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 #