data_A1IY6 # _chem_comp.id A1IY6 _chem_comp.name Se-2,6-diaminopurinribosyl-selenohomocysteineamide _chem_comp.type "RNA OH 3 prime terminus" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C14 H22 N8 O4 Se" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "(2S)-2-azanyl-4-[[(2S,3S,4R,5R)-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylselanyl]butanamide; SeDHA" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-01-22 _chem_comp.pdbx_modified_date 2025-02-07 _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 445.336 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1IY6 _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 9FN3 _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 A1IY6 C5 C1 C 0 1 Y N N N N N 25.012 45.638 37.512 -4.650 -1.686 0.527 C5 A1IY6 1 A1IY6 C6 C2 C 0 1 Y N N N N N 23.936 45.699 38.482 -5.968 -2.123 0.306 C6 A1IY6 2 A1IY6 N1 N1 N 0 1 Y N N N N N 22.877 46.499 38.260 -6.746 -1.410 -0.501 N1 A1IY6 3 A1IY6 C2 C3 C 0 1 Y N N N N N 22.810 47.234 37.153 -6.297 -0.308 -1.090 C2 A1IY6 4 A1IY6 "C3'" C4 C 0 1 N N S N N N 27.704 46.950 32.762 -0.771 2.550 0.933 "C3'" A1IY6 5 A1IY6 C02 C5 C 0 1 N N N N N N 26.477 41.984 26.174 7.534 -1.597 -0.214 C02 A1IY6 6 A1IY6 C04 C6 C 0 1 N N S N N N 26.143 42.358 27.620 6.560 -0.705 0.512 C04 A1IY6 7 A1IY6 C06 C7 C 0 1 N N N N N N 25.143 43.543 27.678 5.267 -0.596 -0.298 C06 A1IY6 8 A1IY6 C07 C8 C 0 1 N N N N N N 25.571 44.720 28.605 4.234 0.206 0.496 C07 A1IY6 9 A1IY6 N01 N2 N 0 1 N N N N N N 26.916 43.033 25.222 7.411 -2.936 -0.134 N01 A1IY6 10 A1IY6 N05 N3 N 0 1 N N N N N N 27.410 42.652 28.354 7.149 0.630 0.678 N05 A1IY6 11 A1IY6 O03 O1 O 0 1 N N N N N N 26.378 40.835 25.806 8.430 -1.109 -0.871 O03 A1IY6 12 A1IY6 SE8 SE1 SE 0 0 N N N N N N 25.150 44.255 30.497 2.577 0.346 -0.542 SE8 A1IY6 13 A1IY6 "C4'" C9 C 0 1 N N S N N N 26.322 46.222 32.263 0.085 1.621 0.044 "C4'" A1IY6 14 A1IY6 "O4'" O2 O 0 1 N N N N N N 25.567 46.083 33.310 -0.654 0.382 -0.014 "O4'" A1IY6 15 A1IY6 "C5'" C10 C 0 1 N N N N N N 26.639 44.873 31.672 1.458 1.394 0.679 "C5'" A1IY6 16 A1IY6 "C1'" C11 C 0 1 N N R N N N 26.273 46.787 34.426 -2.039 0.770 -0.143 "C1'" A1IY6 17 A1IY6 C8 C12 C 0 1 Y N N N N N 26.801 45.299 36.275 -2.590 -1.349 1.114 C8 A1IY6 18 A1IY6 C4 C13 C 0 1 Y N N N N N 24.901 46.415 36.383 -4.219 -0.516 -0.117 C4 A1IY6 19 A1IY6 "C2'" C14 C 0 1 N N R N N N 27.782 46.706 33.972 -2.201 1.977 0.807 "C2'" A1IY6 20 A1IY6 N9 N4 N 0 1 Y N N N N N 26.029 46.191 35.617 -2.917 -0.327 0.271 N9 A1IY6 21 A1IY6 N7 N5 N 0 1 Y N N N N N 26.215 44.949 37.416 -3.609 -2.142 1.267 N7 A1IY6 22 A1IY6 N4 N6 N 0 1 N N N N N N 23.989 44.915 39.689 -6.445 -3.270 0.915 N4 A1IY6 23 A1IY6 N2 N7 N 0 1 N N N N N N 21.640 48.091 36.936 -7.148 0.399 -1.923 N2 A1IY6 24 A1IY6 N3 N8 N 0 1 Y N N N N N 23.791 47.208 36.217 -5.065 0.137 -0.909 N3 A1IY6 25 A1IY6 "O2'" O3 O 0 1 N N N N N N 28.608 47.746 34.692 -3.081 2.948 0.238 "O2'" A1IY6 26 A1IY6 "O3'" O6 O 0 1 N N N N N N 27.604 48.413 32.534 -0.726 3.894 0.449 "O3'" A1IY6 27 A1IY6 "H3'" H1 H 0 1 N N N N N N 28.534 46.538 32.170 -0.433 2.507 1.969 "H3'" A1IY6 28 A1IY6 H041 H2 H 0 0 N N N N N N 25.661 41.490 28.092 6.340 -1.130 1.492 H041 A1IY6 29 A1IY6 H062 H3 H 0 0 N N N N N N 25.022 43.938 26.658 5.471 -0.091 -1.242 H062 A1IY6 30 A1IY6 H061 H4 H 0 0 N N N N N N 24.178 43.158 28.039 4.877 -1.594 -0.497 H061 A1IY6 31 A1IY6 H012 H7 H 0 0 N N N N N N 27.130 42.791 24.276 6.694 -3.327 0.391 H012 A1IY6 32 A1IY6 H011 H8 H 0 0 N N N N N N 26.998 43.982 25.526 8.037 -3.510 -0.602 H011 A1IY6 33 A1IY6 H052 H9 H 0 0 N N N N N N 27.198 42.897 29.300 7.969 0.594 1.264 H052 A1IY6 34 A1IY6 H051 H10 H 0 0 N N N N N N 27.997 41.843 28.343 7.362 1.045 -0.217 H051 A1IY6 35 A1IY6 "H4'" H12 H 0 1 N N N N N N 25.865 46.861 31.492 0.193 2.046 -0.954 "H4'" A1IY6 36 A1IY6 "H5'" H13 H 0 1 N N N N N N 26.783 44.147 32.485 1.339 0.852 1.618 "H5'" A1IY6 37 A1IY6 "H5''" H14 H 0 0 N N N N N N 27.562 44.946 31.078 1.933 2.355 0.873 "H5''" A1IY6 38 A1IY6 "H1'" H15 H 0 1 N N N N N N 25.972 47.845 34.437 -2.257 1.062 -1.171 "H1'" A1IY6 39 A1IY6 H8 H16 H 0 1 N N N N N N 27.753 44.926 35.926 -1.628 -1.476 1.590 H8 A1IY6 40 A1IY6 "H2'" H17 H 0 1 N N N N N N 28.168 45.703 34.205 -2.569 1.650 1.780 "H2'" A1IY6 41 A1IY6 H22 H20 H 0 1 N N N N N N 21.736 48.572 36.064 -8.055 0.087 -2.068 H22 A1IY6 42 A1IY6 H21 H21 H 0 1 N N N N N N 20.814 47.528 36.917 -6.837 1.206 -2.362 H21 A1IY6 43 A1IY6 "HO2'" H22 H 0 0 N N N N N N 28.650 47.533 35.617 -3.172 3.754 0.765 "HO2'" A1IY6 44 A1IY6 "HO3'" H23 H 0 0 N Y N N N N 28.405 48.834 32.823 -1.293 4.507 0.936 "HO3'" A1IY6 45 A1IY6 H42 H19 H 0 1 N N N N N N 23.169 45.087 40.235 -5.868 -3.783 1.502 H42 A1IY6 46 A1IY6 H41 H41 H 0 1 N N N N N N 24.035 43.944 39.454 -7.356 -3.561 0.755 H41 A1IY6 47 A1IY6 H71 H71 H 0 1 N N N N N N 26.652 44.895 28.501 4.030 -0.299 1.440 H71 A1IY6 48 A1IY6 H72 H72 H 0 1 N N N N N N 25.023 45.630 28.320 4.624 1.204 0.695 H72 A1IY6 49 # 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 A1IY6 N01 C02 SING N N 1 A1IY6 O03 C02 DOUB N N 2 A1IY6 C02 C04 SING N N 3 A1IY6 C04 C06 SING N N 4 A1IY6 C04 N05 SING N N 5 A1IY6 C06 C07 SING N N 6 A1IY6 C07 SE8 SING N N 7 A1IY6 SE8 "C5'" SING N N 8 A1IY6 "C5'" "C4'" SING N N 9 A1IY6 "C4'" "C3'" SING N N 10 A1IY6 "C4'" "O4'" SING N N 11 A1IY6 "O3'" "C3'" SING N N 12 A1IY6 "C3'" "C2'" SING N N 13 A1IY6 "O4'" "C1'" SING N N 14 A1IY6 "C2'" "C1'" SING N N 15 A1IY6 "C2'" "O2'" SING N N 16 A1IY6 "C1'" N9 SING N N 17 A1IY6 N9 C8 SING Y N 18 A1IY6 N9 C4 SING Y N 19 A1IY6 N3 C4 SING Y N 20 A1IY6 N3 C2 DOUB Y N 21 A1IY6 C8 N7 DOUB Y N 22 A1IY6 C4 C5 DOUB Y N 23 A1IY6 N2 C2 SING N N 24 A1IY6 C2 N1 SING Y N 25 A1IY6 N7 C5 SING Y N 26 A1IY6 C5 C6 SING Y N 27 A1IY6 N1 C6 DOUB Y N 28 A1IY6 C6 N4 SING N N 29 A1IY6 "C3'" "H3'" SING N N 30 A1IY6 C04 H041 SING N N 31 A1IY6 C06 H062 SING N N 32 A1IY6 C06 H061 SING N N 33 A1IY6 N01 H012 SING N N 34 A1IY6 N01 H011 SING N N 35 A1IY6 N05 H052 SING N N 36 A1IY6 N05 H051 SING N N 37 A1IY6 "C4'" "H4'" SING N N 38 A1IY6 "C5'" "H5'" SING N N 39 A1IY6 "C5'" "H5''" SING N N 40 A1IY6 "C1'" "H1'" SING N N 41 A1IY6 C8 H8 SING N N 42 A1IY6 "C2'" "H2'" SING N N 43 A1IY6 N2 H22 SING N N 44 A1IY6 N2 H21 SING N N 45 A1IY6 "O2'" "HO2'" SING N N 46 A1IY6 "O3'" "HO3'" SING N N 47 A1IY6 N4 H42 SING N N 48 A1IY6 N4 H41 SING N N 49 A1IY6 C07 H71 SING N N 50 A1IY6 C07 H72 SING N N 51 # 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 A1IY6 InChI InChI 1.06 "InChI=1S/C14H22N8O4Se/c15-5(11(17)25)1-2-27-3-6-8(23)9(24)13(26-6)22-4-19-7-10(16)20-14(18)21-12(7)22/h4-6,8-9,13,23-24H,1-3,15H2,(H2,17,25)(H4,16,18,20,21)/t5-,6+,8+,9+,13+/m0/s1" A1IY6 InChIKey InChI 1.06 MSXIHLRPNLBPQD-YTMOPEAISA-N A1IY6 SMILES_CANONICAL CACTVS 3.385 "N[C@@H](CC[Se]C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)nc(N)nc23)C(N)=O" A1IY6 SMILES CACTVS 3.385 "N[CH](CC[Se]C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)nc(N)nc23)C(N)=O" A1IY6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc2c(nc(nc2n1[C@H]3[C@@H]([C@@H]([C@H](O3)C[Se]CC[C@@H](C(=O)N)N)O)O)N)N" A1IY6 SMILES "OpenEye OEToolkits" 2.0.7 "c1nc2c(nc(nc2n1C3C(C(C(O3)C[Se]CCC(C(=O)N)N)O)O)N)N" # _pdbx_chem_comp_identifier.comp_id A1IY6 _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})-2-azanyl-4-[[(2~{S},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylselanyl]butanamide" # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 A1IY6 "(2S)-2-azanyl-4-[[(2S,3S,4R,5R)-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylselanyl]butanamide" PDB ? 2 A1IY6 SeDHA AUTHOR ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1IY6 "Create component" 2025-01-22 PDBE A1IY6 "Modify name" 2025-01-27 PDBE A1IY6 "Initial release" 2025-02-05 RCSB A1IY6 "Other modification" 2025-02-07 PDBE #