data_KH9
# 
_chem_comp.id                                    KH9 
_chem_comp.name                                  "2-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[3-[6-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-[(3-azanylpropylcarbamoylamino)methyl]-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]prop-2-ynyl]amino]ethanoic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C29 H38 N14 O9" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-05-25 
_chem_comp.pdbx_modified_date                    2023-01-06 
_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                        726.700 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     KH9 
_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        7ZZA 
_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 
KH9 N1  N1  N 0 1 N N N 15.190 5.775  10.976 3.128   4.896  -0.450 N1  KH9 1  
KH9 C7  C1  C 0 1 N N R 18.639 9.260  15.430 2.525   -1.869 -2.060 C7  KH9 2  
KH9 C8  C2  C 0 1 N N S 18.489 7.765  15.696 2.038   -0.632 -2.852 C8  KH9 3  
KH9 N2  N2  N 0 1 N N N 16.529 6.831  12.493 2.904   2.757  -1.358 N2  KH9 4  
KH9 C9  C3  C 0 1 Y N N 18.560 11.307 12.816 3.846   -2.002 0.851  C9  KH9 5  
KH9 O1  O1  O 0 1 N N N 18.982 8.089  13.413 3.789   -0.026 -1.327 O1  KH9 6  
KH9 C1  C4  C 0 1 N N N 12.815 5.867  10.295 3.621   7.110  0.463  C1  KH9 7  
KH9 O5  O2  O 0 1 N N N 17.791 10.324 7.959  -5.324  2.400  -1.156 O5  KH9 8  
KH9 C5  C5  C 0 1 N N R 18.221 7.227  14.292 2.929   0.518  -2.342 C5  KH9 9  
KH9 C6  C6  C 0 1 N N R 19.492 9.186  14.162 3.944   -1.432 -1.615 C6  KH9 10 
KH9 N3  N3  N 0 1 Y N N 19.584 10.426 13.350 4.356   -2.162 -0.413 N3  KH9 11 
KH9 C4  C7  C 0 1 N N N 16.769 7.282  13.858 2.057   1.626  -1.747 C4  KH9 12 
KH9 O4  O3  O 0 1 N N N 15.830 8.411  9.936  -3.156  0.056  0.377  O4  KH9 13 
KH9 C3  C8  C 0 1 N N N 15.694 5.804  12.231 2.350   3.855  -0.808 C3  KH9 14 
KH9 O3  O4  O 0 1 N N N 19.699 7.228  16.221 2.231   -0.828 -4.255 O3  KH9 15 
KH9 C2  C9  C 0 1 N N N 14.012 4.989  10.636 2.526   6.087  0.154  C2  KH9 16 
KH9 N4  N4  N 0 1 Y N N 19.064 12.379 12.169 4.451   -2.822 1.678  N4  KH9 17 
KH9 N   N5  N 0 1 N N N 12.323 7.308  8.320  4.044   9.337  1.390  N   KH9 18 
KH9 C   C10 C 0 1 N N N 12.489 5.930  8.813  2.993   8.355  1.094  C   KH9 19 
KH9 O   O5  O 0 1 N N N 15.373 4.985  13.092 1.147   3.908  -0.634 O   KH9 20 
KH9 C10 C11 C 0 1 Y N N 20.477 12.223 12.280 5.370   -3.545 1.001  C10 KH9 21 
KH9 C11 C12 C 0 1 Y N N 21.575 12.995 11.851 6.291   -4.549 1.355  C11 KH9 22 
KH9 C12 C13 C 0 1 Y N N 22.971 11.430 12.818 6.986   -4.639 -0.844 C12 KH9 23 
KH9 C13 C14 C 0 1 Y N N 20.787 11.019 13.007 5.322   -3.134 -0.343 C13 KH9 24 
KH9 C14 C15 C 0 1 N N N 17.264 10.802 12.634 2.815   -1.076 1.214  C14 KH9 25 
KH9 C15 C16 C 0 1 N N N 16.104 10.663 12.884 1.970   -0.317 1.512  C15 KH9 26 
KH9 C16 C17 C 0 1 N N N 14.669 10.369 13.035 0.911   0.634  1.885  C16 KH9 27 
KH9 C17 C18 C 0 1 N N N 14.051 9.887  10.669 -1.331  1.366  1.334  C17 KH9 28 
KH9 C18 C19 C 0 1 N N R 15.366 9.774  9.919  -2.388  1.271  0.233  C18 KH9 29 
KH9 C19 C20 C 0 1 N N R 16.895 8.326  9.007  -4.383  0.294  -0.347 C19 KH9 30 
KH9 C20 C21 C 0 1 N N R 16.683 9.433  7.960  -4.763  1.753  -0.012 C20 KH9 31 
KH9 C21 C22 C 0 1 N N S 15.411 10.145 8.444  -3.421  2.411  0.378  C21 KH9 32 
KH9 C22 C23 C 0 1 Y N N 15.916 6.319  7.798  -5.483  -1.252 1.317  C22 KH9 33 
KH9 C23 C24 C 0 1 Y N N 17.592 5.022  7.688  -7.249  -1.887 0.230  C23 KH9 34 
KH9 C24 C25 C 0 1 Y N N 18.554 4.020  7.457  -8.444  -2.443 -0.256 C24 KH9 35 
KH9 C25 C26 C 0 1 Y N N 20.063 5.354  8.592  -8.136  -1.291 -2.232 C25 KH9 36 
KH9 C26 C27 C 0 1 Y N N 18.018 6.145  8.383  -6.535  -1.014 -0.607 C26 KH9 37 
KH9 C27 C28 C 0 1 N N N 13.004 8.668  12.570 -0.828  -0.998 1.467  C27 KH9 38 
KH9 C28 C29 C 0 1 N N N 11.675 9.372  12.732 -1.286  -1.004 2.902  C28 KH9 39 
KH9 N10 N6  N 0 1 Y N N 16.261 5.146  7.331  -6.552  -1.991 1.387  N10 KH9 40 
KH9 N11 N7  N 0 1 N N N 18.304 2.890  6.785  -9.191  -3.309 0.523  N11 KH9 41 
KH9 N12 N8  N 0 1 Y N N 19.802 4.224  7.929  -8.841  -2.117 -1.482 N12 KH9 42 
KH9 N13 N9  N 0 1 Y N N 19.244 6.369  8.870  -7.011  -0.747 -1.819 N13 KH9 43 
KH9 N5  N10 N 0 1 N N N 21.450 14.143 11.176 6.384   -4.994 2.662  N5  KH9 44 
KH9 N6  N11 N 0 1 Y N N 22.824 12.568 12.138 7.069   -5.058 0.406  N6  KH9 45 
KH9 N7  N12 N 0 1 Y N N 22.028 10.609 13.282 6.141   -3.704 -1.222 N7  KH9 46 
KH9 N8  N13 N 0 1 N N N 14.155 9.412  12.057 -0.309  0.332  1.123  N8  KH9 47 
KH9 N9  N14 N 0 1 Y N N 16.930 6.983  8.442  -5.429  -0.626 0.107  N9  KH9 48 
KH9 O2  O6  O 0 1 N N N 19.328 9.954  16.463 2.588   -3.022 -2.902 O2  KH9 49 
KH9 O6  O7  O 0 1 N N N 15.529 11.551 8.246  -3.111  3.484  -0.513 O6  KH9 50 
KH9 O7  O8  O 0 1 N N N 11.697 10.670 12.588 -1.131  -0.023 3.590  O7  KH9 51 
KH9 O8  O9  O 0 1 N N N 10.663 8.755  12.987 -1.867  -2.099 3.417  O8  KH9 52 
KH9 H1  H1  H 0 1 N N N 15.640 6.309  10.260 4.087   4.854  -0.589 H1  KH9 53 
KH9 H2  H2  H 0 1 N N N 17.661 9.712  15.209 1.886   -2.054 -1.197 H2  KH9 54 
KH9 H3  H3  H 0 1 N N N 17.629 7.573  16.355 0.989   -0.429 -2.637 H3  KH9 55 
KH9 H4  H4  H 0 1 N N N 16.992 7.292  11.736 3.863   2.715  -1.497 H4  KH9 56 
KH9 H5  H5  H 0 1 N N N 13.026 6.888  10.645 4.340   6.675  1.157  H5  KH9 57 
KH9 H6  H6  H 0 1 N N N 11.936 5.472  10.825 4.130   7.388  -0.460 H6  KH9 58 
KH9 H7  H7  H 0 1 N N N 18.566 9.866  7.657  -5.525  3.335  -1.020 H7  KH9 59 
KH9 H8  H8  H 0 1 N N N 18.585 6.191  14.224 3.528   0.914  -3.161 H8  KH9 60 
KH9 H9  H9  H 0 1 N N N 20.513 8.932  14.483 4.662   -1.582 -2.421 H9  KH9 61 
KH9 H10 H10 H 0 1 N N N 16.425 8.323  13.941 1.534   1.246  -0.870 H10 KH9 62 
KH9 H11 H11 H 0 1 N N N 16.183 6.646  14.538 1.331   1.955  -2.490 H11 KH9 63 
KH9 H12 H12 H 0 1 N N N 19.847 7.574  17.093 1.738   -1.577 -4.618 H12 KH9 64 
KH9 H13 H13 H 0 1 N N N 13.751 4.352  11.494 1.808   6.523  -0.540 H13 KH9 65 
KH9 H14 H14 H 0 1 N N N 14.247 4.356  9.767  2.018   5.809  1.077  H14 KH9 66 
KH9 H15 H15 H 0 1 N N N 12.111 7.290  7.343  3.654   10.169 1.808  H15 KH9 67 
KH9 H16 H16 H 0 1 N N N 11.576 7.751  8.815  4.757   8.936  1.981  H16 KH9 68 
KH9 H18 H18 H 0 1 N N N 11.554 5.379  8.636  2.274   8.790  0.400  H18 KH9 69 
KH9 H19 H19 H 0 1 N N N 13.307 5.453  8.253  2.484   8.077  2.017  H19 KH9 70 
KH9 H20 H20 H 0 1 N N N 23.990 11.134 13.020 7.638   -5.081 -1.584 H20 KH9 71 
KH9 H21 H21 H 0 1 N N N 14.109 11.310 12.926 0.704   0.548  2.951  H21 KH9 72 
KH9 H22 H22 H 0 1 N N N 14.504 9.958  14.042 1.238   1.649  1.659  H22 KH9 73 
KH9 H23 H23 H 0 1 N N N 13.739 10.942 10.679 -0.863  2.351  1.305  H23 KH9 74 
KH9 H24 H24 H 0 1 N N N 13.293 9.286  10.146 -1.803  1.218  2.306  H24 KH9 75 
KH9 H25 H25 H 0 1 N N N 16.102 10.402 10.442 -1.916  1.307  -0.749 H25 KH9 76 
KH9 H26 H26 H 0 1 N N N 17.848 8.523  9.520  -4.219  0.181  -1.419 H26 KH9 77 
KH9 H27 H27 H 0 1 N N N 16.514 8.988  6.968  -5.462  1.785  0.824  H27 KH9 78 
KH9 H28 H28 H 0 1 N N N 14.532 9.736  7.924  -3.455  2.766  1.408  H28 KH9 79 
KH9 H29 H29 H 0 1 N N N 14.923 6.728  7.687  -4.750  -1.146 2.103  H29 KH9 80 
KH9 H30 H30 H 0 1 N N N 21.076 5.460  8.952  -8.495  -1.053 -3.223 H30 KH9 81 
KH9 H31 H31 H 0 1 N N N 12.838 7.824  11.885 -0.041  -1.741 1.334  H31 KH9 82 
KH9 H32 H32 H 0 1 N N N 13.286 8.285  13.562 -1.668  -1.240 0.816  H32 KH9 83 
KH9 H33 H33 H 0 1 N N N 19.137 2.339  6.736  -8.891  -3.539 1.416  H33 KH9 84 
KH9 H34 H34 H 0 1 N N N 17.590 2.373  7.257  -10.015 -3.687 0.176  H34 KH9 85 
KH9 H35 H35 H 0 1 N N N 22.357 14.518 10.984 7.023   -5.687 2.894  H35 KH9 86 
KH9 H36 H36 H 0 1 N N N 20.971 13.973 10.315 5.811   -4.614 3.346  H36 KH9 87 
KH9 H38 H38 H 0 1 N N N 18.783 9.989  17.240 1.735   -3.280 -3.279 H38 KH9 88 
KH9 H39 H39 H 0 1 N N N 14.738 11.981 8.548  -3.760  4.200  -0.507 H39 KH9 89 
KH9 H40 H40 H 0 1 N N N 9.933  9.359  13.058 -2.145  -2.055 4.342  H40 KH9 90 
# 
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 
KH9 N11 C24 SING N N 1  
KH9 N10 C23 SING Y N 2  
KH9 N10 C22 DOUB Y N 3  
KH9 C24 C23 DOUB Y N 4  
KH9 C24 N12 SING Y N 5  
KH9 C23 C26 SING Y N 6  
KH9 C22 N9  SING Y N 7  
KH9 N12 C25 DOUB Y N 8  
KH9 O5  C20 SING N N 9  
KH9 C20 C21 SING N N 10 
KH9 C20 C19 SING N N 11 
KH9 O6  C21 SING N N 12 
KH9 N   C   SING N N 13 
KH9 C26 N9  SING Y N 14 
KH9 C26 N13 DOUB Y N 15 
KH9 N9  C19 SING N N 16 
KH9 C21 C18 SING N N 17 
KH9 C25 N13 SING Y N 18 
KH9 C   C1  SING N N 19 
KH9 C19 O4  SING N N 20 
KH9 C18 O4  SING N N 21 
KH9 C18 C17 SING N N 22 
KH9 C1  C2  SING N N 23 
KH9 C2  N1  SING N N 24 
KH9 C17 N8  SING N N 25 
KH9 N1  C3  SING N N 26 
KH9 N5  C11 SING N N 27 
KH9 C11 N6  DOUB Y N 28 
KH9 C11 C10 SING Y N 29 
KH9 N8  C27 SING N N 30 
KH9 N8  C16 SING N N 31 
KH9 N6  C12 SING Y N 32 
KH9 N4  C10 SING Y N 33 
KH9 N4  C9  DOUB Y N 34 
KH9 C3  N2  SING N N 35 
KH9 C3  O   DOUB N N 36 
KH9 C10 C13 DOUB Y N 37 
KH9 N2  C4  SING N N 38 
KH9 C27 C28 SING N N 39 
KH9 O7  C28 DOUB N N 40 
KH9 C14 C9  SING N N 41 
KH9 C14 C15 TRIP N N 42 
KH9 C28 O8  SING N N 43 
KH9 C9  N3  SING Y N 44 
KH9 C12 N7  DOUB Y N 45 
KH9 C15 C16 SING N N 46 
KH9 C13 N7  SING Y N 47 
KH9 C13 N3  SING Y N 48 
KH9 N3  C6  SING N N 49 
KH9 O1  C6  SING N N 50 
KH9 O1  C5  SING N N 51 
KH9 C4  C5  SING N N 52 
KH9 C6  C7  SING N N 53 
KH9 C5  C8  SING N N 54 
KH9 C7  C8  SING N N 55 
KH9 C7  O2  SING N N 56 
KH9 C8  O3  SING N N 57 
KH9 N1  H1  SING N N 58 
KH9 C7  H2  SING N N 59 
KH9 C8  H3  SING N N 60 
KH9 N2  H4  SING N N 61 
KH9 C1  H5  SING N N 62 
KH9 C1  H6  SING N N 63 
KH9 O5  H7  SING N N 64 
KH9 C5  H8  SING N N 65 
KH9 C6  H9  SING N N 66 
KH9 C4  H10 SING N N 67 
KH9 C4  H11 SING N N 68 
KH9 O3  H12 SING N N 69 
KH9 C2  H13 SING N N 70 
KH9 C2  H14 SING N N 71 
KH9 N   H15 SING N N 72 
KH9 N   H16 SING N N 73 
KH9 C   H18 SING N N 74 
KH9 C   H19 SING N N 75 
KH9 C12 H20 SING N N 76 
KH9 C16 H21 SING N N 77 
KH9 C16 H22 SING N N 78 
KH9 C17 H23 SING N N 79 
KH9 C17 H24 SING N N 80 
KH9 C18 H25 SING N N 81 
KH9 C19 H26 SING N N 82 
KH9 C20 H27 SING N N 83 
KH9 C21 H28 SING N N 84 
KH9 C22 H29 SING N N 85 
KH9 C25 H30 SING N N 86 
KH9 C27 H31 SING N N 87 
KH9 C27 H32 SING N N 88 
KH9 N11 H33 SING N N 89 
KH9 N11 H34 SING N N 90 
KH9 N5  H35 SING N N 91 
KH9 N5  H36 SING N N 92 
KH9 O2  H38 SING N N 93 
KH9 O6  H39 SING N N 94 
KH9 O8  H40 SING N N 95 
# 
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 
KH9 InChI            InChI                1.06  "InChI=1S/C29H38N14O9/c30-4-2-5-33-29(50)34-7-13-19(46)22(49)28(51-13)43-15(40-18-24(32)36-11-38-26(18)43)3-1-6-41(9-16(44)45)8-14-20(47)21(48)27(52-14)42-12-39-17-23(31)35-10-37-25(17)42/h10-14,19-22,27-28,46-49H,2,4-9,30H2,(H,44,45)(H2,31,35,37)(H2,32,36,38)(H2,33,34,50)/t13-,14-,19-,20-,21-,22-,27-,28-/m1/s1" 
KH9 InChIKey         InChI                1.06  PFWXIFMXYVCTQE-CGZJSAOLSA-N                                                                                                                                                                                                                                                                                               
KH9 SMILES_CANONICAL CACTVS               3.385 "NCCCNC(=O)NC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2c(nc3c(N)ncnc23)C#CCN(C[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)CC(O)=O"                                                                                                                                                                                               
KH9 SMILES           CACTVS               3.385 "NCCCNC(=O)NC[CH]1O[CH]([CH](O)[CH]1O)n2c(nc3c(N)ncnc23)C#CCN(C[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)CC(O)=O"                                                                                                                                                                                                         
KH9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CN(CC#Cc4nc5c(ncnc5n4[C@H]6[C@@H]([C@@H]([C@H](O6)CNC(=O)NCCCN)O)O)N)CC(=O)O)O)O)N"                                                                                                                                                                                       
KH9 SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CN(CC#Cc4nc5c(ncnc5n4C6C(C(C(O6)CNC(=O)NCCCN)O)O)N)CC(=O)O)O)O)N"                                                                                                                                                                                                                           
# 
_pdbx_chem_comp_identifier.comp_id           KH9 
_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-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[3-[6-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-[(3-azanylpropylcarbamoylamino)methyl]-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]prop-2-ynyl]amino]ethanoic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
KH9 "Create component"  2022-05-25 PDBE 
KH9 "Modify descriptor" 2022-08-22 RCSB 
KH9 "Initial release"   2023-01-11 RCSB 
# 
