data_SDU # _chem_comp.id SDU _chem_comp.name "(2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[(3~{S})-pyrrolidin-3-yl]amino]-2-azanyl-butanoic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H28 N8 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-08-30 _chem_comp.pdbx_modified_date 2024-09-06 _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 436.466 _chem_comp.one_letter_code ? _chem_comp.three_letter_code SDU _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 8QDG _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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_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 SDU C17 C1 C 0 1 N N S N N N -33.567 -6.622 -12.599 1.046 -2.496 1.222 C17 SDU 1 SDU C16 C2 C 0 1 N N N N N N -35.782 -2.439 -15.267 -3.324 -0.676 -1.921 C16 SDU 2 SDU C12 C3 C 0 1 N N N N N N -38.305 -2.154 -11.264 -5.718 2.740 0.053 C12 SDU 3 SDU C13 C4 C 0 1 N N S N N N -34.660 -2.702 -14.286 -2.645 -1.496 -0.808 C13 SDU 4 SDU C15 C5 C 0 1 N N N N N N -33.938 -1.212 -15.856 -4.800 -2.441 -1.375 C15 SDU 5 SDU C14 C6 C 0 1 N N N N N N -33.457 -2.459 -15.162 -3.763 -2.390 -0.225 C14 SDU 6 SDU C5 C7 C 0 1 Y N N N N N -32.654 -9.241 -15.904 2.917 1.372 0.948 C5 SDU 7 SDU C6 C8 C 0 1 N N R N N N -33.973 -8.592 -13.840 2.217 -0.816 -0.097 C6 SDU 8 SDU C7 C9 C 0 1 N N R N N N -34.801 -6.454 -13.508 0.114 -1.614 0.363 C7 SDU 9 SDU C4 C10 C 0 1 Y N N N N N -33.513 -11.174 -16.305 4.914 1.628 0.143 C4 SDU 10 SDU C3 C11 C 0 1 Y N N N N N -34.151 -10.702 -15.173 4.403 0.428 -0.380 C3 SDU 11 SDU C2 C12 C 0 1 Y N N N N N -35.355 -12.516 -14.970 6.369 0.111 -1.526 C2 SDU 12 SDU C18 C13 C 0 1 N N R N N N -32.819 -7.807 -13.225 2.461 -1.959 0.913 C18 SDU 13 SDU N1 N1 N 0 1 N N N N N N -33.378 -13.005 -17.857 6.764 3.193 0.242 N1 SDU 14 SDU C1 C14 C 0 1 Y N N N N N -33.888 -12.438 -16.771 6.209 2.019 -0.237 C1 SDU 15 SDU N2 N2 N 0 1 Y N N N N N -34.850 -13.089 -16.070 6.890 1.234 -1.065 N2 SDU 16 SDU N3 N3 N 0 1 Y N N N N N -35.049 -11.349 -14.425 5.158 -0.291 -1.204 N3 SDU 17 SDU N4 N4 N 0 1 Y N N N N N -32.608 -10.238 -16.767 3.956 2.155 0.942 N4 SDU 18 SDU N5 N5 N 0 1 Y N N N N N -33.575 -9.477 -14.895 3.145 0.290 0.150 N5 SDU 19 SDU O1 O1 O 0 1 N N N N N N -34.842 -7.624 -14.380 0.857 -0.395 0.145 O1 SDU 20 SDU C8 C15 C 0 1 N N N N N N -34.835 -5.174 -14.369 -1.185 -1.319 1.116 C8 SDU 21 SDU N6 N6 N 0 1 N N N N N N -34.880 -3.877 -13.627 -2.113 -0.603 0.231 N6 SDU 22 SDU C9 C16 C 0 1 N N N N N N -36.302 -3.775 -13.113 -3.200 0.018 0.999 C9 SDU 23 SDU C10 C17 C 0 1 N N N N N N -36.518 -3.986 -11.691 -3.997 0.956 0.090 C10 SDU 24 SDU C11 C18 C 0 1 N N S N N N -37.910 -3.615 -11.112 -5.019 1.729 0.925 C11 SDU 25 SDU N7 N7 N 0 1 N N N N N N -39.056 -4.488 -11.550 -6.007 0.794 1.479 N7 SDU 26 SDU O2 O2 O 0 1 N N N N N N -39.254 -1.913 -12.020 -6.817 2.500 -0.388 O2 SDU 27 SDU O3 O3 O 0 1 N N N N N N -37.586 -1.316 -10.655 -5.120 3.907 -0.234 O3 SDU 28 SDU N8 N8 N 0 1 N N N N N N -35.329 -1.456 -16.232 -4.750 -1.066 -1.944 N8 SDU 29 SDU O4 O4 O 0 1 N N N N N N -33.935 -6.872 -11.246 0.935 -3.867 0.836 O4 SDU 30 SDU O5 O5 O 0 1 N N N N N N -31.975 -8.533 -12.359 3.268 -2.982 0.326 O5 SDU 31 SDU H25 H1 H 0 1 N N N N N N -32.941 -5.720 -12.672 0.816 -2.379 2.282 H25 SDU 32 SDU H24 H2 H 0 1 N N N N N N -36.662 -2.054 -14.730 -3.233 0.388 -1.706 H24 SDU 33 SDU H23 H3 H 0 1 N N N N N N -36.048 -3.372 -15.785 -2.862 -0.901 -2.882 H23 SDU 34 SDU H17 H4 H 0 1 N N N N N N -34.686 -1.882 -13.553 -1.847 -2.111 -1.224 H17 SDU 35 SDU H20 H5 H 0 1 N N N N N N -33.874 -0.350 -15.176 -4.504 -3.177 -2.122 H20 SDU 36 SDU H21 H6 H 0 1 N N N N N N -33.331 -1.018 -16.752 -5.796 -2.662 -0.991 H21 SDU 37 SDU H19 H7 H 0 1 N N N N N N -32.545 -2.281 -14.574 -3.383 -3.388 -0.004 H19 SDU 38 SDU H18 H8 H 0 1 N N N N N N -33.283 -3.285 -15.867 -4.196 -1.935 0.666 H18 SDU 39 SDU H4 H9 H 0 1 N N N N N N -32.048 -8.350 -15.975 2.009 1.549 1.506 H4 SDU 40 SDU H5 H10 H 0 1 N N N N N N -34.479 -9.159 -13.044 2.325 -1.182 -1.118 H5 SDU 41 SDU H6 H11 H 0 1 N N N N N N -35.695 -6.454 -12.868 -0.102 -2.104 -0.587 H6 SDU 42 SDU H3 H12 H 0 1 N N N N N N -36.117 -13.084 -14.457 6.957 -0.497 -2.199 H3 SDU 43 SDU H27 H13 H 0 1 N N N N N N -32.216 -7.409 -14.054 2.930 -1.574 1.819 H27 SDU 44 SDU H2 H14 H 0 1 N N N N N N -33.813 -13.893 -18.005 7.659 3.451 -0.027 H2 SDU 45 SDU H1 H15 H 0 1 N N N N N N -33.543 -12.417 -18.649 6.257 3.758 0.846 H1 SDU 46 SDU H7 H16 H 0 1 N N N N N N -33.932 -5.169 -14.998 -1.639 -2.256 1.437 H7 SDU 47 SDU H8 H17 H 0 1 N N N N N N -35.728 -5.225 -15.010 -0.967 -0.703 1.988 H8 SDU 48 SDU H9 H19 H 0 1 N N N N N N -36.669 -2.767 -13.356 -3.860 -0.759 1.387 H9 SDU 49 SDU H10 H20 H 0 1 N N N N N N -36.902 -4.523 -13.652 -2.780 0.586 1.829 H10 SDU 50 SDU H11 H21 H 0 1 N N N N N N -36.351 -5.054 -11.488 -3.316 1.657 -0.393 H11 SDU 51 SDU H12 H22 H 0 1 N N N N N N -35.768 -3.389 -11.152 -4.515 0.371 -0.670 H12 SDU 52 SDU H13 H23 H 0 1 N N N N N N -37.818 -3.778 -10.028 -4.509 2.243 1.739 H13 SDU 53 SDU H16 H24 H 0 1 N N N N N N -39.902 -4.167 -11.124 -6.494 0.305 0.743 H16 SDU 54 SDU H14 H25 H 0 1 N N N N N N -39.147 -4.445 -12.545 -5.572 0.145 2.118 H14 SDU 55 SDU H30 H27 H 0 1 N N N N N N -37.880 -0.437 -10.861 -5.607 4.523 -0.797 H30 SDU 56 SDU H22 H28 H 0 1 N N N N N N -35.868 -0.617 -16.165 -5.119 -1.050 -2.882 H22 SDU 57 SDU H26 H30 H 0 1 N N N N N N -33.152 -6.970 -10.717 1.543 -4.458 1.302 H26 SDU 58 SDU H28 H31 H 0 1 N N N N N N -31.561 -9.241 -12.839 3.403 -3.751 0.896 H28 SDU 59 # 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 SDU N1 C1 SING N N 1 SDU C1 N2 DOUB Y N 2 SDU N2 C2 SING Y N 3 SDU C2 N3 DOUB Y N 4 SDU N3 C3 SING Y N 5 SDU C3 C4 DOUB Y N 6 SDU C4 N4 SING Y N 7 SDU N4 C5 DOUB Y N 8 SDU C5 N5 SING Y N 9 SDU N5 C6 SING N N 10 SDU C6 O1 SING N N 11 SDU O1 C7 SING N N 12 SDU C7 C8 SING N N 13 SDU C8 N6 SING N N 14 SDU N6 C9 SING N N 15 SDU C9 C10 SING N N 16 SDU C10 C11 SING N N 17 SDU C11 N7 SING N N 18 SDU C11 C12 SING N N 19 SDU C12 O2 DOUB N N 20 SDU C12 O3 SING N N 21 SDU N6 C13 SING N N 22 SDU C13 C14 SING N N 23 SDU C14 C15 SING N N 24 SDU C15 N8 SING N N 25 SDU N8 C16 SING N N 26 SDU C7 C17 SING N N 27 SDU C17 O4 SING N N 28 SDU C17 C18 SING N N 29 SDU C18 O5 SING N N 30 SDU C1 C4 SING Y N 31 SDU C6 C18 SING N N 32 SDU C3 N5 SING Y N 33 SDU C13 C16 SING N N 34 SDU C17 H25 SING N N 35 SDU C16 H24 SING N N 36 SDU C16 H23 SING N N 37 SDU C13 H17 SING N N 38 SDU C15 H20 SING N N 39 SDU C15 H21 SING N N 40 SDU C14 H19 SING N N 41 SDU C14 H18 SING N N 42 SDU C5 H4 SING N N 43 SDU C6 H5 SING N N 44 SDU C7 H6 SING N N 45 SDU C2 H3 SING N N 46 SDU C18 H27 SING N N 47 SDU N1 H2 SING N N 48 SDU N1 H1 SING N N 49 SDU C8 H7 SING N N 50 SDU C8 H8 SING N N 51 SDU C9 H9 SING N N 52 SDU C9 H10 SING N N 53 SDU C10 H11 SING N N 54 SDU C10 H12 SING N N 55 SDU C11 H13 SING N N 56 SDU N7 H16 SING N N 57 SDU N7 H14 SING N N 58 SDU O3 H30 SING N N 59 SDU N8 H22 SING N N 60 SDU O4 H26 SING N N 61 SDU O5 H28 SING N N 62 # 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 SDU InChI InChI 1.06 "InChI=1S/C18H28N8O5/c19-10(18(29)30)2-4-25(9-1-3-21-5-9)6-11-13(27)14(28)17(31-11)26-8-24-12-15(20)22-7-23-16(12)26/h7-11,13-14,17,21,27-28H,1-6,19H2,(H,29,30)(H2,20,22,23)/t9-,10-,11+,13+,14+,17+/m0/s1" SDU InChIKey InChI 1.06 TZJIJYUFASCLJJ-GTAFEMJLSA-N SDU SMILES_CANONICAL CACTVS 3.385 "N[C@@H](CCN(C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)[C@H]4CCNC4)C(O)=O" SDU SMILES CACTVS 3.385 "N[CH](CCN(C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)[CH]4CCNC4)C(O)=O" SDU SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CN(CC[C@@H](C(=O)O)N)[C@H]4CCNC4)O)O)N" SDU SMILES "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CN(CCC(C(=O)O)N)C4CCNC4)O)O)N" # _pdbx_chem_comp_identifier.comp_id SDU _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~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[(3~{S})-pyrrolidin-3-yl]amino]-2-azanyl-butanoic 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 SDU "Create component" 2023-08-30 PDBE SDU "Initial release" 2024-09-11 RCSB #