data_KGJ # _chem_comp.id KGJ _chem_comp.name "[1-[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]ethylamino]-1-oxidanylidene-propan-2-ylidene]-bis(oxidanidyl)azanium" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C24 H39 N9 O19 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge -1 _chem_comp.pdbx_initial_date 2018-12-03 _chem_comp.pdbx_modified_date 2019-04-05 _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 850.537 _chem_comp.one_letter_code ? _chem_comp.three_letter_code KGJ _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 6N94 _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 KGJ N1 N1 N 0 1 Y N N 26.989 22.089 15.596 7.705 -5.932 3.529 N1 KGJ 1 KGJ C2 C1 C 0 1 Y N N 26.452 23.191 14.969 8.318 -4.764 3.456 C2 KGJ 2 KGJ N3 N2 N 0 1 Y N N 25.344 23.787 15.410 7.885 -3.786 2.689 N3 KGJ 3 KGJ C4 C2 C 0 1 Y N N 24.785 23.314 16.550 6.796 -3.941 1.944 C4 KGJ 4 KGJ C5 C3 C 0 1 Y N N 25.325 22.163 17.294 6.108 -5.165 1.985 C5 KGJ 5 KGJ C6 C4 C 0 1 Y N N 26.501 21.569 16.742 6.608 -6.179 2.820 C6 KGJ 6 KGJ N6 N3 N 0 1 N N N 27.056 20.544 17.397 5.974 -7.406 2.902 N6 KGJ 7 KGJ N7 N4 N 0 1 Y N N 24.525 21.911 18.369 5.051 -5.058 1.145 N7 KGJ 8 KGJ C8 C5 C 0 1 Y N N 23.562 22.852 18.347 5.046 -3.874 0.604 C8 KGJ 9 KGJ N9 N5 N 0 1 Y N N 23.741 23.676 17.256 6.102 -3.147 1.065 N9 KGJ 10 KGJ "C1'" C6 C 0 1 N N R 22.925 24.863 16.836 6.437 -1.771 0.691 "C1'" KGJ 11 KGJ "C2'" C7 C 0 1 N N R 21.492 24.437 16.534 7.412 -1.761 -0.507 "C2'" KGJ 12 KGJ "O2'" O1 O 0 1 N N N 21.283 23.786 15.241 8.756 -1.581 -0.058 "O2'" KGJ 13 KGJ "C3'" C8 C 0 1 N N S 20.836 25.790 16.755 6.957 -0.549 -1.352 "C3'" KGJ 14 KGJ "O3'" O2 O 0 1 N N N 20.916 26.522 15.539 8.006 0.416 -1.449 "O3'" KGJ 15 KGJ "C4'" C9 C 0 1 N N R 21.639 26.460 17.887 5.760 0.030 -0.563 "C4'" KGJ 16 KGJ "O4'" O3 O 0 1 N N N 22.997 25.920 17.863 5.261 -1.079 0.216 "O4'" KGJ 17 KGJ "C5'" C10 C 0 1 N N N 20.975 26.170 19.230 4.682 0.533 -1.525 "C5'" KGJ 18 KGJ "O5'" O4 O 0 1 N N N 20.517 24.818 19.157 3.640 1.168 -0.782 "O5'" KGJ 19 KGJ O31 O5 O 0 1 N N N 20.292 27.982 13.743 9.086 -0.275 -3.623 O31 KGJ 20 KGJ P3 P1 P 0 1 N N N 19.704 27.523 15.058 8.623 0.902 -2.855 P3 KGJ 21 KGJ O32 O6 O 0 1 N N N 19.722 28.658 16.077 7.493 1.682 -3.695 O32 KGJ 22 KGJ O33 O7 O 0 1 N N N 18.460 26.639 15.063 9.866 1.888 -2.583 O33 KGJ 23 KGJ P1 P2 P 0 1 N N N 19.112 24.191 19.567 2.339 1.817 -1.475 P1 KGJ 24 KGJ O11 O8 O 0 1 N N N 18.833 22.789 19.050 1.470 0.657 -2.176 O11 KGJ 25 KGJ O12 O9 O 0 1 N N N 18.232 25.308 19.048 2.763 2.801 -2.495 O12 KGJ 26 KGJ O6 O10 O 0 1 N N N 18.904 24.051 21.181 1.447 2.554 -0.356 O6 KGJ 27 KGJ P2 P3 P 0 1 N N N 18.344 22.828 22.086 0.240 3.618 -0.410 P2 KGJ 28 KGJ O21 O11 O 0 1 N N N 16.947 22.475 21.696 -0.736 3.204 -1.444 O21 KGJ 29 KGJ O22 O12 O 0 1 N N N 18.422 23.471 23.434 0.823 5.074 -0.775 O22 KGJ 30 KGJ O7 O13 O 0 1 N N N 19.162 21.430 22.154 -0.490 3.676 1.024 O7 KGJ 31 KGJ CPB C11 C 0 1 N N N 20.511 21.455 22.512 -1.666 4.449 1.268 CPB KGJ 32 KGJ CPA C12 C 0 1 N N N 21.114 20.193 21.973 -2.094 4.280 2.727 CPA KGJ 33 KGJ CP9 C13 C 0 1 N N N 20.547 19.011 22.750 -2.387 2.805 3.005 CP9 KGJ 34 KGJ CP8 C14 C 0 1 N N N 22.607 20.309 22.257 -0.969 4.758 3.647 CP8 KGJ 35 KGJ CP7 C15 C 0 1 N N R 20.847 20.061 20.456 -3.354 5.109 2.989 CP7 KGJ 36 KGJ OP3 O14 O 0 1 N N N 21.221 21.250 19.787 -3.058 6.495 2.807 OP3 KGJ 37 KGJ CP6 C16 C 0 1 N N N 21.658 18.968 19.866 -4.436 4.695 2.025 CP6 KGJ 38 KGJ OP2 O15 O 0 1 N N N 21.456 17.781 20.166 -4.765 5.439 1.126 OP2 KGJ 39 KGJ NP2 N6 N 0 1 N N N 22.675 19.364 19.112 -5.039 3.497 2.162 NP2 KGJ 40 KGJ CP5 C17 C 0 1 N N N 23.581 18.388 18.553 -6.017 3.051 1.167 CP5 KGJ 41 KGJ CP4 C18 C 0 1 N N N 24.441 17.772 19.625 -6.546 1.669 1.556 CP4 KGJ 42 KGJ CP3 C19 C 0 1 N N N 25.412 16.812 18.979 -7.552 1.210 0.533 CP3 KGJ 43 KGJ OP1 O16 O 0 1 N N N 24.981 15.789 18.511 -7.820 1.919 -0.415 OP1 KGJ 44 KGJ NP1 N7 N 0 1 N N N 26.696 17.130 18.928 -8.155 0.013 0.670 NP1 KGJ 45 KGJ CP2 C20 C 0 1 N N N 27.708 16.265 18.421 -9.133 -0.434 -0.325 CP2 KGJ 46 KGJ CP1 C21 C 0 1 N N N 28.435 16.813 17.253 -9.662 -1.816 0.064 CP1 KGJ 47 KGJ N N8 N 0 1 N N N 29.300 15.714 16.812 -10.641 -2.262 -0.932 N KGJ 48 KGJ CS1 C22 C 0 1 N N N 30.708 15.634 17.230 -11.243 -3.459 -0.794 CS1 KGJ 49 KGJ OS1 O17 O 0 1 N N N 31.212 16.420 18.009 -11.049 -4.126 0.200 OS1 KGJ 50 KGJ CS2 C23 C 0 1 N N N 31.541 14.589 16.587 -12.147 -3.964 -1.863 CS2 KGJ 51 KGJ CS3 C24 C 0 1 N N N 33.043 14.716 16.731 -12.298 -3.193 -3.149 CS3 KGJ 52 KGJ NS4 N9 N 1 1 N N N 31.027 13.681 15.846 -12.889 -5.210 -1.666 NS4 KGJ 53 KGJ OS4 O18 O -1 1 N N N 29.850 13.710 15.538 -13.656 -5.752 -2.725 OS4 KGJ 54 KGJ OS5 O19 O -1 1 N N N 31.740 12.849 15.337 -12.841 -5.872 -0.415 OS5 KGJ 55 KGJ H1 H1 H 0 1 N N N 26.944 23.585 14.092 9.206 -4.606 4.049 H1 KGJ 56 KGJ H2 H2 H 0 1 N N N 27.872 20.237 16.907 6.329 -8.098 3.482 H2 KGJ 57 KGJ H3 H3 H 0 1 N N N 27.312 20.837 18.318 5.174 -7.574 2.380 H3 KGJ 58 KGJ H4 H4 H 0 1 N N N 22.769 22.947 19.074 4.313 -3.520 -0.106 H4 KGJ 59 KGJ H5 H5 H 0 1 N N N 23.358 25.258 15.905 6.871 -1.242 1.540 H5 KGJ 60 KGJ H6 H6 H 0 1 N N N 21.160 23.759 17.334 7.320 -2.682 -1.082 H6 KGJ 61 KGJ H7 H7 H 0 1 N N N 21.741 22.954 15.227 9.093 -2.312 0.477 H7 KGJ 62 KGJ H8 H8 H 0 1 N N N 19.792 25.653 17.073 6.640 -0.872 -2.343 H8 KGJ 63 KGJ H9 H9 H 0 1 N N N 21.660 27.547 17.719 6.092 0.836 0.090 H9 KGJ 64 KGJ H10 H10 H 0 1 N N N 21.701 26.284 20.048 5.121 1.249 -2.220 H10 KGJ 65 KGJ H11 H11 H 0 1 N N N 20.128 26.853 19.393 4.271 -0.309 -2.082 H11 KGJ 66 KGJ H12 H12 H 0 1 N N N 20.102 29.434 15.681 7.143 2.466 -3.251 H12 KGJ 67 KGJ H13 H13 H 0 1 N N N 18.186 26.472 14.169 10.288 2.220 -3.387 H13 KGJ 68 KGJ H14 H14 H 0 1 N N N 18.105 22.815 18.440 1.158 -0.024 -1.565 H14 KGJ 69 KGJ H15 H15 H 0 1 N N N 17.550 23.539 23.804 1.470 5.409 -0.139 H15 KGJ 70 KGJ H16 H16 H 0 1 N N N 20.614 21.489 23.607 -1.457 5.501 1.070 H16 KGJ 71 KGJ H17 H17 H 0 1 N N N 21.006 22.332 22.070 -2.468 4.109 0.613 H17 KGJ 72 KGJ H18 H18 H 0 1 N N N 20.757 19.142 23.822 -2.758 2.693 4.024 H18 KGJ 73 KGJ H19 H19 H 0 1 N N N 19.460 18.957 22.593 -3.140 2.445 2.303 H19 KGJ 74 KGJ H20 H20 H 0 1 N N N 21.015 18.081 22.396 -1.473 2.224 2.885 H20 KGJ 75 KGJ H21 H21 H 0 1 N N N 22.768 20.401 23.341 -0.698 5.782 3.388 H21 KGJ 76 KGJ H22 H22 H 0 1 N N N 23.122 19.411 21.885 -1.307 4.724 4.683 H22 KGJ 77 KGJ H23 H23 H 0 1 N N N 23.009 21.198 21.749 -0.101 4.110 3.527 H23 KGJ 78 KGJ H24 H24 H 0 1 N N N 19.778 19.851 20.302 -3.693 4.940 4.011 H24 KGJ 79 KGJ H25 H25 H 0 1 N N N 20.723 21.980 20.136 -2.750 6.718 1.918 H25 KGJ 80 KGJ H26 H26 H 0 1 N N N 22.814 20.338 18.931 -4.825 2.931 2.920 H26 KGJ 81 KGJ H27 H27 H 0 1 N N N 22.997 17.596 18.061 -6.844 3.759 1.128 H27 KGJ 82 KGJ H28 H28 H 0 1 N N N 24.228 18.881 17.812 -5.540 2.995 0.189 H28 KGJ 83 KGJ H29 H29 H 0 1 N N N 24.997 18.561 20.152 -5.718 0.961 1.595 H29 KGJ 84 KGJ H30 H30 H 0 1 N N N 23.807 17.230 20.342 -7.023 1.725 2.535 H30 KGJ 85 KGJ H31 H31 H 0 1 N N N 26.972 18.030 19.265 -7.941 -0.554 1.428 H31 KGJ 86 KGJ H32 H32 H 0 1 N N N 27.236 15.317 18.122 -9.961 0.275 -0.364 H32 KGJ 87 KGJ H33 H33 H 0 1 N N N 28.435 16.075 19.224 -8.656 -0.489 -1.304 H33 KGJ 88 KGJ H34 H34 H 0 1 N N N 29.035 17.688 17.544 -8.835 -2.524 0.103 H34 KGJ 89 KGJ H35 H35 H 0 1 N N N 27.732 17.099 16.456 -10.139 -1.760 1.042 H35 KGJ 90 KGJ H36 H36 H 0 1 N N N 28.925 15.005 16.215 -10.854 -1.695 -1.689 H36 KGJ 91 KGJ H38 H38 H 0 1 N N N 33.278 15.552 17.406 -11.554 -3.537 -3.868 H38 KGJ 92 KGJ H39 H39 H 0 1 N N N 33.452 13.783 17.147 -13.297 -3.354 -3.555 H39 KGJ 93 KGJ H40 H40 H 0 1 N N N 33.491 14.905 15.744 -12.151 -2.131 -2.955 H40 KGJ 94 # # 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 KGJ O31 P3 DOUB N N 1 KGJ C2 N3 DOUB Y N 2 KGJ C2 N1 SING Y N 3 KGJ P3 O33 SING N N 4 KGJ P3 "O3'" SING N N 5 KGJ P3 O32 SING N N 6 KGJ "O2'" "C2'" SING N N 7 KGJ OS5 NS4 SING N N 8 KGJ N3 C4 SING Y N 9 KGJ OS4 NS4 SING N N 10 KGJ "O3'" "C3'" SING N N 11 KGJ N1 C6 DOUB Y N 12 KGJ NS4 CS2 DOUB N N 13 KGJ "C2'" "C3'" SING N N 14 KGJ "C2'" "C1'" SING N N 15 KGJ C4 N9 SING Y N 16 KGJ C4 C5 DOUB Y N 17 KGJ CS2 CS3 SING N N 18 KGJ CS2 CS1 SING N N 19 KGJ C6 C5 SING Y N 20 KGJ C6 N6 SING N N 21 KGJ "C3'" "C4'" SING N N 22 KGJ N CS1 SING N N 23 KGJ N CP1 SING N N 24 KGJ "C1'" N9 SING N N 25 KGJ "C1'" "O4'" SING N N 26 KGJ CS1 OS1 DOUB N N 27 KGJ CP1 CP2 SING N N 28 KGJ N9 C8 SING Y N 29 KGJ C5 N7 SING Y N 30 KGJ "O4'" "C4'" SING N N 31 KGJ "C4'" "C5'" SING N N 32 KGJ C8 N7 DOUB Y N 33 KGJ CP2 NP1 SING N N 34 KGJ OP1 CP3 DOUB N N 35 KGJ CP5 NP2 SING N N 36 KGJ CP5 CP4 SING N N 37 KGJ NP1 CP3 SING N N 38 KGJ CP3 CP4 SING N N 39 KGJ O12 P1 DOUB N N 40 KGJ O11 P1 SING N N 41 KGJ NP2 CP6 SING N N 42 KGJ "O5'" "C5'" SING N N 43 KGJ "O5'" P1 SING N N 44 KGJ P1 O6 SING N N 45 KGJ OP3 CP7 SING N N 46 KGJ CP6 OP2 DOUB N N 47 KGJ CP6 CP7 SING N N 48 KGJ CP7 CPA SING N N 49 KGJ O6 P2 SING N N 50 KGJ O21 P2 DOUB N N 51 KGJ CPA CP8 SING N N 52 KGJ CPA CPB SING N N 53 KGJ CPA CP9 SING N N 54 KGJ P2 O7 SING N N 55 KGJ P2 O22 SING N N 56 KGJ O7 CPB SING N N 57 KGJ C2 H1 SING N N 58 KGJ N6 H2 SING N N 59 KGJ N6 H3 SING N N 60 KGJ C8 H4 SING N N 61 KGJ "C1'" H5 SING N N 62 KGJ "C2'" H6 SING N N 63 KGJ "O2'" H7 SING N N 64 KGJ "C3'" H8 SING N N 65 KGJ "C4'" H9 SING N N 66 KGJ "C5'" H10 SING N N 67 KGJ "C5'" H11 SING N N 68 KGJ O32 H12 SING N N 69 KGJ O33 H13 SING N N 70 KGJ O11 H14 SING N N 71 KGJ O22 H15 SING N N 72 KGJ CPB H16 SING N N 73 KGJ CPB H17 SING N N 74 KGJ CP9 H18 SING N N 75 KGJ CP9 H19 SING N N 76 KGJ CP9 H20 SING N N 77 KGJ CP8 H21 SING N N 78 KGJ CP8 H22 SING N N 79 KGJ CP8 H23 SING N N 80 KGJ CP7 H24 SING N N 81 KGJ OP3 H25 SING N N 82 KGJ NP2 H26 SING N N 83 KGJ CP5 H27 SING N N 84 KGJ CP5 H28 SING N N 85 KGJ CP4 H29 SING N N 86 KGJ CP4 H30 SING N N 87 KGJ NP1 H31 SING N N 88 KGJ CP2 H32 SING N N 89 KGJ CP2 H33 SING N N 90 KGJ CP1 H34 SING N N 91 KGJ CP1 H35 SING N N 92 KGJ N H36 SING N N 93 KGJ CS3 H38 SING N N 94 KGJ CS3 H39 SING N N 95 KGJ CS3 H40 SING N N 96 # # 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 KGJ SMILES ACDLabs 12.01 "n1c(c2c(nc1)n(cn2)C3OC(C(C3O)OP(=O)(O)O)COP(OP(OCC(C)(C)C(O)C(=O)NCCC(=O)NCCNC(=O)/C(C)=[N+](\[O-])[O-])(O)=O)(O)=O)N" KGJ InChI InChI 1.03 "InChI=1S/C24H39N9O19P3/c1-12(33(39)40)21(37)28-7-6-26-14(34)4-5-27-22(38)18(36)24(2,3)9-49-55(46,47)52-54(44,45)48-8-13-17(51-53(41,42)43)16(35)23(50-13)32-11-31-15-19(25)29-10-30-20(15)32/h10-11,13,16-18,23,35-36H,4-9H2,1-3H3,(H9-,25,26,27,28,29,30,34,37,38,39,40,41,42,43,44,45,46,47)/q-1/t13-,16-,17-,18+,23-/m1/s1" KGJ InChIKey InChI 1.03 NCNYDGGYTDSUKJ-CUDSEXNASA-N KGJ SMILES_CANONICAL CACTVS 3.385 "CC(C(=O)NCCNC(=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)=[N+]([O-])[O-]" KGJ SMILES CACTVS 3.385 "CC(C(=O)NCCNC(=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)=[N+]([O-])[O-]" KGJ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(=[N+]([O-])[O-])C(=O)NCCNC(=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" KGJ SMILES "OpenEye OEToolkits" 2.0.7 "CC(=[N+]([O-])[O-])C(=O)NCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(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 KGJ "SYSTEMATIC NAME" ACDLabs 12.01 "[(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-20-(dioxido-lambda~5~-azanylidene)-3,5,9-trihydroxy-8,8,20-trimethyl-3,5-dioxido-10,14,19-trioxo-2,4,6-trioxa-11,15,18-triaza-3lambda~5~,5lambda~5~-diphosphaicos-1-yl]oxidanide (non-preferred name)" KGJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[1-[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]ethylamino]-1-oxidanylidene-propan-2-ylidene]-bis(oxidanidyl)azanium" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site KGJ "Create component" 2018-12-03 RCSB KGJ "Modify formal charge" 2019-02-25 RCSB KGJ "Initial release" 2019-04-10 RCSB ##