28(44)33-8-7-20(40)32-9-10-60-21(41)6-4-16-3-5-17(38)18(39)11-16)13-53-59(50,51)56-58(48,49)52-12-19-24(55-57(45,46)47)23(42)29(54-19)37-15-36-22-26(31)34-14-35-27(22)37/h3-6,11,14-15,19,23-25,29,38-39,42-43H,7-10,12-13H2,1-2H3,(H,32,40)(H,33,44)(H,48,49)(H,50,51)(H2,31,34,35)(H2,45,46,47)/b6-4+/t19-,23-,24-,25+,29-/m1/s1" H5L InChIKey InChI 1.03 QHRGJMIMHCLHRG-ZSELIEHESA-N H5L SMILES_CANONICAL CACTVS 3.385 "CC(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)[C@@H](O)C(=O)NCCC(=O)NCCSC(=O)\C=C\c4ccc(O)c(O)c4" H5L SMILES CACTVS 3.385 "CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCSC(=O)C=Cc4ccc(O)c(O)c4" H5L SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)(COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCSC(=O)/C=C/c4ccc(c(c4)O)O)O" H5L SMILES "OpenEye OEToolkits" 2.0.7 "CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSC(=O)C=Cc4ccc(c(c4)O)O)O" # _pdbx_chem_comp_identifier.comp_id H5L _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})-3-[3,4-bis(oxidanyl)phenyl]prop-2-enethioate" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id H5L _pdbx_chem_comp_synonyms.name Caffeoyl-CoA _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site H5L "Create component" 2020-11-13 PDBJ H5L "Other modification" 2020-12-02 PDBJ H5L "Modify synonyms" 2021-03-01 PDBE H5L "Initial release" 2021-09-15 RCSB ##