data_K2F
# 
_chem_comp.id                                    K2F 
_chem_comp.name                                  "2'-methoxyethyl-adenosine-5'-thiophosphate" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C13 H20 N5 O7 P S" 
_chem_comp.mon_nstd_parent_comp_id               DA 
_chem_comp.pdbx_synonyms                         "(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-2-[bis(oxidanyl)phosphinothioyloxymethyl]-4-(2-methoxyethoxy)oxolan-3-ol" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-05-16 
_chem_comp.pdbx_modified_date                    2022-09-09 
_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                        421.366 
_chem_comp.one_letter_code                       A 
_chem_comp.three_letter_code                     K2F 
_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        7ZVN 
_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 
K2F C2     C1  C 0 1 Y N N -15.160 -10.411 -14.184 4.779  -1.069 1.030  C2     K2F 1  
K2F C4     C2  C 0 1 Y N N -14.570 -8.571  -15.235 2.567  -1.271 0.441  C4     K2F 2  
K2F "C1'"  C3  C 0 1 N N R -14.037 -6.216  -14.486 0.456  0.098  0.717  "C1'"  K2F 3  
K2F "C2'"  C4  C 0 1 N N R -12.712 -6.287  -13.710 0.547  1.252  -0.313 "C2'"  K2F 4  
K2F "C3'"  C5  C 0 1 N N R -11.849 -5.322  -14.498 -0.742 2.056  -0.014 "C3'"  K2F 5  
K2F "C4'"  C6  C 0 1 N N R -12.852 -4.224  -14.821 -1.655 1.049  0.712  "C4'"  K2F 6  
K2F C5     C7  C 0 1 Y N N -14.647 -9.185  -16.471 2.852  -2.508 -0.162 C5     K2F 7  
K2F "C5'"  C8  C 0 1 N N N -12.475 -3.267  -15.927 -2.967 0.886  -0.059 "C5'"  K2F 8  
K2F C6     C9  C 0 1 Y N N -15.039 -10.536 -16.490 4.175  -2.979 -0.116 C6     K2F 9  
K2F C8     C10 C 0 1 Y N N -14.059 -7.178  -16.847 0.732  -2.136 -0.423 C8     K2F 10 
K2F "CA'"  C11 C 0 1 N N N -12.655 -6.657  -11.336 2.245  2.649  -1.267 "CA'"  K2F 11 
K2F "CB'"  C12 C 0 1 N N N -13.894 -7.429  -11.027 3.481  3.476  -0.905 "CB'"  K2F 12 
K2F "CD'"  C13 C 0 1 N N N -14.652 -9.612  -10.547 5.713  3.283  -0.054 "CD'"  K2F 13 
K2F N1     N1  N 0 1 Y N N -15.292 -11.133 -15.304 5.095  -2.228 0.482  N1     K2F 14 
K2F N3     N2  N 0 1 Y N N -14.812 -9.135  -14.038 3.552  -0.592 1.019  N3     K2F 15 
K2F N6     N3  N 0 1 N N N -15.197 -11.246 -17.610 4.516  -4.191 -0.691 N6     K2F 16 
K2F N7     N4  N 0 1 Y N N -14.315 -8.295  -17.483 1.689  -2.983 -0.669 N7     K2F 17 
K2F N9     N5  N 0 1 Y N N -14.202 -7.270  -15.484 1.223  -1.064 0.260  N9     K2F 18 
K2F "O2'"  O1  O 0 1 N N N -12.912 -5.748  -12.406 1.710  2.050  -0.085 "O2'"  K2F 19 
K2F "O3'"  O2  O 0 1 N N N -10.741 -4.831  -13.742 -0.452 3.169  0.833  "O3'"  K2F 20 
K2F "O4'"  O3  O 0 1 N N N -14.060 -4.947  -15.149 -0.955 -0.205 0.761  "O4'"  K2F 21 
K2F "O5'"  O4  O 0 1 N N N -12.469 -3.920  -17.204 -3.852 0.043  0.680  "O5'"  K2F 22 
K2F "OC'"  O5  O 0 1 N N N -13.559 -8.704  -10.512 4.509  2.608  -0.422 "OC'"  K2F 23 
K2F OP2    O6  O 0 1 N Y N -11.246 -2.062  -18.315 -6.311 0.915  0.354  OP2    K2F 24 
K2F P      P1  P 0 1 N N N -12.299 -3.082  -18.547 -5.327 -0.346 0.165  P      K2F 25 
K2F SP1    SP1 S 0 1 N N N -12.035 -4.392  -19.900 -5.254 -0.811 -1.638 SP1    K2F 26 
K2F "H1'"  H1  H 0 1 N N N -15.366 -10.941 -13.266 5.557  -0.492 1.509  "H1'"  K2F 27 
K2F H1     H2  H 0 1 N N N -14.863 -6.270  -13.762 0.808  0.428  1.695  H1     K2F 28 
K2F "H2'"  H3  H 0 1 N N N -12.296 -7.305  -13.706 0.537  0.865  -1.332 "H2'"  K2F 29 
K2F "H3'"  H4  H 0 1 N N N -11.511 -5.800  -15.429 -1.205 2.394  -0.942 "H3'"  K2F 30 
K2F "H4'"  H5  H 0 1 N N N -13.022 -3.639  -13.905 -1.861 1.398  1.724  "H4'"  K2F 31 
K2F "H5'"  H6  H 0 1 N N N -11.471 -2.865  -15.726 -3.429 1.863  -0.200 "H5'"  K2F 32 
K2F "H5''" H7  H 0 0 N N N -13.202 -2.442  -15.950 -2.764 0.437  -1.031 "H5''" K2F 33 
K2F H8     H8  H 0 1 N N N -13.763 -6.269  -17.349 -0.299 -2.265 -0.716 H8     K2F 34 
K2F H9     H9  H 0 1 N N N -11.854 -7.352  -11.630 1.493  3.298  -1.717 H9     K2F 35 
K2F H10    H10 H 0 1 N N N -12.343 -6.094  -10.444 2.524  1.870  -1.975 H10    K2F 36 
K2F H11    H11 H 0 1 N N N -14.488 -6.880  -10.281 3.836  4.004  -1.789 H11    K2F 37 
K2F H12    H12 H 0 1 N N N -14.484 -7.552  -11.947 3.221  4.197  -0.130 H12    K2F 38 
K2F H13    H13 H 0 1 N N N -14.336 -10.583 -10.137 6.115  3.807  -0.921 H13    K2F 39 
K2F H14    H14 H 0 1 N N N -15.481 -9.211  -9.945  5.500  4.001  0.738  H14    K2F 40 
K2F H15    H15 H 0 1 N N N -14.985 -9.745  -11.587 6.443  2.556  0.301  H15    K2F 41 
K2F H61    H16 H 0 1 N N N -15.498 -12.171 -17.379 3.838  -4.726 -1.133 H61    K2F 42 
K2F H62    H17 H 0 1 N N N -15.884 -10.807 -18.189 5.433  -4.505 -0.652 H62    K2F 43 
K2F "HO3'" H18 H 0 0 N Y N -10.140 -5.544  -13.561 -1.224 3.708  1.053  "HO3'" K2F 44 
K2F HOP2   H19 H 0 0 N Y N -10.525 -2.208  -18.917 -6.397 1.212  1.271  HOP2   K2F 45 
K2F OP3    O8  O 0 1 N N N -13.728 -2.369  -18.722 -5.883 -1.592 1.019  OP3    K2F 46 
K2F HOP3   H20 H 0 0 N N N -14.177 -2.738  -19.474 -6.769 -1.881 0.762  HOP3   K2F 47 
# 
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 
K2F SP1   P      DOUB N N 1  
K2F P     OP2    SING N N 2  
K2F P     "O5'"  SING N N 3  
K2F N6    C6     SING N N 4  
K2F N7    C8     DOUB Y N 5  
K2F N7    C5     SING Y N 6  
K2F "O5'" "C5'"  SING N N 7  
K2F C8    N9     SING Y N 8  
K2F C6    C5     DOUB Y N 9  
K2F C6    N1     SING Y N 10 
K2F C5    C4     SING Y N 11 
K2F "C5'" "C4'"  SING N N 12 
K2F N9    C4     SING Y N 13 
K2F N9    "C1'"  SING N N 14 
K2F N1    C2     DOUB Y N 15 
K2F C4    N3     DOUB Y N 16 
K2F "O4'" "C4'"  SING N N 17 
K2F "O4'" "C1'"  SING N N 18 
K2F "C4'" "C3'"  SING N N 19 
K2F "C3'" "O3'"  SING N N 20 
K2F "C3'" "C2'"  SING N N 21 
K2F "C1'" "C2'"  SING N N 22 
K2F C2    N3     SING Y N 23 
K2F "C2'" "O2'"  SING N N 24 
K2F "O2'" "CA'"  SING N N 25 
K2F "CA'" "CB'"  SING N N 26 
K2F "CB'" "OC'"  SING N N 27 
K2F "CD'" "OC'"  SING N N 28 
K2F C2    "H1'"  SING N N 29 
K2F "C1'" H1     SING N N 30 
K2F "C2'" "H2'"  SING N N 31 
K2F "C3'" "H3'"  SING N N 32 
K2F "C4'" "H4'"  SING N N 33 
K2F "C5'" "H5'"  SING N N 34 
K2F "C5'" "H5''" SING N N 35 
K2F C8    H8     SING N N 36 
K2F "CA'" H9     SING N N 37 
K2F "CA'" H10    SING N N 38 
K2F "CB'" H11    SING N N 39 
K2F "CB'" H12    SING N N 40 
K2F "CD'" H13    SING N N 41 
K2F "CD'" H14    SING N N 42 
K2F "CD'" H15    SING N N 43 
K2F N6    H61    SING N N 44 
K2F N6    H62    SING N N 45 
K2F "O3'" "HO3'" SING N N 46 
K2F OP2   HOP2   SING N N 47 
K2F P     OP3    SING N N 48 
K2F OP3   HOP3   SING N N 49 
# 
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 
K2F InChI            InChI                1.06  "InChI=1S/C13H20N5O7PS/c1-22-2-3-23-10-9(19)7(4-24-26(20,21)27)25-13(10)18-6-17-8-11(14)15-5-16-12(8)18/h5-7,9-10,13,19H,2-4H2,1H3,(H2,14,15,16)(H2,20,21,27)/t7-,9-,10-,13-/m1/s1" 
K2F InChIKey         InChI                1.06  ZQSIUNNJVQJWJZ-QYVSTXNMSA-N                                                                                                                                                         
K2F SMILES_CANONICAL CACTVS               3.385 "COCCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=S)O[C@H]1n2cnc3c(N)ncnc23"                                                                                                                  
K2F SMILES           CACTVS               3.385 "COCCO[CH]1[CH](O)[CH](CO[P](O)(O)=S)O[CH]1n2cnc3c(N)ncnc23"                                                                                                                        
K2F SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "COCCO[C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2ncnc3N)COP(=S)(O)O)O"                                                                                                                      
K2F SMILES           "OpenEye OEToolkits" 2.0.7 "COCCOC1C(C(OC1n2cnc3c2ncnc3N)COP(=S)(O)O)O"                                                                                                                                        
# 
_pdbx_chem_comp_identifier.comp_id           K2F 
_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~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-2-[bis(oxidanyl)phosphinothioyloxymethyl]-4-(2-methoxyethoxy)oxolan-3-ol" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      K2F 
_pdbx_chem_comp_synonyms.name         "(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-2-[bis(oxidanyl)phosphinothioyloxymethyl]-4-(2-methoxyethoxy)oxolan-3-ol" 
_pdbx_chem_comp_synonyms.provenance   PDB 
_pdbx_chem_comp_synonyms.type         ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
K2F "Create component"    2022-05-16 PDBE 
K2F "Modify linking type" 2022-06-15 PDBE 
K2F "Modify descriptor"   2022-08-22 RCSB 
K2F "Initial release"     2022-09-14 RCSB 
# 
