data_I1K
# 
_chem_comp.id                                    I1K 
_chem_comp.name                                  "5'-{[2-(benzylcarbamamido)ethyl][3-(N'-cyclopentylcarbamimidamido)propyl]amino}-5'-deoxyadenosine" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C29 H43 N11 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-05-01 
_chem_comp.pdbx_modified_date                    2024-04-19 
_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                        609.723 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     I1K 
_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        8SIH 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
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.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
I1K N1  N1  N 0 1 Y N N N N N 7.183  19.818 -29.249 1.972   7.414  2.157  N1  I1K 1  
I1K C7  C1  C 0 1 N N N N N N 1.761  25.856 -28.013 0.172   0.168  -2.396 C7  I1K 2  
I1K C8  C2  C 0 1 N N N N N N 2.809  28.042 -28.752 -1.855  -0.847 -1.545 C8  I1K 3  
I1K N2  N2  N 0 1 Y N N N N N 5.640  21.401 -30.216 0.679   6.281  0.612  N2  I1K 4  
I1K C9  C3  C 0 1 N N N N N N 1.989  28.371 -29.988 -2.479  -1.397 -0.261 C9  I1K 5  
I1K O1  O1  O 0 1 N N N N N N 1.398  30.667 -31.556 -4.183  -2.259 1.643  O1  I1K 6  
I1K C1  C4  C 0 1 Y N N N N N 6.737  20.633 -30.209 0.955   7.358  1.317  C1  I1K 7  
I1K C5  C5  C 0 1 N N R N N N 3.167  23.045 -29.443 0.452   3.454  -0.841 C5  I1K 8  
I1K C6  C6  C 0 1 N N R N N N 2.411  25.229 -29.227 -0.166  1.628  -2.087 C6  I1K 9  
I1K N3  N3  N 0 1 Y N N N N N 4.403  20.679 -26.945 3.109   3.979  1.525  N3  I1K 10 
I1K C4  C7  C 0 1 Y N N N N N 3.568  21.578 -27.411 2.460   3.240  0.673  C4  I1K 11 
I1K C3  C8  C 0 1 Y N N N N N 5.296  20.487 -27.989 2.523   5.198  1.603  C3  I1K 12 
I1K O3  O2  O 0 1 N N N N N N 1.170  22.005 -30.393 0.279   4.972  -2.749 O3  I1K 13 
I1K C2  C9  C 0 1 Y N N N N N 4.962  21.285 -29.074 1.429   5.189  0.722  C2  I1K 14 
I1K N4  N4  N 0 1 Y N N N N N 3.841  21.987 -28.692 1.414   3.942  0.150  N4  I1K 15 
I1K C10 C10 C 0 1 N N N N N N 2.547  30.190 -31.571 -4.703  -1.876 0.613  C10 I1K 16 
I1K N7  N5  N 0 1 N N N N N N 3.561  30.720 -32.292 -6.044  -1.902 0.484  N7  I1K 17 
I1K C11 C11 C 0 1 N N N N N N 3.406  31.933 -33.087 -6.876  -2.392 1.586  C11 I1K 18 
I1K C12 C12 C 0 1 Y N N N N N 3.394  33.219 -32.296 -8.328  -2.318 1.191  C12 I1K 19 
I1K C17 C13 C 0 1 Y N N N N N 4.034  33.309 -31.059 -8.930  -3.394 0.565  C17 I1K 20 
I1K C16 C14 C 0 1 Y N N N N N 4.105  34.521 -30.388 -10.262 -3.326 0.202  C16 I1K 21 
I1K C15 C15 C 0 1 Y N N N N N 3.547  35.666 -30.947 -10.993 -2.182 0.465  C15 I1K 22 
I1K C14 C16 C 0 1 Y N N N N N 2.906  35.587 -32.167 -10.391 -1.106 1.090  C14 I1K 23 
I1K C13 C17 C 0 1 Y N N N N N 2.807  34.368 -32.827 -9.060  -1.176 1.459  C13 I1K 24 
I1K N6  N6  N 0 1 N N N N N N 2.872  29.063 -30.916 -3.937  -1.426 -0.401 N6  I1K 25 
I1K N5  N7  N 0 1 N N N N N N 2.139  27.240 -27.719 -0.405  -0.698 -1.360 N5  I1K 26 
I1K C18 C18 C 0 1 N N N N N N 1.170  27.956 -26.886 0.259   -2.009 -1.339 C18 I1K 27 
I1K C19 C19 C 0 1 N N N N N N 1.566  27.893 -25.420 1.715   -1.835 -0.899 C19 I1K 28 
I1K C20 C20 C 0 1 N N N N N N 1.255  29.137 -24.619 2.407   -3.199 -0.877 C20 I1K 29 
I1K N8  N8  N 0 1 N N N N N N -0.175 29.378 -24.423 3.800   -3.033 -0.456 N8  I1K 30 
I1K C21 C21 C 0 1 N N N N N N -0.708 30.573 -24.641 4.625   -4.129 -0.361 C21 I1K 31 
I1K N10 N9  N 0 1 N N N N N N 0.064  31.494 -25.119 4.167   -5.316 -0.646 N10 I1K 32 
I1K N9  N10 N 0 1 N N N N N N -2.049 30.766 -24.414 5.932   -3.974 0.034  N9  I1K 33 
I1K C22 C22 C 0 1 N N N N N N -2.800 32.012 -24.642 6.811   -5.141 0.135  C22 I1K 34 
I1K C26 C23 C 0 1 N N N N N N -2.673 32.975 -23.488 8.280   -4.712 -0.029 C26 I1K 35 
I1K C25 C24 C 0 1 N N N N N N -2.658 34.374 -24.158 9.000   -5.098 1.279  C25 I1K 36 
I1K C24 C25 C 0 1 N N N N N N -1.891 34.267 -25.315 8.131   -6.236 1.870  C24 I1K 37 
I1K C23 C26 C 0 1 N N N N N N -2.314 32.884 -25.899 6.691   -5.774 1.537  C23 I1K 38 
I1K O   O3  O 0 1 N N N N N N 3.452  24.291 -28.834 0.384   2.012  -0.808 O   I1K 39 
I1K C27 C27 C 0 1 N N S N N N 1.315  24.408 -29.915 0.515   2.566  -3.108 C27 I1K 40 
I1K O2  O4  O 0 1 N N N N N N 1.412  24.665 -31.311 -0.407  2.947  -4.131 O2  I1K 41 
I1K C28 C28 C 0 1 N N R N N N 1.643  22.974 -29.473 0.931   3.795  -2.269 C28 I1K 42 
I1K C   C29 C 0 1 Y N N N N N 6.461  19.704 -28.106 2.777   6.372  2.334  C   I1K 43 
I1K N   N11 N 0 1 N N N N N N 6.859  18.820 -27.181 3.841   6.440  3.216  N   I1K 44 
I1K H1  H1  H 0 1 N N N N N N 0.672  25.831 -28.165 -0.241  -0.103 -3.368 H1  I1K 45 
I1K H2  H2  H 0 1 N N N N N N 2.023  25.243 -27.138 1.255   0.042  -2.413 H2  I1K 46 
I1K H3  H3  H 0 1 N N N N N N 3.701  27.488 -29.080 -2.047  -1.536 -2.367 H3  I1K 47 
I1K H4  H4  H 0 1 N N N N N N 3.116  28.992 -28.291 -2.293  0.125  -1.775 H4  I1K 48 
I1K H5  H5  H 0 1 N N N N N N 1.143  29.020 -29.718 -2.112  -2.407 -0.083 H5  I1K 49 
I1K H6  H6  H 0 1 N N N N N N 1.610  27.446 -30.447 -2.207  -0.757 0.578  H6  I1K 50 
I1K H7  H7  H 0 1 N N N N N N 7.344  20.679 -31.101 0.325   8.228  1.204  H7  I1K 51 
I1K H8  H8  H 0 1 N N N N N N 3.535  23.043 -30.480 -0.533  3.884  -0.656 H8  I1K 52 
I1K H9  H9  H 0 1 N N N N N N 2.797  26.003 -29.907 -1.246  1.776  -2.095 H9  I1K 53 
I1K H10 H10 H 0 1 N N N N N N 2.738  21.962 -26.836 2.712   2.222  0.417  H10 I1K 54 
I1K H11 H11 H 0 1 N N N N N N 1.394  21.136 -30.081 0.498   5.198  -3.663 H11 I1K 55 
I1K H12 H12 H 0 1 N N N N N N 4.450  30.263 -32.280 -6.459  -1.597 -0.338 H12 I1K 56 
I1K H13 H13 H 0 1 N N N N N N 2.456  31.862 -33.636 -6.613  -3.426 1.809  H13 I1K 57 
I1K H14 H14 H 0 1 N N N N N N 4.240  31.981 -33.802 -6.708  -1.776 2.470  H14 I1K 58 
I1K H15 H15 H 0 1 N N N N N N 4.478  32.427 -30.620 -8.359  -4.287 0.359  H15 I1K 59 
I1K H16 H16 H 0 1 N N N N N N 4.596  34.576 -29.427 -10.732 -4.166 -0.288 H16 I1K 60 
I1K H17 H17 H 0 1 N N N N N N 3.615  36.611 -30.429 -12.033 -2.128 0.181  H17 I1K 61 
I1K H18 H18 H 0 1 N N N N N N 2.480  36.475 -32.610 -10.962 -0.212 1.296  H18 I1K 62 
I1K H19 H19 H 0 1 N N N N N N 2.269  34.309 -33.762 -8.591  -0.337 1.951  H19 I1K 63 
I1K H20 H20 H 0 1 N N N N N N 3.779  28.674 -31.076 -4.352  -1.120 -1.223 H20 I1K 64 
I1K H22 H22 H 0 1 N N N N N N 1.130  29.008 -27.204 -0.256  -2.666 -0.639 H22 I1K 65 
I1K H23 H23 H 0 1 N N N N N N 0.178  27.497 -27.011 0.231   -2.446 -2.336 H23 I1K 66 
I1K H24 H24 H 0 1 N N N N N N 1.033  27.048 -24.959 2.230   -1.178 -1.599 H24 I1K 67 
I1K H25 H25 H 0 1 N N N N N N 2.650  27.715 -25.367 1.743   -1.397 0.099  H25 I1K 68 
I1K H26 H26 H 0 1 N N N N N N 1.728  29.039 -23.631 1.891   -3.857 -0.177 H26 I1K 69 
I1K H27 H27 H 0 1 N N N N N N 1.683  30.003 -25.146 2.378   -3.637 -1.875 H27 I1K 70 
I1K H28 H28 H 0 1 N N N N N N -0.762 28.627 -24.119 4.141   -2.150 -0.244 H28 I1K 71 
I1K H29 H29 H 0 1 N N N N N N -0.432 32.344 -25.297 4.749   -6.089 -0.579 H29 I1K 72 
I1K H30 H30 H 0 1 N N N N N N -2.565 29.986 -24.060 6.273   -3.091 0.246  H30 I1K 73 
I1K H31 H31 H 0 1 N N N N N N -3.864 31.774 -24.791 6.549   -5.873 -0.629 H31 I1K 74 
I1K H32 H32 H 0 1 N N N N N N -3.529 32.879 -22.804 8.730   -5.236 -0.872 H32 I1K 75 
I1K H33 H33 H 0 1 N N N N N N -1.740 32.798 -22.934 8.338   -3.635 -0.184 H33 I1K 76 
I1K H34 H34 H 0 1 N N N N N N -2.212 35.114 -23.477 10.007  -5.458 1.068  H34 I1K 77 
I1K H35 H35 H 0 1 N N N N N N -3.683 34.681 -24.412 9.035   -4.248 1.961  H35 I1K 78 
I1K H36 H36 H 0 1 N N N N N N -0.817 34.283 -25.079 8.355   -7.185 1.383  H36 I1K 79 
I1K H37 H37 H 0 1 N N N N N N -2.124 35.080 -26.019 8.276   -6.312 2.948  H37 I1K 80 
I1K H38 H38 H 0 1 N N N N N N -3.135 33.007 -26.621 6.350   -5.034 2.261  H38 I1K 81 
I1K H39 H39 H 0 1 N N N N N N -1.460 32.399 -26.395 6.012   -6.627 1.513  H39 I1K 82 
I1K H40 H40 H 0 1 N N N N N N 0.330  24.701 -29.522 1.392   2.085  -3.542 H40 I1K 83 
I1K H41 H41 H 0 1 N N N N N N 1.191  25.573 -31.482 -0.049  3.582  -4.766 H41 I1K 84 
I1K H42 H42 H 0 1 N N N N N N 1.254  22.796 -28.460 2.013   3.923  -2.291 H42 I1K 85 
I1K H43 H43 H 0 1 N N N N N N 7.682  18.351 -27.500 4.006   7.256  3.714  H43 I1K 86 
I1K H44 H44 H 0 1 N N N N N N 7.059  19.299 -26.326 4.422   5.673  3.336  H44 I1K 87 
# 
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 
I1K C11 C12 SING N N 1  
I1K C11 N7  SING N N 2  
I1K C13 C12 DOUB Y N 3  
I1K C13 C14 SING Y N 4  
I1K C12 C17 SING Y N 5  
I1K N7  C10 SING N N 6  
I1K C14 C15 DOUB Y N 7  
I1K C10 O1  DOUB N N 8  
I1K C10 N6  SING N N 9  
I1K O2  C27 SING N N 10 
I1K C17 C16 DOUB Y N 11 
I1K C15 C16 SING Y N 12 
I1K N6  C9  SING N N 13 
I1K O3  C28 SING N N 14 
I1K N2  C1  DOUB Y N 15 
I1K N2  C2  SING Y N 16 
I1K C1  N1  SING Y N 17 
I1K C9  C8  SING N N 18 
I1K C27 C28 SING N N 19 
I1K C27 C6  SING N N 20 
I1K C28 C5  SING N N 21 
I1K C5  O   SING N N 22 
I1K C5  N4  SING N N 23 
I1K N1  C   DOUB Y N 24 
I1K C6  O   SING N N 25 
I1K C6  C7  SING N N 26 
I1K C2  N4  SING Y N 27 
I1K C2  C3  DOUB Y N 28 
I1K C8  N5  SING N N 29 
I1K N4  C4  SING Y N 30 
I1K C   C3  SING Y N 31 
I1K C   N   SING N N 32 
I1K C7  N5  SING N N 33 
I1K C3  N3  SING Y N 34 
I1K N5  C18 SING N N 35 
I1K C4  N3  DOUB Y N 36 
I1K C18 C19 SING N N 37 
I1K C23 C24 SING N N 38 
I1K C23 C22 SING N N 39 
I1K C19 C20 SING N N 40 
I1K C24 C25 SING N N 41 
I1K N10 C21 DOUB N N 42 
I1K C22 N9  SING N N 43 
I1K C22 C26 SING N N 44 
I1K C21 N8  SING N N 45 
I1K C21 N9  SING N N 46 
I1K C20 N8  SING N N 47 
I1K C25 C26 SING N N 48 
I1K C7  H1  SING N N 49 
I1K C7  H2  SING N N 50 
I1K C8  H3  SING N N 51 
I1K C8  H4  SING N N 52 
I1K C9  H5  SING N N 53 
I1K C9  H6  SING N N 54 
I1K C1  H7  SING N N 55 
I1K C5  H8  SING N N 56 
I1K C6  H9  SING N N 57 
I1K C4  H10 SING N N 58 
I1K O3  H11 SING N N 59 
I1K N7  H12 SING N N 60 
I1K C11 H13 SING N N 61 
I1K C11 H14 SING N N 62 
I1K C17 H15 SING N N 63 
I1K C16 H16 SING N N 64 
I1K C15 H17 SING N N 65 
I1K C14 H18 SING N N 66 
I1K C13 H19 SING N N 67 
I1K N6  H20 SING N N 68 
I1K C18 H22 SING N N 69 
I1K C18 H23 SING N N 70 
I1K C19 H24 SING N N 71 
I1K C19 H25 SING N N 72 
I1K C20 H26 SING N N 73 
I1K C20 H27 SING N N 74 
I1K N8  H28 SING N N 75 
I1K N10 H29 SING N N 76 
I1K N9  H30 SING N N 77 
I1K C22 H31 SING N N 78 
I1K C26 H32 SING N N 79 
I1K C26 H33 SING N N 80 
I1K C25 H34 SING N N 81 
I1K C25 H35 SING N N 82 
I1K C24 H36 SING N N 83 
I1K C24 H37 SING N N 84 
I1K C23 H38 SING N N 85 
I1K C23 H39 SING N N 86 
I1K C27 H40 SING N N 87 
I1K O2  H41 SING N N 88 
I1K C28 H42 SING N N 89 
I1K N   H43 SING N N 90 
I1K N   H44 SING N N 91 
# 
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 
I1K SMILES           ACDLabs              12.01 "N=C(NC1CCCC1)NCCCN(CCNC(=O)NCc1ccccc1)CC1OC(n2cnc3c(N)ncnc32)C(O)C1O"                                                                                                                                                                                                           
I1K InChI            InChI                1.06  "InChI=1S/C29H43N11O4/c30-25-22-26(36-17-35-25)40(18-37-22)27-24(42)23(41)21(44-27)16-39(13-6-11-32-28(31)38-20-9-4-5-10-20)14-12-33-29(43)34-15-19-7-2-1-3-8-19/h1-3,7-8,17-18,20-21,23-24,27,41-42H,4-6,9-16H2,(H2,30,35,36)(H3,31,32,38)(H2,33,34,43)/t21-,23-,24-,27-/m1/s1" 
I1K InChIKey         InChI                1.06  BGNWKEZAKOEUDI-VBHAUSMQSA-N                                                                                                                                                                                                                                                      
I1K SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CN(CCCNC(=N)NC4CCCC4)CCNC(=O)NCc5ccccc5)[C@@H](O)[C@H]3O"                                                                                                                                                                                         
I1K SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CN(CCCNC(=N)NC4CCCC4)CCNC(=O)NCc5ccccc5)[CH](O)[CH]3O"                                                                                                                                                                                               
I1K SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(\NCCCN(CCNC(=O)NCc1ccccc1)C[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)/NC5CCCC5"                                                                                                                                                                                   
I1K SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CNC(=O)NCCN(CCCNC(=N)NC2CCCC2)CC3C(C(C(O3)n4cnc5c4ncnc5N)O)O"                                                                                                                                                                                                         
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
I1K "SYSTEMATIC NAME" ACDLabs              12.01 "5'-{[2-(benzylcarbamamido)ethyl][3-(N'-cyclopentylcarbamimidamido)propyl]amino}-5'-deoxyadenosine"                                                                            
I1K "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "1-[2-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[3-[(~{N}-cyclopentylcarbamimidoyl)amino]propyl]amino]ethyl]-3-(phenylmethyl)urea" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
I1K "Create component" 2023-05-01 RCSB 
I1K "Initial release"  2024-04-24 RCSB 
# 
