data_8JD # _chem_comp.id 8JD _chem_comp.name "[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (3R)-4-[(3-{[2-(ethylsulfanyl)ethyl]amino}-3-oxopropyl)amino]-3-hydroxy-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate (non-preferred name)" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C23 H39 N7 O13 P2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "Ethyl Coenzyme A" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-02-09 _chem_comp.pdbx_modified_date 2021-03-01 _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 715.607 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 8JD _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 5UQR _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # 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 8JD N6A N1 N 0 1 N N N 42.769 -35.668 -33.255 8.481 6.421 2.177 N6A 8JD 1 8JD C6A C1 C 0 1 Y N N 43.087 -35.621 -31.946 8.251 5.724 1.003 C6A 8JD 2 8JD N1A N2 N 0 1 Y N N 44.043 -34.804 -31.456 8.413 6.310 -0.178 N1A 8JD 3 8JD C2A C2 C 0 1 Y N N 44.336 -34.796 -30.138 8.196 5.653 -1.303 C2A 8JD 4 8JD N3A N3 N 0 1 Y N N 43.723 -35.569 -29.206 7.812 4.395 -1.324 N3A 8JD 5 8JD C4A C3 C 0 1 Y N N 42.735 -36.426 -29.589 7.624 3.725 -0.191 C4A 8JD 6 8JD C5A C4 C 0 1 Y N N 42.370 -36.508 -31.011 7.847 4.378 1.033 C5A 8JD 7 8JD N9A N4 N 0 1 Y N N 41.960 -37.320 -28.987 7.239 2.448 0.127 N9A 8JD 8 8JD N7A N5 N 0 1 Y N N 41.390 -37.419 -31.137 7.594 3.481 2.016 N7A 8JD 9 8JD C8A C5 C 0 1 Y N N 41.145 -37.902 -29.900 7.228 2.350 1.487 C8A 8JD 10 8JD C1M C6 C 0 1 N N N 33.230 -34.874 -40.174 -14.824 5.677 0.745 C1M 8JD 11 8JD CP C7 C 0 1 N N N 33.207 -34.112 -38.875 -13.826 4.625 1.233 CP 8JD 12 8JD O3X O1 O 0 1 N N N 41.192 -37.131 -24.658 7.868 -1.347 -2.673 O3X 8JD 13 8JD S1 S1 S 0 1 N N N 33.672 -34.918 -37.502 -12.794 4.080 -0.155 S1 8JD 14 8JD N4 N6 N 0 1 N N N 36.672 -33.764 -35.185 -9.857 1.304 0.168 N4 8JD 15 8JD C5 C8 C 0 1 N N N 37.972 -33.524 -35.390 -8.931 0.671 -0.579 C5 8JD 16 8JD O5 O2 O 0 1 N N N 38.567 -33.875 -36.406 -8.832 0.919 -1.762 O5 8JD 17 8JD C6 C9 C 0 1 N N N 38.711 -32.814 -34.265 -8.017 -0.346 0.056 C6 8JD 18 8JD C7 C10 C 0 1 N N N 39.723 -33.747 -33.573 -7.068 -0.910 -1.003 C7 8JD 19 8JD N8 N7 N 0 1 N N N 39.184 -35.035 -33.157 -6.180 -1.898 -0.386 N8 8JD 20 8JD C9 C11 C 0 1 N N N 38.704 -35.260 -31.926 -5.253 -2.531 -1.132 C9 8JD 21 8JD O9 O3 O 0 1 N N N 38.650 -34.388 -31.057 -5.215 -2.353 -2.331 O9 8JD 22 8JD C13 C12 C 0 1 N N N 35.927 -35.634 -31.235 -2.965 -1.428 0.173 C13 8JD 23 8JD C11 C13 C 0 1 N N N 36.694 -36.792 -31.880 -2.879 -2.812 -0.475 C11 8JD 24 8JD C14 C14 C 0 1 N N N 36.447 -36.789 -33.383 -2.379 -2.671 -1.914 C14 8JD 25 8JD C12 C15 C 0 1 N N N 36.234 -38.126 -31.300 -1.907 -3.687 0.320 C12 8JD 26 8JD P1A P1 P 0 1 N N N 38.687 -40.709 -28.380 3.553 -3.139 0.825 P1A 8JD 27 8JD O2A O4 O 0 1 N N N 39.824 -41.046 -29.312 3.842 -4.458 0.220 O2A 8JD 28 8JD O1A O5 O 0 1 N N N 37.925 -41.856 -27.757 4.030 -3.137 2.363 O1A 8JD 29 8JD O3A O6 O 0 1 N N N 37.738 -39.633 -29.140 1.970 -2.851 0.753 O3A 8JD 30 8JD O5X O7 O 0 1 N N N 39.294 -39.767 -27.246 4.344 -1.993 0.017 O5X 8JD 31 8JD C4X C16 C 0 1 N N R 41.247 -39.124 -25.995 6.180 -0.790 -0.994 C4X 8JD 32 8JD O4X O8 O 0 1 N N N 42.117 -38.878 -27.110 6.044 0.404 -0.193 O4X 8JD 33 8JD C1X C17 C 0 1 N N R 41.945 -37.530 -27.525 6.900 1.383 -0.821 C1X 8JD 34 8JD C2X C18 C 0 1 N N R 40.580 -37.065 -26.998 8.168 0.599 -1.224 C2X 8JD 35 8JD O2X O9 O 0 1 N N N 40.491 -35.639 -26.831 8.666 1.063 -2.480 O2X 8JD 36 8JD C3X C19 C 0 1 N N S 40.499 -37.822 -25.694 7.684 -0.864 -1.341 C3X 8JD 37 8JD C5X C20 C 0 1 N N N 40.313 -40.255 -26.377 5.757 -2.023 -0.193 C5X 8JD 38 8JD P2A P2 P 0 1 N N N 36.181 -39.260 -28.876 0.658 -3.730 1.066 P2A 8JD 39 8JD O4A O10 O 0 1 N N N 35.327 -40.410 -29.324 0.863 -5.112 0.579 O4A 8JD 40 8JD O5A O11 O 0 1 N N N 35.984 -38.669 -27.505 0.396 -3.754 2.655 O5A 8JD 41 8JD O6A O12 O 0 1 N N N 36.039 -38.017 -29.893 -0.613 -3.080 0.322 O6A 8JD 42 8JD C10 C21 C 0 1 N N R 38.198 -36.648 -31.598 -4.264 -3.461 -0.477 C10 8JD 43 8JD O10 O13 O 0 1 N N N 38.921 -37.684 -32.295 -4.672 -3.719 0.868 O10 8JD 44 8JD C3 C22 C 0 1 N N N 35.886 -34.632 -36.055 -10.745 2.292 -0.450 C3 8JD 45 8JD C2 C23 C 0 1 N N N 35.075 -33.902 -37.091 -11.694 2.856 0.609 C2 8JD 46 8JD H1 H1 H 0 1 N N N 43.341 -35.022 -33.761 8.763 7.348 2.143 H1 8JD 47 8JD H2 H2 H 0 1 N N N 42.923 -36.593 -33.602 8.355 5.983 3.033 H2 8JD 48 8JD H3 H3 H 0 1 N N N 45.114 -34.127 -29.801 8.340 6.168 -2.242 H3 8JD 49 8JD H4 H4 H 0 1 N N N 40.401 -38.650 -29.670 6.967 1.462 2.042 H4 8JD 50 8JD H5 H5 H 0 1 N N N 32.899 -34.216 -40.991 -14.282 6.530 0.338 H5 8JD 51 8JD H6 H6 H 0 1 N N N 34.253 -35.223 -40.376 -15.457 5.245 -0.030 H6 8JD 52 8JD H7 H7 H 0 1 N N N 32.554 -35.739 -40.103 -15.444 6.004 1.579 H7 8JD 53 8JD H8 H8 H 0 1 N N N 33.875 -33.246 -38.990 -13.193 5.057 2.008 H8 8JD 54 8JD H9 H9 H 0 1 N N N 32.176 -33.762 -38.717 -14.368 3.771 1.641 H9 8JD 55 8JD H10 H10 H 0 1 N N N 41.127 -37.625 -23.849 8.794 -1.414 -2.943 H10 8JD 56 8JD H11 H11 H 0 1 N N N 36.221 -33.331 -34.404 -9.936 1.105 1.114 H11 8JD 57 8JD H12 H12 H 0 1 N N N 39.249 -31.950 -34.681 -7.437 0.131 0.846 H12 8JD 58 8JD H13 H13 H 0 1 N N N 37.979 -32.467 -33.521 -8.612 -1.155 0.479 H13 8JD 59 8JD H14 H14 H 0 1 N N N 40.551 -33.933 -34.273 -7.647 -1.387 -1.794 H14 8JD 60 8JD H15 H15 H 0 1 N N N 40.107 -33.233 -32.680 -6.473 -0.101 -1.426 H15 8JD 61 8JD H16 H16 H 0 1 N N N 39.172 -35.784 -33.819 -6.258 -2.097 0.561 H16 8JD 62 8JD H17 H17 H 0 1 N N N 36.105 -35.635 -30.149 -3.321 -1.528 1.198 H17 8JD 63 8JD H18 H18 H 0 1 N N N 36.274 -34.682 -31.662 -1.978 -0.965 0.175 H18 8JD 64 8JD H19 H19 H 0 1 N N N 34.851 -35.753 -31.430 -3.657 -0.804 -0.393 H19 8JD 65 8JD H20 H20 H 0 1 N N N 35.369 -36.892 -33.578 -3.028 -1.985 -2.459 H20 8JD 66 8JD H21 H21 H 0 1 N N N 36.808 -35.843 -33.812 -1.361 -2.281 -1.908 H21 8JD 67 8JD H22 H22 H 0 1 N N N 36.985 -37.630 -33.845 -2.391 -3.646 -2.400 H22 8JD 68 8JD H23 H23 H 0 1 N N N 35.286 -38.420 -31.775 -2.263 -3.787 1.345 H23 8JD 69 8JD H24 H24 H 0 1 N N N 36.998 -38.891 -31.501 -1.845 -4.672 -0.141 H24 8JD 70 8JD H25 H25 H 0 1 N N N 38.290 -42.680 -28.057 3.870 -2.302 2.823 H25 8JD 71 8JD H26 H26 H 0 1 N N N 41.830 -39.417 -25.110 5.585 -0.706 -1.903 H26 8JD 72 8JD H27 H27 H 0 1 N N N 42.722 -36.900 -27.067 6.414 1.801 -1.702 H27 8JD 73 8JD H28 H28 H 0 1 N N N 39.792 -37.422 -27.677 8.934 0.689 -0.454 H28 8JD 74 8JD H29 H29 H 0 1 N N N 39.629 -35.411 -26.504 9.462 0.604 -2.782 H29 8JD 75 8JD H30 H30 H 0 1 N N N 39.453 -38.031 -25.426 8.210 -1.498 -0.627 H30 8JD 76 8JD H31 H31 H 0 1 N N N 39.851 -40.670 -25.469 6.267 -2.023 0.770 H31 8JD 77 8JD H32 H32 H 0 1 N N N 40.884 -41.043 -26.890 6.023 -2.924 -0.746 H32 8JD 78 8JD H33 H33 H 0 1 N N N 35.288 -39.134 -27.056 0.253 -2.881 3.043 H33 8JD 79 8JD H34 H34 H 0 1 N N N 38.338 -36.800 -30.518 -4.225 -4.398 -1.031 H34 8JD 80 8JD H35 H35 H 0 1 N N N 38.567 -38.533 -32.057 -4.729 -2.927 1.420 H35 8JD 81 8JD H36 H36 H 0 1 N N N 35.197 -35.216 -35.427 -10.150 3.101 -0.873 H36 8JD 82 8JD H37 H37 H 0 1 N N N 36.575 -35.314 -36.575 -11.325 1.815 -1.241 H37 8JD 83 8JD H38 H38 H 0 1 N N N 35.686 -33.727 -37.989 -11.115 3.332 1.400 H38 8JD 84 8JD H39 H39 H 0 1 N N N 34.733 -32.938 -36.687 -12.290 2.047 1.032 H39 8JD 85 # # 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 8JD C1M CP SING N N 1 8JD CP S1 SING N N 2 8JD S1 C2 SING N N 3 8JD C2 C3 SING N N 4 8JD O5 C5 DOUB N N 5 8JD C3 N4 SING N N 6 8JD C5 N4 SING N N 7 8JD C5 C6 SING N N 8 8JD C6 C7 SING N N 9 8JD C7 N8 SING N N 10 8JD C14 C11 SING N N 11 8JD N6A C6A SING N N 12 8JD N8 C9 SING N N 13 8JD O10 C10 SING N N 14 8JD C6A N1A DOUB Y N 15 8JD C6A C5A SING Y N 16 8JD C9 C10 SING N N 17 8JD C9 O9 DOUB N N 18 8JD C11 C10 SING N N 19 8JD C11 C12 SING N N 20 8JD C11 C13 SING N N 21 8JD N1A C2A SING Y N 22 8JD C12 O6A SING N N 23 8JD N7A C5A SING Y N 24 8JD N7A C8A DOUB Y N 25 8JD C5A C4A DOUB Y N 26 8JD C2A N3A DOUB Y N 27 8JD C8A N9A SING Y N 28 8JD O6A P2A SING N N 29 8JD C4A N3A SING Y N 30 8JD C4A N9A SING Y N 31 8JD O4A P2A DOUB N N 32 8JD O2A P1A DOUB N N 33 8JD O3A P2A SING N N 34 8JD O3A P1A SING N N 35 8JD N9A C1X SING N N 36 8JD P2A O5A SING N N 37 8JD P1A O1A SING N N 38 8JD P1A O5X SING N N 39 8JD C1X O4X SING N N 40 8JD C1X C2X SING N N 41 8JD O5X C5X SING N N 42 8JD O4X C4X SING N N 43 8JD C2X O2X SING N N 44 8JD C2X C3X SING N N 45 8JD C5X C4X SING N N 46 8JD C4X C3X SING N N 47 8JD C3X O3X SING N N 48 8JD N6A H1 SING N N 49 8JD N6A H2 SING N N 50 8JD C2A H3 SING N N 51 8JD C8A H4 SING N N 52 8JD C1M H5 SING N N 53 8JD C1M H6 SING N N 54 8JD C1M H7 SING N N 55 8JD CP H8 SING N N 56 8JD CP H9 SING N N 57 8JD O3X H10 SING N N 58 8JD N4 H11 SING N N 59 8JD C6 H12 SING N N 60 8JD C6 H13 SING N N 61 8JD C7 H14 SING N N 62 8JD C7 H15 SING N N 63 8JD N8 H16 SING N N 64 8JD C13 H17 SING N N 65 8JD C13 H18 SING N N 66 8JD C13 H19 SING N N 67 8JD C14 H20 SING N N 68 8JD C14 H21 SING N N 69 8JD C14 H22 SING N N 70 8JD C12 H23 SING N N 71 8JD C12 H24 SING N N 72 8JD O1A H25 SING N N 73 8JD C4X H26 SING N N 74 8JD C1X H27 SING N N 75 8JD C2X H28 SING N N 76 8JD O2X H29 SING N N 77 8JD C3X H30 SING N N 78 8JD C5X H31 SING N N 79 8JD C5X H32 SING N N 80 8JD O5A H33 SING N N 81 8JD C10 H34 SING N N 82 8JD O10 H35 SING N N 83 8JD C3 H36 SING N N 84 8JD C3 H37 SING N N 85 8JD C2 H38 SING N N 86 8JD C2 H39 SING N N 87 # # 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 8JD SMILES ACDLabs 12.01 "Nc2ncnc3n(C1OC(C(O)C1O)COP(O)(=O)OP(O)(=O)OCC(C)(C(C(NCCC(NCCSCC)=O)=O)O)C)cnc23" 8JD InChI InChI 1.03 "InChI=1S/C23H39N7O13P2S/c1-4-46-8-7-25-14(31)5-6-26-21(35)18(34)23(2,3)10-41-45(38,39)43-44(36,37)40-9-13-16(32)17(33)22(42-13)30-12-29-15-19(24)27-11-28-20(15)30/h11-13,16-18,22,32-34H,4-10H2,1-3H3,(H,25,31)(H,26,35)(H,36,37)(H,38,39)(H2,24,27,28)/t13-,16-,17-,18+,22-/m1/s1" 8JD InChIKey InChI 1.03 ZYQGAGMIMDQCKA-ZSJPKINUSA-N 8JD SMILES_CANONICAL CACTVS 3.385 "CCSCCNC(=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)n2cnc3c(N)ncnc23" 8JD SMILES CACTVS 3.385 "CCSCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23" 8JD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CCSCCNC(=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)O)O" 8JD SMILES "OpenEye OEToolkits" 2.0.6 "CCSCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)O" # # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier 8JD "SYSTEMATIC NAME" ACDLabs 12.01 "[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (3R)-4-[(3-{[2-(ethylsulfanyl)ethyl]amino}-3-oxopropyl)amino]-3-hydroxy-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate (non-preferred name)" 8JD "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{R})-4-[[3-(2-ethylsulfanylethylamino)-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] 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 8JD "Create component" 2017-02-09 RCSB 8JD "Other modification" 2018-02-27 RCSB 8JD "Initial release" 2018-03-14 RCSB 8JD "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 8JD _pdbx_chem_comp_synonyms.name "Ethyl Coenzyme A" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##