data_A1LVZ # _chem_comp.id A1LVZ _chem_comp.name "[[(2~{R},3~{R},4~{S},5~{R})-4-fluoranyl-5-(5-iodanyl-4-methyl-pyrrolo[2,3-d]pyrimidin-7-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H16 F I N3 O12 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2024-01-10 _chem_comp.pdbx_modified_date 2024-11-29 _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 633.092 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1LVZ _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 8XPO _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ _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 A1LVZ C5 C1 C 0 1 Y N N N N N 121.960 111.816 128.609 5.009 0.209 -1.105 C5 A1LVZ 1 A1LVZ "C1'" C2 C 0 1 N N R N N N 124.853 111.104 126.537 2.101 -2.007 -1.013 "C1'" A1LVZ 2 A1LVZ "C4'" C3 C 0 1 N N R N N N 126.348 109.451 125.505 0.171 -2.680 0.076 "C4'" A1LVZ 3 A1LVZ "C5'" C4 C 0 1 N N N N N N 127.155 108.382 126.257 -0.864 -2.245 1.116 "C5'" A1LVZ 4 A1LVZ C06 C5 C 0 1 N N N N N N 119.837 112.371 129.869 7.048 1.690 -1.217 C06 A1LVZ 5 A1LVZ C6 C6 C 0 1 Y N N N N N 120.650 112.269 128.573 6.227 0.524 -1.705 C6 A1LVZ 6 A1LVZ C2 C7 C 0 1 Y N N N N N 120.759 112.554 126.305 5.933 -1.248 -3.146 C2 A1LVZ 7 A1LVZ C4 C8 C 0 1 Y N N N N N 122.628 111.754 127.403 4.279 -0.896 -1.592 C4 A1LVZ 8 A1LVZ C8 C9 C 0 1 Y N N N N N 124.020 111.063 128.907 3.114 0.009 0.099 C8 A1LVZ 9 A1LVZ C7 C10 C 0 1 Y N N N N N 122.857 111.367 129.589 4.220 0.765 -0.006 C7 A1LVZ 10 A1LVZ "C3'" C11 C 0 1 N N R N N N 126.912 110.626 125.643 1.305 -3.498 0.743 "C3'" A1LVZ 11 A1LVZ "C2'" C12 C 0 1 N N S N N N 126.092 111.340 126.867 2.481 -3.285 -0.241 "C2'" A1LVZ 12 A1LVZ "F2'" F1 F 0 1 N N N N N N 126.485 110.677 128.034 3.678 -3.096 0.458 "F2'" A1LVZ 13 A1LVZ I7 I1 I 0 1 N N N N N N 122.602 111.160 131.691 4.718 2.420 1.177 I7 A1LVZ 14 A1LVZ N1 N1 N 0 1 Y N N N N N 120.094 112.626 127.430 6.646 -0.224 -2.712 N1 A1LVZ 15 A1LVZ N3 N2 N 0 1 Y N N N N N 122.007 112.121 126.300 4.782 -1.590 -2.608 N3 A1LVZ 16 A1LVZ N9 N3 N 0 1 Y N N N N N 123.860 111.301 127.611 3.141 -0.991 -0.839 N9 A1LVZ 17 A1LVZ "O4'" O1 O 0 1 N N N N N N 124.937 109.595 126.146 0.858 -1.532 -0.468 "O4'" A1LVZ 18 A1LVZ "O5'" O2 O 0 1 N N N N N N 126.432 107.217 126.284 -1.954 -1.595 0.460 "O5'" A1LVZ 19 A1LVZ O1A O3 O 0 1 N N N N N N 128.679 105.895 126.267 -3.833 -2.076 2.076 O1A A1LVZ 20 A1LVZ O2A O4 O 0 1 N N N N N N 127.300 105.871 128.337 -2.756 0.204 2.202 O2A A1LVZ 21 A1LVZ O3A O5 O 0 1 N N N N N N 126.442 104.492 126.318 -4.313 -0.466 0.192 O3A A1LVZ 22 A1LVZ O2B O6 O 0 1 N N N N N N 125.613 103.591 128.591 -6.765 -1.393 0.395 O2B A1LVZ 23 A1LVZ O1B O7 O 0 1 N N N N N N 125.576 102.081 126.663 -6.083 0.773 1.497 O1B A1LVZ 24 A1LVZ O3B O8 O 0 1 N N N N N N 127.850 102.597 127.691 -6.292 0.773 -1.018 O3B A1LVZ 25 A1LVZ O2G O9 O 0 1 N N N N N N 128.909 103.152 129.983 -7.157 2.588 -2.712 O2G A1LVZ 26 A1LVZ O3G O10 O 0 1 N N N N N N 127.033 101.590 129.863 -8.857 0.941 -1.567 O3G A1LVZ 27 A1LVZ O1G O11 O 0 1 N N N N N N 129.202 100.884 129.052 -7.675 2.738 -0.246 O1G A1LVZ 28 A1LVZ "O3'" O12 O 0 1 N N N N N N 126.747 111.406 124.417 0.955 -4.881 0.828 "O3'" A1LVZ 29 A1LVZ PA P1 P 0 1 N N N N N N 127.239 105.871 126.819 -3.228 -1.007 1.250 PA A1LVZ 30 A1LVZ PB P2 P 0 1 N N N N N N 126.328 103.157 127.317 -5.868 -0.060 0.293 PB A1LVZ 31 A1LVZ PG P3 P 0 1 N N N N N N 128.244 102.036 129.185 -7.499 1.781 -1.361 PG A1LVZ 32 A1LVZ H1 H1 H 0 1 N N N N N N 124.547 111.674 125.648 1.980 -2.235 -2.072 H1 A1LVZ 33 A1LVZ H2 H2 H 0 1 N N N N N N 126.237 109.151 124.453 -0.302 -3.257 -0.719 H2 A1LVZ 34 A1LVZ H3 H3 H 0 1 N N N N N N 128.112 108.211 125.742 -1.231 -3.121 1.651 H3 A1LVZ 35 A1LVZ H4 H4 H 0 1 N N N N N N 127.348 108.721 127.286 -0.401 -1.555 1.822 H4 A1LVZ 36 A1LVZ H5 H5 H 0 1 N N N N N N 118.832 112.756 129.643 7.732 1.353 -0.438 H5 A1LVZ 37 A1LVZ H6 H6 H 0 1 N N N N N N 119.753 111.375 130.328 7.619 2.105 -2.048 H6 A1LVZ 38 A1LVZ H7 H7 H 0 1 N N N N N N 120.343 113.055 130.566 6.386 2.457 -0.813 H7 A1LVZ 39 A1LVZ H8 H8 H 0 1 N N N N N N 120.287 112.849 125.380 6.313 -1.832 -3.971 H8 A1LVZ 40 A1LVZ H9 H9 H 0 1 N N N N N N 124.925 110.687 129.361 2.325 0.161 0.821 H9 A1LVZ 41 A1LVZ H10 H10 H 0 1 N N N N N N 127.974 110.566 125.925 1.546 -3.098 1.728 H10 A1LVZ 42 A1LVZ H11 H11 H 0 1 N N N N N N 126.350 112.409 126.890 2.566 -4.131 -0.923 H11 A1LVZ 43 A1LVZ H12 H12 H 0 1 N N N N N N 128.207 105.886 128.618 -2.349 0.941 1.727 H12 A1LVZ 44 A1LVZ H13 H13 H 0 1 N N N N N N 124.823 103.075 128.703 -6.674 -1.987 -0.363 H13 A1LVZ 45 A1LVZ H14 H14 H 0 1 N N N N N N 129.787 102.886 130.228 -7.843 3.215 -2.980 H14 A1LVZ 46 A1LVZ H15 H15 H 0 1 N N N N N N 127.110 100.667 130.075 -8.814 0.293 -2.284 H15 A1LVZ 47 A1LVZ H16 H16 H 0 1 N N N N N N 127.158 112.256 124.524 1.634 -5.434 1.238 H16 A1LVZ 48 # 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 A1LVZ "O3'" "C3'" SING N N 1 A1LVZ "C4'" "C3'" SING N N 2 A1LVZ "C4'" "O4'" SING N N 3 A1LVZ "C4'" "C5'" SING N N 4 A1LVZ "C3'" "C2'" SING N N 5 A1LVZ "O4'" "C1'" SING N N 6 A1LVZ "C5'" "O5'" SING N N 7 A1LVZ O1A PA DOUB N N 8 A1LVZ "O5'" PA SING N N 9 A1LVZ N3 C2 DOUB Y N 10 A1LVZ N3 C4 SING Y N 11 A1LVZ C2 N1 SING Y N 12 A1LVZ O3A PA SING N N 13 A1LVZ O3A PB SING N N 14 A1LVZ "C1'" "C2'" SING N N 15 A1LVZ "C1'" N9 SING N N 16 A1LVZ O1B PB DOUB N N 17 A1LVZ PA O2A SING N N 18 A1LVZ "C2'" "F2'" SING N N 19 A1LVZ PB O3B SING N N 20 A1LVZ PB O2B SING N N 21 A1LVZ C4 N9 SING Y N 22 A1LVZ C4 C5 DOUB Y N 23 A1LVZ N1 C6 DOUB Y N 24 A1LVZ N9 C8 SING Y N 25 A1LVZ O3B PG SING N N 26 A1LVZ C6 C5 SING Y N 27 A1LVZ C6 C06 SING N N 28 A1LVZ C5 C7 SING Y N 29 A1LVZ C8 C7 DOUB Y N 30 A1LVZ O1G PG DOUB N N 31 A1LVZ PG O3G SING N N 32 A1LVZ PG O2G SING N N 33 A1LVZ C7 I7 SING N N 34 A1LVZ "C1'" H1 SING N N 35 A1LVZ "C4'" H2 SING N N 36 A1LVZ "C5'" H3 SING N N 37 A1LVZ "C5'" H4 SING N N 38 A1LVZ C06 H5 SING N N 39 A1LVZ C06 H6 SING N N 40 A1LVZ C06 H7 SING N N 41 A1LVZ C2 H8 SING N N 42 A1LVZ C8 H9 SING N N 43 A1LVZ "C3'" H10 SING N N 44 A1LVZ "C2'" H11 SING N N 45 A1LVZ O2A H12 SING N N 46 A1LVZ O2B H13 SING N N 47 A1LVZ O2G H14 SING N N 48 A1LVZ O3G H15 SING N N 49 A1LVZ "O3'" H16 SING N N 50 # 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 A1LVZ InChI InChI 1.06 "InChI=1S/C12H16FIN3O12P3/c1-5-8-6(14)2-17(11(8)16-4-15-5)12-9(13)10(18)7(27-12)3-26-31(22,23)29-32(24,25)28-30(19,20)21/h2,4,7,9-10,12,18H,3H2,1H3,(H,22,23)(H,24,25)(H2,19,20,21)/t7-,9+,10-,12-/m1/s1" A1LVZ InChIKey InChI 1.06 SDPCZQPAUGWGIT-DLYFRVTGSA-N A1LVZ SMILES_CANONICAL CACTVS 3.385 "Cc1ncnc2n(cc(I)c12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@@H]3F" A1LVZ SMILES CACTVS 3.385 "Cc1ncnc2n(cc(I)c12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3F" A1LVZ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c2c(cn(c2ncn1)[C@H]3[C@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)F)I" A1LVZ SMILES "OpenEye OEToolkits" 2.0.7 "Cc1c2c(cn(c2ncn1)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)F)I" # _pdbx_chem_comp_identifier.comp_id A1LVZ _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~{S},5~{R})-4-fluoranyl-5-(5-iodanyl-4-methyl-pyrrolo[2,3-d]pyrimidin-7-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono 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 A1LVZ "Create component" 2024-01-10 PDBJ A1LVZ "Initial release" 2024-12-04 RCSB #