data_J5H # _chem_comp.id J5H _chem_comp.name "~{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] naphthalene-2-carbothioate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C32 H42 N7 O17 P3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-01-30 _chem_comp.pdbx_modified_date 2019-05-10 _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 921.699 _chem_comp.one_letter_code ? _chem_comp.three_letter_code J5H _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 6QKR _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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 J5H CBT C1 C 0 1 Y N N -25.844 -7.536 2.482 13.873 2.180 -0.907 CBT J5H 1 J5H CBW C2 C 0 1 Y N N -26.633 -6.414 2.759 15.066 2.837 -0.572 CBW J5H 2 J5H CAV C3 C 0 1 Y N N -26.154 -5.137 2.404 15.833 3.497 -1.549 CAV J5H 3 J5H CAR C4 C 0 1 Y N N -26.964 -4.025 2.649 16.985 4.125 -1.190 CAR J5H 4 J5H CAQ C5 C 0 1 Y N N -28.234 -4.186 3.215 17.419 4.125 0.134 CAQ J5H 5 J5H CAU C6 C 0 1 Y N N -28.722 -5.454 3.554 16.704 3.497 1.107 CAU J5H 6 J5H CBV C7 C 0 1 Y N N -27.901 -6.589 3.332 15.508 2.837 0.776 CBV J5H 7 J5H CAW C8 C 0 1 Y N N -28.359 -7.879 3.718 14.747 2.179 1.759 CAW J5H 8 J5H CAT C9 C 0 1 Y N N -27.586 -9.002 3.427 13.595 1.547 1.416 CAT J5H 9 J5H CBU C10 C 0 1 Y N N -26.318 -8.804 2.860 13.145 1.542 0.083 CBU J5H 10 J5H CBR C11 C 0 1 N N N -25.391 -9.979 2.525 11.887 0.848 -0.263 CBR J5H 11 J5H OAF O1 O 0 1 N N N -25.713 -11.122 2.738 11.495 0.839 -1.414 OAF J5H 12 J5H SBO S1 S 0 1 N N N -23.756 -9.502 1.823 10.956 0.034 0.992 SBO J5H 13 J5H CBA C12 C 0 1 N N N -22.713 -10.960 2.249 9.582 -0.603 0.001 CBA J5H 14 J5H CAY C13 C 0 1 N N N -22.420 -10.940 3.791 8.614 -1.369 0.904 CAY J5H 15 J5H NBH N1 N 0 1 N N N -21.784 -9.650 4.145 7.501 -1.884 0.101 NBH J5H 16 J5H CBP C14 C 0 1 N N N -20.365 -9.400 3.752 6.520 -2.596 0.689 CBP J5H 17 J5H OAD O2 O 0 1 N N N -19.705 -10.220 3.185 6.557 -2.811 1.882 OAD J5H 18 J5H CBB C15 C 0 1 N N N -19.705 -8.056 4.119 5.375 -3.126 -0.136 CBB J5H 19 J5H CAZ C16 C 0 1 N N N -18.284 -8.206 4.742 4.407 -3.893 0.767 CAZ J5H 20 J5H NBI N2 N 0 1 N N N -18.065 -7.097 5.643 3.295 -4.408 -0.035 NBI J5H 21 J5H CBQ C17 C 0 1 N N N -17.512 -5.814 5.141 2.313 -5.120 0.552 CBQ J5H 22 J5H OAE O3 O 0 1 N N N -17.200 -5.678 3.996 2.397 -5.414 1.726 OAE J5H 23 J5H CBZ C18 C 0 1 N N R -17.323 -4.687 6.174 1.112 -5.551 -0.249 CBZ J5H 24 J5H OAK O4 O 0 1 N N N -17.613 -5.157 7.457 1.363 -5.333 -1.639 OAK J5H 25 J5H CCF C19 C 0 1 N N N -18.096 -3.361 5.865 -0.108 -4.735 0.183 CCF J5H 26 J5H CAA C20 C 0 1 N N N -19.626 -3.575 5.862 -0.468 -5.081 1.629 CAA J5H 27 J5H CAB C21 C 0 1 N N N -17.655 -2.754 4.510 0.213 -3.243 0.080 CAB J5H 28 J5H CBD C22 C 0 1 N N N -17.740 -2.313 6.969 -1.292 -5.066 -0.729 CBD J5H 29 J5H OBK O5 O 0 1 N N N -16.395 -1.925 6.796 -2.431 -4.304 -0.326 OBK J5H 30 J5H PCI P1 P 0 1 N N N -15.816 -0.563 7.576 -3.857 -4.400 -1.067 PCI J5H 31 J5H OAP O6 O 0 1 N N N -14.524 -0.082 6.931 -3.682 -4.129 -2.512 OAP J5H 32 J5H OAI O7 O 0 1 N N N -16.869 0.522 7.574 -4.467 -5.877 -0.869 OAI J5H 33 J5H OBN O8 O 0 1 N N N -15.463 -1.062 9.143 -4.865 -3.315 -0.436 OBN J5H 34 J5H PCH P2 P 0 1 N N N -15.049 -0.079 10.441 -6.277 -2.696 -0.900 PCH J5H 35 J5H OAO O9 O 0 1 N N N -15.373 1.384 10.164 -6.255 -2.458 -2.361 OAO J5H 36 J5H OAH O10 O 0 1 N N N -15.884 -0.565 11.608 -7.459 -3.730 -0.543 OAH J5H 37 J5H "O5'" O11 O 0 1 N N N -13.386 -0.280 10.758 -6.531 -1.304 -0.133 "O5'" J5H 38 J5H "C5'" C23 C 0 1 N N N -12.928 -1.607 11.112 -7.650 -0.458 -0.406 "C5'" J5H 39 J5H "C4'" C24 C 0 1 N N R -11.670 -1.967 10.562 -7.588 0.777 0.495 "C4'" J5H 40 J5H "O4'" O12 O 0 1 N N N -11.655 -3.495 10.295 -6.454 1.586 0.138 "O4'" J5H 41 J5H "C3'" C25 C 0 1 N N S -11.276 -1.359 9.148 -8.850 1.638 0.293 "C3'" J5H 42 J5H "O3'" O13 O 0 1 N N N -9.782 -1.295 9.128 -9.571 1.763 1.520 "O3'" J5H 43 J5H PCG P3 P 0 1 N N N -8.977 0.062 9.602 -11.090 1.260 1.700 PCG J5H 44 J5H OAM O14 O 0 1 N N N -9.296 0.375 11.052 -11.624 1.676 3.160 OAM J5H 45 J5H OAN O15 O 0 1 N N N -9.390 1.231 8.731 -11.943 1.886 0.665 OAN J5H 46 J5H OAG O16 O 0 1 N N N -7.495 -0.203 9.454 -11.147 -0.342 1.544 OAG J5H 47 J5H "C2'" C26 C 0 1 N N R -11.695 -2.202 8.269 -8.303 3.013 -0.161 "C2'" J5H 48 J5H "O2'" O17 O 0 1 N N N -10.922 -2.239 7.015 -9.022 4.080 0.461 "O2'" J5H 49 J5H "C1'" C27 C 0 1 N N R -11.701 -3.700 9.010 -6.835 2.962 0.347 "C1'" J5H 50 J5H N9 N3 N 0 1 Y N N -12.889 -4.446 8.740 -5.986 3.860 -0.439 N9 J5H 51 J5H C8 C28 C 0 1 Y N N -14.118 -3.945 8.606 -5.233 3.515 -1.522 C8 J5H 52 J5H N7 N4 N 0 1 Y N N -14.990 -4.929 8.481 -4.608 4.561 -1.980 N7 J5H 53 J5H C5 C29 C 0 1 Y N N -14.327 -6.099 8.535 -4.919 5.640 -1.222 C5 J5H 54 J5H C4 C30 C 0 1 Y N N -12.986 -5.801 8.749 -5.807 5.203 -0.224 C4 J5H 55 J5H N3 N5 N 0 1 Y N N -12.086 -6.804 8.865 -6.271 6.083 0.657 N3 J5H 56 J5H C2 C31 C 0 1 Y N N -12.475 -8.078 8.769 -5.902 7.345 0.603 C2 J5H 57 J5H N1 N6 N 0 1 Y N N -13.759 -8.396 8.562 -5.067 7.801 -0.313 N1 J5H 58 J5H C6 C32 C 0 1 Y N N -14.700 -7.459 8.449 -4.556 6.997 -1.240 C6 J5H 59 J5H N6 N7 N 0 1 N N N -16.072 -7.831 8.243 -3.685 7.485 -2.198 N6 J5H 60 J5H H1 H1 H 0 1 N N N -24.890 -7.430 1.988 13.523 2.176 -1.929 H1 J5H 61 J5H H2 H2 H 0 1 N N N -25.180 -5.020 1.952 15.508 3.504 -2.579 H2 J5H 62 J5H H3 H3 H 0 1 N N N -26.608 -3.036 2.400 17.572 4.630 -1.943 H3 J5H 63 J5H H4 H4 H 0 1 N N N -28.849 -3.316 3.394 18.338 4.631 0.393 H4 J5H 64 J5H H5 H5 H 0 1 N N N -29.709 -5.566 3.978 17.054 3.505 2.129 H5 J5H 65 J5H H6 H6 H 0 1 N N N -29.301 -7.988 4.234 15.078 2.176 2.787 H6 J5H 66 J5H H7 H7 H 0 1 N N N -27.953 -9.997 3.632 13.016 1.044 2.176 H7 J5H 67 J5H H8 H8 H 0 1 N N N -23.246 -11.885 1.986 9.058 0.229 -0.470 H8 J5H 68 J5H H9 H9 H 0 1 N N N -21.766 -10.912 1.692 9.968 -1.271 -0.768 H9 J5H 69 J5H H10 H10 H 0 1 N N N -23.363 -11.051 4.347 9.137 -2.201 1.375 H10 J5H 70 J5H H11 H11 H 0 1 N N N -21.743 -11.768 4.048 8.227 -0.700 1.673 H11 J5H 71 J5H H12 H12 H 0 1 N N N -22.300 -8.953 4.643 7.471 -1.713 -0.853 H12 J5H 72 J5H H13 H13 H 0 1 N N N -19.621 -7.449 3.205 4.852 -2.295 -0.607 H13 J5H 73 J5H H14 H14 H 0 1 N N N -20.350 -7.539 4.845 5.761 -3.795 -0.905 H14 J5H 74 J5H H15 H15 H 0 1 N N N -18.219 -9.154 5.296 4.931 -4.725 1.238 H15 J5H 75 J5H H16 H16 H 0 1 N N N -17.525 -8.194 3.946 4.021 -3.224 1.536 H16 J5H 76 J5H H17 H17 H 0 1 N N N -18.288 -7.195 6.613 3.265 -4.236 -0.990 H17 J5H 77 J5H H18 H18 H 0 1 N N N -16.255 -4.425 6.146 0.920 -6.610 -0.076 H18 J5H 78 J5H H19 H19 H 0 1 N N N -17.494 -4.455 8.086 1.542 -4.411 -1.866 H19 J5H 79 J5H H20 H20 H 0 1 N N N -19.938 -4.006 6.825 0.344 -4.774 2.289 H20 J5H 80 J5H H21 H21 H 0 1 N N N -20.131 -2.609 5.712 -1.382 -4.559 1.911 H21 J5H 81 J5H H22 H22 H 0 1 N N N -19.898 -4.262 5.047 -0.621 -6.156 1.719 H22 J5H 82 J5H H23 H23 H 0 1 N N N -16.566 -2.602 4.513 0.469 -2.997 -0.951 H23 J5H 83 J5H H24 H24 H 0 1 N N N -17.927 -3.441 3.695 -0.656 -2.662 0.387 H24 J5H 84 J5H H25 H25 H 0 1 N N N -18.159 -1.788 4.360 1.056 -3.007 0.730 H25 J5H 85 J5H H26 H26 H 0 1 N N N -18.395 -1.435 6.873 -1.036 -4.819 -1.760 H26 J5H 86 J5H H27 H27 H 0 1 N N N -17.872 -2.762 7.964 -1.521 -6.129 -0.656 H27 J5H 87 J5H H28 H28 H 0 1 N N N -16.517 1.304 7.166 -4.608 -6.123 0.056 H28 J5H 88 J5H H29 H29 H 0 1 N N N -16.434 0.144 11.922 -7.532 -3.932 0.400 H29 J5H 89 J5H H30 H30 H 0 1 N N N -13.676 -2.333 10.760 -7.625 -0.147 -1.451 H30 J5H 90 J5H H31 H31 H 0 1 N N N -12.851 -1.662 12.208 -8.574 -1.003 -0.211 H31 J5H 91 J5H H32 H32 H 0 1 N N N -10.863 -1.730 11.271 -7.511 0.471 1.538 H32 J5H 92 J5H H33 H33 H 0 1 N N N -11.709 -0.353 9.050 -9.486 1.206 -0.480 H33 J5H 93 J5H H34 H34 H 0 1 N N N -9.688 1.238 11.111 -12.535 1.404 3.339 H34 J5H 94 J5H H35 H35 H 0 1 N N N -7.121 0.420 8.842 -10.609 -0.819 2.191 H35 J5H 95 J5H H36 H36 H 0 1 N N N -12.744 -1.996 8.010 -8.336 3.105 -1.247 H36 J5H 96 J5H H37 H37 H 0 1 N N N -10.932 -1.379 6.611 -8.659 4.957 0.278 H37 J5H 97 J5H H38 H38 H 0 1 N N N -10.819 -4.246 8.644 -6.787 3.216 1.406 H38 J5H 98 J5H H39 H39 H 0 1 N N N -14.363 -2.893 8.601 -5.165 2.521 -1.938 H39 J5H 99 J5H H40 H40 H 0 1 N N N -11.741 -8.865 8.860 -6.298 8.034 1.334 H40 J5H 100 J5H H41 H41 H 0 1 N N N -16.146 -8.828 8.209 -3.317 6.887 -2.868 H41 J5H 101 J5H H42 H42 H 0 1 N N N -16.629 -7.481 8.996 -3.442 8.424 -2.200 H42 J5H 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 J5H SBO CBA SING N N 1 J5H SBO CBR SING N N 2 J5H CBA CAY SING N N 3 J5H CAV CAR DOUB Y N 4 J5H CAV CBW SING Y N 5 J5H CBT CBW DOUB Y N 6 J5H CBT CBU SING Y N 7 J5H CBR OAF DOUB N N 8 J5H CBR CBU SING N N 9 J5H CAR CAQ SING Y N 10 J5H CBW CBV SING Y N 11 J5H CBU CAT DOUB Y N 12 J5H OAD CBP DOUB N N 13 J5H CAQ CAU DOUB Y N 14 J5H CBV CAU SING Y N 15 J5H CBV CAW DOUB Y N 16 J5H CAT CAW SING Y N 17 J5H CBP CBB SING N N 18 J5H CBP NBH SING N N 19 J5H CAY NBH SING N N 20 J5H OAE CBQ DOUB N N 21 J5H CBB CAZ SING N N 22 J5H CAB CCF SING N N 23 J5H CAZ NBI SING N N 24 J5H CBQ NBI SING N N 25 J5H CBQ CBZ SING N N 26 J5H CAA CCF SING N N 27 J5H CCF CBZ SING N N 28 J5H CCF CBD SING N N 29 J5H CBZ OAK SING N N 30 J5H OBK CBD SING N N 31 J5H OBK PCI SING N N 32 J5H OAP PCI DOUB N N 33 J5H "O2'" "C2'" SING N N 34 J5H OAI PCI SING N N 35 J5H PCI OBN SING N N 36 J5H N6 C6 SING N N 37 J5H "C2'" "C1'" SING N N 38 J5H "C2'" "C3'" SING N N 39 J5H C6 C5 DOUB Y N 40 J5H C6 N1 SING Y N 41 J5H N7 C5 SING Y N 42 J5H N7 C8 DOUB Y N 43 J5H C5 C4 SING Y N 44 J5H N1 C2 DOUB Y N 45 J5H C8 N9 SING Y N 46 J5H OAN PCG DOUB N N 47 J5H N9 C4 SING Y N 48 J5H N9 "C1'" SING N N 49 J5H C4 N3 DOUB Y N 50 J5H C2 N3 SING Y N 51 J5H "C1'" "O4'" SING N N 52 J5H "O3'" "C3'" SING N N 53 J5H "O3'" PCG SING N N 54 J5H OBN PCH SING N N 55 J5H "C3'" "C4'" SING N N 56 J5H OAG PCG SING N N 57 J5H PCG OAM SING N N 58 J5H OAO PCH DOUB N N 59 J5H "O4'" "C4'" SING N N 60 J5H PCH "O5'" SING N N 61 J5H PCH OAH SING N N 62 J5H "C4'" "C5'" SING N N 63 J5H "O5'" "C5'" SING N N 64 J5H CBT H1 SING N N 65 J5H CAV H2 SING N N 66 J5H CAR H3 SING N N 67 J5H CAQ H4 SING N N 68 J5H CAU H5 SING N N 69 J5H CAW H6 SING N N 70 J5H CAT H7 SING N N 71 J5H CBA H8 SING N N 72 J5H CBA H9 SING N N 73 J5H CAY H10 SING N N 74 J5H CAY H11 SING N N 75 J5H NBH H12 SING N N 76 J5H CBB H13 SING N N 77 J5H CBB H14 SING N N 78 J5H CAZ H15 SING N N 79 J5H CAZ H16 SING N N 80 J5H NBI H17 SING N N 81 J5H CBZ H18 SING N N 82 J5H OAK H19 SING N N 83 J5H CAA H20 SING N N 84 J5H CAA H21 SING N N 85 J5H CAA H22 SING N N 86 J5H CAB H23 SING N N 87 J5H CAB H24 SING N N 88 J5H CAB H25 SING N N 89 J5H CBD H26 SING N N 90 J5H CBD H27 SING N N 91 J5H OAI H28 SING N N 92 J5H OAH H29 SING N N 93 J5H "C5'" H30 SING N N 94 J5H "C5'" H31 SING N N 95 J5H "C4'" H32 SING N N 96 J5H "C3'" H33 SING N N 97 J5H OAM H34 SING N N 98 J5H OAG H35 SING N N 99 J5H "C2'" H36 SING N N 100 J5H "O2'" H37 SING N N 101 J5H "C1'" H38 SING N N 102 J5H C8 H39 SING N N 103 J5H C2 H40 SING N N 104 J5H N6 H41 SING N N 105 J5H N6 H42 SING N N 106 # # 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 J5H InChI InChI 1.03 "InChI=1S/C32H42N7O17P3S/c1-32(2,26(42)29(43)35-10-9-22(40)34-11-12-60-31(44)20-8-7-18-5-3-4-6-19(18)13-20)15-53-59(50,51)56-58(48,49)52-14-21-25(55-57(45,46)47)24(41)30(54-21)39-17-38-23-27(33)36-16-37-28(23)39/h3-8,13,16-17,21,24-26,30,41-42H,9-12,14-15H2,1-2H3,(H,34,40)(H,35,43)(H,48,49)(H,50,51)(H2,33,36,37)(H2,45,46,47)/t21-,24-,25-,26+,30-/m1/s1" J5H InChIKey InChI 1.03 DPWZDDZXXDPFNM-YGFBVEKBSA-N J5H 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)c4ccc5ccccc5c4" J5H 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)c4ccc5ccccc5c4" J5H SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "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)c4ccc5ccccc5c4)O" J5H SMILES "OpenEye OEToolkits" 2.0.6 "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)c4ccc5ccccc5c4)O" # _pdbx_chem_comp_identifier.comp_id J5H _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.6 _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] naphthalene-2-carbothioate" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site J5H "Create component" 2019-01-30 EBI J5H "Initial release" 2019-05-15 RCSB ##