data_9SO # _chem_comp.id 9SO _chem_comp.name "[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(2R,3R,4R,5R)-3,5-dihydroxy-4-(phosphonooxy)oxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H24 N5 O17 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-07-14 _chem_comp.pdbx_modified_date 2023-11-03 _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 639.296 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 9SO _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 8TG4 _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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 9SO C02 C1 C 0 1 Y N N N N N 5.966 -22.453 -18.608 7.929 4.183 0.993 C02 9SO 1 9SO C03 C2 C 0 1 Y N N N N N 5.087 -21.361 -18.538 7.157 3.010 1.041 C03 9SO 2 9SO C05 C3 C 0 1 Y N N N N N 3.506 -19.888 -18.617 5.935 1.283 1.516 C05 9SO 3 9SO C07 C4 C 0 1 N N R N N N 4.660 -17.931 -17.444 5.701 0.181 -0.741 C07 9SO 4 9SO C09 C5 C 0 1 N N R N N N 3.841 -16.654 -15.767 4.430 -1.726 -0.892 C09 9SO 5 9SO C10 C6 C 0 1 N N N N N N 2.579 -16.908 -14.963 3.560 -2.700 -0.095 C10 9SO 6 9SO C20 C7 C 0 1 N N N N N N -2.656 -13.234 -15.978 -4.290 -1.495 0.504 C20 9SO 7 9SO C21 C8 C 0 1 N N R N N N -3.170 -11.818 -15.952 -4.873 -0.097 0.289 C21 9SO 8 9SO C23 C9 C 0 1 N N R N N N -3.372 -10.728 -18.026 -5.738 1.333 -1.285 C23 9SO 9 9SO C25 C10 C 0 1 N N R N N N -4.631 -10.444 -17.146 -6.974 0.865 -0.480 C25 9SO 10 9SO C31 C11 C 0 1 N N R N N N -4.499 -11.670 -16.194 -6.390 -0.097 0.579 C31 9SO 11 9SO C33 C12 C 0 1 N N S N N N 3.589 -15.980 -16.907 5.885 -2.238 -0.963 C33 9SO 12 9SO C35 C13 C 0 1 N N R N N N 3.571 -17.010 -18.039 6.741 -0.955 -0.862 C35 9SO 13 9SO C37 C14 C 0 1 Y N N N N N 5.543 -20.216 -17.924 6.952 2.301 -0.154 C37 9SO 14 9SO C39 C15 C 0 1 Y N N N N N 7.562 -21.192 -17.502 8.206 3.866 -1.277 C39 9SO 15 9SO N01 N1 N 0 1 N N N N N N 5.585 -23.682 -19.219 8.170 4.921 2.139 N01 9SO 16 9SO N04 N2 N 0 1 Y N N N N N 3.819 -21.120 -18.934 6.510 2.335 2.022 N04 9SO 17 9SO N06 N3 N 0 1 Y N N N N N 4.549 -19.336 -18.005 6.178 1.217 0.177 N06 9SO 18 9SO N38 N4 N 0 1 Y N N N N N 6.773 -20.133 -17.410 7.490 2.761 -1.279 N38 9SO 19 9SO N40 N5 N 0 1 Y N N N N N 7.167 -22.324 -18.088 8.427 4.566 -0.179 N40 9SO 20 9SO O08 O1 O 0 1 N N N N N N 4.382 -17.975 -16.076 4.519 -0.456 -0.209 O08 9SO 21 9SO O11 O2 O 0 1 N N N N N N 2.280 -15.737 -14.278 2.204 -2.250 -0.109 O11 9SO 22 9SO O13 O3 O 0 1 N N N N N N 0.793 -13.907 -13.416 1.261 -3.013 2.223 O13 9SO 23 9SO O14 O4 O 0 1 N N N N N N -0.070 -16.305 -13.512 0.975 -4.438 0.159 O14 9SO 24 9SO O15 O5 O 0 1 N N N N N N 0.201 -15.178 -15.619 -0.392 -2.320 0.299 O15 9SO 25 9SO O17 O6 O 0 1 N N N N N N 1.163 -13.037 -16.596 -2.310 -3.823 -0.688 O17 9SO 26 9SO O18 O7 O 0 1 N N N N N N -0.555 -14.430 -17.855 -2.141 -3.366 1.789 O18 9SO 27 9SO O19 O8 O 0 1 N N N N N N -1.258 -13.074 -15.728 -2.875 -1.457 0.310 O19 9SO 28 9SO O22 O9 O 0 1 N N N N N N -2.440 -11.158 -17.050 -4.759 0.287 -1.098 O22 9SO 29 9SO O24 O10 O 0 1 N N N N N N -3.662 -11.750 -18.918 -6.066 1.466 -2.669 O24 9SO 30 9SO O26 O11 O 0 1 N N N N N N -4.419 -9.303 -16.484 -7.612 1.978 0.150 O26 9SO 31 9SO O28 O12 O 0 1 N N N N N N -6.589 -8.095 -15.723 -9.565 3.592 0.851 O28 9SO 32 9SO O29 O13 O 0 1 N N N N N N -4.528 -6.866 -16.091 -9.324 2.830 -1.654 O29 9SO 33 9SO O30 O14 O 0 1 N N N N N N -5.694 -7.853 -18.055 -10.016 1.209 0.153 O30 9SO 34 9SO O32 O15 O 0 1 N N N N N N -5.278 -11.326 -14.992 -6.649 0.393 1.896 O32 9SO 35 9SO O34 O16 O 0 1 N N N N N N 4.702 -14.967 -17.179 6.122 -2.904 -2.206 O34 9SO 36 9SO O36 O17 O 0 1 N N N N N N 3.971 -16.602 -19.287 7.532 -0.787 -2.039 O36 9SO 37 9SO P12 P1 P 0 1 N N N N N N 0.736 -15.248 -14.116 1.011 -3.036 0.633 P12 9SO 38 9SO P16 P2 P 0 1 N N N N N N -0.075 -13.880 -16.581 -1.934 -2.755 0.457 P16 9SO 39 9SO P27 P3 P 0 1 N N N N N N -5.362 -7.975 -16.594 -9.148 2.376 -0.119 P27 9SO 40 9SO H1 H1 H 0 1 N N N N N N 2.562 -19.404 -18.818 5.351 0.567 2.076 H1 9SO 41 9SO H2 H2 H 0 1 N N N N N N 5.657 -17.515 -17.651 5.492 0.609 -1.721 H2 9SO 42 9SO H3 H3 H 0 1 N N N N N N 4.555 -16.107 -15.135 4.026 -1.591 -1.896 H3 9SO 43 9SO H4 H4 H 0 1 N N N N N N 1.750 -17.171 -15.637 3.619 -3.691 -0.545 H4 9SO 44 9SO H5 H5 H 0 1 N N N N N N 2.746 -17.729 -14.250 3.917 -2.747 0.934 H5 9SO 45 9SO H6 H6 H 0 1 N N N N N N -3.131 -13.841 -15.193 -4.509 -1.828 1.519 H6 9SO 46 9SO H7 H7 H 0 1 N N N N N N -2.831 -13.700 -16.959 -4.736 -2.188 -0.209 H7 9SO 47 9SO H8 H8 H 0 1 N N N N N N -2.888 -11.353 -14.996 -4.365 0.627 0.927 H8 9SO 48 9SO H9 H9 H 0 1 N N N N N N -3.049 -9.805 -18.530 -5.363 2.277 -0.890 H9 9SO 49 9SO H10 H10 H 0 1 N N N N N N -5.558 -10.485 -17.737 -7.676 0.341 -1.129 H10 9SO 50 9SO H11 H11 H 0 1 N N N N N N -4.929 -12.555 -16.686 -6.803 -1.098 0.454 H11 9SO 51 9SO H12 H12 H 0 1 N N N N N N 2.621 -15.458 -16.874 6.097 -2.905 -0.128 H12 9SO 52 9SO H13 H13 H 0 1 N N N N N N 2.605 -17.536 -18.057 7.375 -0.988 0.024 H13 9SO 53 9SO H14 H14 H 0 1 N N N N N N 8.558 -21.138 -17.089 8.630 4.213 -2.208 H14 9SO 54 9SO H15 H15 H 0 1 N N N N N N 6.344 -24.331 -19.165 7.804 4.629 2.989 H15 9SO 55 9SO H16 H16 H 0 1 N N N N N N 4.790 -24.058 -18.743 8.704 5.729 2.092 H16 9SO 56 9SO H17 H17 H 0 1 N N N N N N 0.263 -13.938 -12.628 1.297 -2.124 2.603 H17 9SO 57 9SO H18 H18 H 0 1 N N N N N N 1.490 -12.969 -17.486 -2.198 -3.489 -1.589 H18 9SO 58 9SO H19 H19 H 0 1 N N N N N N -2.899 -11.927 -19.456 -5.328 1.757 -3.222 H19 9SO 59 9SO H20 H20 H 0 1 N N N N N N -7.368 -8.071 -16.267 -10.480 3.885 0.743 H20 9SO 60 9SO H21 H21 H 0 1 N N N N N N -4.347 -6.259 -16.799 -8.783 3.592 -1.903 H21 9SO 61 9SO H22 H22 H 0 1 N N N N N N -5.234 -12.043 -14.370 -6.304 -0.173 2.601 H22 9SO 62 9SO H23 H23 H 0 1 N N N N N N 4.722 -14.323 -16.481 7.021 -3.246 -2.304 H23 9SO 63 9SO H24 H24 H 0 1 N N N N N N 3.308 -16.035 -19.663 8.202 -1.473 -2.165 H24 9SO 64 # 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 9SO O36 C35 SING N N 1 9SO N01 C02 SING N N 2 9SO N04 C05 DOUB Y N 3 9SO N04 C03 SING Y N 4 9SO O24 C23 SING N N 5 9SO C05 N06 SING Y N 6 9SO C02 C03 DOUB Y N 7 9SO C02 N40 SING Y N 8 9SO C03 C37 SING Y N 9 9SO N40 C39 DOUB Y N 10 9SO O30 P27 DOUB N N 11 9SO C35 C07 SING N N 12 9SO C35 C33 SING N N 13 9SO C23 C25 SING N N 14 9SO C23 O22 SING N N 15 9SO N06 C37 SING Y N 16 9SO N06 C07 SING N N 17 9SO C37 N38 DOUB Y N 18 9SO O18 P16 DOUB N N 19 9SO C39 N38 SING Y N 20 9SO C07 O08 SING N N 21 9SO O34 C33 SING N N 22 9SO C25 O26 SING N N 23 9SO C25 C31 SING N N 24 9SO O22 C21 SING N N 25 9SO C33 C09 SING N N 26 9SO O17 P16 SING N N 27 9SO P27 O26 SING N N 28 9SO P27 O29 SING N N 29 9SO P27 O28 SING N N 30 9SO P16 O19 SING N N 31 9SO P16 O15 SING N N 32 9SO C31 C21 SING N N 33 9SO C31 O32 SING N N 34 9SO O08 C09 SING N N 35 9SO C20 C21 SING N N 36 9SO C20 O19 SING N N 37 9SO C09 C10 SING N N 38 9SO O15 P12 SING N N 39 9SO C10 O11 SING N N 40 9SO O11 P12 SING N N 41 9SO P12 O14 DOUB N N 42 9SO P12 O13 SING N N 43 9SO C05 H1 SING N N 44 9SO C07 H2 SING N N 45 9SO C09 H3 SING N N 46 9SO C10 H4 SING N N 47 9SO C10 H5 SING N N 48 9SO C20 H6 SING N N 49 9SO C20 H7 SING N N 50 9SO C21 H8 SING N N 51 9SO C23 H9 SING N N 52 9SO C25 H10 SING N N 53 9SO C31 H11 SING N N 54 9SO C33 H12 SING N N 55 9SO C35 H13 SING N N 56 9SO C39 H14 SING N N 57 9SO N01 H15 SING N N 58 9SO N01 H16 SING N N 59 9SO O13 H17 SING N N 60 9SO O17 H18 SING N N 61 9SO O24 H19 SING N N 62 9SO O28 H20 SING N N 63 9SO O29 H21 SING N N 64 9SO O32 H22 SING N N 65 9SO O34 H23 SING N N 66 9SO O36 H24 SING N N 67 # 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 9SO SMILES ACDLabs 12.01 "OP(=O)(O)OC1C(O)C(COP(=O)(O)OP(=O)(O)OCC2OC(n3cnc4c(N)ncnc43)C(O)C2O)OC1O" 9SO InChI InChI 1.06 "InChI=1S/C15H24N5O17P3/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(34-14)1-32-39(28,29)37-40(30,31)33-2-6-9(22)11(15(24)35-6)36-38(25,26)27/h3-6,8-11,14-15,21-24H,1-2H2,(H,28,29)(H,30,31)(H2,16,17,18)(H2,25,26,27)/t5-,6-,8-,9-,10-,11-,14-,15-/m1/s1" 9SO InChIKey InChI 1.06 MWRFFSMPOUTGDW-KEOHHSTQSA-N 9SO SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@@H](O)[C@H](O[P](O)(O)=O)[C@@H]4O)[C@@H](O)[C@H]3O" 9SO SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH](O)[CH](O[P](O)(O)=O)[CH]4O)[CH](O)[CH]3O" 9SO SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)O)OP(=O)(O)O)O)O)O)N" 9SO SMILES "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)OP(=O)(O)O)O)O)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 9SO "SYSTEMATIC NAME" ACDLabs 12.01 "[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(2R,3R,4R,5R)-3,5-dihydroxy-4-(phosphonooxy)oxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)" 9SO "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R})-3,5-bis(oxidanyl)-4-phosphonooxy-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 9SO "Create component" 2023-07-14 RCSB 9SO "Initial release" 2023-11-08 RCSB #