data_A1IVA
# 
_chem_comp.id                                    A1IVA 
_chem_comp.name                                  "(1~{S},2~{S},4~{S},5~{R})-6-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-bis(oxidanylidene)-$l^{6}-phosphanyl]oxy-bis(oxidanylidene)-$l^{6}-phosphanyl]methyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxycyclohexane-1,2,3,4,5-pentol" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C17 H25 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                     2024-11-27 
_chem_comp.pdbx_modified_date                    2025-11-28 
_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                        664.325 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1IVA 
_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        9HHM 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_chem_comp.pdbx_pcm                              ? 
# 
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_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_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 
A1IVA C4     C1  C 0 1 Y N N N N N 57.383 64.771 20.190 7.272   -2.090 0.402  C4     A1IVA 1  
A1IVA "C1'"  C2  C 0 1 N N R N N N 55.654 62.928 19.973 6.109   0.126  0.778  "C1'"  A1IVA 2  
A1IVA C2     C3  C 0 1 Y N N N N N 59.570 64.880 19.923 9.037   -3.229 1.334  C2     A1IVA 3  
A1IVA "C2'"  C4  C 0 1 N N R N N N 55.391 62.092 21.230 6.996   1.222  0.133  "C2'"  A1IVA 4  
A1IVA "C3'"  C5  C 0 1 N N S N N N 53.894 62.317 21.443 6.223   2.515  0.487  "C3'"  A1IVA 5  
A1IVA C3B    C6  C 0 1 N N N N N N 48.153 63.355 20.236 -2.533  0.632  0.229  C3B    A1IVA 6  
A1IVA "C4'"  C7  C 0 1 N N R N N N 53.370 62.381 20.013 4.791   2.030  0.784  "C4'"  A1IVA 7  
A1IVA C5     C8  C 0 1 Y N N N N N 57.305 66.112 20.535 7.076   -3.152 -0.497 C5     A1IVA 8  
A1IVA "C5'"  C9  C 0 1 N N N N N N 52.115 63.197 19.837 3.799   2.720  -0.156 "C5'"  A1IVA 9  
A1IVA C6     C10 C 0 1 Y N N N N N 58.510 66.838 20.554 7.936   -4.260 -0.413 C6     A1IVA 10 
A1IVA C8     C11 C 0 1 Y N N N N N 55.320 65.362 20.611 5.573   -1.650 -0.933 C8     A1IVA 11 
A1IVA CI1    C12 C 0 1 N N N N N N 41.947 64.993 21.294 -8.860  -2.367 0.941  CI1    A1IVA 12 
A1IVA CI2    C13 C 0 1 N N S N N N 41.774 64.024 20.125 -8.663  -0.956 1.498  CI2    A1IVA 13 
A1IVA CI3    C14 C 0 1 N N S N N N 43.072 63.830 19.349 -7.168  -0.684 1.680  CI3    A1IVA 14 
A1IVA CI4    C15 C 0 1 N N N N N N 44.267 64.001 20.274 -6.459  -0.803 0.329  CI4    A1IVA 15 
A1IVA CI5    C16 C 0 1 N N R N N N 44.381 65.441 20.755 -6.657  -2.214 -0.227 CI5    A1IVA 16 
A1IVA CI6    C17 C 0 1 N N S N N N 43.005 66.055 21.001 -8.152  -2.486 -0.410 CI6    A1IVA 17 
A1IVA N1     N1  N 0 1 Y N N N N N 59.646 66.177 20.236 8.891   -4.251 0.510  N1     A1IVA 18 
A1IVA N3     N2  N 0 1 Y N N N N N 58.491 64.092 19.871 8.256   -2.171 1.292  N3     A1IVA 19 
A1IVA N6     N3  N 0 1 N N N N N N 58.596 68.132 20.879 7.790   -5.336 -1.271 N6     A1IVA 20 
A1IVA N7     N4  N 0 1 Y N N N N N 55.990 66.471 20.799 6.024   -2.819 -1.283 N7     A1IVA 21 
A1IVA N9     N5  N 0 1 Y N N N N N 56.097 64.293 20.241 6.307   -1.160 0.106  N9     A1IVA 22 
A1IVA O1A    O1  O 0 1 N N N N N N 50.707 64.170 22.025 1.401   2.806  -2.044 O1A    A1IVA 23 
A1IVA O1B    O2  O 0 1 N N N N N N 47.646 65.627 18.896 -1.771  1.801  -2.087 O1B    A1IVA 24 
A1IVA O1G    O3  O 0 1 N N N N N N 46.185 62.852 22.022 -4.897  1.942  0.128  O1G    A1IVA 25 
A1IVA "O2'"  O4  O 0 1 N N N N N N 55.686 60.721 20.986 8.300   1.230  0.717  "O2'"  A1IVA 26 
A1IVA O2A    O5  O 0 1 N N N N N N 51.586 66.514 21.581 0.907   4.286  -0.198 O2A    A1IVA 27 
A1IVA O2B    O6  O 0 1 N N N N N N 47.782 65.805 21.355 -2.265  3.282  -0.242 O2B    A1IVA 28 
A1IVA O2G    O7  O 0 1 N N N N N N 46.388 61.296 20.121 -4.403  0.461  -1.717 O2G    A1IVA 29 
A1IVA "O3'"  O8  O 0 1 N N N N N N 53.292 61.251 22.170 6.790   3.136  1.643  "O3'"  A1IVA 30 
A1IVA O3A    O9  O 0 1 N N N N N N 49.936 65.464 20.055 -0.106  1.974  -0.198 O3A    A1IVA 31 
A1IVA "O4'"  O10 O 0 1 N N N N N N 54.437 62.982 19.247 4.764   0.609  0.565  "O4'"  A1IVA 32 
A1IVA "O5'"  O11 O 0 1 N N N N N N 52.426 64.563 20.180 2.467   2.342  0.197  "O5'"  A1IVA 33 
A1IVA OI1    O12 O 0 1 N N N N N N 42.234 64.295 22.504 -10.256 -2.620 0.771  OI1    A1IVA 34 
A1IVA OI2    O13 O 0 1 N N N N N N 41.296 62.770 20.600 -9.212  -0.002 0.586  OI2    A1IVA 35 
A1IVA OI3    O14 O 0 1 N N N N N N 43.096 62.538 18.751 -6.983  0.634  2.200  OI3    A1IVA 36 
A1IVA OI4    O15 O 0 1 N N N N N N 45.427 63.656 19.587 -5.064  -0.549 0.500  OI4    A1IVA 37 
A1IVA OI5    O16 O 0 1 N N N N N N 45.165 65.504 21.943 -5.996  -2.326 -1.489 OI5    A1IVA 38 
A1IVA OI6    O17 O 0 1 N N N N N N 42.610 66.866 19.898 -8.337  -3.804 -0.930 OI6    A1IVA 39 
A1IVA PA     P1  P 0 1 N N N N N N 51.144 65.202 21.063 1.166   2.881  -0.584 PA     A1IVA 40 
A1IVA PB     P2  P 0 1 N N N N N N 48.375 65.149 20.129 -1.659  1.986  -0.623 PB     A1IVA 41 
A1IVA PG     P3  P 0 1 N N N N N N 46.480 62.745 20.544 -4.291  0.646  -0.253 PG     A1IVA 42 
A1IVA "H1'"  H1  H 0 1 N N N N N N 56.419 62.413 19.374 6.321   0.039  1.843  "H1'"  A1IVA 43 
A1IVA H2     H2  H 0 1 N N N N N N 60.508 64.403 19.679 9.827   -3.263 2.070  H2     A1IVA 44 
A1IVA "H2'"  H3  H 0 1 N N N N N N 55.963 62.491 22.081 7.056   1.087  -0.947 "H2'"  A1IVA 45 
A1IVA "H3'"  H4  H 0 1 N N N N N N 53.731 63.283 21.943 6.228   3.206  -0.356 "H3'"  A1IVA 46 
A1IVA H3B    H5  H 0 1 N N N N N N 48.793 62.991 21.053 -2.087  -0.322 -0.052 H3B    A1IVA 47 
A1IVA H3B1   H6  H 0 0 N N N N N N 48.492 62.922 19.283 -2.451  0.769  1.307  H3B1   A1IVA 48 
A1IVA "H4'"  H7  H 0 1 N N N N N N 53.185 61.357 19.657 4.536   2.251  1.820  "H4'"  A1IVA 49 
A1IVA "H5'2" H8  H 0 0 N N N N N N 51.324 62.815 20.500 3.906   3.801  -0.067 "H5'2" A1IVA 50 
A1IVA "H5'1" H9  H 0 0 N N N N N N 51.776 63.141 18.792 4.002   2.418  -1.184 "H5'1" A1IVA 51 
A1IVA H8     H10 H 0 1 N N N N N N 54.249 65.294 20.736 4.739   -1.143 -1.395 H8     A1IVA 52 
A1IVA HI1    H11 H 0 1 N N N N N N 40.989 65.519 21.419 -8.441  -3.094 1.637  HI1    A1IVA 53 
A1IVA HI2    H12 H 0 1 N N N N N N 41.032 64.456 19.437 -9.167  -0.871 2.460  HI2    A1IVA 54 
A1IVA HI3    H13 H 0 1 N N N N N N 43.126 64.601 18.567 -6.749  -1.411 2.376  HI3    A1IVA 55 
A1IVA HI4    H14 H 0 1 N N N N N N 44.130 63.348 21.149 -6.879  -0.076 -0.366 HI4    A1IVA 56 
A1IVA HI5    H15 H 0 1 N N N N N N 44.875 66.024 19.964 -6.238  -2.941 0.468  HI5    A1IVA 57 
A1IVA HI6    H16 H 0 1 N N N N N N 43.085 66.692 21.894 -8.571  -1.759 -1.105 HI6    A1IVA 58 
A1IVA HN61   H17 H 0 0 N N N N N N 59.551 68.425 20.832 7.088   -5.331 -1.941 HN61   A1IVA 59 
A1IVA HN62   H18 H 0 0 N N N N N N 58.050 68.673 20.240 8.390   -6.095 -1.203 HN62   A1IVA 60 
A1IVA "HO2'" H19 H 0 0 N N N N N N 56.621 60.616 20.858 8.892   1.899  0.347  "HO2'" A1IVA 61 
A1IVA "HO3'" H20 H 0 0 N N N N N N 53.637 61.236 23.055 7.711   3.408  1.531  "HO3'" A1IVA 62 
A1IVA HIO1   H21 H 0 0 N N N N N N 42.337 64.919 23.213 -10.456 -3.499 0.420  HIO1   A1IVA 63 
A1IVA HIO2   H22 H 0 0 N N N N N N 41.191 62.173 19.869 -10.159 -0.115 0.423  HIO2   A1IVA 64 
A1IVA HIO3   H23 H 0 0 N N N N N N 43.908 62.426 18.270 -7.407  0.782  3.057  HIO3   A1IVA 65 
A1IVA HIO5   H24 H 0 0 N N N N N N 46.081 65.610 21.713 -6.079  -3.196 -1.902 HIO5   A1IVA 66 
A1IVA HIO6   H25 H 0 0 N N N N N N 43.278 67.520 19.730 -9.262  -4.045 -1.071 HIO6   A1IVA 67 
# 
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 
A1IVA PG    O1G    DOUB N N 1  
A1IVA PG    O2G    DOUB N N 2  
A1IVA PG    C3B    SING N N 3  
A1IVA PG    OI4    SING N N 4  
A1IVA PB    O1B    DOUB N N 5  
A1IVA PB    O2B    DOUB N N 6  
A1IVA PB    C3B    SING N N 7  
A1IVA PB    O3A    SING N N 8  
A1IVA PA    O1A    DOUB N N 9  
A1IVA PA    O2A    DOUB N N 10 
A1IVA PA    O3A    SING N N 11 
A1IVA PA    "O5'"  SING N N 12 
A1IVA "O5'" "C5'"  SING N N 13 
A1IVA "C5'" "C4'"  SING N N 14 
A1IVA "C4'" "O4'"  SING N N 15 
A1IVA "C4'" "C3'"  SING N N 16 
A1IVA "O4'" "C1'"  SING N N 17 
A1IVA "C3'" "O3'"  SING N N 18 
A1IVA "C3'" "C2'"  SING N N 19 
A1IVA "C2'" "O2'"  SING N N 20 
A1IVA "C2'" "C1'"  SING N N 21 
A1IVA "C1'" N9     SING N N 22 
A1IVA N9    C8     SING Y N 23 
A1IVA N9    C4     SING Y N 24 
A1IVA C8    N7     DOUB Y N 25 
A1IVA N7    C5     SING Y N 26 
A1IVA C5    C6     SING Y N 27 
A1IVA C5    C4     DOUB Y N 28 
A1IVA C6    N6     SING N N 29 
A1IVA C6    N1     DOUB Y N 30 
A1IVA N1    C2     SING Y N 31 
A1IVA C2    N3     DOUB Y N 32 
A1IVA N3    C4     SING Y N 33 
A1IVA CI1   CI2    SING N N 34 
A1IVA CI1   CI6    SING N N 35 
A1IVA CI1   OI1    SING N N 36 
A1IVA CI2   CI3    SING N N 37 
A1IVA CI2   OI2    SING N N 38 
A1IVA CI3   CI4    SING N N 39 
A1IVA CI3   OI3    SING N N 40 
A1IVA CI4   CI5    SING N N 41 
A1IVA CI4   OI4    SING N N 42 
A1IVA CI5   CI6    SING N N 43 
A1IVA CI5   OI5    SING N N 44 
A1IVA CI6   OI6    SING N N 45 
A1IVA "C1'" "H1'"  SING N N 46 
A1IVA C2    H2     SING N N 47 
A1IVA "C2'" "H2'"  SING N N 48 
A1IVA "C3'" "H3'"  SING N N 49 
A1IVA C3B   H3B    SING N N 50 
A1IVA C3B   H3B1   SING N N 51 
A1IVA "C4'" "H4'"  SING N N 52 
A1IVA "C5'" "H5'2" SING N N 53 
A1IVA "C5'" "H5'1" SING N N 54 
A1IVA C8    H8     SING N N 55 
A1IVA CI1   HI1    SING N N 56 
A1IVA CI2   HI2    SING N N 57 
A1IVA CI3   HI3    SING N N 58 
A1IVA CI4   HI4    SING N N 59 
A1IVA CI5   HI5    SING N N 60 
A1IVA CI6   HI6    SING N N 61 
A1IVA N6    HN61   SING N N 62 
A1IVA N6    HN62   SING N N 63 
A1IVA "O2'" "HO2'" SING N N 64 
A1IVA "O3'" "HO3'" SING N N 65 
A1IVA OI1   HIO1   SING N N 66 
A1IVA OI2   HIO2   SING N N 67 
A1IVA OI3   HIO3   SING N N 68 
A1IVA OI5   HIO5   SING N N 69 
A1IVA OI6   HIO6   SING N N 70 
# 
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 
A1IVA InChI            InChI                1.06  "InChI=1S/C17H25N5O17P3/c18-15-6-16(20-2-19-15)22(3-21-6)17-13(29)7(23)5(37-17)1-36-42(34,35)39-41(32,33)4-40(30,31)38-14-11(27)9(25)8(24)10(26)12(14)28/h2-3,5,7-14,17,23-29H,1,4H2,(H2,18,19,20)" 
A1IVA InChIKey         InChI                1.06  SXKKMVQPOLWBJB-UHFFFAOYSA-N                                                                                                                                                                         
A1IVA SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](=O)(=O)O[P](=O)(=O)C[P](=O)(=O)O[C@@H]4[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)[C@H]4O)[C@@H](O)[C@H]3O"                                                            
A1IVA SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](=O)(=O)O[P](=O)(=O)C[P](=O)(=O)O[CH]4[CH](O)[CH](O)[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O"                                                                            
A1IVA 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)CP(=O)(=O)OC4[C@@H]([C@H](C([C@@H]([C@@H]4O)O)O)O)O)O)O)N"                                                                     
A1IVA SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(=O)OP(=O)(=O)CP(=O)(=O)OC4C(C(C(C(C4O)O)O)O)O)O)O)N"                                                                                                          
# 
_pdbx_chem_comp_identifier.comp_id           A1IVA 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "(1~{S},2~{S},4~{S},5~{R})-6-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-bis(oxidanylidene)-$l^{6}-phosphanyl]oxy-bis(oxidanylidene)-$l^{6}-phosphanyl]methyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxycyclohexane-1,2,3,4,5-pentol" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1IVA "Create component" 2024-11-27 PDBE 
A1IVA "Initial release"  2025-12-03 RCSB 
# 
