data_ILK
# 
_chem_comp.id                                    ILK 
_chem_comp.name                                  "[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(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 H13 N2 O8 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                        387.142 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     ILK 
_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 
ILK "C1'" C1  C  0 1 N N R 1.752  2.247  26.857 1.377  1.048  0.175  "C1'" ILK 1  
ILK C2    C2  C  0 1 N N N -0.617 2.499  27.592 3.638  0.263  -0.252 C2    ILK 2  
ILK "C2'" C3  C  0 1 N N R 2.721  2.548  28.011 0.477  1.168  -1.090 "C2'" ILK 3  
ILK "C3'" C4  C  0 1 N N S 3.436  1.252  28.509 -0.813 1.918  -0.786 "C3'" ILK 4  
ILK C4    C5  C  0 1 N N N -2.044 0.650  28.121 4.207  -2.003 -0.239 C4    ILK 5  
ILK "C4'" C6  C  0 1 N N R 4.058  0.598  27.276 -1.376 1.722  0.634  "C4'" ILK 6  
ILK C5    C7  C  0 1 N N N -0.948 -0.290 27.885 2.862  -2.328 0.062  C5    ILK 7  
ILK "C5'" C8  C  0 1 N N N 4.407  -0.866 27.516 -2.721 0.994  0.584  "C5'" ILK 8  
ILK C6    C9  C  0 1 N N N 0.274  0.262  27.511 1.959  -1.332 0.192  C6    ILK 9  
ILK N1    N1  N  0 1 N N N 0.504  1.620  27.311 2.356  -0.032 0.033  N1    ILK 10 
ILK N3    N2  N  0 1 N N N -1.881 1.956  27.971 4.558  -0.710 -0.387 N3    ILK 11 
ILK O2    O1  O  0 1 N N N -0.387 3.710  27.432 3.968  1.424  -0.393 O2    ILK 12 
ILK "O2'" O2  O  0 1 N N N 3.676  3.487  27.552 1.195  1.866  -2.109 "O2'" ILK 13 
ILK "O3'" O3  O  0 1 N N N 4.411  1.683  29.455 -0.577 3.313  -0.985 "O3'" ILK 14 
ILK O4    O4  O  0 1 N N N -3.282 0.135  28.501 5.039  -2.884 -0.361 O4    ILK 15 
ILK "O5'" O5  O  0 1 N N N 3.256  -1.502 27.931 -2.571 -0.235 -0.130 "O5'" ILK 16 
ILK OP1   O6  O  0 1 N N N 4.227  -3.573 29.076 -4.401 -1.620 0.921  OP1   ILK 17 
ILK OP2   O7  O  0 1 N N N 1.694  -3.427 28.755 -4.894 -0.563 -1.317 OP2   ILK 18 
ILK P     P1  P  0 1 N N N 3.067  -3.198 28.236 -3.788 -1.260 -0.377 P     ILK 19 
ILK SE4   SE1 SE 0 0 N N N 2.766  0.903  25.891 -0.009 0.598  1.530  SE4   ILK 20 
ILK H1    H1  H  0 1 N N N 1.604  3.107  26.187 1.866  1.995  0.405  H1    ILK 21 
ILK H2    H2  H  0 1 N N N 2.147  2.969  28.850 0.233  0.168  -1.449 H2    ILK 22 
ILK H3    H3  H  0 1 N N N 2.699  0.575  28.966 -1.571 1.597  -1.500 H3    ILK 23 
ILK H4    H4  H  0 1 N N N 4.958  1.153  26.972 -1.480 2.681  1.141  H4    ILK 24 
ILK H5    H5  H  0 1 N N N -1.080 -1.356 27.995 2.562  -3.358 0.185  H5    ILK 25 
ILK H6    H6  H  0 1 N N N 4.774  -1.323 26.585 -3.060 0.786  1.598  H6    ILK 26 
ILK H7    H7  H  0 1 N N N 5.181  -0.945 28.293 -3.455 1.621  0.077  H7    ILK 27 
ILK H8    H8  H  0 1 N N N 1.104  -0.413 27.365 0.929  -1.560 0.421  H8    ILK 28 
ILK H9    H9  H  0 1 N N N -2.655 2.570  28.126 5.477  -0.480 -0.593 H9    ILK 29 
ILK H10   H10 H  0 1 N N N 4.286  3.687  28.252 0.698  1.980  -2.931 H10   ILK 30 
ILK H11   H11 H  0 1 N N N 3.976  2.081  30.200 -0.328 3.545  -1.890 H11   ILK 31 
ILK H13   H13 H  0 1 N N N 1.743  -3.813 29.622 -4.562 -0.300 -2.186 H13   ILK 32 
ILK OP3   OP3 O  0 1 N N N 3.357  -3.954 26.905 -3.233 -2.589 -1.095 OP3   ILK 33 
ILK H12   H12 H  0 1 N N N 4.172  -4.436 26.985 -3.914 -3.253 -1.275 H12   ILK 34 
# 
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 
ILK SE4   "C1'" SING N N 1  
ILK SE4   "C4'" SING N N 2  
ILK "C1'" N1    SING N N 3  
ILK "C1'" "C2'" SING N N 4  
ILK "C4'" "C5'" SING N N 5  
ILK "C4'" "C3'" SING N N 6  
ILK N1    C6    SING N N 7  
ILK N1    C2    SING N N 8  
ILK O2    C2    DOUB N N 9  
ILK C6    C5    DOUB N N 10 
ILK "C5'" "O5'" SING N N 11 
ILK "O2'" "C2'" SING N N 12 
ILK C2    N3    SING N N 13 
ILK C5    C4    SING N N 14 
ILK "O5'" P     SING N N 15 
ILK N3    C4    SING N N 16 
ILK "C2'" "C3'" SING N N 17 
ILK C4    O4    DOUB N N 18 
ILK P     OP2   SING N N 19 
ILK P     OP1   DOUB N N 20 
ILK "C3'" "O3'" SING N N 21 
ILK "C1'" H1    SING N N 22 
ILK "C2'" H2    SING N N 23 
ILK "C3'" H3    SING N N 24 
ILK "C4'" H4    SING N N 25 
ILK C5    H5    SING N N 26 
ILK "C5'" H6    SING N N 27 
ILK "C5'" H7    SING N N 28 
ILK C6    H8    SING N N 29 
ILK N3    H9    SING N N 30 
ILK "O2'" H10   SING N N 31 
ILK "O3'" H11   SING N N 32 
ILK OP2   H13   SING N N 33 
ILK P     OP3   SING N N 34 
ILK OP3   H12   SING N N 35 
# 
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 
ILK InChI            InChI                1.06  "InChI=1S/C9H13N2O8PSe/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(21-8)3-19-20(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1" 
ILK InChIKey         InChI                1.06  QLPCUUUELDONBL-XVFCMESISA-N                                                                                                                           
ILK SMILES_CANONICAL CACTVS               3.385 "O[C@H]1[C@@H](O)[C@@H]([Se][C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O"                                                                                     
ILK SMILES           CACTVS               3.385 "O[CH]1[CH](O)[CH]([Se][CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O"                                                                                            
ILK SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H]([Se]2)COP(=O)(O)O)O)O"                                                                                    
ILK SMILES           "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)C2C(C(C([Se]2)COP(=O)(O)O)O)O"                                                                                                      
# 
_pdbx_chem_comp_identifier.comp_id           ILK 
_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-[2,4-bis(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 
ILK "Create component" 2022-07-07 PDBJ 
ILK "Initial release"  2023-05-03 RCSB 
# 
