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 
# 
