data_QXD # _chem_comp.id QXD _chem_comp.name "5'-deoxy-5'-({[(2R)-2-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}-2-(3-hydroxyphenyl)ethyl]sulfonyl}amino)adenosine" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C29 H43 N8 O13 P S2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-01-13 _chem_comp.pdbx_modified_date 2020-06-19 _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 806.801 _chem_comp.one_letter_code ? _chem_comp.three_letter_code QXD _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 6VHY _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 QXD C10 C1 C 0 1 N N R -6.886 90.986 35.030 10.885 1.945 -1.100 C10 QXD 1 QXD C15 C2 C 0 1 N N N -5.276 89.736 38.473 7.105 1.408 -1.353 C15 QXD 2 QXD C17 C3 C 0 1 N N N -3.168 88.504 37.313 4.702 1.226 -0.768 C17 QXD 3 QXD C20 C4 C 0 1 N N N -1.988 86.435 38.297 2.299 0.956 -0.470 C20 QXD 4 QXD C21 C5 C 0 1 N N N -1.347 86.919 39.628 1.261 1.137 0.640 C21 QXD 5 QXD C24 C6 C 0 1 N N N 2.412 86.664 39.586 -2.916 0.764 1.035 C24 QXD 6 QXD C02 C7 C 0 1 N N N -8.012 92.017 34.713 11.269 0.831 -0.123 C02 QXD 7 QXD C03 C8 C 0 1 N N N -7.955 93.275 35.569 10.346 0.882 1.096 C03 QXD 8 QXD C04 C9 C 0 1 N N N -7.862 92.459 33.157 11.125 -0.526 -0.816 C04 QXD 9 QXD O13 O1 O 0 1 N N N -7.748 90.212 37.203 9.368 1.389 -2.820 O13 QXD 10 QXD C16 C10 C 0 1 N N N -4.126 88.644 38.550 6.067 1.589 -0.243 C16 QXD 11 QXD N19 N1 N 0 1 N N N -2.177 87.456 37.235 3.626 1.309 0.040 N19 QXD 12 QXD C23 C11 C 0 1 N N R 1.553 86.364 40.843 -1.457 0.973 1.444 C23 QXD 13 QXD C29 C12 C 0 1 N N N 4.429 86.880 36.759 -5.969 1.837 0.393 C29 QXD 14 QXD C30 C13 C 0 1 N N R 5.955 86.618 36.796 -7.348 1.816 -0.270 C30 QXD 15 QXD O31 O2 O 0 1 N N N 6.626 87.860 36.334 -7.679 0.478 -0.701 O31 QXD 16 QXD N33 N2 N 0 1 Y N N 7.199 89.516 37.863 -9.622 -0.908 -0.787 N33 QXD 17 QXD C36 C14 C 0 1 Y N N 6.883 91.695 38.554 -10.868 -2.728 -1.017 C36 QXD 18 QXD C37 C15 C 0 1 Y N N 7.086 93.107 38.468 -11.996 -3.450 -1.442 C37 QXD 19 QXD C40 C16 C 0 1 Y N N 8.442 92.738 36.627 -12.854 -1.508 -2.347 C40 QXD 20 QXD C42 C17 C 0 1 Y N N 7.541 90.865 37.579 -10.810 -1.355 -1.308 C42 QXD 21 QXD C01 C18 C 0 1 N N N -9.369 91.346 34.865 12.719 1.023 0.326 C01 QXD 22 QXD C12 C19 C 0 1 N N N -6.784 90.459 36.525 9.508 1.678 -1.650 C12 QXD 23 QXD C32 C20 C 0 1 N N R 7.601 88.239 37.160 -9.116 0.466 -0.837 C32 QXD 24 QXD C34 C21 C 0 1 Y N N 6.352 89.628 38.990 -9.001 -1.976 -0.210 C34 QXD 25 QXD C43 C22 C 0 1 N N R 7.967 87.057 38.160 -9.634 1.273 0.375 C43 QXD 26 QXD C45 C23 C 0 1 N N S 6.593 86.384 38.194 -8.443 2.182 0.756 C45 QXD 27 QXD C47 C24 C 0 1 Y N N 1.374 87.481 41.894 -1.096 -0.002 2.534 C47 QXD 28 QXD C48 C25 C 0 1 Y N N 1.548 87.290 43.276 -1.186 -1.362 2.303 C48 QXD 29 QXD C49 C26 C 0 1 Y N N 1.373 88.327 44.201 -0.856 -2.259 3.302 C49 QXD 30 QXD C50 C27 C 0 1 Y N N 1.018 89.617 43.805 -0.434 -1.798 4.534 C50 QXD 31 QXD C51 C28 C 0 1 Y N N 0.840 89.813 42.431 -0.341 -0.434 4.768 C51 QXD 32 QXD C53 C29 C 0 1 Y N N 1.010 88.791 41.504 -0.669 0.464 3.763 C53 QXD 33 QXD N14 N3 N 0 1 N N N -5.470 90.240 37.112 8.432 1.761 -0.843 N14 QXD 34 QXD N28 N4 N 0 1 N N N 3.469 85.813 37.089 -4.937 1.606 -0.621 N28 QXD 35 QXD N35 N5 N 0 1 Y N N 6.143 90.878 39.414 -9.733 -3.043 -0.346 N35 QXD 36 QXD N38 N6 N 0 1 N N N 6.498 94.042 39.365 -12.109 -4.805 -1.184 N38 QXD 37 QXD N39 N7 N 0 1 Y N N 7.873 93.636 37.493 -12.953 -2.801 -2.098 N39 QXD 38 QXD N41 N8 N 0 1 Y N N 8.350 91.377 36.576 -11.816 -0.792 -1.969 N41 QXD 39 QXD O05 O3 O 0 1 N N N -7.316 91.438 32.429 11.483 -1.566 0.096 O05 QXD 40 QXD O08 O4 O 0 1 N N N -6.794 90.265 30.137 12.036 -4.001 0.921 O08 QXD 41 QXD O09 O5 O 0 1 N N N -9.097 89.928 31.310 9.930 -3.572 -0.594 O09 QXD 42 QXD O11 O6 O 0 1 N N N -5.583 91.465 34.750 11.828 1.983 -2.173 O11 QXD 43 QXD O18 O7 O 0 1 N N N -3.242 89.288 36.392 4.572 0.859 -1.916 O18 QXD 44 QXD O26 O8 O 0 1 N N N 1.947 84.364 38.472 -3.372 3.266 0.227 O26 QXD 45 QXD O27 O9 O 0 1 N N N 4.136 84.697 39.236 -2.659 1.622 -1.478 O27 QXD 46 QXD O44 O10 O 0 1 N N N 8.769 86.130 37.465 -10.767 2.061 0.005 O44 QXD 47 QXD O46 O11 O 0 1 N N N 6.808 84.971 38.375 -8.805 3.559 0.633 O46 QXD 48 QXD O52 O12 O 0 1 N N N 0.483 91.108 42.066 0.073 0.022 5.980 O52 QXD 49 QXD P06 P1 P 0 1 N N N -7.982 90.855 30.877 11.449 -3.127 -0.297 P06 QXD 50 QXD S22 S1 S 0 1 N N N -0.169 85.676 40.384 -0.382 0.700 0.008 S22 QXD 51 QXD S25 S2 S 0 1 N N N 3.006 85.317 38.611 -3.351 1.938 -0.278 S25 QXD 52 QXD H1 H1 H 0 1 N N N -7.077 90.104 34.401 10.889 2.902 -0.579 H1 QXD 53 QXD H2 H2 H 0 1 N N N -5.009 90.578 39.128 7.107 0.370 -1.683 H2 QXD 54 QXD H3 H3 H 0 1 N N N -6.217 89.285 38.821 6.854 2.056 -2.193 H3 QXD 55 QXD H4 H4 H 0 1 N N N -2.977 86.017 38.537 2.301 -0.083 -0.800 H4 QXD 56 QXD H5 H5 H 0 1 N N N -1.345 85.643 37.886 2.048 1.604 -1.311 H5 QXD 57 QXD H6 H6 H 0 1 N N N -0.793 87.848 39.430 1.512 0.489 1.480 H6 QXD 58 QXD H7 H7 H 0 1 N N N -2.152 87.119 40.350 1.259 2.176 0.970 H7 QXD 59 QXD H8 H8 H 0 1 N N N 3.293 87.229 39.925 -3.049 -0.255 0.671 H8 QXD 60 QXD H9 H9 H 0 1 N N N 1.803 87.297 38.924 -3.562 0.928 1.898 H9 QXD 61 QXD H10 H10 H 0 1 N N N -8.055 93.002 36.630 10.362 1.885 1.522 H10 QXD 62 QXD H11 H11 H 0 1 N N N -6.992 93.783 35.410 9.329 0.632 0.793 H11 QXD 63 QXD H12 H12 H 0 1 N N N -8.777 93.949 35.285 10.689 0.164 1.841 H12 QXD 64 QXD H13 H13 H 0 1 N N N -7.210 93.342 33.091 10.092 -0.663 -1.136 H13 QXD 65 QXD H14 H14 H 0 1 N N N -8.854 92.705 32.751 11.783 -0.562 -1.684 H14 QXD 66 QXD H15 H15 H 0 1 N N N -4.610 87.668 38.703 6.318 0.941 0.597 H15 QXD 67 QXD H16 H16 H 0 1 N N N -3.502 88.885 39.423 6.065 2.628 0.087 H16 QXD 68 QXD H17 H17 H 0 1 N N N -1.590 87.416 36.427 3.730 1.603 0.958 H17 QXD 69 QXD H18 H18 H 0 1 N N N 2.035 85.520 41.359 -1.324 1.992 1.808 H18 QXD 70 QXD H19 H19 H 0 1 N N N 4.236 87.703 37.462 -5.806 2.807 0.863 H19 QXD 71 QXD H20 H20 H 0 1 N N N 4.193 87.208 35.736 -5.918 1.054 1.149 H20 QXD 72 QXD H21 H21 H 0 1 N N N 6.202 85.776 36.132 -7.373 2.506 -1.114 H21 QXD 73 QXD H22 H22 H 0 1 N N N 9.063 93.179 35.861 -13.654 -1.019 -2.883 H22 QXD 74 QXD H23 H23 H 0 1 N N N -9.508 91.031 35.910 12.808 1.962 0.872 H23 QXD 75 QXD H24 H24 H 0 1 N N N -10.162 92.056 34.587 13.011 0.197 0.974 H24 QXD 76 QXD H25 H25 H 0 1 N N N -9.418 90.466 34.207 13.370 1.048 -0.548 H25 QXD 77 QXD H26 H26 H 0 1 N N N 8.513 88.454 36.585 -9.414 0.946 -1.769 H26 QXD 78 QXD H27 H27 H 0 1 N N N 5.908 88.769 39.471 -8.042 -1.941 0.286 H27 QXD 79 QXD H28 H28 H 0 1 N N N 8.335 87.402 39.138 -9.884 0.606 1.199 H28 QXD 80 QXD H29 H29 H 0 1 N N N 5.962 86.816 38.985 -8.106 1.964 1.769 H29 QXD 81 QXD H30 H30 H 0 1 N N N 1.826 86.311 43.636 -1.516 -1.724 1.341 H30 QXD 82 QXD H31 H31 H 0 1 N N N 1.517 88.122 45.252 -0.928 -3.321 3.118 H31 QXD 83 QXD H32 H32 H 0 1 N N N 0.888 90.418 44.518 -0.176 -2.499 5.314 H32 QXD 84 QXD H33 H33 H 0 1 N N N 0.860 89.003 40.456 -0.594 1.526 3.941 H33 QXD 85 QXD H34 H34 H 0 1 N N N -4.662 90.443 36.560 8.536 2.055 0.075 H34 QXD 86 QXD H35 H35 H 0 1 N N N 2.619 86.082 36.636 -5.182 1.258 -1.492 H35 QXD 87 QXD H36 H36 H 0 1 N N N 6.778 94.968 39.112 -11.405 -5.267 -0.704 H36 QXD 88 QXD H37 H37 H 0 1 N N N 5.502 93.970 39.316 -12.893 -5.292 -1.483 H37 QXD 89 QXD H38 H38 H 0 1 N N N -6.650 90.749 29.332 12.045 -4.953 0.754 H38 QXD 90 QXD H39 H39 H 0 1 N N N -9.929 90.267 31.002 9.332 -3.454 0.156 H39 QXD 91 QXD H40 H40 H 0 1 N N N -4.946 90.794 34.963 11.878 1.162 -2.682 H40 QXD 92 QXD H41 H41 H 0 1 N N N 9.000 85.414 38.044 -11.132 2.589 0.728 H41 QXD 93 QXD H42 H42 H 0 1 N N N 6.008 84.566 38.689 -9.490 3.842 1.254 H42 QXD 94 QXD H43 H43 H 0 1 N N N 0.419 91.650 42.843 1.030 0.146 6.047 H43 QXD 95 QXD O1 O13 O 0 1 N N N -8.582 92.082 30.054 12.273 -3.350 -1.506 O1 QXD 96 # # 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 QXD O08 P06 SING N N 1 QXD P06 O09 SING N N 2 QXD P06 O05 SING N N 3 QXD O05 C04 SING N N 4 QXD C04 C02 SING N N 5 QXD C02 C01 SING N N 6 QXD C02 C10 SING N N 7 QXD C02 C03 SING N N 8 QXD O11 C10 SING N N 9 QXD C10 C12 SING N N 10 QXD O31 C30 SING N N 11 QXD O31 C32 SING N N 12 QXD O18 C17 DOUB N N 13 QXD C12 N14 SING N N 14 QXD C12 O13 DOUB N N 15 QXD N41 C40 DOUB Y N 16 QXD N41 C42 SING Y N 17 QXD C40 N39 SING Y N 18 QXD C29 C30 SING N N 19 QXD C29 N28 SING N N 20 QXD C30 C45 SING N N 21 QXD N28 S25 SING N N 22 QXD N14 C15 SING N N 23 QXD C32 N33 SING N N 24 QXD C32 C43 SING N N 25 QXD N19 C17 SING N N 26 QXD N19 C20 SING N N 27 QXD C17 C16 SING N N 28 QXD O44 C43 SING N N 29 QXD N39 C37 DOUB Y N 30 QXD C42 N33 SING Y N 31 QXD C42 C36 DOUB Y N 32 QXD N33 C34 SING Y N 33 QXD C43 C45 SING N N 34 QXD C45 O46 SING N N 35 QXD C20 C21 SING N N 36 QXD C37 C36 SING Y N 37 QXD C37 N38 SING N N 38 QXD O26 S25 DOUB N N 39 QXD C15 C16 SING N N 40 QXD C36 N35 SING Y N 41 QXD S25 O27 DOUB N N 42 QXD S25 C24 SING N N 43 QXD C34 N35 DOUB Y N 44 QXD C24 C23 SING N N 45 QXD C21 S22 SING N N 46 QXD S22 C23 SING N N 47 QXD C23 C47 SING N N 48 QXD C53 C47 DOUB Y N 49 QXD C53 C51 SING Y N 50 QXD C47 C48 SING Y N 51 QXD O52 C51 SING N N 52 QXD C51 C50 DOUB Y N 53 QXD C48 C49 DOUB Y N 54 QXD C50 C49 SING Y N 55 QXD C10 H1 SING N N 56 QXD C15 H2 SING N N 57 QXD C15 H3 SING N N 58 QXD C20 H4 SING N N 59 QXD C20 H5 SING N N 60 QXD C21 H6 SING N N 61 QXD C21 H7 SING N N 62 QXD C24 H8 SING N N 63 QXD C24 H9 SING N N 64 QXD C03 H10 SING N N 65 QXD C03 H11 SING N N 66 QXD C03 H12 SING N N 67 QXD C04 H13 SING N N 68 QXD C04 H14 SING N N 69 QXD C16 H15 SING N N 70 QXD C16 H16 SING N N 71 QXD N19 H17 SING N N 72 QXD C23 H18 SING N N 73 QXD C29 H19 SING N N 74 QXD C29 H20 SING N N 75 QXD C30 H21 SING N N 76 QXD C40 H22 SING N N 77 QXD C01 H23 SING N N 78 QXD C01 H24 SING N N 79 QXD C01 H25 SING N N 80 QXD C32 H26 SING N N 81 QXD C34 H27 SING N N 82 QXD C43 H28 SING N N 83 QXD C45 H29 SING N N 84 QXD C48 H30 SING N N 85 QXD C49 H31 SING N N 86 QXD C50 H32 SING N N 87 QXD C53 H33 SING N N 88 QXD N14 H34 SING N N 89 QXD N28 H35 SING N N 90 QXD N38 H36 SING N N 91 QXD N38 H37 SING N N 92 QXD O08 H38 SING N N 93 QXD O09 H39 SING N N 94 QXD O11 H40 SING N N 95 QXD O44 H41 SING N N 96 QXD O46 H42 SING N N 97 QXD O52 H43 SING N N 98 QXD P06 O1 DOUB N N 99 # # 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 QXD SMILES ACDLabs 12.01 "C(C(=O)NCCC(NCCSC(CS(NCC1C(C(C(O1)n2cnc3c(N)ncnc23)O)O)(=O)=O)c4cccc(c4)O)=O)(C(C)(C)COP(O)(O)=O)O" QXD InChI InChI 1.03 "InChI=1S/C29H43N8O13PS2/c1-29(2,13-49-51(44,45)46)24(42)27(43)32-7-6-20(39)31-8-9-52-19(16-4-3-5-17(38)10-16)12-53(47,48)36-11-18-22(40)23(41)28(50-18)37-15-35-21-25(30)33-14-34-26(21)37/h3-5,10,14-15,18-19,22-24,28,36,38,40-42H,6-9,11-13H2,1-2H3,(H,31,39)(H,32,43)(H2,30,33,34)(H2,44,45,46)/t18-,19+,22-,23-,24+,28-/m1/s1" QXD InChIKey InChI 1.03 ADMPPCCGBBJHMD-XCYBABBZSA-N QXD SMILES_CANONICAL CACTVS 3.385 "CC(C)(CO[P](O)(O)=O)[C@@H](O)C(=O)NCCC(=O)NCCS[C@@H](C[S](=O)(=O)NC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)c4cccc(O)c4" QXD SMILES CACTVS 3.385 "CC(C)(CO[P](O)(O)=O)[CH](O)C(=O)NCCC(=O)NCCS[CH](C[S](=O)(=O)NC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)c4cccc(O)c4" QXD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)(COP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCS[C@@H](CS(=O)(=O)NC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)c4cccc(c4)O)O" QXD SMILES "OpenEye OEToolkits" 2.0.7 "CC(C)(COP(=O)(O)O)C(C(=O)NCCC(=O)NCCSC(CS(=O)(=O)NCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)c4cccc(c4)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 QXD "SYSTEMATIC NAME" ACDLabs 12.01 "5'-deoxy-5'-({[(2R)-2-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}-2-(3-hydroxyphenyl)ethyl]sulfonyl}amino)adenosine" QXD "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(3~{R})-4-[[3-[2-[(1~{R})-2-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfamoyl]-1-(3-hydroxyphenyl)ethyl]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 QXD "Create component" 2020-01-13 RCSB QXD "Modify coordinates" 2020-01-15 RCSB QXD "Modify coordinates" 2020-01-27 RCSB QXD "Initial release" 2020-06-24 RCSB ##