data_A1IDY # _chem_comp.id A1IDY _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-(methylamino)propyl]amino]-2-azanyl-butanoic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H30 N8 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2024-06-07 _chem_comp.pdbx_modified_date 2025-06-13 _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 438.481 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1IDY _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 9FKW _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 A1IDY C5 C1 C 0 1 N N N N N N -36.683 -4.098 -12.904 3.427 -0.653 0.636 C5 A1IDY 1 A1IDY C2 C2 C 0 1 N N N N N N -35.187 -2.486 -15.659 4.823 2.962 -1.268 C2 A1IDY 2 A1IDY C7 C3 C 0 1 N N S N N N -38.153 -3.740 -10.821 3.564 -3.142 0.473 C7 A1IDY 3 A1IDY C13 C4 C 0 1 Y N N N N N -33.483 -11.389 -16.332 -4.319 -0.762 -1.121 C13 A1IDY 4 A1IDY N6 N1 N 0 1 N N N N N N -33.305 -13.205 -17.891 -6.117 -1.980 -2.197 N6 A1IDY 5 A1IDY C8 C5 C 0 1 N N N N N N -38.399 -2.265 -11.147 2.759 -4.415 0.440 C8 A1IDY 6 A1IDY C4 C6 C 0 1 N N N N N N -34.400 -3.244 -13.457 3.305 1.742 0.297 C4 A1IDY 7 A1IDY C3 C7 C 0 1 N N N N N N -34.863 -2.084 -14.287 4.021 1.676 -1.054 C3 A1IDY 8 A1IDY C1 C8 C 0 1 N N N N N N -33.956 -0.783 -17.040 6.292 4.119 -2.806 C1 A1IDY 9 A1IDY N1 N2 N 0 1 N N N N N N -35.240 -1.374 -16.645 5.511 2.899 -2.565 N1 A1IDY 10 A1IDY N2 N3 N 0 1 N N N N N N -35.305 -4.362 -13.305 2.536 0.507 0.503 N2 A1IDY 11 A1IDY C6 C9 C 0 1 N N N N N N -36.803 -4.180 -11.389 2.618 -1.940 0.458 C6 A1IDY 12 A1IDY N3 N4 N 0 1 N N N N N N -39.226 -4.588 -11.420 4.443 -3.088 -0.702 N3 A1IDY 13 A1IDY O1 O1 O 0 1 N N N N N N -39.286 -2.017 -11.998 2.638 -5.028 -0.594 O1 A1IDY 14 A1IDY O2 O2 O 0 1 N N N N N N -37.688 -1.418 -10.568 2.175 -4.869 1.561 O2 A1IDY 15 A1IDY C9 C10 C 0 1 N N N N N N -35.085 -5.495 -14.191 1.650 0.628 1.669 C9 A1IDY 16 A1IDY C10 C11 C 0 1 N N R N N N -34.899 -6.785 -13.416 0.446 1.500 1.308 C10 A1IDY 17 A1IDY O3 O3 O 0 1 N N N N N N -34.840 -7.896 -14.341 -0.320 0.868 0.269 O3 A1IDY 18 A1IDY C11 C12 C 0 1 N N R N N N -33.949 -8.848 -13.805 -1.706 1.194 0.510 C11 A1IDY 19 A1IDY N4 N5 N 0 1 Y N N N N N -33.535 -9.718 -14.897 -2.585 0.226 -0.150 N4 A1IDY 20 A1IDY C12 C13 C 0 1 Y N N N N N -32.638 -9.476 -15.908 -2.260 -1.050 -0.503 C12 A1IDY 21 A1IDY N5 N6 N 0 1 Y N N N N N -32.583 -10.447 -16.790 -3.279 -1.629 -1.070 N5 A1IDY 22 A1IDY C14 C14 C 0 1 Y N N N N N -33.841 -12.663 -16.797 -5.636 -0.826 -1.605 C14 A1IDY 23 A1IDY N7 N7 N 0 1 Y N N N N N -34.751 -13.358 -16.067 -6.409 0.248 -1.481 N7 A1IDY 24 A1IDY C15 C15 C 0 1 Y N N N N N -35.262 -12.802 -14.956 -5.959 1.353 -0.917 C15 A1IDY 25 A1IDY N8 N8 N 0 1 Y N N N N N -34.984 -11.623 -14.424 -4.733 1.459 -0.449 N8 A1IDY 26 A1IDY C16 C16 C 0 1 Y N N N N N -34.089 -10.948 -15.162 -3.887 0.437 -0.529 C16 A1IDY 27 A1IDY C17 C17 C 0 1 N N R N N N -32.820 -8.044 -13.192 -1.839 1.090 2.050 C17 A1IDY 28 A1IDY O4 O4 O 0 1 N N N N N N -32.010 -8.770 -12.289 -2.919 1.896 2.525 O4 A1IDY 29 A1IDY C18 C18 C 0 1 N N S N N N -33.613 -6.882 -12.559 -0.478 1.650 2.532 C18 A1IDY 30 A1IDY O5 O5 O 0 1 N N N N N N -33.935 -7.074 -11.176 -0.605 3.025 2.898 O5 A1IDY 31 A1IDY H11 H1 H 0 1 N N N N N N -36.975 -3.092 -13.240 4.203 -0.604 -0.127 H11 A1IDY 32 A1IDY H12 H2 H 0 1 N N N N N N -37.347 -4.845 -13.364 3.887 -0.646 1.624 H12 A1IDY 33 A1IDY H5 H3 H 0 1 N N N N N N -36.171 -2.978 -15.647 4.148 3.817 -1.256 H5 A1IDY 34 A1IDY H6 H4 H 0 1 N N N N N N -34.423 -3.203 -15.994 5.559 3.068 -0.472 H6 A1IDY 35 A1IDY H15 H5 H 0 1 N N N N N N -38.145 -3.871 -9.729 4.168 -3.118 1.380 H15 A1IDY 36 A1IDY H25 H6 H 0 1 N N N N N N -33.681 -14.121 -18.028 -5.543 -2.758 -2.282 H25 A1IDY 37 A1IDY H24 H7 H 0 1 N N N N N N -33.519 -12.635 -18.684 -7.028 -2.012 -2.528 H24 A1IDY 38 A1IDY H9 H8 H 0 1 N N N N N N -33.476 -3.628 -13.914 4.041 1.848 1.094 H9 A1IDY 39 A1IDY H10 H9 H 0 1 N N N N N N -34.179 -2.861 -12.450 2.630 2.597 0.309 H10 A1IDY 40 A1IDY H7 H10 H 0 1 N N N N N N -34.065 -1.328 -14.317 3.285 1.570 -1.850 H7 A1IDY 41 A1IDY H8 H11 H 0 1 N N N N N N -35.761 -1.651 -13.822 4.696 0.821 -1.066 H8 A1IDY 42 A1IDY H1 H12 H 0 1 N N N N N N -34.131 0.023 -17.768 6.791 4.046 -3.773 H1 A1IDY 43 A1IDY H2 H13 H 0 1 N N N N N N -33.453 -0.372 -16.152 5.627 4.983 -2.804 H2 A1IDY 44 A1IDY H3 H14 H 0 1 N N N N N N -33.321 -1.557 -17.496 7.038 4.234 -2.020 H3 A1IDY 45 A1IDY H31 H15 H 0 1 N N N N N N -35.801 -0.646 -16.251 4.855 2.736 -3.315 H31 A1IDY 46 A1IDY H13 H18 H 0 1 N N N N N N -36.631 -5.224 -11.089 1.900 -2.033 1.273 H13 A1IDY 47 A1IDY H14 H19 H 0 1 N N N N N N -36.024 -3.540 -10.950 2.087 -1.907 -0.493 H14 A1IDY 48 A1IDY H16 H20 H 0 1 N N N N N N -40.114 -4.309 -11.055 3.906 -3.110 -1.556 H16 A1IDY 49 A1IDY H17 H21 H 0 1 N N N N N N -39.223 -4.476 -12.414 5.040 -2.276 -0.671 H17 A1IDY 50 A1IDY H33 H23 H 0 1 N N N N N N -37.921 -0.548 -10.871 1.668 -5.690 1.490 H33 A1IDY 51 A1IDY H19 H24 H 0 1 N N N N N N -35.954 -5.601 -14.857 1.306 -0.363 1.967 H19 A1IDY 52 A1IDY H20 H25 H 0 1 N N N N N N -34.183 -5.307 -14.793 2.196 1.086 2.494 H20 A1IDY 53 A1IDY H21 H26 H 0 1 N N N N N N -35.763 -6.915 -12.747 0.786 2.480 0.975 H21 A1IDY 54 A1IDY H22 H27 H 0 1 N N N N N N -34.440 -9.440 -13.018 -1.927 2.205 0.170 H22 A1IDY 55 A1IDY H23 H28 H 0 1 N N N N N N -32.039 -8.579 -15.971 -1.298 -1.513 -0.337 H23 A1IDY 56 A1IDY H26 H29 H 0 1 N N N N N N -35.995 -13.394 -14.429 -6.621 2.203 -0.836 H26 A1IDY 57 A1IDY H27 H30 H 0 1 N N N N N N -32.201 -7.635 -14.004 -1.965 0.052 2.361 H27 A1IDY 58 A1IDY H28 H31 H 0 1 N N N N N N -31.328 -8.203 -11.948 -3.042 1.865 3.483 H28 A1IDY 59 A1IDY H29 H32 H 0 1 N N N N N N -33.037 -5.954 -12.687 -0.100 1.064 3.370 H29 A1IDY 60 A1IDY H30 H33 H 0 1 N N N N N N -34.420 -6.323 -10.856 -1.176 3.178 3.663 H30 A1IDY 61 # 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 A1IDY C1 N1 SING N N 1 A1IDY N1 C2 SING N N 2 A1IDY C2 C3 SING N N 3 A1IDY C3 C4 SING N N 4 A1IDY C4 N2 SING N N 5 A1IDY N2 C5 SING N N 6 A1IDY C5 C6 SING N N 7 A1IDY C6 C7 SING N N 8 A1IDY C7 N3 SING N N 9 A1IDY C7 C8 SING N N 10 A1IDY C8 O1 DOUB N N 11 A1IDY C8 O2 SING N N 12 A1IDY N2 C9 SING N N 13 A1IDY C9 C10 SING N N 14 A1IDY C10 O3 SING N N 15 A1IDY O3 C11 SING N N 16 A1IDY C11 N4 SING N N 17 A1IDY N4 C12 SING Y N 18 A1IDY C12 N5 DOUB Y N 19 A1IDY N5 C13 SING Y N 20 A1IDY C13 C14 DOUB Y N 21 A1IDY C14 N6 SING N N 22 A1IDY C14 N7 SING Y N 23 A1IDY N7 C15 DOUB Y N 24 A1IDY C15 N8 SING Y N 25 A1IDY N8 C16 DOUB Y N 26 A1IDY C11 C17 SING N N 27 A1IDY C17 O4 SING N N 28 A1IDY C17 C18 SING N N 29 A1IDY C18 O5 SING N N 30 A1IDY C10 C18 SING N N 31 A1IDY N4 C16 SING Y N 32 A1IDY C13 C16 SING Y N 33 A1IDY C5 H11 SING N N 34 A1IDY C5 H12 SING N N 35 A1IDY C2 H5 SING N N 36 A1IDY C2 H6 SING N N 37 A1IDY C7 H15 SING N N 38 A1IDY N6 H25 SING N N 39 A1IDY N6 H24 SING N N 40 A1IDY C4 H9 SING N N 41 A1IDY C4 H10 SING N N 42 A1IDY C3 H7 SING N N 43 A1IDY C3 H8 SING N N 44 A1IDY C1 H1 SING N N 45 A1IDY C1 H2 SING N N 46 A1IDY C1 H3 SING N N 47 A1IDY N1 H31 SING N N 48 A1IDY C6 H13 SING N N 49 A1IDY C6 H14 SING N N 50 A1IDY N3 H16 SING N N 51 A1IDY N3 H17 SING N N 52 A1IDY O2 H33 SING N N 53 A1IDY C9 H19 SING N N 54 A1IDY C9 H20 SING N N 55 A1IDY C10 H21 SING N N 56 A1IDY C11 H22 SING N N 57 A1IDY C12 H23 SING N N 58 A1IDY C15 H26 SING N N 59 A1IDY C17 H27 SING N N 60 A1IDY O4 H28 SING N N 61 A1IDY C18 H29 SING N N 62 A1IDY O5 H30 SING N N 63 # 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 A1IDY InChI InChI 1.06 "InChI=1S/C18H30N8O5/c1-21-4-2-5-25(6-3-10(19)18(29)30)7-11-13(27)14(28)17(31-11)26-9-24-12-15(20)22-8-23-16(12)26/h8-11,13-14,17,21,27-28H,2-7,19H2,1H3,(H,29,30)(H2,20,22,23)/t10-,11+,13+,14+,17+/m0/s1" A1IDY InChIKey InChI 1.06 LVDGLILGWFMHER-YRGUDCOPSA-N A1IDY SMILES_CANONICAL CACTVS 3.385 "CNCCCN(CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23" A1IDY SMILES CACTVS 3.385 "CNCCCN(CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23" A1IDY SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CNCCCN(CC[C@@H](C(=O)O)N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O" A1IDY SMILES "OpenEye OEToolkits" 2.0.7 "CNCCCN(CCC(C(=O)O)N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O" # _pdbx_chem_comp_identifier.comp_id A1IDY _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-(methylamino)propyl]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 A1IDY "Create component" 2024-06-07 PDBE A1IDY "Initial release" 2025-06-18 RCSB #