data_IKS
# 
_chem_comp.id                                    IKS 
_chem_comp.name                                  "[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)selenolan-2-yl]methyl dihydrogen phosphate" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C9 H14 N3 O7 P Se" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-07-07 
_chem_comp.pdbx_modified_date                    2023-04-28 
_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                        386.157 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     IKS 
_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        7Y8P 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
# 
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 
IKS P     P1  P  0 1 N N N -0.005 -7.970 25.931 4.031  1.085  -0.416 P     IKS 1  
IKS OP1   O1  O  0 1 N N N 0.913  -9.032 26.379 5.070  0.235  -1.039 OP1   IKS 2  
IKS OP2   O2  O  0 1 N N N -1.073 -7.503 26.835 3.686  2.316  -1.394 OP2   IKS 3  
IKS "O5'" O3  O  0 1 N N N 0.985  -6.549 25.788 2.703  0.211  -0.164 "O5'" IKS 4  
IKS "C5'" C1  C  0 1 N N N 2.311  -6.527 25.390 2.703  -1.010 0.579  "C5'" IKS 5  
IKS "C4'" C2  C  0 1 N N R 2.603  -5.154 24.827 1.284  -1.579 0.626  "C4'" IKS 6  
IKS "C3'" C3  C  0 1 N N S 2.336  -4.098 25.891 0.706  -1.749 -0.799 "C3'" IKS 7  
IKS "O3'" O4  O  0 1 N N N 3.357  -3.954 26.905 0.927  -3.099 -1.213 "O3'" IKS 8  
IKS "C2'" C4  C  0 1 N N R 2.146  -2.810 24.988 -0.771 -1.442 -0.948 "C2'" IKS 9  
IKS "O2'" O5  O  0 1 N N N 3.468  -2.462 24.480 -1.422 -2.612 -1.449 "O2'" IKS 10 
IKS "C1'" C5  C  0 1 N N R 1.138  -2.950 23.821 -1.497 -1.002 0.344  "C1'" IKS 11 
IKS N1    N1  N  0 1 N N N -0.179 -2.898 24.424 -2.495 0.032  0.061  N1    IKS 12 
IKS C2    C6  C  0 1 N N N -0.819 -1.593 24.390 -3.800 -0.292 0.010  C2    IKS 13 
IKS O2    O6  O  0 1 N N N -0.179 -0.678 23.819 -4.138 -1.449 0.201  O2    IKS 14 
IKS N3    N2  N  0 1 N N N -2.099 -1.324 24.961 -4.728 0.628  -0.244 N3    IKS 15 
IKS C4    C7  C  0 1 N N N -2.794 -2.309 25.581 -4.388 1.893  -0.456 C4    IKS 16 
IKS N4    N3  N  0 1 N N N -4.050 -2.097 26.142 -5.356 2.835  -0.718 N4    IKS 17 
IKS C5    C8  C  0 1 N N N -2.164 -3.650 25.614 -3.029 2.266  -0.411 C5    IKS 18 
IKS C6    C9  C  0 1 N N N -0.908 -3.889 25.076 -2.098 1.320  -0.145 C6    IKS 19 
IKS SE4   SE1 SE 0 0 N N N 1.494  -4.767 23.268 0.013  -0.265 1.410  SE4   IKS 20 
IKS H2    H2  H  0 1 N N N -1.029 -7.984 27.653 4.442  2.886  -1.590 H2    IKS 21 
IKS H3    H3  H  0 1 N N N 2.483  -7.292 24.618 3.367  -1.728 0.097  H3    IKS 22 
IKS H4    H4  H  0 1 N N N 2.964  -6.724 26.253 3.051  -0.818 1.594  H4    IKS 23 
IKS H5    H5  H  0 1 N N N 3.644  -5.093 24.477 1.260  -2.522 1.173  H5    IKS 24 
IKS H6    H6  H  0 1 N N N 1.370  -4.319 26.369 1.260  -1.094 -1.472 H6    IKS 25 
IKS H7    H7  H  0 1 N N N 3.101  -3.276 27.519 0.595  -3.298 -2.099 H7    IKS 26 
IKS H8    H8  H  0 1 N N N 1.791  -2.000 25.642 -0.882 -0.650 -1.689 H8    IKS 27 
IKS H9    H9  H  0 1 N N N 4.075  -2.380 25.206 -1.108 -2.895 -2.319 H9    IKS 28 
IKS H10   H10 H  0 1 N N N 1.317  -2.268 22.977 -1.953 -1.855 0.847  H10   IKS 29 
IKS H11   H11 H  0 1 N N N -4.472 -1.191 26.096 -6.290 2.575  -0.748 H11   IKS 30 
IKS H12   H12 H  0 1 N N N -4.531 -2.850 26.591 -5.104 3.759  -0.872 H12   IKS 31 
IKS H13   H13 H  0 1 N N N -2.700 -4.468 26.072 -2.736 3.291  -0.581 H13   IKS 32 
IKS H14   H14 H  0 1 N N N -0.481 -4.877 25.166 -1.051 1.581  -0.100 H14   IKS 33 
IKS OP3   OP3 O  0 1 N N N -0.398 -8.379 24.486 4.574  1.652  0.990  OP3   IKS 34 
IKS H1    H1  H  0 1 N N N 0.039  -9.190 24.256 3.944  2.219  1.455  H1    IKS 35 
# 
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 
IKS SE4   "C1'" SING N N 1  
IKS SE4   "C4'" SING N N 2  
IKS O2    C2    DOUB N N 3  
IKS "C1'" N1    SING N N 4  
IKS "C1'" "C2'" SING N N 5  
IKS C2    N1    SING N N 6  
IKS C2    N3    SING N N 7  
IKS N1    C6    SING N N 8  
IKS "O2'" "C2'" SING N N 9  
IKS "C4'" "C5'" SING N N 10 
IKS "C4'" "C3'" SING N N 11 
IKS N3    C4    DOUB N N 12 
IKS "C2'" "C3'" SING N N 13 
IKS C6    C5    DOUB N N 14 
IKS "C5'" "O5'" SING N N 15 
IKS C4    C5    SING N N 16 
IKS C4    N4    SING N N 17 
IKS "O5'" P     SING N N 18 
IKS "C3'" "O3'" SING N N 19 
IKS P     OP1   DOUB N N 20 
IKS P     OP2   SING N N 21 
IKS OP2   H2    SING N N 22 
IKS "C5'" H3    SING N N 23 
IKS "C5'" H4    SING N N 24 
IKS "C4'" H5    SING N N 25 
IKS "C3'" H6    SING N N 26 
IKS "O3'" H7    SING N N 27 
IKS "C2'" H8    SING N N 28 
IKS "O2'" H9    SING N N 29 
IKS "C1'" H10   SING N N 30 
IKS N4    H11   SING N N 31 
IKS N4    H12   SING N N 32 
IKS C5    H13   SING N N 33 
IKS C6    H14   SING N N 34 
IKS P     OP3   SING N N 35 
IKS OP3   H1    SING N N 36 
# 
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 
IKS InChI            InChI                1.06  "InChI=1S/C9H14N3O7PSe/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(21-8)3-19-20(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1" 
IKS InChIKey         InChI                1.06  PXFLZUCOUFTIFX-XVFCMESISA-N                                                                                                                            
IKS SMILES_CANONICAL CACTVS               3.385 "NC1=NC(=O)N(C=C1)[C@@H]2[Se][C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O"                                                                                     
IKS SMILES           CACTVS               3.385 "NC1=NC(=O)N(C=C1)[CH]2[Se][CH](CO[P](O)(O)=O)[CH](O)[CH]2O"                                                                                           
IKS SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H]([Se]2)COP(=O)(O)O)O)O"                                                                                     
IKS SMILES           "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N=C1N)C2C(C(C([Se]2)COP(=O)(O)O)O)O"                                                                                                       
# 
_pdbx_chem_comp_identifier.comp_id           IKS 
_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-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)selenolan-2-yl]methyl dihydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
IKS "Create component" 2022-07-07 PDBJ 
IKS "Initial release"  2023-05-03 RCSB 
# 
