data_YO7 # _chem_comp.id YO7 _chem_comp.name "[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4R,5R,6S)-6-[(1R)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-2-yl dihydrogen diphosphate (non-preferred name)" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H27 N5 O17 P2" _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 2021-03-19 _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 635.367 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YO7 _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 7M15 _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 YO7 O3B O1 O 0 1 N N N 11.481 -27.205 25.254 2.905 -0.049 1.880 O3B YO7 1 YO7 PB P1 P 0 1 N N N 11.405 -26.389 23.954 3.061 1.165 0.835 PB YO7 2 YO7 O2B O2 O 0 1 N N N 12.478 -25.290 23.760 3.742 2.301 1.496 O2B YO7 3 YO7 O1B O3 O 0 1 N N N 11.283 -27.373 22.693 3.933 0.678 -0.428 O1B YO7 4 YO7 C11 C1 C 0 1 N N R 11.896 -27.220 21.397 5.308 0.300 -0.325 C11 YO7 5 YO7 C21 C2 C 0 1 N N S 10.975 -27.747 20.302 6.022 0.610 -1.643 C21 YO7 6 YO7 O21 O4 O 0 1 N N N 9.863 -26.858 20.151 5.982 2.017 -1.890 O21 YO7 7 YO7 C31 C3 C 0 1 N N R 11.712 -27.910 18.953 7.479 0.148 -1.546 C31 YO7 8 YO7 O31 O5 O 0 1 N N N 10.841 -28.483 17.956 8.134 0.366 -2.797 O31 YO7 9 YO7 C41 C4 C 0 1 N N R 12.978 -28.760 19.161 7.508 -1.346 -1.206 C41 YO7 10 YO7 O41 O6 O 0 1 N N N 13.781 -28.969 17.987 8.862 -1.772 -1.041 O41 YO7 11 YO7 C51 C5 C 0 1 N N S 13.880 -28.160 20.272 6.736 -1.580 0.095 C51 YO7 12 YO7 C61 C6 C 0 1 N N R 15.132 -29.014 20.637 6.709 -3.076 0.411 C61 YO7 13 YO7 C71 C7 C 0 1 N N N 16.185 -28.257 21.463 5.834 -3.323 1.641 C71 YO7 14 YO7 O71 O7 O 0 1 N N N 16.845 -27.411 20.515 5.902 -4.703 2.005 O71 YO7 15 YO7 O6A O8 O 0 1 N N N 14.743 -30.134 21.423 6.173 -3.789 -0.706 O6A YO7 16 YO7 O51 O9 O 0 1 N N N 13.075 -28.016 21.432 5.399 -1.100 -0.053 O51 YO7 17 YO7 O3A O10 O 0 1 N N N 10.021 -25.580 23.792 1.604 1.631 0.332 O3A YO7 18 YO7 PA P2 P 0 1 N N N 8.531 -26.208 23.582 0.450 2.562 0.960 PA YO7 19 YO7 O1A O11 O 0 1 N N N 8.205 -26.630 22.173 0.336 2.296 2.411 O1A YO7 20 YO7 O2A O12 O 0 1 N N N 8.312 -27.291 24.645 0.824 4.111 0.726 O2A YO7 21 YO7 "O5'" O13 O 0 1 N N N 7.606 -24.909 23.900 -0.953 2.235 0.241 "O5'" YO7 22 YO7 "C5'" C8 C 0 1 N N N 7.599 -24.393 25.246 -2.191 2.822 0.648 "C5'" YO7 23 YO7 "C4'" C9 C 0 1 N N R 6.471 -23.366 25.331 -3.320 2.297 -0.241 "C4'" YO7 24 YO7 "C3'" C10 C 0 1 N N S 5.145 -23.936 24.855 -4.655 2.983 0.124 "C3'" YO7 25 YO7 "O3'" O14 O 0 1 N N N 4.150 -23.445 25.747 -4.931 4.055 -0.780 "O3'" YO7 26 YO7 "C2'" C11 C 0 1 N N R 4.919 -23.338 23.473 -5.708 1.862 -0.028 "C2'" YO7 27 YO7 "O2'" O15 O 0 1 N N N 3.547 -23.039 23.169 -6.667 2.206 -1.030 "O2'" YO7 28 YO7 "O4'" O16 O 0 1 N N N 6.756 -22.231 24.469 -3.545 0.892 0.009 "O4'" YO7 29 YO7 "C1'" C12 C 0 1 N N R 5.693 -22.024 23.543 -4.884 0.631 -0.467 "C1'" YO7 30 YO7 N9 N1 N 0 1 Y N N 6.270 -21.631 22.279 -5.417 -0.586 0.150 N9 YO7 31 YO7 C4 C13 C 0 1 Y N N 6.231 -20.411 21.760 -6.450 -1.348 -0.324 C4 YO7 32 YO7 N3 N2 N 0 1 N N N 5.689 -19.251 22.196 -7.252 -1.272 -1.392 N3 YO7 33 YO7 C2 C14 C 0 1 N N N 5.780 -18.082 21.501 -8.188 -2.170 -1.605 C2 YO7 34 YO7 N2 N3 N 0 1 N N N 5.186 -16.987 22.076 -8.987 -2.050 -2.714 N2 YO7 35 YO7 C8 C15 C 0 1 Y N N 6.983 -22.433 21.441 -4.971 -1.170 1.300 C8 YO7 36 YO7 N7 N4 N 0 1 Y N N 7.352 -21.707 20.367 -5.672 -2.235 1.555 N7 YO7 37 YO7 C5 C16 C 0 1 Y N N 6.928 -20.447 20.571 -6.605 -2.401 0.586 C5 YO7 38 YO7 C6 C17 C 0 1 N N N 7.050 -19.171 19.791 -7.619 -3.358 0.347 C6 YO7 39 YO7 O6 O17 O 0 1 N N N 7.673 -19.193 18.709 -7.789 -4.292 1.112 O6 YO7 40 YO7 N1 N5 N 0 1 N N N 6.467 -18.036 20.293 -8.388 -3.217 -0.756 N1 YO7 41 YO7 H1 H1 H 0 1 N N N 12.213 -26.901 25.777 2.466 -0.829 1.514 H1 YO7 42 YO7 H2 H2 H 0 1 N N N 12.137 -26.165 21.201 5.779 0.859 0.484 H2 YO7 43 YO7 H3 H3 H 0 1 N N N 10.610 -28.738 20.609 5.527 0.083 -2.459 H3 YO7 44 YO7 H4 H4 H 0 1 N N N 9.342 -26.864 20.945 5.088 2.378 -1.958 H4 YO7 45 YO7 H5 H5 H 0 1 N N N 12.029 -26.910 18.621 7.989 0.710 -0.763 H5 YO7 46 YO7 H6 H6 H 0 1 N N N 10.072 -27.934 17.854 8.153 1.291 -3.075 H6 YO7 47 YO7 H7 H7 H 0 1 N N N 12.644 -29.743 19.524 7.043 -1.912 -2.012 H7 YO7 48 YO7 H8 H8 H 0 1 N N N 14.536 -29.501 18.210 9.412 -1.648 -1.827 H8 YO7 49 YO7 H9 H9 H 0 1 N N N 14.228 -27.173 19.934 7.226 -1.046 0.910 H9 YO7 50 YO7 H10 H10 H 0 1 N N N 15.601 -29.354 19.702 7.723 -3.424 0.610 H10 YO7 51 YO7 H11 H11 H 0 1 N N N 16.898 -28.959 21.920 6.191 -2.711 2.469 H11 YO7 52 YO7 H12 H12 H 0 1 N N N 15.704 -27.658 22.250 4.802 -3.058 1.412 H12 YO7 53 YO7 H13 H13 H 0 1 N N N 17.518 -26.905 20.956 5.370 -4.932 2.780 H13 YO7 54 YO7 H14 H14 H 0 1 N N N 15.510 -30.650 21.642 5.271 -3.530 -0.941 H14 YO7 55 YO7 H15 H15 H 0 1 N N N 7.994 -28.084 24.229 0.915 4.358 -0.205 H15 YO7 56 YO7 H16 H16 H 0 1 N N N 7.420 -25.209 25.961 -2.394 2.560 1.686 H16 YO7 57 YO7 H17 H17 H 0 1 N N N 8.563 -23.913 25.471 -2.128 3.906 0.552 H17 YO7 58 YO7 H18 H18 H 0 1 N N N 6.367 -23.032 26.374 -3.083 2.462 -1.292 H18 YO7 59 YO7 H19 H19 H 0 1 N N N 5.175 -25.035 24.813 -4.629 3.348 1.151 H19 YO7 60 YO7 H20 H20 H 0 1 N N N 4.288 -23.816 26.611 -5.758 4.521 -0.597 H20 YO7 61 YO7 H21 H21 H 0 1 N N N 5.361 -23.991 22.706 -6.201 1.671 0.925 H21 YO7 62 YO7 H22 H22 H 0 1 N N N 3.049 -23.847 23.121 -7.212 2.973 -0.807 H22 YO7 63 YO7 H23 H23 H 0 1 N N N 5.019 -21.235 23.909 -4.888 0.539 -1.553 H23 YO7 64 YO7 H24 H24 H 0 1 N N N 4.720 -17.075 22.957 -8.857 -1.310 -3.328 H24 YO7 65 YO7 H25 H25 H 0 1 N N N 5.219 -16.100 21.615 -9.682 -2.705 -2.884 H25 YO7 66 YO7 H26 H26 H 0 1 N N N 7.214 -23.475 21.609 -4.157 -0.802 1.908 H26 YO7 67 YO7 H27 H27 H 0 1 N N N 6.536 -17.175 19.790 -9.089 -3.862 -0.940 H27 YO7 68 # # 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 YO7 O31 C31 SING N N 1 YO7 O41 C41 SING N N 2 YO7 O6 C6 DOUB N N 3 YO7 C31 C41 SING N N 4 YO7 C31 C21 SING N N 5 YO7 C41 C51 SING N N 6 YO7 C6 N1 SING N N 7 YO7 C6 C5 SING N N 8 YO7 O21 C21 SING N N 9 YO7 C51 C61 SING N N 10 YO7 C51 O51 SING N N 11 YO7 N1 C2 SING N N 12 YO7 C21 C11 SING N N 13 YO7 N7 C5 SING Y N 14 YO7 N7 C8 DOUB Y N 15 YO7 O71 C71 SING N N 16 YO7 C5 C4 DOUB Y N 17 YO7 C61 O6A SING N N 18 YO7 C61 C71 SING N N 19 YO7 C11 O51 SING N N 20 YO7 C11 O1B SING N N 21 YO7 C8 N9 SING Y N 22 YO7 C2 N2 SING N N 23 YO7 C2 N3 DOUB N N 24 YO7 C4 N3 SING N N 25 YO7 C4 N9 SING Y N 26 YO7 O1A PA DOUB N N 27 YO7 N9 "C1'" SING N N 28 YO7 O1B PB SING N N 29 YO7 "O2'" "C2'" SING N N 30 YO7 "C2'" "C1'" SING N N 31 YO7 "C2'" "C3'" SING N N 32 YO7 "C1'" "O4'" SING N N 33 YO7 PA O3A SING N N 34 YO7 PA "O5'" SING N N 35 YO7 PA O2A SING N N 36 YO7 O2B PB DOUB N N 37 YO7 O3A PB SING N N 38 YO7 "O5'" "C5'" SING N N 39 YO7 PB O3B SING N N 40 YO7 "O4'" "C4'" SING N N 41 YO7 "C3'" "C4'" SING N N 42 YO7 "C3'" "O3'" SING N N 43 YO7 "C5'" "C4'" SING N N 44 YO7 O3B H1 SING N N 45 YO7 C11 H2 SING N N 46 YO7 C21 H3 SING N N 47 YO7 O21 H4 SING N N 48 YO7 C31 H5 SING N N 49 YO7 O31 H6 SING N N 50 YO7 C41 H7 SING N N 51 YO7 O41 H8 SING N N 52 YO7 C51 H9 SING N N 53 YO7 C61 H10 SING N N 54 YO7 C71 H11 SING N N 55 YO7 C71 H12 SING N N 56 YO7 O71 H13 SING N N 57 YO7 O6A H14 SING N N 58 YO7 O2A H15 SING N N 59 YO7 "C5'" H16 SING N N 60 YO7 "C5'" H17 SING N N 61 YO7 "C4'" H18 SING N N 62 YO7 "C3'" H19 SING N N 63 YO7 "O3'" H20 SING N N 64 YO7 "C2'" H21 SING N N 65 YO7 "O2'" H22 SING N N 66 YO7 "C1'" H23 SING N N 67 YO7 N2 H24 SING N N 68 YO7 N2 H25 SING N N 69 YO7 C8 H26 SING N N 70 YO7 N1 H27 SING N N 71 # # 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 YO7 SMILES ACDLabs 12.01 "NC1=Nc2c(ncn2C2OC(COP(=O)(O)OP(=O)(O)OC3OC(C(O)C(O)C3O)C(O)CO)C(O)C2O)C(=O)N1" YO7 InChI InChI 1.03 "InChI=1S/C17H27N5O17P2/c18-17-20-13-6(14(30)21-17)19-3-22(13)15-10(28)7(25)5(36-15)2-35-40(31,32)39-41(33,34)38-16-11(29)8(26)9(27)12(37-16)4(24)1-23/h3-5,7-12,15-16,23-29H,1-2H2,(H,31,32)(H,33,34)(H3,18,20,21,30)/t4-,5-,7-,8-,9-,10-,11+,12+,15-,16-/m1/s1" YO7 InChIKey InChI 1.03 HRUXIQZFNLQZQA-GVGRRHNDSA-N YO7 SMILES_CANONICAL CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[C@H]4O[C@@H]([C@H](O)CO)[C@H](O)[C@@H](O)[C@@H]4O)[C@@H](O)[C@H]3O" YO7 SMILES CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]4O[CH]([CH](O)CO)[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O" YO7 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)O[C@@H]4[C@H]([C@@H]([C@H]([C@@H](O4)[C@@H](CO)O)O)O)O)O)O)N=C(NC2=O)N" YO7 SMILES "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OC4C(C(C(C(O4)C(CO)O)O)O)O)O)O)N=C(NC2=O)N" # # 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 YO7 "SYSTEMATIC NAME" ACDLabs 12.01 "[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4R,5R,6S)-6-[(1R)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-2-yl dihydrogen diphosphate (non-preferred name)" YO7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R},6~{S})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl] 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 YO7 "Create component" 2021-03-16 RCSB YO7 "Initial release" 2021-03-24 RCSB ##