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 #