data_YOA # _chem_comp.id YOA _chem_comp.name "5'-{[(2R,3S)-3-amino-2-({2-[(N-{(2R)-4-[(dihydroxyphosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-beta-alanyl)amino]ethyl}sulfanyl)-4-sulfanylbutane-1-sulfonyl]amino}-5'-deoxyadenosine" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C25 H44 N9 O12 P S3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-03-16 _chem_comp.pdbx_modified_date 2022-06-29 _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 789.839 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ? _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 7LY7 _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 YOA C11 C1 C 0 1 N N R -3.638 61.354 -9.605 -9.141 0.573 -0.639 C11 YOA 1 YOA C13 C2 C 0 1 N N R -4.466 60.887 -11.736 -7.418 2.048 -0.175 C13 YOA 2 YOA C14 C3 C 0 1 N N N -4.534 59.797 -12.796 -6.047 2.006 0.505 C14 YOA 3 YOA C17 C4 C 0 1 N N N -4.126 55.918 -12.239 -3.018 0.851 1.114 C17 YOA 4 YOA C18 C5 C 0 1 N N R -3.300 54.824 -12.930 -1.561 1.013 1.553 C18 YOA 5 YOA C19 C6 C 0 1 N N S -1.790 55.046 -12.866 -1.222 -0.052 2.598 C19 YOA 6 YOA C02 C7 C 0 1 Y N N 0.378 60.861 -6.893 -11.657 -3.578 -1.304 C02 YOA 7 YOA C04 C8 C 0 1 Y N N -0.640 62.951 -6.705 -12.896 -1.663 -1.663 C04 YOA 8 YOA C06 C9 C 0 1 Y N N -1.612 61.370 -8.118 -10.697 -1.380 -1.057 C06 YOA 9 YOA C07 C10 C 0 1 Y N N -0.610 60.475 -7.787 -10.544 -2.775 -1.001 C07 YOA 10 YOA C09 C11 C 0 1 Y N N -1.965 59.529 -9.203 -8.634 -1.894 -0.474 C09 YOA 11 YOA C21 C12 C 0 1 N N N -1.221 55.626 -14.156 -1.368 -1.442 1.976 C21 YOA 12 YOA C24 C13 C 0 1 N N N -5.373 53.136 -11.869 1.156 1.279 0.772 C24 YOA 13 YOA C25 C14 C 0 1 N N N -5.643 52.602 -10.467 2.222 1.051 -0.301 C25 YOA 14 YOA C27 C15 C 0 1 N N N -5.224 50.277 -9.911 4.633 1.305 -0.546 C27 YOA 15 YOA C28 C16 C 0 1 N N N -5.783 48.876 -9.873 5.984 1.689 -0.001 C28 YOA 16 YOA C29 C17 C 0 1 N N N -7.296 48.961 -9.720 7.051 1.460 -1.074 C29 YOA 17 YOA C31 C18 C 0 1 N N N -8.163 49.169 -7.467 9.462 1.714 -1.318 C31 YOA 18 YOA C32 C19 C 0 1 N N R -8.712 48.451 -6.272 10.826 1.991 -0.739 C32 YOA 19 YOA C34 C20 C 0 1 N N N -10.234 48.524 -6.225 11.208 0.865 0.224 C34 YOA 20 YOA C35 C21 C 0 1 N N N -10.844 48.920 -7.564 12.556 1.186 0.874 C35 YOA 21 YOA C36 C22 C 0 1 N N N -10.645 49.528 -5.153 10.137 0.737 1.309 C36 YOA 22 YOA C37 C23 C 0 1 N N N -10.758 47.141 -5.874 11.314 -0.452 -0.547 C37 YOA 23 YOA C53 C24 C 0 1 N N S -3.285 61.821 -11.921 -8.518 2.346 0.867 C53 YOA 24 YOA C55 C25 C 0 1 N N R -3.179 62.450 -10.552 -9.474 1.133 0.767 C55 YOA 25 YOA N01 N1 N 0 1 N N N 1.372 60.005 -6.553 -11.566 -4.958 -1.266 N01 YOA 26 YOA N03 N2 N 0 1 Y N N 0.340 62.103 -6.369 -12.800 -2.980 -1.624 N03 YOA 27 YOA N05 N3 N 0 1 Y N N -1.607 62.605 -7.563 -11.880 -0.873 -1.392 N05 YOA 28 YOA N08 N4 N 0 1 Y N N -0.846 59.338 -8.468 -9.262 -3.021 -0.640 N08 YOA 29 YOA N10 N5 N 0 1 Y N N -2.432 60.761 -8.981 -9.477 -0.851 -0.720 N10 YOA 30 YOA N15 N6 N 0 1 N N N -4.909 58.506 -12.200 -5.005 1.826 -0.509 N15 YOA 31 YOA N20 N7 N 0 1 N N N -1.106 53.772 -12.574 -2.139 0.073 3.739 N20 YOA 32 YOA N26 N8 N 0 1 N N N -5.998 51.198 -10.476 3.536 1.424 0.228 N26 YOA 33 YOA N30 N9 N 0 1 N N N -7.750 48.396 -8.467 8.365 1.833 -0.544 N30 YOA 34 YOA O12 O1 O 0 1 N N N -4.307 60.373 -10.410 -7.715 0.766 -0.754 O12 YOA 35 YOA O33 O2 O 0 1 N N N -8.298 47.079 -6.319 11.786 2.061 -1.795 O33 YOA 36 YOA O38 O3 O 0 1 N N N -11.801 47.287 -4.915 11.672 -1.503 0.353 O38 YOA 37 YOA O40 O4 O 0 1 N N N -13.688 45.773 -5.832 10.651 -3.494 -0.815 O40 YOA 38 YOA O48 O5 O 0 1 N N N -13.726 48.180 -6.387 13.130 -3.124 -1.117 O48 YOA 39 YOA O49 O6 O 0 1 N N N -8.097 50.389 -7.493 9.351 1.385 -2.480 O49 YOA 40 YOA O50 O7 O 0 1 N N N -4.120 50.524 -9.453 4.532 0.889 -1.681 O50 YOA 41 YOA O51 O8 O 0 1 N N N -2.528 57.898 -11.964 -3.430 3.406 0.464 O51 YOA 42 YOA O52 O9 O 0 1 N N N -3.517 57.693 -14.034 -2.716 1.865 -1.336 O52 YOA 43 YOA O54 O10 O 0 1 N N N -3.548 62.805 -12.922 -9.205 3.554 0.536 O54 YOA 44 YOA O56 O11 O 0 1 N N N -4.070 63.563 -10.462 -10.838 1.552 0.839 O56 YOA 45 YOA P39 P1 P 0 1 N N N -13.367 47.170 -5.313 11.871 -3.030 -0.117 P39 YOA 46 YOA S16 S1 S 0 1 N N N -3.734 57.498 -12.634 -3.420 2.113 -0.126 S16 YOA 47 YOA S22 S2 S 0 1 N N N -0.601 57.309 -13.913 -0.966 -2.704 3.215 S22 YOA 48 YOA S23 S3 S 0 1 N N N -3.637 53.288 -12.122 -0.471 0.817 0.116 S23 YOA 49 YOA H1 H1 H 0 1 N N N -4.308 61.770 -8.839 -9.668 1.134 -1.411 H1 YOA 50 YOA H2 H2 H 0 1 N N N -5.390 61.481 -11.792 -7.424 2.815 -0.949 H2 YOA 51 YOA H3 H3 H 0 1 N N N -3.549 59.699 -13.275 -5.878 2.941 1.038 H3 YOA 52 YOA H4 H4 H 0 1 N N N -5.283 60.076 -13.551 -6.016 1.175 1.209 H4 YOA 53 YOA H5 H5 H 0 1 N N N -5.182 55.758 -12.502 -3.159 -0.140 0.682 H5 YOA 54 YOA H6 H6 H 0 1 N N N -3.997 55.801 -11.153 -3.673 0.968 1.977 H6 YOA 55 YOA H7 H7 H 0 1 N N N -3.621 54.718 -13.977 -1.419 2.003 1.984 H7 YOA 56 YOA H8 H8 H 0 1 N N N -1.583 55.755 -12.051 -0.196 0.087 2.939 H8 YOA 57 YOA H9 H9 H 0 1 N N N -0.650 63.940 -6.272 -13.844 -1.219 -1.927 H9 YOA 58 YOA H10 H10 H 0 1 N N N -2.411 58.801 -9.865 -7.598 -1.798 -0.185 H10 YOA 59 YOA H11 H11 H 0 1 N N N -2.013 55.644 -14.919 -2.394 -1.582 1.635 H11 YOA 60 YOA H12 H12 H 0 1 N N N -0.394 54.987 -14.500 -0.688 -1.535 1.129 H12 YOA 61 YOA H13 H13 H 0 1 N N N -5.847 54.122 -11.982 1.382 0.668 1.645 H13 YOA 62 YOA H14 H14 H 0 1 N N N -5.791 52.441 -12.612 1.147 2.331 1.057 H14 YOA 63 YOA H15 H15 H 0 1 N N N -4.737 52.735 -9.857 2.231 -0.002 -0.587 H15 YOA 64 YOA H16 H16 H 0 1 N N N -6.471 53.174 -10.023 1.995 1.662 -1.175 H16 YOA 65 YOA H17 H17 H 0 1 N N N -5.534 48.352 -10.808 5.976 2.741 0.284 H17 YOA 66 YOA H18 H18 H 0 1 N N N -5.354 48.329 -9.020 6.211 1.077 0.873 H18 YOA 67 YOA H19 H19 H 0 1 N N N -7.598 50.018 -9.762 7.059 0.408 -1.359 H19 YOA 68 YOA H20 H20 H 0 1 N N N -7.768 48.412 -10.548 6.824 2.071 -1.947 H20 YOA 69 YOA H21 H21 H 0 1 N N N -8.314 48.925 -5.363 10.807 2.939 -0.201 H21 YOA 70 YOA H22 H22 H 0 1 N N N -11.940 48.957 -7.472 12.458 2.078 1.492 H22 YOA 71 YOA H23 H23 H 0 1 N N N -10.468 49.910 -7.860 12.870 0.347 1.494 H23 YOA 72 YOA H24 H24 H 0 1 N N N -10.565 48.179 -8.327 13.300 1.363 0.097 H24 YOA 73 YOA H25 H25 H 0 1 N N N -10.202 49.238 -4.189 9.204 0.398 0.860 H25 YOA 74 YOA H26 H26 H 0 1 N N N -10.288 50.530 -5.433 10.463 0.014 2.057 H26 YOA 75 YOA H27 H27 H 0 1 N N N -11.741 49.541 -5.064 9.982 1.706 1.783 H27 YOA 76 YOA H28 H28 H 0 1 N N N -11.150 46.651 -6.778 10.354 -0.680 -1.009 H28 YOA 77 YOA H29 H29 H 0 1 N N N -9.946 46.532 -5.450 12.078 -0.360 -1.320 H29 YOA 78 YOA H30 H30 H 0 1 N N N -2.376 61.245 -12.149 -8.088 2.412 1.867 H30 YOA 79 YOA H31 H31 H 0 1 N N N -2.139 62.737 -10.336 -9.253 0.398 1.541 H31 YOA 80 YOA H32 H32 H 0 1 N N N 1.991 60.452 -5.907 -12.342 -5.501 -1.474 H32 YOA 81 YOA H33 H33 H 0 1 N N N 0.979 59.189 -6.129 -10.726 -5.382 -1.032 H33 YOA 82 YOA H34 H34 H 0 1 N N N -4.961 58.579 -11.204 -5.243 1.539 -1.404 H34 YOA 83 YOA H35 H35 H 0 1 N N N -1.472 53.383 -11.729 -2.123 1.009 4.115 H35 YOA 84 YOA H36 H36 H 0 1 N N N -1.256 53.133 -13.328 -3.077 -0.197 3.480 H36 YOA 85 YOA H38 H38 H 0 1 N N N -6.848 50.914 -10.919 3.616 1.756 1.136 H38 YOA 86 YOA H39 H39 H 0 1 N N N -7.753 47.403 -8.351 8.445 2.166 0.364 H39 YOA 87 YOA H40 H40 H 0 1 N N N -8.643 46.618 -5.564 11.856 1.250 -2.317 H40 YOA 88 YOA H41 H41 H 0 1 N Y N -13.468 45.130 -5.168 12.268 -4.893 0.962 H41 YOA 89 YOA H42 H42 H 0 1 N N N -14.071 47.726 -7.147 13.965 -2.834 -0.726 H42 YOA 90 YOA H43 H43 H 0 1 N N N -2.792 63.373 -13.015 -9.908 3.790 1.158 H43 YOA 91 YOA H44 H44 H 0 1 N N N -4.001 63.956 -9.600 -11.072 1.991 1.668 H44 YOA 92 YOA H45 H45 H 0 1 N N N -1.407 57.765 -13.001 -1.135 -3.856 2.540 H45 YOA 93 YOA O1 O99 O 0 1 N Y N ? ? ? 12.139 -3.957 1.171 O1 YOA 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 YOA C21 S22 SING N N 1 YOA C21 C19 SING N N 2 YOA O52 S16 DOUB N N 3 YOA C18 C19 SING N N 4 YOA C18 C17 SING N N 5 YOA C18 S23 SING N N 6 YOA O54 C53 SING N N 7 YOA C19 N20 SING N N 8 YOA C14 N15 SING N N 9 YOA C14 C13 SING N N 10 YOA S16 C17 SING N N 11 YOA S16 N15 SING N N 12 YOA S16 O51 DOUB N N 13 YOA S23 C24 SING N N 14 YOA C53 C13 SING N N 15 YOA C53 C55 SING N N 16 YOA C24 C25 SING N N 17 YOA C13 O12 SING N N 18 YOA C55 O56 SING N N 19 YOA C55 C11 SING N N 20 YOA N26 C25 SING N N 21 YOA N26 C27 SING N N 22 YOA O12 C11 SING N N 23 YOA C27 C28 SING N N 24 YOA C27 O50 DOUB N N 25 YOA C28 C29 SING N N 26 YOA C29 N30 SING N N 27 YOA C11 N10 SING N N 28 YOA C09 N10 SING Y N 29 YOA C09 N08 DOUB Y N 30 YOA N10 C06 SING Y N 31 YOA N08 C07 SING Y N 32 YOA N30 C31 SING N N 33 YOA C06 C07 DOUB Y N 34 YOA C06 N05 SING Y N 35 YOA C07 C02 SING Y N 36 YOA C35 C34 SING N N 37 YOA N05 C04 DOUB Y N 38 YOA O49 C31 DOUB N N 39 YOA C31 C32 SING N N 40 YOA C02 N01 SING N N 41 YOA C02 N03 DOUB Y N 42 YOA C04 N03 SING Y N 43 YOA O48 P39 SING N N 44 YOA O33 C32 SING N N 45 YOA C32 C34 SING N N 46 YOA C34 C37 SING N N 47 YOA C34 C36 SING N N 48 YOA C37 O38 SING N N 49 YOA O40 P39 DOUB N N 50 YOA P39 O38 SING N N 51 YOA C11 H1 SING N N 52 YOA C13 H2 SING N N 53 YOA C14 H3 SING N N 54 YOA C14 H4 SING N N 55 YOA C17 H5 SING N N 56 YOA C17 H6 SING N N 57 YOA C18 H7 SING N N 58 YOA C19 H8 SING N N 59 YOA C04 H9 SING N N 60 YOA C09 H10 SING N N 61 YOA C21 H11 SING N N 62 YOA C21 H12 SING N N 63 YOA C24 H13 SING N N 64 YOA C24 H14 SING N N 65 YOA C25 H15 SING N N 66 YOA C25 H16 SING N N 67 YOA C28 H17 SING N N 68 YOA C28 H18 SING N N 69 YOA C29 H19 SING N N 70 YOA C29 H20 SING N N 71 YOA C32 H21 SING N N 72 YOA C35 H22 SING N N 73 YOA C35 H23 SING N N 74 YOA C35 H24 SING N N 75 YOA C36 H25 SING N N 76 YOA C36 H26 SING N N 77 YOA C36 H27 SING N N 78 YOA C37 H28 SING N N 79 YOA C37 H29 SING N N 80 YOA C53 H30 SING N N 81 YOA C55 H31 SING N N 82 YOA N01 H32 SING N N 83 YOA N01 H33 SING N N 84 YOA N15 H34 SING N N 85 YOA N20 H35 SING N N 86 YOA N20 H36 SING N N 87 YOA N26 H38 SING N N 88 YOA N30 H39 SING N N 89 YOA O33 H40 SING N N 90 YOA O48 H42 SING N N 91 YOA O54 H43 SING N N 92 YOA O56 H44 SING N N 93 YOA S22 H45 SING N N 94 YOA P39 O1 SING N N 95 YOA O1 H41 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 YOA 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)CS" YOA InChI InChI 1.06 "InChI=1S/C25H44N9O12PS3/c1-25(2,10-45-47(40,41)42)20(38)23(39)29-4-3-16(35)28-5-6-49-15(13(26)8-48)9-50(43,44)33-7-14-18(36)19(37)24(46-14)34-12-32-17-21(27)30-11-31-22(17)34/h11-15,18-20,24,33,36-38,48H,3-10,26H2,1-2H3,(H,28,35)(H,29,39)(H2,27,30,31)(H2,40,41,42)/t13-,14+,15-,18+,19+,20-,24+/m0/s1" YOA InChIKey InChI 1.06 DMSHVJWQIKPFOK-DROAMXOMSA-N YOA 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)[C@@H](N)CS" YOA 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)[CH](N)CS" YOA 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)[C@H](CS)N)O" YOA 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)C(CS)N)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 YOA "SYSTEMATIC NAME" ACDLabs 12.01 "5'-{[(2R,3S)-3-amino-2-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}-4-sulfanylbutane-1-sulfonyl]amino}-5'-deoxyadenosine" YOA "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(3~{R})-4-[[3-[2-[(2~{R},3~{S})-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-sulfanyl-butan-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 YOA "Create component" 2021-03-16 RCSB YOA "Initial release" 2022-02-02 RCSB YOA "Other modification" 2022-06-29 RCSB #