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 
# 
