data_OK6
# 
_chem_comp.id                                    OK6 
_chem_comp.name                                  "2-azanyl-9-[(1~{R},6~{R},8~{R},9~{R},10~{S},15~{R},17~{R},18~{R})-8-(4-azanyl-5-phenyl-pyrrolo[2,3-d]pyrimidin-7-yl)-3,9,12,18-tetrakis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{6,10}]octadecan-17-yl]-1~{H}-purin-6-one" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C27 H29 N9 O13 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "2',3'-cyclic-GMP-7-deazaphenyl-AMP" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-09-13 
_chem_comp.pdbx_modified_date                    2023-05-15 
_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                        749.519 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     OK6 
_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        8A2H 
_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 
OK6 N1    N1  N 0 1 Y N N 0.212  27.049 3.745  -7.197 2.376  1.043  N1    OK6 1  
OK6 N3    N2  N 0 1 Y N N 2.586  27.142 3.987  -5.052 3.138  0.630  N3    OK6 2  
OK6 C4    C1  C 0 1 Y N N 2.543  28.462 4.325  -4.667 1.947  0.171  C4    OK6 3  
OK6 C5    C2  C 0 1 Y N N 1.238  29.153 4.394  -5.607 0.902  0.146  C5    OK6 4  
OK6 C6    C3  C 0 1 Y N N 0.021  28.356 4.067  -6.907 1.154  0.603  C6    OK6 5  
OK6 C7    C4  C 0 1 Y N N -1.596 32.509 5.282  -6.688 -3.523 0.186  C7    OK6 6  
OK6 C8    C5  C 0 1 Y N N 2.903  30.761 4.970  -3.636 0.134  -0.660 C8    OK6 7  
OK6 C10   C6  C 0 1 Y N N 0.309  33.950 5.100  -5.840 -3.507 -2.059 C10   OK6 8  
OK6 C11   C7  C 0 1 Y N N 1.105  32.815 4.935  -5.310 -2.250 -1.856 C11   OK6 9  
OK6 C12   C8  C 0 1 Y N N 1.511  30.436 4.772  -4.905 -0.266 -0.401 C12   OK6 10 
OK6 C9    C9  C 0 1 Y N N -1.064 33.801 5.270  -6.528 -4.143 -1.041 C9    OK6 11 
OK6 C3    C10 C 0 1 Y N N -0.767 31.389 5.121  -6.167 -2.263 0.398  C3    OK6 12 
OK6 C2    C11 C 0 1 Y N N 1.451  26.483 3.702  -6.284 3.330  1.050  C2    OK6 13 
OK6 C1    C12 C 0 1 Y N N 0.631  31.483 4.945  -5.473 -1.617 -0.624 C1    OK6 14 
OK6 "C1'" C13 C 0 1 N N R 4.901  29.324 4.745  -2.253 2.220  -0.464 "C1'" OK6 15 
OK6 C16   C14 C 0 1 N N N 6.169  32.592 5.350  0.590  0.306  -1.286 C16   OK6 16 
OK6 "C2'" C15 C 0 1 N N R 5.304  29.594 3.321  -1.463 2.203  0.855  "C2'" OK6 17 
OK6 C21   C16 C 0 1 N N R 4.003  34.831 2.910  3.898  -0.019 -0.520 C21   OK6 18 
OK6 C22   C17 C 0 1 N N R 5.435  35.209 2.599  4.796  1.228  -0.737 C22   OK6 19 
OK6 C24   C18 C 0 1 N N R 5.428  35.399 1.087  5.371  1.478  0.673  C24   OK6 20 
OK6 C25   C19 C 0 1 N N N 6.045  34.176 0.419  4.473  2.487  1.400  C25   OK6 21 
OK6 "C3'" C20 C 0 1 N N S 5.837  31.025 3.358  0.007  2.062  0.420  "C3'" OK6 22 
OK6 C32   C21 C 0 1 N N R 3.184  35.412 1.766  4.596  -0.755 0.643  C32   OK6 23 
OK6 C34   C22 C 0 1 Y N N 2.020  33.197 1.204  3.059  -0.815 2.645  C34   OK6 24 
OK6 C36   C23 C 0 1 Y N N 0.827  34.877 1.811  2.990  -2.582 1.329  C36   OK6 25 
OK6 C37   C24 C 0 1 Y N N -0.063 33.740 1.561  2.103  -2.745 2.400  C37   OK6 26 
OK6 C38   C25 C 0 1 N N N -1.512 33.981 1.787  1.347  -3.937 2.477  C38   OK6 27 
OK6 "C4'" C26 C 0 1 N N R 6.377  31.193 4.777  -0.053 1.676  -1.065 "C4'" OK6 28 
OK6 C40   C27 C 0 1 N N N -0.995 36.221 2.392  2.395  -4.652 0.493  C40   OK6 29 
OK6 N01   N3  N 0 1 N N N -1.326 28.963 4.113  -7.866 0.157  0.598  N01   OK6 30 
OK6 N33   N4  N 0 1 Y N N 2.052  34.497 1.563  3.584  -1.362 1.510  N33   OK6 31 
OK6 N35   N5  N 0 1 Y N N 0.741  32.715 1.188  2.189  -1.630 3.166  N35   OK6 32 
OK6 N39   N6  N 0 1 N N N -1.894 35.212 2.185  1.515  -4.868 1.512  N39   OK6 33 
OK6 N41   N7  N 0 1 N N N -1.341 37.612 2.840  2.545  -5.614 -0.473 N41   OK6 34 
OK6 N42   N8  N 0 1 N N N 0.325  36.049 2.203  3.105  -3.548 0.411  N42   OK6 35 
OK6 N9    N9  N 0 1 Y N N 3.409  29.424 4.675  -3.490 1.451  -0.321 N9    OK6 36 
OK6 O17   O1  O 0 1 N N N 4.810  33.005 5.179  1.598  0.399  -2.294 O17   OK6 37 
OK6 O19   O2  O 0 1 N N N 5.544  35.219 6.006  3.020  -0.679 -4.083 O19   OK6 38 
OK6 "O2'" O3  O 0 1 N N N 6.225  28.586 2.888  -1.661 3.433  1.557  "O2'" OK6 39 
OK6 O20   O4  O 0 1 N N N 3.657  35.273 4.221  3.852  -0.807 -1.700 O20   OK6 40 
OK6 O23   O5  O 0 1 N N N 5.818  36.384 3.349  5.845  0.935  -1.659 O23   OK6 41 
OK6 O26   O6  O 0 1 N N N 5.303  33.025 0.771  3.126  2.336  0.951  O26   OK6 42 
OK6 O28   O7  O 0 1 N N N 6.714  31.317 2.267  0.700  3.301  0.592  O28   OK6 43 
OK6 O29   O8  O 0 1 N N N 5.002  30.580 0.549  2.753  4.931  0.833  O29   OK6 44 
OK6 O30   O9  O 0 1 N N N 7.108  31.651 -0.243 2.462  3.480  -1.204 O30   OK6 45 
OK6 O31   O10 O 0 1 N N N 4.063  35.526 0.667  5.333  0.229  1.369  O31   OK6 46 
OK6 "O4'" O11 O 0 1 N N N 5.582  30.295 5.560  -1.426 1.623  -1.464 "O4'" OK6 47 
OK6 O43   O12 O 0 1 N N N -2.330 33.045 1.605  0.563  -4.122 3.393  O43   OK6 48 
OK6 O44   O13 O 0 1 N N N 3.277  34.467 6.520  1.781  -2.214 -2.503 O44   OK6 49 
OK6 P18   P1  P 0 1 N N N 4.346  34.507 5.474  2.571  -0.823 -2.681 P18   OK6 50 
OK6 P27   P2  P 0 1 N N N 6.056  31.608 0.830  2.263  3.504  0.264  P27   OK6 51 
OK6 H1    H1  H 0 1 N N N -2.659 32.371 5.417  -7.226 -4.023 0.977  H1    OK6 52 
OK6 H2    H2  H 0 1 N N N 3.401  31.680 5.243  -2.858 -0.492 -1.072 H2    OK6 53 
OK6 H3    H3  H 0 1 N N N 0.754  34.934 5.096  -5.718 -3.996 -3.014 H3    OK6 54 
OK6 H4    H4  H 0 1 N N N 2.164  32.966 4.788  -4.769 -1.756 -2.650 H4    OK6 55 
OK6 H5    H5  H 0 1 N N N -1.703 34.663 5.390  -6.941 -5.127 -1.203 H5    OK6 56 
OK6 H6    H6  H 0 1 N N N -1.219 30.408 5.132  -6.297 -1.777 1.354  H6    OK6 57 
OK6 H7    H7  H 0 1 N N N 1.525  25.443 3.422  -6.560 4.308  1.414  H7    OK6 58 
OK6 H8    H8  H 0 1 N N N 5.195  28.303 5.028  -2.486 3.248  -0.737 H8    OK6 59 
OK6 H9    H9  H 0 1 N N N 6.413  32.584 6.423  1.034  -0.047 -0.357 H9    OK6 60 
OK6 H10   H10 H 0 1 N N N 6.831  33.299 4.829  -0.167 -0.407 -1.608 H10   OK6 61 
OK6 H11   H11 H 0 1 N N N 4.405  29.573 2.688  -1.770 1.360  1.469  H11   OK6 62 
OK6 H12   H12 H 0 1 N N N 3.921  33.735 2.864  2.902  0.295  -0.210 H12   OK6 63 
OK6 H13   H13 H 0 1 N N N 6.095  34.366 2.852  4.208  2.078  -1.075 H13   OK6 64 
OK6 H14   H14 H 0 1 N N N 6.006  36.297 0.823  6.385  1.837  0.603  H14   OK6 65 
OK6 H15   H15 H 0 1 N N N 7.086  34.059 0.756  4.521  2.300  2.476  H15   OK6 66 
OK6 H16   H16 H 0 1 N N N 6.026  34.305 -0.673 4.823  3.499  1.194  H16   OK6 67 
OK6 H17   H17 H 0 1 N N N 4.963  31.688 3.273  0.504  1.281  0.996  H17   OK6 68 
OK6 H18   H18 H 0 1 N N N 2.809  36.403 2.063  5.259  -1.519 0.252  H18   OK6 69 
OK6 H19   H19 H 0 1 N N N 2.894  32.611 0.960  3.329  0.148  3.052  H19   OK6 70 
OK6 H20   H20 H 0 1 N N N 7.443  30.924 4.811  0.468  2.420  -1.667 H20   OK6 71 
OK6 H21   H21 H 0 1 N N N -2.011 28.273 3.878  -8.763 0.344  0.917  H21   OK6 72 
OK6 H22   H22 H 0 1 N N N -1.504 29.310 5.034  -7.642 -0.730 0.274  H22   OK6 73 
OK6 H23   H23 H 0 1 N N N -2.866 35.392 2.333  1.008  -5.694 1.544  H23   OK6 74 
OK6 H24   H24 H 0 1 N N N -0.618 38.291 2.965  2.029  -6.434 -0.425 H24   OK6 75 
OK6 H25   H25 H 0 1 N N N -2.294 37.859 3.013  3.167  -5.475 -1.204 H25   OK6 76 
OK6 H26   H26 H 0 1 N N N 5.797  27.738 2.901  -2.570 3.574  1.855  H26   OK6 77 
OK6 H27   H27 H 0 1 N N N 5.788  36.191 4.279  6.437  1.680  -1.832 H27   OK6 78 
OK6 H28   H28 H 0 1 N N N 5.199  30.139 -0.269 3.685  5.123  0.661  H28   OK6 79 
OK6 H29   H29 H 0 1 N N N 3.585  34.904 7.305  0.991  -2.292 -3.056 H29   OK6 80 
# 
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 
OK6 O30   P27   DOUB N N 1  
OK6 C25   O26   SING N N 2  
OK6 C25   C24   SING N N 3  
OK6 O29   P27   SING N N 4  
OK6 O31   C24   SING N N 5  
OK6 O31   C32   SING N N 6  
OK6 O26   P27   SING N N 7  
OK6 P27   O28   SING N N 8  
OK6 C24   C22   SING N N 9  
OK6 N35   C34   DOUB Y N 10 
OK6 N35   C37   SING Y N 11 
OK6 C34   N33   SING Y N 12 
OK6 C37   C38   SING N N 13 
OK6 C37   C36   DOUB Y N 14 
OK6 N33   C32   SING N N 15 
OK6 N33   C36   SING Y N 16 
OK6 O43   C38   DOUB N N 17 
OK6 C32   C21   SING N N 18 
OK6 C38   N39   SING N N 19 
OK6 C36   N42   SING N N 20 
OK6 N39   C40   SING N N 21 
OK6 N42   C40   DOUB N N 22 
OK6 O28   "C3'" SING N N 23 
OK6 C40   N41   SING N N 24 
OK6 C22   C21   SING N N 25 
OK6 C22   O23   SING N N 26 
OK6 "O2'" "C2'" SING N N 27 
OK6 C21   O20   SING N N 28 
OK6 "C2'" "C3'" SING N N 29 
OK6 "C2'" "C1'" SING N N 30 
OK6 "C3'" "C4'" SING N N 31 
OK6 C2    N1    DOUB Y N 32 
OK6 C2    N3    SING Y N 33 
OK6 N1    C6    SING Y N 34 
OK6 N3    C4    DOUB Y N 35 
OK6 C6    N01   SING N N 36 
OK6 C6    C5    DOUB Y N 37 
OK6 O20   P18   SING N N 38 
OK6 C4    C5    SING Y N 39 
OK6 C4    N9    SING Y N 40 
OK6 C5    C12   SING Y N 41 
OK6 N9    "C1'" SING N N 42 
OK6 N9    C8    SING Y N 43 
OK6 "C1'" "O4'" SING N N 44 
OK6 C12   C1    SING N N 45 
OK6 C12   C8    DOUB Y N 46 
OK6 "C4'" C16   SING N N 47 
OK6 "C4'" "O4'" SING N N 48 
OK6 C11   C1    DOUB Y N 49 
OK6 C11   C10   SING Y N 50 
OK6 C1    C3    SING Y N 51 
OK6 C10   C9    DOUB Y N 52 
OK6 C3    C7    DOUB Y N 53 
OK6 O17   C16   SING N N 54 
OK6 O17   P18   SING N N 55 
OK6 C9    C7    SING Y N 56 
OK6 P18   O19   DOUB N N 57 
OK6 P18   O44   SING N N 58 
OK6 C7    H1    SING N N 59 
OK6 C8    H2    SING N N 60 
OK6 C10   H3    SING N N 61 
OK6 C11   H4    SING N N 62 
OK6 C9    H5    SING N N 63 
OK6 C3    H6    SING N N 64 
OK6 C2    H7    SING N N 65 
OK6 "C1'" H8    SING N N 66 
OK6 C16   H9    SING N N 67 
OK6 C16   H10   SING N N 68 
OK6 "C2'" H11   SING N N 69 
OK6 C21   H12   SING N N 70 
OK6 C22   H13   SING N N 71 
OK6 C24   H14   SING N N 72 
OK6 C25   H15   SING N N 73 
OK6 C25   H16   SING N N 74 
OK6 "C3'" H17   SING N N 75 
OK6 C32   H18   SING N N 76 
OK6 C34   H19   SING N N 77 
OK6 "C4'" H20   SING N N 78 
OK6 N01   H21   SING N N 79 
OK6 N01   H22   SING N N 80 
OK6 N39   H23   SING N N 81 
OK6 N41   H24   SING N N 82 
OK6 N41   H25   SING N N 83 
OK6 "O2'" H26   SING N N 84 
OK6 O23   H27   SING N N 85 
OK6 O29   H28   SING N N 86 
OK6 O44   H29   SING N N 87 
# 
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 
OK6 InChI            InChI                1.06  "InChI=1S/C27H29N9O13P2/c28-21-15-12(11-4-2-1-3-5-11)6-35(22(15)31-9-30-21)25-18(38)19-14(47-25)8-45-51(42,43)49-20-17(37)13(7-44-50(40,41)48-19)46-26(20)36-10-32-16-23(36)33-27(29)34-24(16)39/h1-6,9-10,13-14,17-20,25-26,37-38H,7-8H2,(H,40,41)(H,42,43)(H2,28,30,31)(H3,29,33,34,39)/t13-,14-,17-,18-,19-,20-,25-,26-/m1/s1" 
OK6 InChIKey         InChI                1.06  FBIPVHNFXGBUQO-RTZOWOBBSA-N                                                                                                                                                                                                                                                                                                       
OK6 SMILES_CANONICAL CACTVS               3.385 "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@@H]4CO[P](O)(=O)O[C@H]5[C@@H](O)[C@@H](O[C@@H]5CO[P](O)(=O)O[C@@H]3[C@@H]4O)n6cc(c7ccccc7)c8c(N)ncnc68"                                                                                                                                                                                          
OK6 SMILES           CACTVS               3.385 "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH]4CO[P](O)(=O)O[CH]5[CH](O)[CH](O[CH]5CO[P](O)(=O)O[CH]3[CH]4O)n6cc(c7ccccc7)c8c(N)ncnc68"                                                                                                                                                                                                         
OK6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)c2cn(c3c2c(ncn3)N)[C@H]4[C@@H]([C@H]5[C@H](O4)COP(=O)(O[C@@H]6[C@@H]([C@@H](COP(=O)(O5)O)O[C@H]6n7cnc8c7N=C(NC8=O)N)O)O)O"                                                                                                                                                                                             
OK6 SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)c2cn(c3c2c(ncn3)N)C4C(C5C(O4)COP(=O)(OC6C(C(COP(=O)(O5)O)OC6n7cnc8c7N=C(NC8=O)N)O)O)O"                                                                                                                                                                                                                                 
# 
_pdbx_chem_comp_identifier.comp_id           OK6 
_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-[(1~{R},6~{R},8~{R},9~{R},10~{S},15~{R},17~{R},18~{R})-8-(4-azanyl-5-phenyl-pyrrolo[2,3-d]pyrimidin-7-yl)-3,9,12,18-tetrakis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{6,10}]octadecan-17-yl]-1~{H}-purin-6-one" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      OK6 
_pdbx_chem_comp_synonyms.name         "2',3'-cyclic-GMP-7-deazaphenyl-AMP" 
_pdbx_chem_comp_synonyms.provenance   AUTHOR 
_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 
OK6 "Create component" 2022-09-13 PDBE 
OK6 "Initial release"  2022-10-12 RCSB 
OK6 "Modify formula"   2023-05-15 PDBE 
# 
