data_K1F
# 
_chem_comp.id                                    K1F 
_chem_comp.name                                  "[(2R,3S,4R,5R)-5-(3-aminocarbonyl-2-oxidanylidene-pyrazin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H14 N3 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "Beta-D-riboruranosyl-3-oxo-2-pyrazinecarboxamide; T1106 nucleoside analogue" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-09-06 
_chem_comp.pdbx_modified_date                    2023-02-08 
_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                        351.207 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     K1F 
_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        8BE0 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
# 
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 
K1F C02    C1  C 0 1 N N N 118.218 135.785 174.382 5.317  -1.054 0.539  C02    K1F 1  
K1F C04    C2  C 0 1 N N N 119.331 136.589 174.595 3.990  -0.966 -0.100 C04    K1F 2  
K1F C06    C3  C 0 1 N N N 120.966 137.507 176.051 2.502  -1.657 -1.709 C06    K1F 3  
K1F C07    C4  C 0 1 N N N 121.536 138.186 174.984 1.547  -0.794 -1.263 C07    K1F 4  
K1F "C1'"  C5  C 0 1 N N R 121.559 138.761 172.564 0.747  0.950  0.247  "C1'"  K1F 5  
K1F "C4'"  C6  C 0 1 N N R 123.592 138.822 171.410 -1.545 1.262  0.363  "C4'"  K1F 6  
K1F "C5'"  C7  C 0 1 N N N 124.919 138.476 172.042 -2.797 0.682  -0.298 "C5'"  K1F 7  
K1F "C3'"  C8  C 0 1 N N S 123.107 140.252 171.657 -1.006 2.436  -0.477 "C3'"  K1F 8  
K1F "C2'"  C9  C 0 1 N N R 122.253 140.071 172.902 0.438  2.012  -0.839 "C2'"  K1F 9  
K1F C22    C10 C 0 1 N N N 119.900 137.269 173.523 2.984  -0.022 0.400  C22    K1F 10 
K1F N01    N1  N 0 1 N N N 117.812 135.715 173.119 6.237  -1.917 0.065  N01    K1F 11 
K1F N05    N2  N 0 1 N N N 119.847 136.701 175.828 3.690  -1.734 -1.135 N05    K1F 12 
K1F N08    N3  N 0 1 N N N 120.971 138.054 173.711 1.782  0.023  -0.217 N08    K1F 13 
K1F O03    O1  O 0 1 N N N 117.672 135.195 175.313 5.582  -0.344 1.490  O03    K1F 14 
K1F "O4'"  O2  O 0 1 N N N 122.569 137.957 171.985 -0.512 0.263  0.413  "O4'"  K1F 15 
K1F "O5'"  O3  O 0 1 N N N 125.252 137.103 171.857 -3.356 -0.328 0.545  "O5'"  K1F 16 
K1F OP2    O4  O 0 1 N Y N 125.151 135.159 170.309 -5.944 -0.150 0.112  OP2    K1F 17 
K1F "O3'"  O5  O 0 1 N N N 122.254 140.633 170.579 -0.996 3.639  0.294  "O3'"  K1F 18 
K1F "O2'"  O6  O 0 1 N N N 121.343 141.116 173.173 1.336  3.120  -0.737 "O2'"  K1F 19 
K1F O23    O7  O 0 1 N N N 119.424 137.165 172.394 3.227  0.704  1.348  O23    K1F 20 
K1F P      P1  P 0 1 N N N 125.669 136.540 170.425 -4.685 -1.153 0.162  P      K1F 21 
K1F OP1    O8  O 0 1 N N N 127.113 136.801 170.226 -4.507 -1.788 -1.163 OP1    K1F 22 
K1F H1     H1  H 0 1 N N N 121.383 137.600 177.043 2.281  -2.298 -2.549 H1     K1F 23 
K1F H2     H2  H 0 1 N N N 122.405 138.809 175.134 0.586  -0.764 -1.756 H2     K1F 24 
K1F "H1'"  H3  H 0 1 N N N 120.771 138.965 171.823 1.051  1.429  1.178  "H1'"  K1F 25 
K1F "H4'"  H4  H 0 1 N N N 123.656 138.652 170.325 -1.780 1.604  1.371  "H4'"  K1F 26 
K1F "H5'"  H5  H 0 1 N N N 125.704 139.097 171.585 -3.529 1.475  -0.449 "H5'"  K1F 27 
K1F "H5''" H6  H 0 0 N N N 124.866 138.687 173.120 -2.532 0.245  -1.261 "H5''" K1F 28 
K1F "H3'"  H7  H 0 1 N N N 123.943 140.947 171.825 -1.603 2.565  -1.380 "H3'"  K1F 29 
K1F "H2'"  H8  H 0 1 N N N 122.915 139.909 173.765 0.477  1.572  -1.835 "H2'"  K1F 30 
K1F H9     H9  H 0 1 N N N 117.017 135.157 172.879 6.027  -2.480 -0.696 H9     K1F 31 
K1F H10    H10 H 0 1 N N N 118.301 136.220 172.408 7.109  -1.974 0.484  H10    K1F 32 
K1F HOP2   H11 H 0 0 N Y N 125.866 134.568 170.106 -6.120 0.302  0.948  HOP2   K1F 33 
K1F "HO3'" H12 H 0 0 N Y N 121.944 141.520 170.718 -0.665 4.411  -0.185 "HO3'" K1F 34 
K1F "HO2'" H13 H 0 0 N N N 120.857 140.916 173.964 1.183  3.811  -1.396 "HO2'" K1F 35 
K1F OP3    O9  O 0 1 N N N 124.841 137.449 169.391 -4.949 -2.290 1.271  OP3    K1F 36 
K1F HOP3   H16 H 0 0 N N N 125.444 137.964 168.868 -5.735 -2.828 1.104  HOP3   K1F 37 
# 
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 
K1F OP1   P      DOUB N N 1  
K1F OP2   P      SING N N 2  
K1F P     "O5'"  SING N N 3  
K1F "O3'" "C3'"  SING N N 4  
K1F "C4'" "C3'"  SING N N 5  
K1F "C4'" "O4'"  SING N N 6  
K1F "C4'" "C5'"  SING N N 7  
K1F "C3'" "C2'"  SING N N 8  
K1F "O5'" "C5'"  SING N N 9  
K1F "O4'" "C1'"  SING N N 10 
K1F O23   C22    DOUB N N 11 
K1F "C1'" "C2'"  SING N N 12 
K1F "C1'" N08    SING N N 13 
K1F "C2'" "O2'"  SING N N 14 
K1F N01   C02    SING N N 15 
K1F C22   N08    SING N N 16 
K1F C22   C04    SING N N 17 
K1F N08   C07    SING N N 18 
K1F C02   C04    SING N N 19 
K1F C02   O03    DOUB N N 20 
K1F C04   N05    DOUB N N 21 
K1F C07   C06    DOUB N N 22 
K1F N05   C06    SING N N 23 
K1F C06   H1     SING N N 24 
K1F C07   H2     SING N N 25 
K1F "C1'" "H1'"  SING N N 26 
K1F "C4'" "H4'"  SING N N 27 
K1F "C5'" "H5'"  SING N N 28 
K1F "C5'" "H5''" SING N N 29 
K1F "C3'" "H3'"  SING N N 30 
K1F "C2'" "H2'"  SING N N 31 
K1F N01   H9     SING N N 32 
K1F N01   H10    SING N N 33 
K1F OP2   HOP2   SING N N 34 
K1F "O3'" "HO3'" SING N N 35 
K1F "O2'" "HO2'" SING N N 36 
K1F P     OP3    SING N N 37 
K1F OP3   HOP3   SING N N 38 
# 
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 
K1F InChI            InChI                1.06  "InChI=1S/C10H14N3O9P/c11-8(16)5-9(17)13(2-1-12-5)10-7(15)6(14)4(22-10)3-21-23(18,19)20/h1-2,4,6-7,10,14-15H,3H2,(H2,11,16)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1" 
K1F InChIKey         InChI                1.06  DZEZSGXCBIFRRE-KQYNXXCUSA-N                                                                                                                                   
K1F SMILES_CANONICAL CACTVS               3.385 "NC(=O)C1=NC=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C1=O"                                                                                            
K1F SMILES           CACTVS               3.385 "NC(=O)C1=NC=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C1=O"                                                                                                  
K1F SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)C(=N1)C(=O)N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O"                                                                                        
K1F SMILES           "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)C(=N1)C(=O)N)C2C(C(C(O2)COP(=O)(O)O)O)O"                                                                                                          
# 
_pdbx_chem_comp_identifier.comp_id           K1F 
_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-(3-aminocarbonyl-2-oxidanylidene-pyrazin-1-yl)-3,4-bis(oxidanyl)oxolan-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 
K1F "Create component"   2022-09-06 PDBJ 
K1F "Initial release"    2022-12-28 RCSB 
K1F "Modify coordinates" 2023-02-08 PDBE 
# 
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 K1F Beta-D-riboruranosyl-3-oxo-2-pyrazinecarboxamide PDB    ? 
2 K1F "T1106 nucleoside analogue"                      AUTHOR ? 
# 
