data_DG9 # _chem_comp.id DG9 _chem_comp.name "5'-({[(2R,3R)-3-amino-2-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-{[oxido(oxo)phosphonio]oxy}butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}-4-methylpentyl]sulfonyl}amino)-5'-deoxyadenosine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C27 H48 N9 O12 P S2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-01-30 _chem_comp.pdbx_modified_date 2022-06-22 _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 785.827 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DG9 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 4DG9 _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 DG9 C C C 0 1 N N R -1.958 -35.577 -2.977 -1.975 -0.221 1.678 C DG9 1 DG9 N N N 0 1 N N N -1.008 -32.723 -1.170 -5.008 1.340 -0.588 N DG9 2 DG9 S S S 0 1 N N N -0.077 -33.729 -1.983 -3.420 1.234 -0.133 S DG9 3 DG9 C1 C1 C 0 1 N N N -0.802 -35.223 -2.027 -3.405 -0.029 1.169 C1 DG9 4 DG9 N1 N1 N 0 1 Y N N -8.728 -30.949 2.282 -13.775 -1.349 -1.771 N1 DG9 5 DG9 O1 O1 O 0 1 N N N -0.950 -32.021 3.300 -8.652 4.134 0.163 O1 DG9 6 DG9 C2 C2 C 0 1 Y N N -7.874 -29.940 2.527 -13.528 -0.055 -1.858 C2 DG9 7 DG9 N2 N2 N 0 1 N N N -2.493 -37.683 -1.826 -2.527 -2.537 2.252 N2 DG9 8 DG9 O2 O2 O 0 1 N N N -2.142 -29.598 2.848 -10.759 2.641 0.481 O2 DG9 9 DG9 C3 C3 C 0 1 N N N -1.234 -33.029 0.229 -6.011 1.826 0.363 C3 DG9 10 DG9 N3 N3 N 0 1 Y N N -6.575 -30.003 2.203 -12.344 0.458 -1.599 N3 DG9 11 DG9 O3 O3 O 0 1 N N N -3.804 -27.392 -14.058 15.370 2.573 -0.800 O3 DG9 12 DG9 C4 C4 C 0 1 Y N N -6.077 -31.109 1.593 -11.333 -0.323 -1.233 C4 DG9 13 DG9 C5 C5 C 0 1 Y N N -6.929 -32.167 1.325 -11.544 -1.708 -1.125 C5 DG9 14 DG9 C6 C6 C 0 1 Y N N -8.279 -32.070 1.681 -12.826 -2.208 -1.412 C6 DG9 15 DG9 N6 N6 N 0 1 N N N -9.153 -33.079 1.440 -13.094 -3.562 -1.322 N6 DG9 16 DG9 N7 N7 N 0 1 Y N N -6.177 -33.123 0.737 -10.369 -2.262 -0.742 N7 DG9 17 DG9 C8 C8 C 0 1 Y N N -4.902 -32.677 0.641 -9.472 -1.329 -0.611 C8 DG9 18 DG9 N9 N9 N 0 1 Y N N -4.848 -31.446 1.158 -10.017 -0.114 -0.903 N9 DG9 19 DG9 CA CA C 0 1 N N R -2.992 -36.298 -2.094 -1.963 -1.286 2.776 CA DG9 20 DG9 CB CB C 0 1 N N N -4.444 -36.364 -2.571 -2.803 -0.805 3.961 CB DG9 21 DG9 "C1'" "C1'" C 0 1 N N R -3.627 -30.605 1.248 -9.326 1.177 -0.871 "C1'" DG9 22 DG9 S1P S1P S 0 1 N N N -2.615 -34.255 -3.961 -0.913 -0.754 0.308 S1P DG9 23 DG9 "C2'" "C2'" C 0 1 N N R -2.951 -30.766 2.605 -9.549 1.882 0.492 "C2'" DG9 24 DG9 P2A P2A P 0 1 N N N -4.163 -27.721 -15.487 14.881 1.172 -0.176 P2A DG9 25 DG9 C2P C2P C 0 1 N N N -3.159 -35.067 -5.437 0.753 -0.643 1.017 C2P DG9 26 DG9 O2P O2P O 0 1 N N N 0.277 -33.189 -3.259 -2.753 0.759 -1.295 O2P DG9 27 DG9 "C3'" "C3'" C 0 1 N N S -2.072 -31.984 2.404 -8.314 2.811 0.582 "C3'" DG9 28 DG9 C3P C3P C 0 1 N N N -2.139 -35.057 -6.574 1.790 -0.942 -0.068 C3P DG9 29 DG9 O3P O3P O 0 1 N N N 1.100 -33.919 -1.190 -3.124 2.513 0.410 O3P DG9 30 DG9 "C4'" "C4'" C 0 1 N N R -1.622 -31.764 0.968 -7.296 2.181 -0.389 "C4'" DG9 31 DG9 "O4'" "O4'" O 0 1 N N N -2.692 -31.088 0.287 -7.896 0.989 -0.923 "O4'" DG9 32 DG9 O4A O4A O 0 1 N N N -3.132 -27.712 -16.582 14.913 1.253 1.302 O4A DG9 33 DG9 N4P N4P N 0 1 N N N -2.369 -33.940 -7.468 3.136 -0.853 0.504 N4P DG9 34 DG9 C5P C5P C 0 1 N N N -2.736 -34.074 -8.739 4.214 -1.079 -0.271 C5P DG9 35 DG9 O5P O5P O 0 1 N N N -2.976 -35.144 -9.273 4.071 -1.356 -1.444 O5P DG9 36 DG9 O6A O6A O 0 1 N N N -4.969 -29.119 -15.588 13.378 0.862 -0.664 O6A DG9 37 DG9 C6P C6P C 0 1 N N N -2.851 -32.793 -9.526 5.598 -0.987 0.317 C6P DG9 38 DG9 C7P C7P C 0 1 N N N -4.305 -32.595 -9.930 6.635 -1.286 -0.767 C7P DG9 39 DG9 N8P N8P N 0 1 N N N -4.466 -31.551 -10.921 7.981 -1.197 -0.195 N8P DG9 40 DG9 C9P C9P C 0 1 N N N -4.347 -31.803 -12.222 9.059 -1.423 -0.971 C9P DG9 41 DG9 O9P O9P O 0 1 N N N -4.114 -32.916 -12.657 8.923 -1.602 -2.162 O9P DG9 42 DG9 CAP CAP C 0 1 N N R -4.513 -30.642 -13.165 10.436 -1.453 -0.357 CAP DG9 43 DG9 OAP OAP O 0 1 N N N -4.581 -29.421 -12.432 10.324 -1.393 1.066 OAP DG9 44 DG9 CBP CBP C 0 1 N N N -5.761 -30.771 -14.039 11.244 -0.254 -0.857 CBP DG9 45 DG9 CCP CCP C 0 1 N N N -6.052 -29.428 -14.707 12.624 -0.258 -0.197 CCP DG9 46 DG9 CDP CDP C 0 1 N N N -5.447 -31.837 -15.075 11.405 -0.346 -2.376 CDP DG9 47 DG9 CEP CEP C 0 1 N N N -6.980 -31.198 -13.232 10.510 1.040 -0.499 CEP DG9 48 DG9 CG1 CG1 C 0 1 N N N -4.727 -37.534 -3.506 -2.774 -1.861 5.069 CG1 DG9 49 DG9 CG2 CG2 C 0 1 N N N -5.359 -36.457 -1.354 -2.229 0.509 4.494 CG2 DG9 50 DG9 H H H 0 1 N N N -1.576 -36.310 -3.702 -1.603 0.721 2.081 H DG9 51 DG9 HN HN H 0 1 N N N -0.588 -31.817 -1.218 -5.275 1.081 -1.484 HN DG9 52 DG9 H1 H1 H 0 1 N N N -1.182 -35.403 -1.011 -3.777 -0.971 0.766 H1 DG9 53 DG9 H1A H1A H 0 1 N N N 0.001 -35.941 -2.250 -4.044 0.291 1.993 H1A DG9 54 DG9 HO1 HO1 H 0 1 N N N -0.435 -32.801 3.131 -9.333 4.557 0.706 HO1 DG9 55 DG9 H2 H2 H 0 1 N N N -8.249 -29.046 3.002 -14.328 0.608 -2.154 H2 DG9 56 DG9 HN2 HN2 H 0 1 N N N -3.152 -38.170 -1.252 -2.471 -3.274 2.938 HN2 DG9 57 DG9 HN2A HN2A H 0 0 N N N -2.381 -38.170 -2.692 -3.478 -2.403 1.941 HN2A DG9 58 DG9 HO2 HO2 H 0 1 N N N -1.712 -29.680 3.691 -10.942 3.101 1.312 HO2 DG9 59 DG9 H3 H3 H 0 1 N N N -2.045 -33.768 0.316 -6.223 1.049 1.097 H3 DG9 60 DG9 H3A H3A H 0 1 N N N -0.313 -33.442 0.667 -5.631 2.712 0.871 H3A DG9 61 DG9 HN6 HN6 H 0 1 N N N -10.061 -32.819 1.768 -13.982 -3.895 -1.523 HN6 DG9 62 DG9 HN6A HN6A H 0 0 N N N -9.192 -33.258 0.457 -12.392 -4.179 -1.059 HN6A DG9 63 DG9 H8 H8 H 0 1 N N N -4.071 -33.223 0.219 -8.446 -1.492 -0.315 H8 DG9 64 DG9 HA HA H 0 1 N N N -3.002 -35.768 -1.130 -0.938 -1.458 3.104 HA DG9 65 DG9 HB HB H 0 1 N N N -4.674 -35.431 -3.106 -3.832 -0.647 3.637 HB DG9 66 DG9 "H1'" "H1'" H 0 1 N N N -3.873 -29.547 1.074 -9.663 1.812 -1.691 "H1'" DG9 67 DG9 "H2'" "H2'" H 0 1 N N N -3.692 -30.936 3.400 -9.553 1.158 1.307 "H2'" DG9 68 DG9 H2P H2P H 0 1 N N N -3.388 -36.114 -5.189 0.916 0.361 1.408 H2P DG9 69 DG9 H2PA H2PA H 0 0 N N N -4.072 -34.565 -5.789 0.853 -1.369 1.824 H2PA DG9 70 DG9 "H3'" "H3'" H 0 1 N N N -2.673 -32.902 2.476 -7.919 2.822 1.598 "H3'" DG9 71 DG9 H3P H3P H 0 1 N N N -1.128 -34.975 -6.149 1.627 -1.946 -0.460 H3P DG9 72 DG9 H3PA H3PA H 0 0 N N N -2.224 -35.995 -7.142 1.690 -0.217 -0.876 H3PA DG9 73 DG9 "H4'" "H4'" H 0 1 N N N -0.742 -31.104 0.990 -7.073 2.880 -1.195 "H4'" DG9 74 DG9 HN4P HN4P H 0 0 N N N -2.245 -33.015 -7.108 3.250 -0.632 1.442 HN4P DG9 75 DG9 H6P H6P H 0 1 N N N -2.521 -31.947 -8.905 5.761 0.017 0.709 H6P DG9 76 DG9 H6PA H6PA H 0 0 N N N -2.222 -32.854 -10.426 5.698 -1.712 1.125 H6PA DG9 77 DG9 H7P H7P H 0 1 N N N -4.688 -33.539 -10.346 6.472 -2.290 -1.159 H7P DG9 78 DG9 H7PA H7PA H 0 0 N N N -4.886 -32.326 -9.036 6.535 -0.561 -1.575 H7PA DG9 79 DG9 HN8P HN8P H 0 0 N N N -4.671 -30.620 -10.621 8.095 -0.975 0.743 HN8P DG9 80 DG9 HAP HAP H 0 1 N N N -3.638 -30.615 -13.831 10.940 -2.376 -0.643 HAP DG9 81 DG9 HOAP HOAP H 0 0 N N N -4.686 -28.694 -13.035 9.884 -0.596 1.393 HOAP DG9 82 DG9 HCP HCP H 0 1 N N N -6.143 -28.644 -13.941 13.146 -1.180 -0.451 HCP DG9 83 DG9 HCPA HCPA H 0 0 N N N -6.989 -29.493 -15.279 12.509 -0.193 0.886 HCPA DG9 84 DG9 HDP HDP H 0 1 N N N -6.315 -31.973 -15.736 10.435 -0.208 -2.853 HDP DG9 85 DG9 HDPA HDPA H 0 0 N N N -4.578 -31.524 -15.672 12.091 0.431 -2.716 HDPA DG9 86 DG9 HDPB HDPB H 0 0 N N N -5.220 -32.786 -14.567 11.805 -1.325 -2.641 HDPB DG9 87 DG9 HEP HEP H 0 1 N N N -7.852 -31.278 -13.898 10.395 1.105 0.583 HEP DG9 88 DG9 HEPA HEPA H 0 0 N N N -6.786 -32.174 -12.764 11.086 1.894 -0.856 HEPA DG9 89 DG9 HEPB HEPB H 0 0 N N N -7.183 -30.450 -12.451 9.527 1.043 -0.970 HEPB DG9 90 DG9 HG1 HG1 H 0 1 N N N -5.785 -37.517 -3.806 -1.745 -2.019 5.393 HG1 DG9 91 DG9 HG1A HG1A H 0 0 N N N -4.091 -37.451 -4.400 -3.372 -1.519 5.913 HG1A DG9 92 DG9 HG1B HG1B H 0 0 N N N -4.509 -38.479 -2.987 -3.183 -2.797 4.689 HG1B DG9 93 DG9 HG2 HG2 H 0 1 N N N -6.407 -36.505 -1.685 -1.207 0.347 4.836 HG2 DG9 94 DG9 HG2A HG2A H 0 0 N N N -5.114 -37.363 -0.780 -2.233 1.255 3.700 HG2A DG9 95 DG9 HG2B HG2B H 0 0 N N N -5.216 -35.570 -0.719 -2.839 0.861 5.326 HG2B DG9 96 DG9 O4 O4 O 0 1 N Y N ? ? ? 15.859 -0.007 -0.670 O4 DG9 97 DG9 H4 H4 H 0 1 N N N -2.876 -27.196 -14.001 16.269 2.823 -0.548 H4 DG9 98 DG9 H5 H5 H 0 1 N Y N ? ? ? 15.888 -0.118 -1.630 H5 DG9 99 # 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 DG9 C C1 SING N N 1 DG9 C CA SING N N 2 DG9 C S1P SING N N 3 DG9 N S SING N N 4 DG9 N C3 SING N N 5 DG9 S C1 SING N N 6 DG9 S O2P DOUB N N 7 DG9 S O3P DOUB N N 8 DG9 N1 C2 DOUB Y N 9 DG9 N1 C6 SING Y N 10 DG9 O1 "C3'" SING N N 11 DG9 C2 N3 SING Y N 12 DG9 N2 CA SING N N 13 DG9 O2 "C2'" SING N N 14 DG9 C3 "C4'" SING N N 15 DG9 N3 C4 DOUB Y N 16 DG9 O3 P2A SING N N 17 DG9 C4 C5 SING Y N 18 DG9 C4 N9 SING Y N 19 DG9 C5 C6 DOUB Y N 20 DG9 C5 N7 SING Y N 21 DG9 C6 N6 SING N N 22 DG9 N7 C8 DOUB Y N 23 DG9 C8 N9 SING Y N 24 DG9 N9 "C1'" SING N N 25 DG9 CA CB SING N N 26 DG9 CB CG1 SING N N 27 DG9 CB CG2 SING N N 28 DG9 "C1'" "C2'" SING N N 29 DG9 "C1'" "O4'" SING N N 30 DG9 S1P C2P SING N N 31 DG9 "C2'" "C3'" SING N N 32 DG9 P2A O4A DOUB N N 33 DG9 P2A O6A SING N N 34 DG9 C2P C3P SING N N 35 DG9 "C3'" "C4'" SING N N 36 DG9 C3P N4P SING N N 37 DG9 "C4'" "O4'" SING N N 38 DG9 N4P C5P SING N N 39 DG9 C5P O5P DOUB N N 40 DG9 C5P C6P SING N N 41 DG9 O6A CCP SING N N 42 DG9 C6P C7P SING N N 43 DG9 C7P N8P SING N N 44 DG9 N8P C9P SING N N 45 DG9 C9P O9P DOUB N N 46 DG9 C9P CAP SING N N 47 DG9 CAP OAP SING N N 48 DG9 CAP CBP SING N N 49 DG9 CBP CCP SING N N 50 DG9 CBP CDP SING N N 51 DG9 CBP CEP SING N N 52 DG9 C H SING N N 53 DG9 N HN SING N N 54 DG9 C1 H1 SING N N 55 DG9 C1 H1A SING N N 56 DG9 O1 HO1 SING N N 57 DG9 C2 H2 SING N N 58 DG9 N2 HN2 SING N N 59 DG9 N2 HN2A SING N N 60 DG9 O2 HO2 SING N N 61 DG9 C3 H3 SING N N 62 DG9 C3 H3A SING N N 63 DG9 N6 HN6 SING N N 64 DG9 N6 HN6A SING N N 65 DG9 C8 H8 SING N N 66 DG9 CA HA SING N N 67 DG9 CB HB SING N N 68 DG9 "C1'" "H1'" SING N N 69 DG9 "C2'" "H2'" SING N N 70 DG9 C2P H2P SING N N 71 DG9 C2P H2PA SING N N 72 DG9 "C3'" "H3'" SING N N 73 DG9 C3P H3P SING N N 74 DG9 C3P H3PA SING N N 75 DG9 "C4'" "H4'" SING N N 76 DG9 N4P HN4P SING N N 77 DG9 C6P H6P SING N N 78 DG9 C6P H6PA SING N N 79 DG9 C7P H7P SING N N 80 DG9 C7P H7PA SING N N 81 DG9 N8P HN8P SING N N 82 DG9 CAP HAP SING N N 83 DG9 OAP HOAP SING N N 84 DG9 CCP HCP SING N N 85 DG9 CCP HCPA SING N N 86 DG9 CDP HDP SING N N 87 DG9 CDP HDPA SING N N 88 DG9 CDP HDPB SING N N 89 DG9 CEP HEP SING N N 90 DG9 CEP HEPA SING N N 91 DG9 CEP HEPB SING N N 92 DG9 CG1 HG1 SING N N 93 DG9 CG1 HG1A SING N N 94 DG9 CG1 HG1B SING N N 95 DG9 CG2 HG2 SING N N 96 DG9 CG2 HG2A SING N N 97 DG9 CG2 HG2B SING N N 98 DG9 P2A O4 SING N N 99 DG9 O3 H4 SING N N 100 DG9 O4 H5 SING N N 101 # 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 DG9 SMILES ACDLabs 12.01 "O=P(O)(O)OCC(C)(C)C(O)C(=O)NCCC(=O)NCCSC(CS(=O)(=O)NCC1OC(n2cnc3c(N)ncnc32)C(O)C1O)C(N)C(C)C" DG9 InChI InChI 1.06 "InChI=1S/C27H48N9O12PS2/c1-14(2)18(28)16(50-8-7-30-17(37)5-6-31-25(41)22(40)27(3,4)11-47-49(42,43)44)10-51(45,46)35-9-15-20(38)21(39)26(48-15)36-13-34-19-23(29)32-12-33-24(19)36/h12-16,18,20-22,26,35,38-40H,5-11,28H2,1-4H3,(H,30,37)(H,31,41)(H2,29,32,33)(H2,42,43,44)/t15-,16+,18-,20-,21-,22+,26-/m1/s1" DG9 InChIKey InChI 1.06 LAWRAYXGFUHBCH-AWSFPXBRSA-N DG9 SMILES_CANONICAL CACTVS 3.385 "CC(C)[C@@H](N)[C@H](C[S](=O)(=O)NC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(O)=O" DG9 SMILES CACTVS 3.385 "CC(C)[CH](N)[CH](C[S](=O)(=O)NC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(O)=O" DG9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)[C@H]([C@H](CS(=O)(=O)NC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)O)O)N" DG9 SMILES "OpenEye OEToolkits" 2.0.7 "CC(C)C(C(CS(=O)(=O)NCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)O)O)N" # 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 DG9 "SYSTEMATIC NAME" ACDLabs 12.01 "5'-{[(2R,3R)-3-amino-2-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}-4-methylpentane-1-sulfonyl]amino}-5'-deoxyadenosine" DG9 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(3~{R})-4-[[3-[2-[(2~{R},3~{R})-1-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfamoyl]-3-azanyl-4-methyl-pentan-2-yl]sulfanylethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen 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 DG9 "Create component" 2012-01-30 RCSB DG9 "Modify leaving atom flag" 2022-06-22 RCSB #