data_YDZ
# 
_chem_comp.id                                    YDZ 
_chem_comp.name                                  
;[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanyl-purin-7-ium-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl hydrogen phosphate
;
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C22 H32 N10 O16 P3 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2016-11-11 
_chem_comp.pdbx_modified_date                    2017-12-15 
_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                        817.533 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YDZ 
_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        5M83 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  EBI 
# 
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 
YDZ C1  C2    C 0 1 Y N N 8.569   2.784  1.981  -8.545  -4.119 1.319  C1  YDZ 1  
YDZ C2  C8    C 0 1 Y N N 7.585   -0.594 -0.756 -6.655  -0.106 1.318  C2  YDZ 2  
YDZ C3  C4    C 0 1 Y N N 7.666   1.052  0.659  -7.401  -2.152 0.966  C3  YDZ 3  
YDZ C4  C5    C 0 1 Y N N 8.935   0.792  0.173  -7.913  -1.651 2.175  C4  YDZ 4  
YDZ C5  C6    C 0 1 Y N N 10.036  1.540  0.596  -8.761  -2.476 2.930  C5  YDZ 5  
YDZ N1  N6A   N 0 1 N N N -12.616 0.034  1.731  8.808   -4.636 -3.650 N1  YDZ 6  
YDZ C6  C6A   C 0 1 Y N N -11.486 0.703  1.033  8.634   -4.468 -2.287 C6  YDZ 7  
YDZ N2  N1A   N 0 1 Y N N -11.661 1.914  0.443  9.075   -5.381 -1.428 N2  YDZ 8  
YDZ C7  C2A   C 0 1 Y N N -10.642 2.527  -0.192 8.913   -5.229 -0.126 C7  YDZ 9  
YDZ N3  N3A   N 0 1 Y N N -9.424  1.955  -0.258 8.314   -4.179 0.394  N3  YDZ 10 
YDZ C8  C4A   C 0 1 Y N N -9.196  0.741  0.317  7.841   -3.213 -0.388 C8  YDZ 11 
YDZ C9  C5A   C 0 1 Y N N -10.233 0.093  0.976  7.993   -3.325 -1.780 C9  YDZ 12 
YDZ N4  N7A   N 0 1 Y N N -9.745  -1.071 1.446  7.431   -2.224 -2.333 N4  YDZ 13 
YDZ C10 C8A   C 0 1 Y N N -8.443  -1.144 1.089  6.955   -1.462 -1.391 C10 YDZ 14 
YDZ N5  N9A   N 0 1 Y N N -8.113  -0.038 0.401  7.187   -2.027 -0.173 N5  YDZ 15 
YDZ C11 C1P   C 0 1 N N R -6.780  0.291  -0.179 6.806   -1.470 1.128  C11 YDZ 16 
YDZ O1  O4P   O 0 1 N N N -5.938  -0.866 -0.226 5.775   -0.472 0.971  O1  YDZ 17 
YDZ C12 C2P   C 0 1 N N R -6.069  1.343  0.667  7.985   -0.677 1.748  C12 YDZ 18 
YDZ O2  O2P   O 0 1 N N N -5.960  2.578  -0.054 8.851   -1.543 2.483  O2  YDZ 19 
YDZ C13 C3P   C 0 1 N N S -4.709  0.756  1.017  7.253   0.306  2.694  C13 YDZ 20 
YDZ O3  O3P   O 0 1 N N N -3.627  1.594  0.587  7.258   -0.192 4.034  O3  YDZ 21 
YDZ C14 C4P   C 0 1 N N R -4.640  -0.600 0.315  5.815   0.361  2.142  C14 YDZ 22 
YDZ C15 C5P   C 0 1 N N N -4.208  -1.760 1.218  5.457   1.801  1.769  C15 YDZ 23 
YDZ O4  O5P   O 0 1 N N N -2.931  -2.250 0.807  4.091   1.859  1.353  O4  YDZ 24 
YDZ P1  PA    P 0 1 N N N -2.784  -3.372 -0.342 3.373   3.223  0.887  P1  YDZ 25 
YDZ O5  OA2   O 0 1 N N N -3.989  -3.323 -1.252 4.154   3.843  -0.206 O5  YDZ 26 
YDZ O6  OA1   O 0 1 N N N -2.676  -4.730 0.309  3.294   4.240  2.133  O6  YDZ 27 
YDZ O7  OAB   O 0 1 N N N -1.459  -3.106 -1.222 1.885   2.896  0.366  O7  YDZ 28 
YDZ P2  PB    P 0 1 N N S -0.260  -2.171 -0.687 0.833   3.673  -0.573 P2  YDZ 29 
YDZ O8  OB    O 0 1 N N N 0.318   -2.748 0.547  1.428   3.884  -1.911 O8  YDZ 30 
YDZ S1  SB    S 0 1 N N N -0.985  -0.273 -0.268 0.363   5.549  0.296  S1  YDZ 31 
YDZ O9  OBC   O 0 1 N N N 0.864   -2.042 -1.835 -0.509  2.795  -0.715 O9  YDZ 32 
YDZ P3  PC    P 0 1 N N N 1.742   -3.283 -2.375 -1.903  3.002  -1.493 P3  YDZ 33 
YDZ O10 OC1   O 0 1 N N N 1.833   -4.376 -1.335 -2.801  4.083  -0.708 O10 YDZ 34 
YDZ O11 OC2   O 0 1 N N N 1.114   -3.817 -3.640 -1.635  3.487  -2.865 O11 YDZ 35 
YDZ O12 "O5'" O 0 1 N N N 3.221   -2.740 -2.715 -2.691  1.600  -1.564 O12 YDZ 36 
YDZ C16 "C5'" C 0 1 N N N 4.228   -2.577 -1.713 -3.915  1.430  -2.282 C16 YDZ 37 
YDZ C17 "C4'" C 0 1 N N R 3.883   -1.451 -0.738 -4.391  -0.017 -2.143 C17 YDZ 38 
YDZ O13 "O4'" O 0 1 N N N 4.957   -1.286 0.193  -4.752  -0.284 -0.777 O13 YDZ 39 
YDZ C18 "C3'" C 0 1 N N R 3.660   -0.107 -1.428 -5.652  -0.238 -3.001 C18 YDZ 40 
YDZ O14 "O3'" O 0 1 N N N 2.291   0.300  -1.295 -5.419  -1.252 -3.981 O14 YDZ 41 
YDZ C19 "C2'" C 0 1 N N R 4.622   0.874  -0.774 -6.725  -0.703 -1.987 C19 YDZ 42 
YDZ O15 "O2'" O 0 1 N N N 3.951   1.984  -0.170 -7.517  -1.760 -2.531 O15 YDZ 43 
YDZ C20 CM2   C 0 1 N N N 3.806   3.100  -1.049 -8.694  -1.316 -3.208 C20 YDZ 44 
YDZ C21 "C1'" C 0 1 N N R 5.381   0.078  0.283  -5.858  -1.212 -0.807 C21 YDZ 45 
YDZ N6  N9    N 0 1 Y N N 6.850   0.176  0.066  -6.611  -1.156 0.448  N6  YDZ 46 
YDZ N7  N7    N 1 1 Y N N 8.873   -0.220 -0.697 -7.420  -0.398 2.329  N7  YDZ 47 
YDZ C22 CM7   C 0 1 N N N 9.984   -0.841 -1.465 -7.701  0.489  3.460  C22 YDZ 48 
YDZ N8  N3    N 0 1 Y N N 7.497   2.053  1.566  -7.738  -3.377 0.578  N8  YDZ 49 
YDZ N9  N2    N 0 1 N N N 8.390   3.779  2.884  -8.873  -5.392 0.882  N9  YDZ 50 
YDZ N10 N1    N 0 1 Y N N 9.820   2.530  1.502  -9.046  -3.686 2.469  N10 YDZ 51 
YDZ O16 O6    O 0 1 N N N 11.296  1.308  0.134  -9.282  -2.042 4.103  O16 YDZ 52 
YDZ H1  H8    H 0 1 N N N 7.197   -1.393 -1.371 -6.132  0.830  1.186  H1  YDZ 53 
YDZ H2  HN61  H 0 1 N N N -13.432 0.609  1.673  9.256   -5.427 -3.988 H2  YDZ 54 
YDZ H3  HN62  H 0 1 N N N -12.799 -0.849 1.298  8.482   -3.963 -4.267 H3  YDZ 55 
YDZ H4  H2G   H 0 1 N N N -10.804 3.490  -0.654 9.286   -5.996 0.537  H4  YDZ 56 
YDZ H5  HBI   H 0 1 N N N -7.775  -1.961 1.320  6.453   -0.519 -1.552 H5  YDZ 57 
YDZ H6  HBT   H 0 1 N N N -6.919  0.693  -1.193 6.479   -2.261 1.802  H6  YDZ 58 
YDZ H7  HBV   H 0 1 N N N -6.639  1.497  1.595  8.538   -0.137 0.979  H7  YDZ 59 
YDZ H8  HBU   H 0 1 N N N -5.516  3.222  0.485  9.604   -1.094 2.890  H8  YDZ 60 
YDZ H9  HBX   H 0 1 N N N -4.657  0.597  2.104  7.716   1.291  2.653  H9  YDZ 61 
YDZ H10 HBW   H 0 1 N N N -3.680  2.433  1.030  8.143   -0.301 4.409  H10 YDZ 62 
YDZ H11 HBY   H 0 1 N N N -3.913  -0.521 -0.507 5.117   -0.015 2.889  H11 YDZ 63 
YDZ H12 HBZ   H 0 1 N N N -4.145  -1.408 2.258  5.600   2.447  2.635  H12 YDZ 64 
YDZ H13 H8N   H 0 1 N N N -4.949  -2.570 1.149  6.099   2.136  0.955  H13 YDZ 65 
YDZ H14 H1    H 0 1 N N N -3.391  -5.281 0.013  2.795   3.898  2.888  H14 YDZ 66 
YDZ H15 HSB   H 0 1 N N N -0.707  -0.150 0.996  -0.160  5.208  1.487  H15 YDZ 67 
YDZ H16 H2    H 0 1 N N N 1.475   -5.181 -1.689 -3.016  3.831  0.201  H16 YDZ 68 
YDZ H17 "H5'" H 0 1 N N N 4.326   -3.517 -1.151 -4.671  2.102  -1.876 H17 YDZ 69 
YDZ H18 H5V   H 0 1 N N N 5.184   -2.342 -2.204 -3.753  1.660  -3.335 H18 YDZ 70 
YDZ H19 "H4'" H 0 1 N N N 2.963   -1.725 -0.201 -3.602  -0.699 -2.458 H19 YDZ 71 
YDZ H20 "H3'" H 0 1 N N N 3.922   -0.207 -2.492 -5.958  0.691  -3.481 H20 YDZ 72 
YDZ H21 H8O   H 0 1 N N N 1.728   -0.339 -1.716 -4.755  -1.014 -4.643 H21 YDZ 73 
YDZ H22 "H2'" H 0 1 N N N 5.336   1.230  -1.531 -7.354  0.132  -1.676 H22 YDZ 74 
YDZ H23 H2W   H 0 1 N N N 3.285   3.915  -0.525 -9.328  -0.764 -2.513 H23 YDZ 75 
YDZ H24 H2V   H 0 1 N N N 4.800   3.446  -1.369 -8.413  -0.666 -4.037 H24 YDZ 76 
YDZ H25 HAI   H 0 1 N N N 3.222   2.798  -1.931 -9.241  -2.178 -3.592 H25 YDZ 77 
YDZ H26 H1*   H 0 1 N N N 5.134   0.484  1.275  -5.504  -2.225 -1.000 H26 YDZ 78 
YDZ H27 H8L   H 0 1 N N N 10.929  -0.334 -1.219 -8.582  1.093  3.238  H27 YDZ 79 
YDZ H28 HBG   H 0 1 N N N 10.061  -1.906 -1.202 -7.886  -0.108 4.353  H28 YDZ 80 
YDZ H29 H8M   H 0 1 N N N 9.785   -0.743 -2.542 -6.846  1.143  3.631  H29 YDZ 81 
YDZ H30 H22   H 0 1 N N N 9.269   4.213  3.081  -8.513  -5.725 0.046  H30 YDZ 82 
YDZ H31 H21   H 0 1 N N N 7.759   4.459  2.510  -9.464  -5.949 1.413  H31 YDZ 83 
YDZ H32 H6    H 0 1 N N N 11.900  1.918  0.540  -10.133 -1.591 4.013  H32 YDZ 84 
# 
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 
YDZ O11 P3  DOUB N N 1  
YDZ O12 P3  SING N N 2  
YDZ O12 C16 SING N N 3  
YDZ P3  O9  SING N N 4  
YDZ P3  O10 SING N N 5  
YDZ O9  P2  SING N N 6  
YDZ C16 C17 SING N N 7  
YDZ C22 N7  SING N N 8  
YDZ C18 O14 SING N N 9  
YDZ C18 C19 SING N N 10 
YDZ C18 C17 SING N N 11 
YDZ O5  P1  DOUB N N 12 
YDZ O7  P2  SING N N 13 
YDZ O7  P1  SING N N 14 
YDZ C20 O15 SING N N 15 
YDZ C19 O15 SING N N 16 
YDZ C19 C21 SING N N 17 
YDZ C2  N7  DOUB Y N 18 
YDZ C2  N6  SING Y N 19 
YDZ C17 O13 SING N N 20 
YDZ N7  C4  SING Y N 21 
YDZ P2  S1  SING N N 22 
YDZ P2  O8  DOUB N N 23 
YDZ P1  O6  SING N N 24 
YDZ P1  O4  SING N N 25 
YDZ N3  C7  DOUB Y N 26 
YDZ N3  C8  SING Y N 27 
YDZ O1  C11 SING N N 28 
YDZ O1  C14 SING N N 29 
YDZ C7  N2  SING Y N 30 
YDZ C11 N5  SING N N 31 
YDZ C11 C12 SING N N 32 
YDZ O2  C12 SING N N 33 
YDZ N6  C21 SING N N 34 
YDZ N6  C3  SING Y N 35 
YDZ O16 C5  SING N N 36 
YDZ C4  C5  DOUB Y N 37 
YDZ C4  C3  SING Y N 38 
YDZ O13 C21 SING N N 39 
YDZ C14 C13 SING N N 40 
YDZ C14 C15 SING N N 41 
YDZ C8  N5  SING Y N 42 
YDZ C8  C9  DOUB Y N 43 
YDZ N5  C10 SING Y N 44 
YDZ N2  C6  DOUB Y N 45 
YDZ O3  C13 SING N N 46 
YDZ C5  N10 SING Y N 47 
YDZ C3  N8  DOUB Y N 48 
YDZ C12 C13 SING N N 49 
YDZ O4  C15 SING N N 50 
YDZ C9  C6  SING Y N 51 
YDZ C9  N4  SING Y N 52 
YDZ C6  N1  SING N N 53 
YDZ C10 N4  DOUB Y N 54 
YDZ N10 C1  DOUB Y N 55 
YDZ N8  C1  SING Y N 56 
YDZ C1  N9  SING N N 57 
YDZ C2  H1  SING N N 58 
YDZ N1  H2  SING N N 59 
YDZ N1  H3  SING N N 60 
YDZ C7  H4  SING N N 61 
YDZ C10 H5  SING N N 62 
YDZ C11 H6  SING N N 63 
YDZ C12 H7  SING N N 64 
YDZ O2  H8  SING N N 65 
YDZ C13 H9  SING N N 66 
YDZ O3  H10 SING N N 67 
YDZ C14 H11 SING N N 68 
YDZ C15 H12 SING N N 69 
YDZ C15 H13 SING N N 70 
YDZ O6  H14 SING N N 71 
YDZ S1  H15 SING N N 72 
YDZ O10 H16 SING N N 73 
YDZ C16 H17 SING N N 74 
YDZ C16 H18 SING N N 75 
YDZ C17 H19 SING N N 76 
YDZ C18 H20 SING N N 77 
YDZ O14 H21 SING N N 78 
YDZ C19 H22 SING N N 79 
YDZ C20 H23 SING N N 80 
YDZ C20 H24 SING N N 81 
YDZ C20 H25 SING N N 82 
YDZ C21 H26 SING N N 83 
YDZ C22 H27 SING N N 84 
YDZ C22 H28 SING N N 85 
YDZ C22 H29 SING N N 86 
YDZ N9  H30 SING N N 87 
YDZ N9  H31 SING N N 88 
YDZ O16 H32 SING N N 89 
# 
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 
YDZ InChI            InChI                1.03  
;InChI=1S/C22H31N10O16P3S/c1-30-7-32(18-11(30)19(36)29-22(24)28-18)21-15(42-2)13(34)9(46-21)4-44-50(39,40)48-51(41,52)47-49(37,38)43-3-8-12(33)14(35)20(45-8)31-6-27-10-16(23)25-5-26-17(10)31/h5-9,12-15,20-21,33-35H,3-4H2,1-2H3,(H7-,23,24,25,26,28,29,36,37,38,39,40,41,52)/p+1/t8-,9-,12-,13-,14-,15-,20-,21-,51+/m1/s1
;
YDZ InChIKey         InChI                1.03  LVAVASOWNAXXPY-KVLYALRXSA-O 
YDZ SMILES_CANONICAL CACTVS               3.385 "CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(=O)O[P@](S)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34)O[C@H]1n5c[n+](C)c6c(O)nc(N)nc56" 
YDZ SMILES           CACTVS               3.385 "CO[CH]1[CH](O)[CH](CO[P](O)(=O)O[P](S)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34)O[CH]1n5c[n+](C)c6c(O)nc(N)nc56" 
YDZ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C[n+]1cn(c2c1c(nc(n2)N)O)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O[P@](=O)(OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)S)O)OC" 
YDZ SMILES           "OpenEye OEToolkits" 2.0.6 "C[n+]1cn(c2c1c(nc(n2)N)O)C3C(C(C(O3)COP(=O)(O)OP(=O)(OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)S)O)OC" 
# 
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 
YDZ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 
;[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanyl-purin-7-ium-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl 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 
YDZ "Create component" 2016-11-11 EBI  
YDZ "Initial release"  2017-12-20 RCSB 
# 
