data_K39
# 
_chem_comp.id                                    K39 
_chem_comp.name                                  "2'-methoxyethyl-guanosine-5'-thiophosphate" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C13 H20 N5 O8 P S" 
_chem_comp.mon_nstd_parent_comp_id               DG 
_chem_comp.pdbx_synonyms                         "2-azanyl-9-[(2R,3R,4R,5R)-5-[bis(oxidanyl)phosphinothioyloxymethyl]-3-(2-methoxyethoxy)-4-oxidanyl-oxolan-2-yl]-1H-purin-6-one" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-05-17 
_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                        437.365 
_chem_comp.one_letter_code                       G 
_chem_comp.three_letter_code                     K39 
_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 
K39 "C1'"  C1  C 0 1 N N R -10.130 -21.968 -24.872 -0.285 -0.024 0.610  "C1'"  K39 1  
K39 C2     C2  C 0 1 N N N -9.309  -21.022 -20.723 -4.648 0.950  0.870  C2     K39 2  
K39 "C2'"  C3  C 0 1 N N R -11.623 -22.275 -24.748 -0.318 -1.216 -0.380 "C2'"  K39 3  
K39 "C3'"  C4  C 0 1 N N R -12.171 -21.705 -26.042 0.999  -1.956 -0.041 "C3'"  K39 4  
K39 C4     C5  C 0 1 Y N N -9.514  -20.535 -22.875 -2.438 1.255  0.269  C4     K39 5  
K39 "C4'"  C6  C 0 1 N N R -11.056 -22.029 -27.030 1.863  -0.888 0.658  "C4'"  K39 6  
K39 C5     C7  C 0 1 Y N N -9.145  -19.214 -22.736 -2.766 2.451  -0.379 C5     K39 7  
K39 "C5'"  C8  C 0 1 N N N -10.993 -21.160 -28.261 3.174  -0.697 -0.109 "C5'"  K39 8  
K39 C6     C9  C 0 1 N N N -8.802  -18.733 -21.444 -4.114 2.879  -0.371 C6     K39 9  
K39 C8     C10 C 0 1 Y N N -9.523  -19.490 -24.813 -0.631 2.158  -0.612 C8     K39 10 
K39 "CA'"  C11 C 0 1 N N N -11.308 -24.270 -23.449 -1.948 -2.715 -1.298 "CA'"  K39 11 
K39 "CB'"  C12 C 0 1 N N N -11.065 -25.730 -23.660 -3.153 -3.577 -0.918 "CB'"  K39 12 
K39 "CD'"  C13 C 0 1 N N N -10.308 -27.104 -25.411 -5.400 -3.446 -0.095 "CD'"  K39 13 
K39 N1     N1  N 0 1 N N N -8.915  -19.730 -20.481 -5.028 2.106  0.256  N1     K39 14 
K39 N2     N2  N 0 1 N N N -9.347  -21.839 -19.659 -5.599 0.185  1.498  N2     K39 15 
K39 N3     N3  N 0 1 N N N -9.628  -21.484 -21.921 -3.398 0.544  0.873  N3     K39 16 
K39 N7     N4  N 0 1 Y N N -9.164  -18.565 -23.964 -1.619 2.955  -0.897 N7     K39 17 
K39 N9     N5  N 0 1 Y N N -9.744  -20.711 -24.219 -1.090 1.090  0.103  N9     K39 18 
K39 "O2'"  O1  O 0 1 N N N -11.803 -23.687 -24.658 -1.450 -2.053 -0.133 "O2'"  K39 19 
K39 "O3'"  O2  O 0 1 N N N -13.395 -22.342 -26.412 0.745  -3.052 0.841  "O3'"  K39 20 
K39 "O4'"  O3  O 0 1 N N N -9.842  -21.864 -26.266 1.112  0.338  0.655  "O4'"  K39 21 
K39 "O5'"  O4  O 0 1 N N N -11.091 -19.780 -27.878 4.010  0.221  0.599  "O5'"  K39 22 
K39 O6     O5  O 0 1 N N N -8.422  -17.602 -21.118 -4.444 3.915  -0.923 O6     K39 23 
K39 "OC'"  O6  O 0 1 N N N -11.139 -26.019 -25.037 -4.220 -2.736 -0.476 "OC'"  K39 24 
K39 OP2    O7  O 0 1 N Y N -11.750 -18.710 -30.043 6.276  1.367  1.278  OP2    K39 25 
K39 P      P1  P 0 1 N N N -10.783 -18.613 -28.918 5.470  0.656  0.080  P      K39 26 
K39 SP1    S8  S 0 1 N N N -10.773 -17.048 -27.840 6.404  -0.854 -0.487 SP1    K39 27 
K39 "H1'"  H1  H 0 1 N N N -9.562  -22.800 -24.431 -0.636 -0.333 1.595  "H1'"  K39 28 
K39 "H2'"  H2  H 0 1 N N N -12.052 -21.750 -23.882 -0.313 -0.865 -1.412 "H2'"  K39 29 
K39 "H3'"  H3  H 0 1 N N N -12.294 -20.615 -25.955 1.486  -2.305 -0.951 "H3'"  K39 30 
K39 "H4'"  H4  H 0 1 N N N -11.158 -23.079 -27.342 2.073  -1.193 1.683  "H4'"  K39 31 
K39 "H5'"  H5  H 0 1 N N N -11.826 -21.414 -28.932 3.684  -1.656 -0.202 "H5'"  K39 32 
K39 "H5''" H6  H 0 0 N N N -10.039 -21.329 -28.781 2.960  -0.301 -1.102 "H5''" K39 33 
K39 H8     H7  H 0 1 N N N -9.635  -19.314 -25.873 0.398  2.317  -0.899 H8     K39 34 
K39 H2     H8  H 0 1 N N N -10.365 -23.779 -23.165 -1.166 -3.347 -1.718 H2     K39 35 
K39 H9     H9  H 0 1 N N N -12.048 -24.134 -22.647 -2.251 -1.972 -2.036 H9     K39 36 
K39 H10    H10 H 0 1 N N N -11.827 -26.311 -23.121 -3.478 -4.150 -1.786 H10    K39 37 
K39 H11    H11 H 0 1 N N N -10.067 -25.995 -23.282 -2.873 -4.260 -0.116 H11    K39 38 
K39 H12    H12 H 0 1 N N N -10.405 -27.285 -26.492 -6.163 -2.737 0.228  H12    K39 39 
K39 H13    H13 H 0 1 N N N -9.262  -26.864 -25.172 -5.772 -4.017 -0.946 H13    K39 40 
K39 H14    H14 H 0 1 N N N -10.612 -28.006 -24.860 -5.167 -4.127 0.724  H14    K39 41 
K39 H1     H15 H 0 1 N N N -8.691  -19.486 -19.537 -5.960 2.375  0.268  H1     K39 42 
K39 H21    H16 H 0 1 N N N -9.616  -22.795 -19.772 -6.526 0.470  1.500  H21    K39 43 
K39 H22    H17 H 0 1 N N N -9.106  -21.491 -18.753 -5.343 -0.640 1.939  H22    K39 44 
K39 "HO3'" H18 H 0 0 N Y N -14.070 -22.123 -25.780 1.536  -3.551 1.086  "HO3'" K39 45 
K39 HOP2   H19 H 0 0 N Y N -12.275 -17.919 -30.079 7.167  1.657  1.036  HOP2   K39 46 
K39 OP3    O9  O 0 1 N N N -9.302  -18.957 -29.432 5.318  1.686  -1.149 OP3    K39 47 
K39 HOP3   H20 H 0 0 N N N -8.692  -18.309 -29.099 4.841  2.497  -0.926 HOP3   K39 48 
# 
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 
K39 OP2   P      SING N N 1  
K39 P     "O5'"  SING N N 2  
K39 P     SP1    DOUB N N 3  
K39 "C5'" "O5'"  SING N N 4  
K39 "C5'" "C4'"  SING N N 5  
K39 "C4'" "O4'"  SING N N 6  
K39 "C4'" "C3'"  SING N N 7  
K39 "O3'" "C3'"  SING N N 8  
K39 "O4'" "C1'"  SING N N 9  
K39 "C3'" "C2'"  SING N N 10 
K39 "CD'" "OC'"  SING N N 11 
K39 "OC'" "CB'"  SING N N 12 
K39 "C1'" "C2'"  SING N N 13 
K39 "C1'" N9     SING N N 14 
K39 C8    N9     SING Y N 15 
K39 C8    N7     DOUB Y N 16 
K39 "C2'" "O2'"  SING N N 17 
K39 "O2'" "CA'"  SING N N 18 
K39 N9    C4     SING Y N 19 
K39 N7    C5     SING Y N 20 
K39 "CB'" "CA'"  SING N N 21 
K39 C4    C5     DOUB Y N 22 
K39 C4    N3     SING N N 23 
K39 C5    C6     SING N N 24 
K39 N3    C2     DOUB N N 25 
K39 C6    O6     DOUB N N 26 
K39 C6    N1     SING N N 27 
K39 C2    N1     SING N N 28 
K39 C2    N2     SING N N 29 
K39 "C1'" "H1'"  SING N N 30 
K39 "C2'" "H2'"  SING N N 31 
K39 "C3'" "H3'"  SING N N 32 
K39 "C4'" "H4'"  SING N N 33 
K39 "C5'" "H5'"  SING N N 34 
K39 "C5'" "H5''" SING N N 35 
K39 C8    H8     SING N N 36 
K39 "CA'" H2     SING N N 37 
K39 "CA'" H9     SING N N 38 
K39 "CB'" H10    SING N N 39 
K39 "CB'" H11    SING N N 40 
K39 "CD'" H12    SING N N 41 
K39 "CD'" H13    SING N N 42 
K39 "CD'" H14    SING N N 43 
K39 N1    H1     SING N N 44 
K39 N2    H21    SING N N 45 
K39 N2    H22    SING N N 46 
K39 "O3'" "HO3'" SING N N 47 
K39 OP2   HOP2   SING N N 48 
K39 P     OP3    SING N N 49 
K39 OP3   HOP3   SING N N 50 
# 
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 
K39 InChI            InChI                1.06  "InChI=1S/C13H20N5O8PS/c1-23-2-3-24-9-8(19)6(4-25-27(21,22)28)26-12(9)18-5-15-7-10(18)16-13(14)17-11(7)20/h5-6,8-9,12,19H,2-4H2,1H3,(H2,21,22,28)(H3,14,16,17,20)/t6-,8-,9-,12-/m1/s1" 
K39 InChIKey         InChI                1.06  QOLXKMFPGMBQJQ-WOUKDFQISA-N                                                                                                                                                            
K39 SMILES_CANONICAL CACTVS               3.385 "COCCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=S)O[C@H]1n2cnc3C(=O)NC(=Nc23)N"                                                                                                                
K39 SMILES           CACTVS               3.385 "COCCO[CH]1[CH](O)[CH](CO[P](O)(O)=S)O[CH]1n2cnc3C(=O)NC(=Nc23)N"                                                                                                                      
K39 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "COCCO[C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2N=C(NC3=O)N)COP(=S)(O)O)O"                                                                                                                    
K39 SMILES           "OpenEye OEToolkits" 2.0.7 "COCCOC1C(C(OC1n2cnc3c2N=C(NC3=O)N)COP(=S)(O)O)O"                                                                                                                                      
# 
_pdbx_chem_comp_identifier.comp_id           K39 
_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-azanyl-9-[(2~{R},3~{R},4~{R},5~{R})-5-[bis(oxidanyl)phosphinothioyloxymethyl]-3-(2-methoxyethoxy)-4-oxidanyl-oxolan-2-yl]-1~{H}-purin-6-one" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      K39 
_pdbx_chem_comp_synonyms.name         "2-azanyl-9-[(2R,3R,4R,5R)-5-[bis(oxidanyl)phosphinothioyloxymethyl]-3-(2-methoxyethoxy)-4-oxidanyl-oxolan-2-yl]-1H-purin-6-one" 
_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 
K39 "Create component"    2022-05-17 PDBE 
K39 "Modify linking type" 2022-06-15 PDBE 
K39 "Modify descriptor"   2022-08-22 RCSB 
K39 "Initial release"     2022-09-14 RCSB 
# 
