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 
# 
