data_USB # _chem_comp.id USB _chem_comp.name "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2~{S})-2-azanyl-4-methyl-pentanoate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H25 N6 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-03-11 _chem_comp.pdbx_modified_date 2022-08-26 _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 460.379 _chem_comp.one_letter_code ? _chem_comp.three_letter_code USB _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 7NU8 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # 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.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 USB C2 C1 C 0 1 Y N N -12.728 -7.380 -28.745 6.851 -1.200 1.055 C2 USB 1 USB C4 C2 C 0 1 Y N N -10.631 -7.121 -28.117 4.721 -0.870 0.259 C4 USB 2 USB C5 C3 C 0 1 Y N N -10.903 -7.574 -26.833 4.850 -2.023 -0.534 C5 USB 3 USB C6 C4 C 0 1 Y N N -12.238 -7.923 -26.550 6.061 -2.734 -0.477 C6 USB 4 USB C8 C5 C 0 1 Y N N -8.821 -7.146 -26.886 2.873 -1.209 -0.896 C8 USB 5 USB N N1 N 0 1 N N N -0.548 -3.912 -28.566 -7.284 -0.408 -0.054 N USB 6 USB CA C6 C 0 1 N N S -1.746 -3.057 -28.503 -5.908 -0.691 0.376 CA USB 7 USB C C7 C 0 1 N N N -3.026 -3.778 -28.054 -4.968 0.295 -0.268 C USB 8 USB O O1 O 0 1 N N N -4.074 -3.198 -28.013 -5.309 0.898 -1.258 O USB 9 USB CB C8 C 0 1 N N N -1.995 -2.415 -29.872 -5.524 -2.111 -0.045 CB USB 10 USB CG C9 C 0 1 N N N -0.957 -1.383 -30.313 -6.398 -3.119 0.704 CG USB 11 USB CD1 C10 C 0 1 N N N -0.985 -0.142 -29.434 -6.101 -4.530 0.193 CD1 USB 12 USB CD2 C11 C 0 1 N N N -1.157 -1.004 -31.775 -6.092 -3.045 2.201 CD2 USB 13 USB "C1'" C12 C 0 1 N N R -8.549 -6.235 -29.241 2.865 0.814 0.613 "C1'" USB 14 USB "C2'" C13 C 0 1 N N R -7.999 -4.847 -28.932 3.270 2.083 -0.179 "C2'" USB 15 USB "C3'" C14 C 0 1 N N S -6.889 -4.740 -29.975 2.115 3.057 0.155 "C3'" USB 16 USB "C4'" C15 C 0 1 N N R -6.378 -6.184 -30.088 0.964 2.138 0.608 "C4'" USB 17 USB "C5'" C16 C 0 1 N N N -5.073 -6.453 -29.375 -0.258 2.354 -0.286 "C5'" USB 18 USB N1 N2 N 0 1 Y N N -13.139 -7.821 -27.552 7.019 -2.290 0.328 N1 USB 19 USB N3 N3 N 0 1 Y N N -11.504 -7.003 -29.123 5.737 -0.500 1.031 N3 USB 20 USB N6 N4 N 0 1 N N N -12.670 -8.295 -25.337 6.246 -3.878 -1.235 N6 USB 21 USB N7 N5 N 0 1 Y N N -9.747 -7.590 -26.067 3.688 -2.173 -1.214 N7 USB 22 USB N9 N6 N 0 1 Y N N -9.289 -6.833 -28.135 3.462 -0.382 0.014 N9 USB 23 USB O1P O2 O 0 1 N N N -3.374 -7.418 -26.893 -2.664 1.198 -1.911 O1P USB 24 USB "O2'" O3 O 0 1 N N N -9.023 -3.887 -29.156 4.521 2.595 0.285 "O2'" USB 25 USB O2P O4 O 0 1 N N N -4.519 -5.456 -25.718 -3.464 3.038 -0.380 O2P USB 26 USB "O3'" O5 O 0 1 N N N -7.433 -4.272 -31.204 2.497 3.942 1.210 "O3'" USB 27 USB "O4'" O6 O 0 1 N N N -7.420 -7.031 -29.542 1.427 0.782 0.484 "O4'" USB 28 USB "O5'" O7 O 0 1 N N N -5.260 -6.173 -27.970 -1.355 1.585 0.212 "O5'" USB 29 USB OPP O8 O 0 1 N N N -2.986 -5.068 -27.689 -3.751 0.504 0.259 OPP USB 30 USB P P1 P 0 1 N N N -4.022 -6.089 -26.959 -2.805 1.573 -0.487 P USB 31 USB H1 H1 H 0 1 N N N -13.490 -7.320 -29.508 7.656 -0.874 1.697 H1 USB 32 USB H2 H2 H 0 1 N N N -7.785 -7.038 -26.601 1.876 -1.085 -1.292 H2 USB 33 USB H3 H3 H 0 1 N N N -0.388 -4.329 -27.671 -7.584 0.500 0.268 H3 USB 34 USB H4 H4 H 0 1 N N N -0.686 -4.630 -29.249 -7.372 -0.483 -1.056 H4 USB 35 USB H6 H6 H 0 1 N N N -1.554 -2.246 -27.786 -5.840 -0.603 1.460 H6 USB 36 USB H7 H7 H 0 1 N N N -2.975 -1.917 -29.840 -5.676 -2.226 -1.119 H7 USB 37 USB H8 H8 H 0 1 N N N -2.016 -3.218 -30.624 -4.476 -2.290 0.194 H8 USB 38 USB H9 H9 H 0 1 N N N 0.037 -1.843 -30.217 -7.449 -2.885 0.535 H9 USB 39 USB H10 H10 H 0 1 N N N -0.839 -0.433 -28.383 -5.050 -4.765 0.361 H10 USB 40 USB H11 H11 H 0 1 N N N -0.180 0.542 -29.740 -6.723 -5.249 0.727 H11 USB 41 USB H12 H12 H 0 1 N N N -1.956 0.363 -29.543 -6.318 -4.583 -0.874 H12 USB 42 USB H13 H13 H 0 1 N N N -0.400 -0.262 -32.069 -6.304 -2.039 2.566 H13 USB 43 USB H14 H14 H 0 1 N N N -1.054 -1.901 -32.404 -6.715 -3.763 2.735 H14 USB 44 USB H15 H15 H 0 1 N N N -2.161 -0.576 -31.909 -5.041 -3.279 2.370 H15 USB 45 USB H16 H16 H 0 1 N N N -9.204 -6.163 -30.122 3.157 0.905 1.659 H16 USB 46 USB H17 H17 H 0 1 N N N -7.589 -4.801 -27.912 3.309 1.878 -1.249 H17 USB 47 USB H18 H18 H 0 1 N N N -6.086 -4.083 -29.609 1.825 3.623 -0.730 H18 USB 48 USB H19 H19 H 0 1 N N N -6.245 -6.417 -31.155 0.708 2.349 1.647 H19 USB 49 USB H20 H20 H 0 1 N N N -4.785 -7.506 -29.510 -0.525 3.411 -0.286 H20 USB 50 USB H21 H21 H 0 1 N N N -4.285 -5.803 -29.783 -0.024 2.039 -1.303 H21 USB 51 USB H22 H22 H 0 1 N N N -13.658 -8.449 -25.367 5.536 -4.196 -1.814 H22 USB 52 USB H23 H23 H 0 1 N N N -12.209 -9.140 -25.064 7.086 -4.360 -1.188 H23 USB 53 USB H24 H24 H 0 1 N N N -9.696 -3.980 -28.492 4.818 3.389 -0.180 H24 USB 54 USB H25 H25 H 0 1 N N N -4.346 -6.027 -24.979 -3.587 3.349 0.527 H25 USB 55 USB H26 H26 H 0 1 N N N -7.738 -3.379 -31.096 3.254 4.504 0.998 H26 USB 56 # 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 USB CD2 CG SING N N 1 USB "O3'" "C3'" SING N N 2 USB CG CB SING N N 3 USB CG CD1 SING N N 4 USB "C4'" "C3'" SING N N 5 USB "C4'" "O4'" SING N N 6 USB "C4'" "C5'" SING N N 7 USB "C3'" "C2'" SING N N 8 USB CB CA SING N N 9 USB "O4'" "C1'" SING N N 10 USB "C5'" "O5'" SING N N 11 USB "C1'" "C2'" SING N N 12 USB "C1'" N9 SING N N 13 USB "O2'" "C2'" SING N N 14 USB N3 C2 DOUB Y N 15 USB N3 C4 SING Y N 16 USB C2 N1 SING Y N 17 USB N CA SING N N 18 USB CA C SING N N 19 USB N9 C4 SING Y N 20 USB N9 C8 SING Y N 21 USB C4 C5 DOUB Y N 22 USB C O DOUB N N 23 USB C OPP SING N N 24 USB "O5'" P SING N N 25 USB OPP P SING N N 26 USB N1 C6 DOUB Y N 27 USB P O1P DOUB N N 28 USB P O2P SING N N 29 USB C8 N7 DOUB Y N 30 USB C5 C6 SING Y N 31 USB C5 N7 SING Y N 32 USB C6 N6 SING N N 33 USB C2 H1 SING N N 34 USB C8 H2 SING N N 35 USB N H3 SING N N 36 USB N H4 SING N N 37 USB CA H6 SING N N 38 USB CB H7 SING N N 39 USB CB H8 SING N N 40 USB CG H9 SING N N 41 USB CD1 H10 SING N N 42 USB CD1 H11 SING N N 43 USB CD1 H12 SING N N 44 USB CD2 H13 SING N N 45 USB CD2 H14 SING N N 46 USB CD2 H15 SING N N 47 USB "C1'" H16 SING N N 48 USB "C2'" H17 SING N N 49 USB "C3'" H18 SING N N 50 USB "C4'" H19 SING N N 51 USB "C5'" H20 SING N N 52 USB "C5'" H21 SING N N 53 USB N6 H22 SING N N 54 USB N6 H23 SING N N 55 USB "O2'" H24 SING N N 56 USB O2P H25 SING N N 57 USB "O3'" H26 SING N N 58 # 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 USB InChI InChI 1.03 "InChI=1S/C16H25N6O8P/c1-7(2)3-8(17)16(25)30-31(26,27)28-4-9-11(23)12(24)15(29-9)22-6-21-10-13(18)19-5-20-14(10)22/h5-9,11-12,15,23-24H,3-4,17H2,1-2H3,(H,26,27)(H2,18,19,20)/t8-,9+,11+,12+,15+/m0/s1" USB InChIKey InChI 1.03 AXWPLGAOCISUCB-OPYVMVOTSA-N USB SMILES_CANONICAL CACTVS 3.385 "CC(C)C[C@H](N)C(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23" USB SMILES CACTVS 3.385 "CC(C)C[CH](N)C(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23" USB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)C[C@@H](C(=O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)N" USB SMILES "OpenEye OEToolkits" 2.0.7 "CC(C)CC(C(=O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)N" # _pdbx_chem_comp_identifier.comp_id USB _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~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2~{S})-2-azanyl-4-methyl-pentanoate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site USB "Create component" 2021-03-11 PDBE USB "Initial release" 2022-08-31 RCSB #