data_UBG # _chem_comp.id UBG _chem_comp.name "[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name)" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C27 H34 N9 O18 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-05-06 _chem_comp.pdbx_modified_date 2020-05-15 _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 865.530 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UBG _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 6WUG _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 UBG PA P1 P 0 1 N N N 15.080 -2.789 17.152 -2.809 1.561 2.502 PA UBG 1 UBG O1A O1 O 0 1 N N N 13.886 -2.188 17.872 -3.450 0.945 3.845 O1A UBG 2 UBG O2A O2 O 0 1 N N N 16.019 -1.655 16.807 -2.794 3.038 2.595 O2A UBG 3 UBG O5B O3 O 0 1 N N N 14.566 -3.694 15.867 -3.692 1.113 1.232 O5B UBG 4 UBG C5B C1 C 0 1 N N N 15.584 -4.420 15.187 -5.045 1.528 1.039 C5B UBG 5 UBG C4B C2 C 0 1 N N R 14.992 -5.738 14.779 -5.584 0.925 -0.260 C4B UBG 6 UBG O4B O4 O 0 1 N N N 14.515 -6.524 15.893 -5.675 -0.504 -0.134 O4B UBG 7 UBG C3B C3 C 0 1 N N S 13.739 -5.481 13.954 -7.005 1.453 -0.533 C3B UBG 8 UBG O3B O5 O 0 1 N N N 14.105 -5.180 12.619 -7.049 2.152 -1.778 O3B UBG 9 UBG C2B C4 C 0 1 N N R 13.022 -6.793 13.993 -7.878 0.176 -0.598 C2B UBG 10 UBG O2B O6 O 0 1 N N N 13.486 -7.729 13.038 -8.837 0.267 -1.653 O2B UBG 11 UBG C1B C5 C 0 1 N N R 13.300 -7.226 15.346 -6.826 -0.921 -0.899 C1B UBG 12 UBG N9A N1 N 0 1 Y N N 12.343 -6.801 16.384 -7.301 -2.230 -0.444 N9A UBG 13 UBG C8A C6 C 0 1 Y N N 12.350 -5.696 17.146 -7.025 -2.816 0.756 C8A UBG 14 UBG N7A N2 N 0 1 Y N N 11.234 -5.682 17.902 -7.608 -3.977 0.829 N7A UBG 15 UBG C5A C7 C 0 1 Y N N 10.489 -6.799 17.577 -8.294 -4.209 -0.316 C5A UBG 16 UBG C6A C8 C 0 1 Y N N 9.263 -7.346 18.008 -9.090 -5.264 -0.794 C6A UBG 17 UBG N6A N3 N 0 1 N N N 8.496 -6.615 19.050 -9.313 -6.390 -0.021 N6A UBG 18 UBG N1A N4 N 0 1 Y N N 8.815 -8.482 17.479 -9.626 -5.154 -2.006 N1A UBG 19 UBG C2A C9 C 0 1 Y N N 9.508 -9.107 16.559 -9.419 -4.083 -2.750 C2A UBG 20 UBG N3A N5 N 0 1 Y N N 10.678 -8.649 16.114 -8.681 -3.072 -2.344 N3A UBG 21 UBG C4A C10 C 0 1 Y N N 11.186 -7.498 16.617 -8.109 -3.089 -1.144 C4A UBG 22 UBG N1 N6 N 0 1 N N N 12.636 -8.472 19.712 8.255 -2.398 0.942 N1 UBG 23 UBG C2 C11 C 0 1 N N N 12.990 -9.580 18.819 8.633 -3.674 0.960 C2 UBG 24 UBG O2 O7 O 0 1 N N N 14.073 -9.609 18.280 8.250 -4.370 1.884 O2 UBG 25 UBG N3 N7 N 0 1 N N N 12.022 -10.647 18.580 9.409 -4.240 0.026 N3 UBG 26 UBG C4 C12 C 0 1 N N N 10.738 -10.619 19.207 9.872 -3.530 -1.029 C4 UBG 27 UBG O4 O8 O 0 1 N N N 9.919 -11.539 18.980 10.576 -4.041 -1.878 O4 UBG 28 UBG C4X C13 C 0 1 N N N 10.374 -9.472 20.147 9.484 -2.104 -1.105 C4X UBG 29 UBG N5 N8 N 0 1 N N N 9.154 -9.434 20.744 9.875 -1.325 -2.081 N5 UBG 30 UBG C5X C14 C 0 1 Y N N 8.854 -8.395 21.564 9.505 -0.039 -2.120 C5X UBG 31 UBG C6 C15 C 0 1 Y N N 7.591 -8.353 22.194 9.937 0.783 -3.180 C6 UBG 32 UBG C7 C16 C 0 1 Y N N 7.271 -7.289 23.043 9.562 2.091 -3.222 C7 UBG 33 UBG C7M C17 C 0 1 N N N 5.901 -7.249 23.727 10.027 2.963 -4.359 C7M UBG 34 UBG C8 C18 C 0 1 Y N N 8.219 -6.255 23.272 8.753 2.632 -2.227 C8 UBG 35 UBG C8M C19 C 0 1 N N N 7.867 -5.074 24.218 8.352 4.083 -2.297 C8M UBG 36 UBG C9 C20 C 0 1 Y N N 9.477 -6.299 22.650 8.316 1.854 -1.179 C9 UBG 37 UBG C9A C21 C 0 1 Y N N 9.797 -7.371 21.795 8.686 0.513 -1.109 C9A UBG 38 UBG N10 N9 N 0 1 N N N 11.009 -7.411 21.188 8.250 -0.271 -0.061 N10 UBG 39 UBG C10 C22 C 0 1 N N N 11.314 -8.440 20.368 8.629 -1.579 -0.027 C10 UBG 40 UBG "C1'" C23 C 0 1 N N N 11.992 -6.354 21.419 7.400 0.291 0.992 "C1'" UBG 41 UBG "C2'" C24 C 0 1 N N S 13.187 -6.880 22.267 5.930 0.127 0.601 "C2'" UBG 42 UBG "O2'" O9 O 0 1 N N N 12.815 -6.911 23.619 5.684 0.815 -0.627 "O2'" UBG 43 UBG "C3'" C25 C 0 1 N N S 14.485 -5.948 22.162 5.042 0.714 1.701 "C3'" UBG 44 UBG "O3'" O10 O 0 1 N N N 14.179 -4.646 22.437 5.288 0.026 2.929 "O3'" UBG 45 UBG "C4'" C26 C 0 1 N N R 15.083 -5.967 20.812 3.572 0.551 1.310 "C4'" UBG 46 UBG "O4'" O11 O 0 1 N N N 15.146 -7.303 20.316 3.326 1.238 0.082 "O4'" UBG 47 UBG "C5'" C27 C 0 1 N N N 16.541 -5.419 20.908 2.684 1.137 2.409 "C5'" UBG 48 UBG "O5'" O12 O 0 1 N N N 17.076 -5.572 19.597 1.312 0.882 2.101 "O5'" UBG 49 UBG P P2 P 0 1 N N N 17.215 -4.112 18.759 0.098 1.359 3.044 P UBG 50 UBG O1P O13 O 0 1 N N N 18.154 -4.375 17.561 0.194 2.818 3.271 O1P UBG 51 UBG O2P O14 O 0 1 N N N 17.699 -2.983 19.647 0.180 0.589 4.456 O2P UBG 52 UBG O3P O15 O 0 1 N N N 15.697 -3.863 18.217 -1.304 1.019 2.328 O3P UBG 53 UBG O52 O16 O 0 1 N N N 13.982 -3.772 10.480 -6.772 4.536 -0.994 O52 UBG 54 UBG O53 O17 O 0 1 N N N 13.552 -2.604 12.660 -7.345 4.179 -3.426 O53 UBG 55 UBG O54 O18 O 0 1 N N N 11.908 -4.123 11.780 -9.114 3.760 -1.528 O54 UBG 56 UBG P51 P3 P 0 1 N N N 13.362 -3.896 11.888 -7.553 3.676 -1.911 P51 UBG 57 UBG H1 H1 H 0 1 N N N 13.998 -1.247 17.942 -3.492 -0.021 3.853 H1 UBG 58 UBG H2 H2 H 0 1 N N N 16.442 -4.583 15.856 -5.653 1.188 1.877 H2 UBG 59 UBG H3 H3 H 0 1 N N N 15.914 -3.863 14.297 -5.086 2.616 0.979 H3 UBG 60 UBG H4 H4 H 0 1 N N N 15.719 -6.308 14.182 -4.925 1.183 -1.089 H4 UBG 61 UBG H5 H5 H 0 1 N N N 13.131 -4.685 14.409 -7.335 2.100 0.281 H5 UBG 62 UBG H6 H6 H 0 1 N N N 11.943 -6.621 13.868 -8.370 -0.008 0.358 H6 UBG 63 UBG H7 H7 H 0 1 N N N 12.990 -8.535 13.117 -9.408 -0.510 -1.734 H7 UBG 64 UBG H8 H8 H 0 1 N N N 13.448 -8.315 15.384 -6.591 -0.946 -1.963 H8 UBG 65 UBG H9 H9 H 0 1 N N N 13.123 -4.942 17.152 -6.413 -2.380 1.532 H9 UBG 66 UBG H10 H10 H 0 1 N N N 7.651 -7.110 19.251 -8.917 -6.458 0.861 H10 UBG 67 UBG H11 H11 H 0 1 N N N 9.047 -6.544 19.881 -9.865 -7.111 -0.363 H11 UBG 68 UBG H12 H12 H 0 1 N N N 9.117 -10.026 16.147 -9.873 -4.035 -3.729 H12 UBG 69 UBG H14 H14 H 0 1 N N N 12.260 -11.404 17.972 9.644 -5.178 0.107 H14 UBG 70 UBG H15 H15 H 0 1 N N N 6.873 -9.141 22.020 10.565 0.375 -3.958 H15 UBG 71 UBG H16 H16 H 0 1 N N N 5.959 -7.768 24.695 9.303 2.917 -5.173 H16 UBG 72 UBG H17 H17 H 0 1 N N N 5.603 -6.203 23.889 10.119 3.993 -4.014 H17 UBG 73 UBG H18 H18 H 0 1 N N N 5.157 -7.747 23.088 10.996 2.611 -4.714 H18 UBG 74 UBG H19 H19 H 0 1 N N N 7.402 -4.264 23.637 7.420 4.175 -2.853 H19 UBG 75 UBG H20 H20 H 0 1 N N N 7.165 -5.420 24.991 8.214 4.471 -1.288 H20 UBG 76 UBG H21 H21 H 0 1 N N N 8.785 -4.702 24.697 9.134 4.652 -2.801 H21 UBG 77 UBG H22 H22 H 0 1 N N N 10.197 -5.513 22.827 7.689 2.283 -0.411 H22 UBG 78 UBG H23 H23 H 0 1 N N N 12.369 -5.995 20.450 7.587 -0.234 1.928 H23 UBG 79 UBG H24 H24 H 0 1 N N N 11.509 -5.524 21.955 7.627 1.349 1.116 H24 UBG 80 UBG H25 H25 H 0 1 N N N 13.457 -7.885 21.912 5.702 -0.931 0.477 H25 UBG 81 UBG H26 H26 H 0 1 N N N 13.541 -7.231 24.141 5.865 1.764 -0.590 H26 UBG 82 UBG H27 H27 H 0 1 N N N 15.222 -6.330 22.883 5.269 1.773 1.825 H27 UBG 83 UBG H28 H28 H 0 1 N N N 13.789 -4.588 23.302 5.106 -0.923 2.891 H28 UBG 84 UBG H29 H29 H 0 1 N N N 14.503 -5.324 20.133 3.344 -0.508 1.186 H29 UBG 85 UBG H30 H30 H 0 1 N N N 14.267 -7.658 20.249 3.507 2.187 0.119 H30 UBG 86 UBG H31 H31 H 0 1 N N N 17.126 -6.001 21.635 2.934 0.674 3.364 H31 UBG 87 UBG H32 H32 H 0 1 N N N 16.538 -4.359 21.204 2.847 2.213 2.473 H32 UBG 88 UBG H33 H33 H 0 1 N N N 18.511 -2.632 19.300 0.123 -0.373 4.383 H33 UBG 89 UBG H34 H34 H 0 1 N N N 14.016 -1.976 12.119 -7.628 5.091 -3.580 H34 UBG 90 UBG H35 H35 H 0 1 N N N 11.658 -4.145 10.864 -9.687 3.220 -2.089 H35 UBG 91 # # 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 UBG O52 P51 DOUB N N 1 UBG O54 P51 SING N N 2 UBG P51 O3B SING N N 3 UBG P51 O53 SING N N 4 UBG O3B C3B SING N N 5 UBG O2B C2B SING N N 6 UBG C3B C2B SING N N 7 UBG C3B C4B SING N N 8 UBG C2B C1B SING N N 9 UBG C4B C5B SING N N 10 UBG C4B O4B SING N N 11 UBG C5B O5B SING N N 12 UBG C1B O4B SING N N 13 UBG C1B N9A SING N N 14 UBG O5B PA SING N N 15 UBG N3A C2A DOUB Y N 16 UBG N3A C4A SING Y N 17 UBG N9A C4A SING Y N 18 UBG N9A C8A SING Y N 19 UBG C2A N1A SING Y N 20 UBG C4A C5A DOUB Y N 21 UBG O2A PA DOUB N N 22 UBG C8A N7A DOUB Y N 23 UBG PA O1A SING N N 24 UBG PA O3P SING N N 25 UBG N1A C6A DOUB Y N 26 UBG O1P P DOUB N N 27 UBG C5A N7A SING Y N 28 UBG C5A C6A SING Y N 29 UBG C6A N6A SING N N 30 UBG O3P P SING N N 31 UBG O2 C2 DOUB N N 32 UBG N3 C2 SING N N 33 UBG N3 C4 SING N N 34 UBG P "O5'" SING N N 35 UBG P O2P SING N N 36 UBG C2 N1 SING N N 37 UBG O4 C4 DOUB N N 38 UBG C4 C4X SING N N 39 UBG "O5'" "C5'" SING N N 40 UBG N1 C10 DOUB N N 41 UBG C4X N5 DOUB N N 42 UBG "O4'" "C4'" SING N N 43 UBG C10 N10 SING N N 44 UBG "C4'" "C5'" SING N N 45 UBG "C4'" "C3'" SING N N 46 UBG N10 "C1'" SING N N 47 UBG "C1'" "C2'" SING N N 48 UBG C5X C9A DOUB Y N 49 UBG C5X C6 SING Y N 50 UBG C9A C9 SING Y N 51 UBG "C3'" "C2'" SING N N 52 UBG "C3'" "O3'" SING N N 53 UBG C6 C7 DOUB Y N 54 UBG "C2'" "O2'" SING N N 55 UBG C9 C8 DOUB Y N 56 UBG C7 C8 SING Y N 57 UBG C7 C7M SING N N 58 UBG C8 C8M SING N N 59 UBG O1A H1 SING N N 60 UBG C5B H2 SING N N 61 UBG C5B H3 SING N N 62 UBG C4B H4 SING N N 63 UBG C3B H5 SING N N 64 UBG C2B H6 SING N N 65 UBG O2B H7 SING N N 66 UBG C1B H8 SING N N 67 UBG C8A H9 SING N N 68 UBG N6A H10 SING N N 69 UBG N6A H11 SING N N 70 UBG C2A H12 SING N N 71 UBG N3 H14 SING N N 72 UBG C6 H15 SING N N 73 UBG C7M H16 SING N N 74 UBG C7M H17 SING N N 75 UBG C7M H18 SING N N 76 UBG C8M H19 SING N N 77 UBG C8M H20 SING N N 78 UBG C8M H21 SING N N 79 UBG C9 H22 SING N N 80 UBG "C1'" H23 SING N N 81 UBG "C1'" H24 SING N N 82 UBG "C2'" H25 SING N N 83 UBG "O2'" H26 SING N N 84 UBG "C3'" H27 SING N N 85 UBG "O3'" H28 SING N N 86 UBG "C4'" H29 SING N N 87 UBG "O4'" H30 SING N N 88 UBG "C5'" H31 SING N N 89 UBG "C5'" H32 SING N N 90 UBG O2P H33 SING N N 91 UBG O53 H34 SING N N 92 UBG O54 H35 SING N N 93 UBG N10 C9A SING N N 94 UBG N5 C5X SING N N 95 UBG C4X C10 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 UBG SMILES ACDLabs 12.01 "P(O)(OP(OCC(C(C(CN2c3c(N=C1C(NC(N=C12)=O)=O)cc(c(C)c3)C)O)O)O)(O)=O)(=O)OCC4OC(C(C4OP(=O)(O)O)O)n5c6c(nc5)c(N)ncn6" UBG InChI InChI 1.03 "InChI=1S/C27H34N9O18P3/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(41)34-27(42)33-24)5-14(37)19(39)15(38)6-50-56(46,47)54-57(48,49)51-7-16-21(53-55(43,44)45)20(40)26(52-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-40H,5-7H2,1-2H3,(H,46,47)(H,48,49)(H2,28,29,30)(H,34,41,42)(H2,43,44,45)/t14-,15+,16+,19-,20+,21+,26+/m0/s1" UBG InChIKey InChI 1.03 QOJVPCDYXUQNMD-UYBVJOGSSA-N UBG SMILES_CANONICAL CACTVS 3.385 "Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O[P](O)(O)=O)n5cnc6c(N)ncnc56)c2cc1C" UBG SMILES CACTVS 3.385 "Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O[P](O)(O)=O)n5cnc6c(N)ncnc56)c2cc1C" UBG SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)OP(=O)(O)O)O)O)O" UBG SMILES "OpenEye OEToolkits" 2.0.7 "Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)OP(=O)(O)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 UBG "SYSTEMATIC NAME" ACDLabs 12.01 "[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name)" UBG "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-5-[7,8-dimethyl-2,4-bis(oxidanylidene)benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] 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 UBG "Create component" 2020-05-06 RCSB UBG "Initial release" 2020-05-20 RCSB ##