data_SO5 # _chem_comp.id SO5 _chem_comp.name "(2~{R})-1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethoxy]-1-oxidanylidene-propane-2-sulfonic acid" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C24 H40 N7 O21 P3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-12-03 _chem_comp.pdbx_modified_date 2019-04-05 _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 887.595 _chem_comp.one_letter_code ? _chem_comp.three_letter_code SO5 _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 6N96 _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 SO5 O56 O1 O 0 1 N N N 31.935 12.512 15.350 -12.466 -4.282 -1.031 O56 SO5 1 SO5 SS4 S1 S 0 1 N N N 31.398 13.454 16.305 -11.163 -3.916 -1.464 SS4 SO5 2 SO5 OS5 O2 O 0 1 N N N 31.962 13.390 17.649 -10.499 -5.240 -1.816 OS5 SO5 3 SO5 OS4 O3 O 0 1 N N N 29.962 13.292 16.313 -10.974 -3.111 -2.619 OS4 SO5 4 SO5 CS2 C1 C 0 1 N N R 31.831 14.982 15.730 -10.188 -3.276 -0.075 CS2 SO5 5 SO5 CS3 C2 C 0 1 N N N 33.343 15.259 15.840 -10.139 -4.322 1.039 CS3 SO5 6 SO5 CS1 C3 C 0 1 N N N 31.056 15.989 16.534 -10.826 -2.015 0.448 CS1 SO5 7 SO5 OS1 O4 O 0 1 N N N 31.482 16.466 17.606 -12.008 -1.824 0.285 OS1 SO5 8 SO5 OPS O5 O 0 1 N N N 29.805 16.389 16.003 -10.082 -1.104 1.094 OPS SO5 9 SO5 CP1 C4 C 0 1 N N N 28.925 17.184 16.830 -10.763 0.087 1.570 CP1 SO5 10 SO5 CP2 C5 C 0 1 N N N 28.385 16.328 17.971 -9.760 1.001 2.276 CP2 SO5 11 SO5 NP1 N1 N 0 1 N N N 27.350 17.053 18.618 -8.771 1.481 1.308 NP1 SO5 12 SO5 CP3 C6 C 0 1 N N N 26.105 16.695 18.508 -7.783 2.307 1.706 CP3 SO5 13 SO5 OP1 O6 O 0 1 N N N 25.745 15.787 17.750 -7.713 2.652 2.867 OP1 SO5 14 SO5 CP4 C7 C 0 1 N N N 25.121 17.512 19.318 -6.766 2.801 0.710 CP4 SO5 15 SO5 CP5 C8 C 0 1 N N N 24.028 17.948 18.386 -5.763 3.715 1.416 CP5 SO5 16 SO5 NP2 N2 N 0 1 N N N 23.089 18.868 18.994 -4.775 4.196 0.447 NP2 SO5 17 SO5 CP6 C9 C 0 1 N N N 22.129 18.454 19.840 -3.786 5.021 0.846 CP6 SO5 18 SO5 OP2 O7 O 0 1 N N N 21.928 17.281 20.169 -3.769 5.440 1.984 OP2 SO5 19 SO5 CP7 C10 C 0 1 N N R 21.272 19.570 20.442 -2.704 5.423 -0.122 CP7 SO5 20 SO5 OP3 O8 O 0 1 N N N 21.463 20.739 19.675 -3.081 5.037 -1.446 OP3 SO5 21 SO5 CPA C11 C 0 1 N N N 21.642 19.923 21.893 -1.395 4.727 0.258 CPA SO5 22 SO5 CP9 C12 C 0 1 N N N 21.160 18.842 22.865 -0.914 5.252 1.612 CP9 SO5 23 SO5 CP8 C13 C 0 1 N N N 23.171 20.128 21.962 -1.628 3.218 0.350 CP8 SO5 24 SO5 CPB C14 C 0 1 N N N 20.982 21.238 22.273 -0.336 5.016 -0.807 CPB SO5 25 SO5 O7 O9 O 0 1 N N N 19.571 21.100 22.197 0.886 4.367 -0.451 O7 SO5 26 SO5 P2 P1 P 0 1 N N N 18.590 22.409 22.119 2.220 4.455 -1.349 P2 SO5 27 SO5 O21 O10 O 0 1 N N N 17.233 21.880 21.818 1.916 4.015 -2.729 O21 SO5 28 SO5 O22 O11 O 0 1 N N N 18.811 23.246 23.305 2.749 5.976 -1.376 O22 SO5 29 SO5 O6 O12 O 0 1 N N N 19.040 23.407 21.001 3.355 3.503 -0.719 O6 SO5 30 SO5 P1 P2 P 0 1 N N N 18.850 23.154 19.434 4.750 2.913 -1.266 P1 SO5 31 SO5 O11 O13 O 0 1 N N N 17.600 23.913 19.112 5.892 4.042 -1.151 O11 SO5 32 SO5 O12 O14 O 0 1 N N N 18.746 21.731 19.000 4.594 2.512 -2.682 O12 SO5 33 SO5 "O5'" O15 O 0 1 N N N 20.092 23.918 18.806 5.172 1.632 -0.388 "O5'" SO5 34 SO5 "C5'" C15 C 0 1 N N N 20.425 25.294 18.944 6.310 0.822 -0.689 "C5'" SO5 35 SO5 "C4'" C16 C 0 1 N N R 21.120 25.667 17.624 6.420 -0.306 0.339 "C4'" SO5 36 SO5 "O4'" O16 O 0 1 N N N 22.445 25.100 17.737 5.308 -1.206 0.199 "O4'" SO5 37 SO5 "C1'" C17 C 0 1 N N R 22.688 24.335 16.576 5.795 -2.529 0.510 "C1'" SO5 38 SO5 "C2'" C18 C 0 1 N N R 21.347 23.769 16.109 7.196 -2.564 -0.153 "C2'" SO5 39 SO5 "O2'" O17 O 0 1 N N N 21.362 23.327 14.749 8.042 -3.516 0.494 "O2'" SO5 40 SO5 "C3'" C19 C 0 1 N N S 20.535 25.033 16.366 7.703 -1.121 0.087 "C3'" SO5 41 SO5 "O3'" O18 O 0 1 N N N 20.710 25.909 15.242 8.558 -1.075 1.232 "O3'" SO5 42 SO5 P3 P3 P 0 1 N N N 19.487 26.930 14.836 10.083 -0.563 1.167 P3 SO5 43 SO5 O31 O19 O 0 1 N N N 20.083 28.283 14.912 10.699 -0.524 2.654 O31 SO5 44 SO5 O32 O20 O 0 1 N N N 18.408 26.886 15.893 10.948 -1.569 0.255 O32 SO5 45 SO5 O33 O21 O 0 1 N N N 18.858 26.197 13.684 10.124 0.794 0.580 O33 SO5 46 SO5 N9 N3 N 0 1 Y N N 23.661 23.289 16.952 4.922 -3.550 -0.075 N9 SO5 47 SO5 C8 C20 C 0 1 Y N N 23.564 22.417 17.992 4.096 -3.387 -1.147 C8 SO5 48 SO5 N7 N4 N 0 1 Y N N 24.684 21.629 18.032 3.467 -4.499 -1.396 N7 SO5 49 SO5 C5 C21 C 0 1 Y N N 25.471 22.003 17.034 3.849 -5.443 -0.503 C5 SO5 50 SO5 C4 C22 C 0 1 Y N N 24.839 23.129 16.359 4.792 -4.848 0.351 C4 SO5 51 SO5 C6 C23 C 0 1 Y N N 26.749 21.551 16.575 3.516 -6.792 -0.287 C6 SO5 52 SO5 N6 N5 N 0 1 N N N 27.433 20.546 17.197 2.599 -7.433 -1.100 N6 SO5 53 SO5 N1 N6 N 0 1 Y N N 27.265 22.173 15.506 4.103 -7.436 0.716 N1 SO5 54 SO5 C2 C24 C 0 1 Y N N 26.595 23.214 14.886 4.980 -6.831 1.497 C2 SO5 55 SO5 N3 N7 N 0 1 Y N N 25.404 23.674 15.277 5.332 -5.575 1.324 N3 SO5 56 SO5 H1 H1 H 0 1 N N N 31.528 15.037 14.674 -9.175 -3.057 -0.413 H1 SO5 57 SO5 H2 H2 H 0 1 N N N 33.561 16.265 15.452 -9.677 -5.234 0.661 H2 SO5 58 SO5 H3 H3 H 0 1 N N N 33.651 15.198 16.894 -9.552 -3.937 1.874 H3 SO5 59 SO5 H4 H4 H 0 1 N N N 33.896 14.511 15.253 -11.152 -4.541 1.377 H4 SO5 60 SO5 H5 H5 H 0 1 N N N 29.483 18.037 17.244 -11.204 0.615 0.725 H5 SO5 61 SO5 H6 H6 H 0 1 N N N 28.087 17.555 16.222 -11.549 -0.199 2.270 H6 SO5 62 SO5 H7 H7 H 0 1 N N N 27.985 15.384 17.572 -10.286 1.851 2.711 H7 SO5 63 SO5 H8 H8 H 0 1 N N N 29.191 16.111 18.687 -9.255 0.444 3.066 H8 SO5 64 SO5 H9 H9 H 0 1 N N N 27.583 17.854 19.169 -8.828 1.206 0.379 H9 SO5 65 SO5 H10 H10 H 0 1 N N N 25.624 18.392 19.745 -6.240 1.951 0.275 H10 SO5 66 SO5 H11 H11 H 0 1 N N N 24.701 16.899 20.130 -7.272 3.357 -0.079 H11 SO5 67 SO5 H12 H12 H 0 1 N N N 23.477 17.056 18.053 -6.289 4.565 1.850 H12 SO5 68 SO5 H13 H13 H 0 1 N N N 24.487 18.441 17.517 -5.258 3.159 2.205 H13 SO5 69 SO5 H14 H14 H 0 1 N N N 23.157 19.842 18.778 -4.831 3.920 -0.481 H14 SO5 70 SO5 H15 H15 H 0 1 N N N 20.217 19.260 20.413 -2.565 6.503 -0.084 H15 SO5 71 SO5 H16 H16 H 0 1 N N N 20.619 21.100 19.431 -3.221 4.086 -1.553 H16 SO5 72 SO5 H17 H17 H 0 1 N N N 21.438 19.121 23.892 -1.632 4.978 2.385 H17 SO5 73 SO5 H18 H18 H 0 1 N N N 20.066 18.747 22.794 0.057 4.815 1.847 H18 SO5 74 SO5 H19 H19 H 0 1 N N N 21.629 17.881 22.607 -0.823 6.338 1.570 H19 SO5 75 SO5 H20 H20 H 0 1 N N N 23.461 20.382 22.992 -1.971 2.844 -0.615 H20 SO5 76 SO5 H21 H21 H 0 1 N N N 23.679 19.202 21.656 -0.696 2.722 0.621 H21 SO5 77 SO5 H22 H22 H 0 1 N N N 23.462 20.946 21.287 -2.383 3.012 1.109 H22 SO5 78 SO5 H23 H23 H 0 1 N N N 21.269 21.509 23.300 -0.679 4.642 -1.771 H23 SO5 79 SO5 H24 H24 H 0 1 N N N 21.311 22.027 21.580 -0.170 6.092 -0.872 H24 SO5 80 SO5 H25 H25 H 0 1 N N N 17.992 23.356 23.773 2.968 6.332 -0.503 H25 SO5 81 SO5 H26 H26 H 0 1 N N N 16.977 23.334 18.689 6.048 4.353 -0.248 H26 SO5 82 SO5 H27 H27 H 0 1 N N N 21.105 25.444 19.795 6.198 0.395 -1.686 H27 SO5 83 SO5 H28 H28 H 0 1 N N N 19.518 25.899 19.088 7.211 1.434 -0.655 H28 SO5 84 SO5 H29 H29 H 0 1 N N N 21.160 26.761 17.515 6.435 0.111 1.346 H29 SO5 85 SO5 H30 H30 H 0 1 N N N 23.109 24.964 15.778 5.874 -2.665 1.588 H30 SO5 86 SO5 H31 H31 H 0 1 N N N 21.021 22.967 16.788 7.117 -2.776 -1.219 H31 SO5 87 SO5 H32 H32 H 0 1 N N N 21.887 22.539 14.678 7.765 -4.435 0.373 H32 SO5 88 SO5 H33 H33 H 0 1 N N N 19.476 24.781 16.523 8.225 -0.749 -0.795 H33 SO5 89 SO5 H34 H34 H 0 1 N N N 20.027 28.702 14.061 11.618 -0.224 2.691 H34 SO5 90 SO5 H35 H35 H 0 1 N N N 17.651 26.423 15.554 10.966 -2.479 0.581 H35 SO5 91 SO5 H36 H36 H 0 1 N N N 22.733 22.356 18.679 3.979 -2.470 -1.706 H36 SO5 92 SO5 H37 H37 H 0 1 N N N 28.304 20.396 16.730 2.177 -6.953 -1.830 H37 SO5 93 SO5 H38 H38 H 0 1 N N N 27.605 20.799 18.149 2.377 -8.364 -0.941 H38 SO5 94 SO5 H39 H39 H 0 1 N N N 27.065 23.683 14.034 5.438 -7.393 2.297 H39 SO5 95 SO5 H40 H40 H 0 1 N N N 31.265 13.252 18.279 -10.917 -5.706 -2.553 H40 SO5 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 SO5 O33 P3 DOUB N N 1 SO5 "O2'" "C2'" SING N N 2 SO5 P3 O31 SING N N 3 SO5 P3 "O3'" SING N N 4 SO5 P3 O32 SING N N 5 SO5 C2 N3 DOUB Y N 6 SO5 C2 N1 SING Y N 7 SO5 "O3'" "C3'" SING N N 8 SO5 N3 C4 SING Y N 9 SO5 O56 SS4 DOUB N N 10 SO5 N1 C6 DOUB Y N 11 SO5 CS2 CS3 SING N N 12 SO5 CS2 SS4 SING N N 13 SO5 CS2 CS1 SING N N 14 SO5 OPS CS1 SING N N 15 SO5 OPS CP1 SING N N 16 SO5 "C2'" "C3'" SING N N 17 SO5 "C2'" "C1'" SING N N 18 SO5 SS4 OS4 DOUB N N 19 SO5 SS4 OS5 SING N N 20 SO5 C4 N9 SING Y N 21 SO5 C4 C5 DOUB Y N 22 SO5 "C3'" "C4'" SING N N 23 SO5 CS1 OS1 DOUB N N 24 SO5 C6 C5 SING Y N 25 SO5 C6 N6 SING N N 26 SO5 "C1'" N9 SING N N 27 SO5 "C1'" "O4'" SING N N 28 SO5 CP1 CP2 SING N N 29 SO5 N9 C8 SING Y N 30 SO5 C5 N7 SING Y N 31 SO5 "C4'" "O4'" SING N N 32 SO5 "C4'" "C5'" SING N N 33 SO5 OP1 CP3 DOUB N N 34 SO5 CP2 NP1 SING N N 35 SO5 C8 N7 DOUB Y N 36 SO5 CP5 NP2 SING N N 37 SO5 CP5 CP4 SING N N 38 SO5 CP3 NP1 SING N N 39 SO5 CP3 CP4 SING N N 40 SO5 "O5'" "C5'" SING N N 41 SO5 "O5'" P1 SING N N 42 SO5 NP2 CP6 SING N N 43 SO5 O12 P1 DOUB N N 44 SO5 O11 P1 SING N N 45 SO5 P1 O6 SING N N 46 SO5 OP3 CP7 SING N N 47 SO5 CP6 OP2 DOUB N N 48 SO5 CP6 CP7 SING N N 49 SO5 CP7 CPA SING N N 50 SO5 O6 P2 SING N N 51 SO5 O21 P2 DOUB N N 52 SO5 CPA CP8 SING N N 53 SO5 CPA CPB SING N N 54 SO5 CPA CP9 SING N N 55 SO5 P2 O7 SING N N 56 SO5 P2 O22 SING N N 57 SO5 O7 CPB SING N N 58 SO5 CS2 H1 SING N N 59 SO5 CS3 H2 SING N N 60 SO5 CS3 H3 SING N N 61 SO5 CS3 H4 SING N N 62 SO5 CP1 H5 SING N N 63 SO5 CP1 H6 SING N N 64 SO5 CP2 H7 SING N N 65 SO5 CP2 H8 SING N N 66 SO5 NP1 H9 SING N N 67 SO5 CP4 H10 SING N N 68 SO5 CP4 H11 SING N N 69 SO5 CP5 H12 SING N N 70 SO5 CP5 H13 SING N N 71 SO5 NP2 H14 SING N N 72 SO5 CP7 H15 SING N N 73 SO5 OP3 H16 SING N N 74 SO5 CP9 H17 SING N N 75 SO5 CP9 H18 SING N N 76 SO5 CP9 H19 SING N N 77 SO5 CP8 H20 SING N N 78 SO5 CP8 H21 SING N N 79 SO5 CP8 H22 SING N N 80 SO5 CPB H23 SING N N 81 SO5 CPB H24 SING N N 82 SO5 O22 H25 SING N N 83 SO5 O11 H26 SING N N 84 SO5 "C5'" H27 SING N N 85 SO5 "C5'" H28 SING N N 86 SO5 "C4'" H29 SING N N 87 SO5 "C1'" H30 SING N N 88 SO5 "C2'" H31 SING N N 89 SO5 "O2'" H32 SING N N 90 SO5 "C3'" H33 SING N N 91 SO5 O31 H34 SING N N 92 SO5 O32 H35 SING N N 93 SO5 C8 H36 SING N N 94 SO5 N6 H37 SING N N 95 SO5 N6 H38 SING N N 96 SO5 C2 H39 SING N N 97 SO5 OS5 H40 SING N N 98 # # 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 SO5 SMILES ACDLabs 12.01 "O=S(=O)(O)C(C)C(=O)OCCNC(CCNC(=O)C(C(C)(COP(O)(=O)OP(O)(=O)OCC3OC(n1cnc2c1ncnc2N)C(C3OP(O)(O)=O)O)C)O)=O" SO5 InChI InChI 1.03 "InChI=1S/C24H40N7O21P3S/c1-12(56(44,45)46)23(36)47-7-6-26-14(32)4-5-27-21(35)18(34)24(2,3)9-49-55(42,43)52-54(40,41)48-8-13-17(51-53(37,38)39)16(33)22(50-13)31-11-30-15-19(25)28-10-29-20(15)31/h10-13,16-18,22,33-34H,4-9H2,1-3H3,(H,26,32)(H,27,35)(H,40,41)(H,42,43)(H2,25,28,29)(H2,37,38,39)(H,44,45,46)/t12-,13-,16-,17-,18+,22-/m1/s1" SO5 InChIKey InChI 1.03 BEMUOEZGNHFKKE-AGCMQPJKSA-N SO5 SMILES_CANONICAL CACTVS 3.385 "C[C@H](C(=O)OCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[S](O)(=O)=O" SO5 SMILES CACTVS 3.385 "C[CH](C(=O)OCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[S](O)(=O)=O" SO5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C[C@H](C(=O)OCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O)S(=O)(=O)O" SO5 SMILES "OpenEye OEToolkits" 2.0.6 "CC(C(=O)OCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O)S(=O)(=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 SO5 "SYSTEMATIC NAME" ACDLabs 12.01 "(3S,5R,9R,20R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-10,14,19-trioxo-2,4,6,18-tetraoxa-11,15-diaza-3,5-diphosphahenicosane-20-sulfonic acid 3,5-dioxide (non-preferred name)" SO5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "(2~{R})-1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethoxy]-1-oxidanylidene-propane-2-sulfonic acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site SO5 "Create component" 2018-12-03 RCSB SO5 "Initial release" 2019-04-10 RCSB ##