data_A1JDM # _chem_comp.id A1JDM _chem_comp.name "[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-fluoranyl-2-(phosphonooxymethyl)oxolan-3-yl]oxy-[2-[(2~{R},3~{S},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-oxolan-2-yl]ethenyl]phosphinic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C21 H25 F N10 O10 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-05-19 _chem_comp.pdbx_modified_date 2026-01-16 _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 658.430 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1JDM _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 9R99 _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 A1JDM C11 C1 C 0 1 N N S N N N -1.041 84.171 3.616 -3.407 0.760 -0.493 C11 A1JDM 1 A1JDM C13 C2 C 0 1 N N R N N N -2.318 83.459 1.757 -2.457 -1.303 -0.158 C13 A1JDM 2 A1JDM C14 C3 C 0 1 N N N N N N -3.785 83.696 1.493 -2.759 -2.765 0.178 C14 A1JDM 3 A1JDM C2 C4 C 0 1 Y N N N N N -2.150 85.981 8.004 -6.680 4.372 -0.986 C2 A1JDM 4 A1JDM C20 C5 C 0 1 N N R N N N -2.023 82.238 2.632 -2.110 -0.517 1.126 C20 A1JDM 5 A1JDM C21 C6 C 0 1 N N R N N N -0.795 82.679 3.421 -2.749 0.872 0.900 C21 A1JDM 6 A1JDM C27 C7 C 0 1 N N N N N N -0.095 79.317 2.624 1.890 -0.759 2.284 C27 A1JDM 7 A1JDM C28 C8 C 0 1 N N N N N N 1.100 79.382 3.178 2.590 -0.040 3.126 C28 A1JDM 8 A1JDM C29 C9 C 0 1 N N S N N N 1.376 79.125 4.625 4.070 0.143 2.912 C29 A1JDM 9 A1JDM C30 C10 C 0 1 N N R N N N 2.700 79.710 5.136 4.413 1.645 2.872 C30 A1JDM 10 A1JDM C32 C11 C 0 1 N N N N N N 3.110 78.691 6.192 5.068 1.848 1.484 C32 A1JDM 11 A1JDM C33 C12 C 0 1 N N R N N N 2.632 77.387 5.581 5.517 0.409 1.123 C33 A1JDM 12 A1JDM C36 C13 C 0 1 Y N N N N N 3.769 77.061 3.336 4.668 -0.240 -1.163 C36 A1JDM 13 A1JDM C38 C14 C 0 1 Y N N N N N 5.088 75.450 3.743 6.361 0.260 -2.422 C38 A1JDM 14 A1JDM C39 C15 C 0 1 Y N N N N N 4.419 75.712 4.930 6.716 0.575 -1.100 C39 A1JDM 15 A1JDM C4 C16 C 0 1 Y N N N N N 0.084 86.050 7.403 -4.503 5.017 -1.403 C4 A1JDM 16 A1JDM C41 C17 C 0 1 Y N N N N N 5.489 74.101 5.990 8.775 1.280 -1.839 C41 A1JDM 17 A1JDM C43 C18 C 0 1 Y N N N N N 6.029 74.402 3.759 7.306 0.494 -3.436 C43 A1JDM 18 A1JDM C6 C19 C 0 1 Y N N N N N -1.299 85.138 5.947 -4.843 2.818 -0.825 C6 A1JDM 19 A1JDM C7 C20 C 0 1 Y N N N N N -2.394 85.352 6.767 -6.221 3.069 -0.722 C7 A1JDM 20 A1JDM C9 C21 C 0 1 Y N N N N N -3.142 84.420 5.016 -5.909 0.977 -0.248 C9 A1JDM 21 A1JDM F22 F1 F 0 1 N N N N N N 0.357 82.557 2.636 -1.768 1.869 0.901 F22 A1JDM 22 A1JDM N1 N1 N 0 1 N N N N N N -3.107 86.273 8.891 -8.026 4.680 -0.896 N1 A1JDM 23 A1JDM N10 N2 N 0 1 Y N N N N N -1.791 84.535 4.813 -4.677 1.491 -0.520 N10 A1JDM 24 A1JDM N3 N3 N 0 1 Y N N N N N -0.874 86.322 8.295 -5.790 5.301 -1.319 N3 A1JDM 25 A1JDM N35 N4 N 0 1 Y N N N N N 3.568 76.755 4.657 5.628 0.253 -0.329 N35 A1JDM 26 A1JDM N37 N5 N 0 1 Y N N N N N 4.666 76.313 2.742 5.102 -0.238 -2.390 N37 A1JDM 27 A1JDM N40 N6 N 0 1 Y N N N N N 4.575 75.071 6.093 7.922 1.078 -0.857 N40 A1JDM 28 A1JDM N42 N7 N 0 1 Y N N N N N 6.207 73.737 4.923 8.487 1.000 -3.097 N42 A1JDM 29 A1JDM N44 N8 N 0 1 N N N N N N 6.748 74.031 2.695 7.014 0.203 -4.757 N44 A1JDM 30 A1JDM N5 N9 N 0 1 Y N N N N N -0.028 85.463 6.207 -4.029 3.812 -1.165 N5 A1JDM 31 A1JDM N8 N10 N 0 1 Y N N N N N -3.556 84.892 6.166 -6.814 1.904 -0.367 N8 A1JDM 32 A1JDM O12 O1 O 0 1 N N N N N N -1.777 84.591 2.478 -3.637 -0.653 -0.681 O12 A1JDM 33 A1JDM O15 O2 O 0 1 N N N N N N -3.979 84.109 0.123 -2.963 -3.499 -1.031 O15 A1JDM 34 A1JDM O17 O3 O 0 1 N N N N N N -6.366 83.355 0.104 -4.739 -5.322 -0.370 O17 A1JDM 35 A1JDM O18 O4 O 0 1 N N N N N N -5.413 84.588 -1.878 -3.337 -5.591 -2.578 O18 A1JDM 36 A1JDM O19 O5 O 0 1 N N N N N N -5.802 85.810 0.296 -2.264 -5.813 -0.304 O19 A1JDM 37 A1JDM O23 O6 O 0 1 N N N N N N -1.856 81.084 1.769 -0.694 -0.398 1.273 O23 A1JDM 38 A1JDM O25 O7 O 0 1 N N N N N N -0.969 79.437 0.110 -0.343 -0.188 3.870 O25 A1JDM 39 A1JDM O26 O8 O 0 1 N N N N N N 0.465 81.340 0.879 -0.193 -2.419 2.699 O26 A1JDM 40 A1JDM O31 O9 O 0 1 N N N N N N 2.472 80.993 5.720 5.334 1.976 3.913 O31 A1JDM 41 A1JDM O34 O10 O 0 1 N N N N N N 1.453 77.706 4.863 4.454 -0.416 1.644 O34 A1JDM 42 A1JDM P16 P1 P 0 1 N N N N N N -5.480 84.490 -0.368 -3.303 -5.073 -1.054 P16 A1JDM 43 A1JDM P24 P2 P 0 1 N N N N N N -0.545 80.316 1.239 0.108 -0.979 2.542 P24 A1JDM 44 A1JDM H11 H1 H 0 1 N N N N N N -0.066 84.681 3.634 -2.735 1.141 -1.262 H11 A1JDM 45 A1JDM H13 H2 H 0 1 N N N N N N -1.795 83.341 0.797 -1.638 -1.240 -0.874 H13 A1JDM 46 A1JDM H14B H3 H 0 0 N N N N N N -4.343 82.766 1.676 -1.920 -3.193 0.726 H14B A1JDM 47 A1JDM H14A H4 H 0 0 N N N N N N -4.154 84.483 2.167 -3.658 -2.818 0.792 H14A A1JDM 48 A1JDM H20 H5 H 0 1 N N N N N N -2.862 82.078 3.325 -2.546 -1.001 2.000 H20 A1JDM 49 A1JDM H21 H6 H 0 1 N N N N N N -0.726 82.153 4.385 -3.501 1.074 1.663 H21 A1JDM 50 A1JDM H27 H7 H 0 1 N N N N N N -0.822 78.630 3.031 2.374 -1.221 1.436 H27 A1JDM 51 A1JDM H28 H8 H 0 1 N N N N N N 1.936 79.638 2.544 2.106 0.422 3.974 H28 A1JDM 52 A1JDM H29 H9 H 0 1 N N N N N N 0.557 79.553 5.222 4.624 -0.342 3.716 H29 A1JDM 53 A1JDM H30 H10 H 0 1 N N N N N N 3.442 79.750 4.325 3.507 2.245 2.961 H30 A1JDM 54 A1JDM H32B H11 H 0 0 N N N N N N 4.200 78.686 6.340 4.341 2.221 0.762 H32B A1JDM 55 A1JDM H32A H12 H 0 0 N N N N N N 2.611 78.888 7.152 5.925 2.518 1.553 H32A A1JDM 56 A1JDM H33 H13 H 0 1 N N N N N N 2.396 76.686 6.395 6.463 0.169 1.610 H33 A1JDM 57 A1JDM H36 H14 H 0 1 N N N N N N 3.234 77.850 2.829 3.694 -0.585 -0.850 H36 A1JDM 58 A1JDM H4 H15 H 0 1 N N N N N N 1.084 86.344 7.687 -3.814 5.802 -1.677 H4 A1JDM 59 A1JDM H41 H16 H 0 1 N N N N N N 5.672 73.535 6.891 9.747 1.690 -1.607 H41 A1JDM 60 A1JDM H9 H17 H 0 1 N N N N N N -3.808 83.978 4.290 -6.106 -0.049 0.026 H9 A1JDM 61 A1JDM H1B H18 H 0 1 N N N N N N -2.700 86.728 9.683 -8.330 5.583 -1.077 H1B A1JDM 62 A1JDM H1A H19 H 0 1 N N N N N N -3.780 86.879 8.467 -8.666 3.993 -0.652 H1A A1JDM 63 A1JDM H44A H20 H 0 0 N N N N N N 7.345 73.268 2.945 6.148 -0.167 -4.992 H44A A1JDM 64 A1JDM H44B H21 H 0 0 N N N N N N 6.133 73.746 1.960 7.674 0.368 -5.448 H44B A1JDM 65 A1JDM H1 H22 H 0 1 N N N N N N -6.982 83.681 0.749 -5.469 -4.866 -0.810 H1 A1JDM 66 A1JDM H2 H23 H 0 1 N N N N N N -5.589 85.482 -2.146 -3.537 -6.533 -2.668 H2 A1JDM 67 A1JDM H3 H24 H 0 1 N N N N N N -0.505 79.689 -0.680 -0.175 0.763 3.837 H3 A1JDM 68 A1JDM H31 H25 H 0 1 N N N N N N 3.295 81.349 6.034 5.584 2.909 3.935 H31 A1JDM 69 # 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 A1JDM N1 C2 SING N N 1 A1JDM C2 N3 DOUB Y N 2 A1JDM N3 C4 SING Y N 3 A1JDM C4 N5 DOUB Y N 4 A1JDM N5 C6 SING Y N 5 A1JDM C6 C7 DOUB Y N 6 A1JDM C7 N8 SING Y N 7 A1JDM N8 C9 DOUB Y N 8 A1JDM C9 N10 SING Y N 9 A1JDM N10 C11 SING N N 10 A1JDM C11 O12 SING N N 11 A1JDM O12 C13 SING N N 12 A1JDM C13 C14 SING N N 13 A1JDM C14 O15 SING N N 14 A1JDM O15 P16 SING N N 15 A1JDM P16 O17 SING N N 16 A1JDM P16 O18 SING N N 17 A1JDM P16 O19 DOUB N N 18 A1JDM C13 C20 SING N N 19 A1JDM C20 C21 SING N N 20 A1JDM C21 F22 SING N N 21 A1JDM C20 O23 SING N N 22 A1JDM O23 P24 SING N N 23 A1JDM P24 O25 SING N N 24 A1JDM P24 O26 DOUB N N 25 A1JDM P24 C27 SING N N 26 A1JDM C27 C28 DOUB N Z 27 A1JDM C28 C29 SING N N 28 A1JDM C29 C30 SING N N 29 A1JDM C30 O31 SING N N 30 A1JDM C30 C32 SING N N 31 A1JDM C32 C33 SING N N 32 A1JDM C33 O34 SING N N 33 A1JDM C33 N35 SING N N 34 A1JDM N35 C36 SING Y N 35 A1JDM C36 N37 DOUB Y N 36 A1JDM N37 C38 SING Y N 37 A1JDM C38 C39 DOUB Y N 38 A1JDM C39 N40 SING Y N 39 A1JDM N40 C41 DOUB Y N 40 A1JDM C41 N42 SING Y N 41 A1JDM N42 C43 DOUB Y N 42 A1JDM C43 N44 SING N N 43 A1JDM C7 C2 SING Y N 44 A1JDM N10 C6 SING Y N 45 A1JDM C21 C11 SING N N 46 A1JDM O34 C29 SING N N 47 A1JDM C39 N35 SING Y N 48 A1JDM C43 C38 SING Y N 49 A1JDM C11 H11 SING N N 50 A1JDM C13 H13 SING N N 51 A1JDM C14 H14B SING N N 52 A1JDM C14 H14A SING N N 53 A1JDM C20 H20 SING N N 54 A1JDM C21 H21 SING N N 55 A1JDM C27 H27 SING N N 56 A1JDM C28 H28 SING N N 57 A1JDM C29 H29 SING N N 58 A1JDM C30 H30 SING N N 59 A1JDM C32 H32B SING N N 60 A1JDM C32 H32A SING N N 61 A1JDM C33 H33 SING N N 62 A1JDM C36 H36 SING N N 63 A1JDM C4 H4 SING N N 64 A1JDM C41 H41 SING N N 65 A1JDM C9 H9 SING N N 66 A1JDM N1 H1B SING N N 67 A1JDM N1 H1A SING N N 68 A1JDM N44 H44A SING N N 69 A1JDM N44 H44B SING N N 70 A1JDM O17 H1 SING N N 71 A1JDM O18 H2 SING N N 72 A1JDM O25 H3 SING N N 73 A1JDM O31 H31 SING N N 74 # 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 A1JDM InChI InChI 1.06 "InChI=1S/C21H25FN10O10P2/c22-13-16(11(4-39-44(36,37)38)41-21(13)32-8-30-15-18(24)26-6-28-20(15)32)42-43(34,35)2-1-10-9(33)3-12(40-10)31-7-29-14-17(23)25-5-27-19(14)31/h1-2,5-13,16,21,33H,3-4H2,(H,34,35)(H2,23,25,27)(H2,24,26,28)(H2,36,37,38)" A1JDM InChIKey InChI 1.06 SGIFLIAUADEBFS-UHFFFAOYSA-N A1JDM SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@H]3C[C@@H](O)[C@@H](O3)\C=C/[P](O)(=O)O[C@H]4[C@@H](F)[C@H](O[C@@H]4CO[P](O)(O)=O)n5cnc6c(N)ncnc56" A1JDM SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](O3)C=C[P](O)(=O)O[CH]4[CH](F)[CH](O[CH]4CO[P](O)(O)=O)n5cnc6c(N)ncnc56" A1JDM SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)C=CP(=O)(O)O[C@@H]4[C@H](O[C@H]([C@@H]4F)n5cnc6c5ncnc6N)COP(=O)(O)O)O)N" A1JDM SMILES "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3CC(C(O3)C=CP(=O)(O)OC4C(OC(C4F)n5cnc6c5ncnc6N)COP(=O)(O)O)O)N" # _pdbx_chem_comp_identifier.comp_id A1JDM _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 "[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-fluoranyl-2-(phosphonooxymethyl)oxolan-3-yl]oxy-[2-[(2~{R},3~{S},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-oxolan-2-yl]ethenyl]phosphinic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1JDM "Create component" 2025-05-19 PDBE A1JDM "Initial release" 2026-01-21 RCSB #