data_5SV # _chem_comp.id 5SV _chem_comp.name "[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl icosyl hydrogen phosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C30 H54 N5 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-11-25 _chem_comp.pdbx_modified_date 2019-09-04 _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 627.753 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 5SV _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 5EY8 _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 5SV C2 C1 C 0 1 Y N N 43.352 -1.329 250.245 11.690 -3.842 1.211 C2 5SV 1 5SV C4 C2 C 0 1 Y N N 43.228 0.916 250.126 10.000 -2.558 0.327 C4 5SV 2 5SV C6 C3 C 0 1 Y N N 42.726 -0.448 248.173 10.538 -4.724 -0.584 C6 5SV 3 5SV C5 C4 C 0 1 Y N N 42.840 0.851 248.757 9.751 -3.561 -0.624 C5 5SV 4 5SV N1 N1 N 0 1 Y N N 42.991 -1.559 248.944 11.489 -4.814 0.340 N1 5SV 5 5SV N3 N2 N 0 1 Y N N 43.493 -0.166 250.924 10.970 -2.739 1.218 N3 5SV 6 5SV C8 C5 C 0 1 Y N N 42.961 2.977 249.257 8.340 -1.956 -0.993 C8 5SV 7 5SV C9 C6 C 0 1 N N N 40.905 7.448 248.145 1.652 2.564 -0.682 C9 5SV 8 5SV C10 C7 C 0 1 N N N 41.030 6.250 247.174 0.547 1.773 0.021 C10 5SV 9 5SV C11 C8 C 0 1 N N N 41.434 6.739 245.783 -0.804 2.112 -0.613 C11 5SV 10 5SV C12 C9 C 0 1 N N N 41.494 5.606 244.742 -1.910 1.322 0.090 C12 5SV 11 5SV C13 C10 C 0 1 N N N 41.656 6.155 243.301 -3.261 1.661 -0.544 C13 5SV 12 5SV C14 C11 C 0 1 N N N 40.327 6.697 242.738 -4.366 0.870 0.159 C14 5SV 13 5SV C15 C12 C 0 1 N N N 40.511 7.360 241.369 -5.717 1.209 -0.475 C15 5SV 14 5SV O2P O1 O 0 1 N N N 40.090 8.060 251.663 4.284 4.482 -0.291 O2P 5SV 15 5SV P P1 P 0 1 N N N 41.261 7.685 250.834 4.301 2.898 -0.582 P 5SV 16 5SV O1P O2 O 0 1 N N N 42.263 8.814 250.327 4.468 2.665 -2.034 O1P 5SV 17 5SV "O5'" O3 O 0 1 N N N 42.283 6.707 251.570 5.525 2.220 0.215 "O5'" 5SV 18 5SV "C5'" C13 C 0 1 N N N 43.538 6.272 251.172 6.895 2.510 -0.070 "C5'" 5SV 19 5SV "C4'" C14 C 0 1 N N R 43.956 5.101 252.080 7.793 1.699 0.866 "C4'" 5SV 20 5SV "O4'" O4 O 0 1 N N N 43.045 4.051 251.861 7.671 0.298 0.568 "O4'" 5SV 21 5SV "C3'" C15 C 0 1 N N S 45.389 4.592 251.794 9.267 2.090 0.647 "C3'" 5SV 22 5SV "O3'" O5 O 0 1 N N N 46.179 5.098 252.819 9.832 2.605 1.855 "O3'" 5SV 23 5SV "C2'" C16 C 0 1 N N R 45.245 3.059 251.851 9.958 0.762 0.250 "C2'" 5SV 24 5SV "O2'" O6 O 0 1 N N N 45.720 2.685 253.099 11.235 0.644 0.879 "O2'" 5SV 25 5SV "C1'" C17 C 0 1 N N R 43.696 2.819 251.755 8.965 -0.298 0.804 "C1'" 5SV 26 5SV N9 N3 N 0 1 Y N N 43.307 2.277 250.440 9.096 -1.559 0.070 N9 5SV 27 5SV N7 N4 N 0 1 Y N N 42.673 2.148 248.234 8.726 -3.131 -1.399 N7 5SV 28 5SV N6 N5 N 0 1 N N N 42.384 -0.642 246.862 10.339 -5.746 -1.496 N6 5SV 29 5SV O3P O7 O 0 1 N N N 40.883 6.958 249.459 2.914 2.247 -0.090 O3P 5SV 30 5SV C16 C18 C 0 1 N N N 39.327 7.085 240.434 -6.823 0.419 0.228 C16 5SV 31 5SV C17 C19 C 0 1 N N N 38.816 8.285 239.629 -8.173 0.757 -0.406 C17 5SV 32 5SV C18 C20 C 0 1 N N N 37.629 7.905 238.738 -9.279 -0.033 0.296 C18 5SV 33 5SV C19 C21 C 0 1 N N N 36.952 9.168 238.203 -10.630 0.306 -0.338 C19 5SV 34 5SV C20 C22 C 0 1 N N N 35.821 8.869 237.195 -11.735 -0.484 0.365 C20 5SV 35 5SV C21 C23 C 0 1 N N N 35.138 10.157 236.722 -13.086 -0.146 -0.269 C21 5SV 36 5SV C22 C24 C 0 1 N N N 34.391 9.977 235.416 -14.192 -0.936 0.434 C22 5SV 37 5SV C23 C25 C 0 1 N N N 33.894 11.299 234.926 -15.542 -0.597 -0.200 C23 5SV 38 5SV C24 C26 C 0 1 N N N 34.332 11.884 233.807 -16.648 -1.388 0.503 C24 5SV 39 5SV H1 H1 H 0 1 N N N 43.557 -2.218 250.822 12.470 -3.957 1.948 H1 5SV 40 5SV H2 H2 H 0 1 N N N 42.931 4.054 249.184 7.540 -1.380 -1.433 H2 5SV 41 5SV H3 H3 H 0 1 N N N 41.765 8.122 248.015 1.671 2.300 -1.739 H3 5SV 42 5SV H4 H4 H 0 1 N N N 39.974 7.997 247.938 1.459 3.631 -0.576 H4 5SV 43 5SV H5 H5 H 0 1 N N N 40.062 5.731 247.110 0.740 0.706 -0.084 H5 5SV 44 5SV H6 H6 H 0 1 N N N 41.794 5.555 247.551 0.528 2.036 1.079 H6 5SV 45 5SV H7 H7 H 0 1 N N N 42.428 7.206 245.850 -0.998 3.180 -0.507 H7 5SV 46 5SV H8 H8 H 0 1 N N N 40.700 7.486 245.447 -0.785 1.849 -1.670 H8 5SV 47 5SV H9 H9 H 0 1 N N N 40.564 5.022 244.798 -1.717 0.254 -0.015 H9 5SV 48 5SV H10 H10 H 0 1 N N N 42.350 4.955 244.973 -1.929 1.585 1.148 H10 5SV 49 5SV H11 H11 H 0 1 N N N 42.013 5.344 242.650 -3.454 2.728 -0.439 H11 5SV 50 5SV H12 H12 H 0 1 N N N 42.396 6.969 243.312 -3.242 1.397 -1.602 H12 5SV 51 5SV H13 H13 H 0 1 N N N 39.920 7.440 243.440 -4.173 -0.197 0.053 H13 5SV 52 5SV H14 H14 H 0 1 N N N 39.618 5.862 242.636 -4.385 1.133 1.216 H14 5SV 53 5SV H15 H15 H 0 1 N N N 41.428 6.968 240.905 -5.910 2.276 -0.370 H15 5SV 54 5SV H16 H16 H 0 1 N N N 40.607 8.447 241.511 -5.698 0.946 -1.533 H16 5SV 55 5SV H17 H17 H 0 1 N N N 40.085 9.000 251.798 4.177 4.709 0.642 H17 5SV 56 5SV H18 H18 H 0 1 N N N 43.500 5.936 250.125 7.115 2.244 -1.104 H18 5SV 57 5SV H19 H19 H 0 1 N N N 44.263 7.093 251.267 7.081 3.573 0.079 H19 5SV 58 5SV H20 H20 H 0 1 N N N 43.909 5.436 253.127 7.510 1.883 1.902 H20 5SV 59 5SV H21 H21 H 0 1 N N N 45.721 4.914 250.796 9.353 2.820 -0.157 H21 5SV 60 5SV H22 H22 H 0 1 N N N 46.236 6.043 252.739 10.774 2.814 1.791 H22 5SV 61 5SV H23 H23 H 0 1 N N N 45.769 2.577 251.013 10.050 0.681 -0.833 H23 5SV 62 5SV H24 H24 H 0 1 N N N 46.657 2.836 253.140 11.861 1.339 0.633 H24 5SV 63 5SV H25 H25 H 0 1 N N N 43.390 2.131 252.557 9.127 -0.454 1.870 H25 5SV 64 5SV H26 H26 H 0 1 N N N 42.381 -1.621 246.659 9.649 -5.664 -2.173 H26 5SV 65 5SV H27 H27 H 0 1 N N N 41.473 -0.264 246.696 10.888 -6.544 -1.457 H27 5SV 66 5SV H28 H28 H 0 1 N N N 38.494 6.711 241.047 -6.629 -0.649 0.122 H28 5SV 67 5SV H29 H29 H 0 1 N N N 39.635 6.307 239.720 -6.841 0.682 1.285 H29 5SV 68 5SV H30 H30 H 0 1 N N N 39.632 8.662 238.995 -8.367 1.825 -0.301 H30 5SV 69 5SV H31 H31 H 0 1 N N N 38.500 9.074 240.327 -8.155 0.494 -1.464 H31 5SV 70 5SV H32 H32 H 0 1 N N N 36.903 7.324 239.326 -9.086 -1.100 0.191 H32 5SV 71 5SV H33 H33 H 0 1 N N N 37.987 7.298 237.894 -9.298 0.230 1.354 H33 5SV 72 5SV H34 H34 H 0 1 N N N 37.711 9.787 237.703 -10.823 1.373 -0.232 H34 5SV 73 5SV H35 H35 H 0 1 N N N 36.527 9.723 239.052 -10.611 0.043 -1.395 H35 5SV 74 5SV H36 H36 H 0 1 N N N 35.073 8.224 237.678 -11.542 -1.552 0.260 H36 5SV 75 5SV H37 H37 H 0 1 N N N 36.246 8.349 236.324 -11.754 -0.221 1.423 H37 5SV 76 5SV H38 H38 H 0 1 N N N 35.906 10.932 236.584 -13.279 0.922 -0.163 H38 5SV 77 5SV H39 H39 H 0 1 N N N 34.424 10.481 237.494 -13.067 -0.409 -1.326 H39 5SV 78 5SV H40 H40 H 0 1 N N N 33.537 9.303 235.575 -13.998 -2.003 0.328 H40 5SV 79 5SV H41 H41 H 0 1 N N N 35.068 9.541 234.666 -14.210 -0.673 1.491 H41 5SV 80 5SV H42 H42 H 0 1 N N N 34.094 12.015 235.737 -15.736 0.470 -0.095 H42 5SV 81 5SV H43 H43 H 0 1 N N N 34.110 12.942 234.009 -16.455 -2.455 0.397 H43 5SV 82 5SV H44 H44 H 0 1 N N N 35.417 11.716 233.880 -16.667 -1.124 1.560 H44 5SV 83 5SV C25 C27 C 0 1 N N N ? ? ? -17.999 -1.049 -0.131 C25 5SV 84 5SV C26 C28 C 0 1 N N N ? ? ? -19.104 -1.839 0.571 C26 5SV 85 5SV C27 C29 C 0 1 N N N ? ? ? -20.455 -1.500 -0.062 C27 5SV 86 5SV C28 C30 C 0 1 N N N ? ? ? -21.561 -2.291 0.640 C28 5SV 87 5SV H45 H45 H 0 1 N N N 32.808 11.183 234.799 -15.524 -0.860 -1.258 H45 5SV 88 5SV H46 H46 H 0 1 N N N ? ? ? -18.192 0.019 -0.026 H46 5SV 89 5SV H47 H47 H 0 1 N N N ? ? ? -17.980 -1.312 -1.189 H47 5SV 90 5SV H48 H48 H 0 1 N N N ? ? ? -18.911 -2.907 0.466 H48 5SV 91 5SV H49 H49 H 0 1 N N N ? ? ? -19.123 -1.576 1.629 H49 5SV 92 5SV H50 H50 H 0 1 N N N ? ? ? -20.649 -0.433 0.043 H50 5SV 93 5SV H51 H51 H 0 1 N N N ? ? ? -20.436 -1.763 -1.120 H51 5SV 94 5SV H52 H52 H 0 1 N N N ? ? ? -21.580 -2.027 1.698 H52 5SV 95 5SV H53 H53 H 0 1 N N N ? ? ? -22.523 -2.049 0.189 H53 5SV 96 5SV H54 H54 H 0 1 N N N ? ? ? -21.368 -3.358 0.535 H54 5SV 97 # # 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 5SV C24 C23 SING N N 1 5SV C23 C22 SING N N 2 5SV C22 C21 SING N N 3 5SV C21 C20 SING N N 4 5SV C20 C19 SING N N 5 5SV C19 C18 SING N N 6 5SV C18 C17 SING N N 7 5SV C17 C16 SING N N 8 5SV C16 C15 SING N N 9 5SV C15 C14 SING N N 10 5SV C14 C13 SING N N 11 5SV C13 C12 SING N N 12 5SV C12 C11 SING N N 13 5SV C11 C10 SING N N 14 5SV N6 C6 SING N N 15 5SV C10 C9 SING N N 16 5SV C9 O3P SING N N 17 5SV C6 C5 DOUB Y N 18 5SV C6 N1 SING Y N 19 5SV N7 C5 SING Y N 20 5SV N7 C8 DOUB Y N 21 5SV C5 C4 SING Y N 22 5SV N1 C2 DOUB Y N 23 5SV C8 N9 SING Y N 24 5SV O3P P SING N N 25 5SV C4 N9 SING Y N 26 5SV C4 N3 DOUB Y N 27 5SV C2 N3 SING Y N 28 5SV O1P P DOUB N N 29 5SV N9 "C1'" SING N N 30 5SV P "O5'" SING N N 31 5SV P O2P SING N N 32 5SV "C5'" "O5'" SING N N 33 5SV "C5'" "C4'" SING N N 34 5SV "C1'" "C2'" SING N N 35 5SV "C1'" "O4'" SING N N 36 5SV "C3'" "C2'" SING N N 37 5SV "C3'" "C4'" SING N N 38 5SV "C3'" "O3'" SING N N 39 5SV "C2'" "O2'" SING N N 40 5SV "O4'" "C4'" SING N N 41 5SV C2 H1 SING N N 42 5SV C8 H2 SING N N 43 5SV C9 H3 SING N N 44 5SV C9 H4 SING N N 45 5SV C10 H5 SING N N 46 5SV C10 H6 SING N N 47 5SV C11 H7 SING N N 48 5SV C11 H8 SING N N 49 5SV C12 H9 SING N N 50 5SV C12 H10 SING N N 51 5SV C13 H11 SING N N 52 5SV C13 H12 SING N N 53 5SV C14 H13 SING N N 54 5SV C14 H14 SING N N 55 5SV C15 H15 SING N N 56 5SV C15 H16 SING N N 57 5SV O2P H17 SING N N 58 5SV "C5'" H18 SING N N 59 5SV "C5'" H19 SING N N 60 5SV "C4'" H20 SING N N 61 5SV "C3'" H21 SING N N 62 5SV "O3'" H22 SING N N 63 5SV "C2'" H23 SING N N 64 5SV "O2'" H24 SING N N 65 5SV "C1'" H25 SING N N 66 5SV N6 H26 SING N N 67 5SV N6 H27 SING N N 68 5SV C16 H28 SING N N 69 5SV C16 H29 SING N N 70 5SV C17 H30 SING N N 71 5SV C17 H31 SING N N 72 5SV C18 H32 SING N N 73 5SV C18 H33 SING N N 74 5SV C19 H34 SING N N 75 5SV C19 H35 SING N N 76 5SV C20 H36 SING N N 77 5SV C20 H37 SING N N 78 5SV C21 H38 SING N N 79 5SV C21 H39 SING N N 80 5SV C22 H40 SING N N 81 5SV C22 H41 SING N N 82 5SV C23 H42 SING N N 83 5SV C24 H43 SING N N 84 5SV C24 H44 SING N N 85 5SV C24 C25 SING N N 86 5SV C25 C26 SING N N 87 5SV C26 C27 SING N N 88 5SV C27 C28 SING N N 89 5SV C23 H45 SING N N 90 5SV C25 H46 SING N N 91 5SV C25 H47 SING N N 92 5SV C26 H48 SING N N 93 5SV C26 H49 SING N N 94 5SV C27 H50 SING N N 95 5SV C27 H51 SING N N 96 5SV C28 H52 SING N N 97 5SV C28 H53 SING N N 98 5SV C28 H54 SING N N 99 # # 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 5SV InChI InChI 1.03 "InChI=1S/C30H54N5O7P/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-40-43(38,39)41-21-24-26(36)27(37)30(42-24)35-23-34-25-28(31)32-22-33-29(25)35/h22-24,26-27,30,36-37H,2-21H2,1H3,(H,38,39)(H2,31,32,33)/t24-,26-,27-,30-/m1/s1" 5SV InChIKey InChI 1.03 JFYKNVSLLXBVHG-BQOYKFDPSA-N 5SV SMILES_CANONICAL CACTVS 3.385 "CCCCCCCCCCCCCCCCCCCCO[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23" 5SV SMILES CACTVS 3.385 "CCCCCCCCCCCCCCCCCCCCO[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23" 5SV SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "CCCCCCCCCCCCCCCCCCCCOP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O" 5SV SMILES "OpenEye OEToolkits" 2.0.4 "CCCCCCCCCCCCCCCCCCCCOP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O" # _pdbx_chem_comp_identifier.comp_id 5SV _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.4 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl icosyl 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 5SV "Create component" 2015-11-25 EBI 5SV "Initial release" 2015-12-16 RCSB 5SV "Other modification" 2019-09-04 EBI ##