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 #