data_I5M
# 
_chem_comp.id                                    I5M 
_chem_comp.name                                  "5'-deoxy-5'-({(2S)-2-({2-[(N-{(2R)-4-[(dioxo-lambda~5~-phosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-beta-alanyl)amino]ethyl}sulfanyl)-2-[(2S)-pyrrolidin-2-yl]ethanesulfonyl}amino)adenosine" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C27 H44 N9 O11 P S2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-01-13 
_chem_comp.pdbx_modified_date                    2022-07-15 
_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                        765.796 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     I5M 
_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        7THN 
_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.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 
I5M N   N1  N 0 1 N N N 8.094  15.962 22.617 2.645   -4.970 -2.299 N   I5M 1  
I5M S   S1  S 0 1 N N N 6.316  16.036 26.795 3.270   -3.113 1.850  S   I5M 2  
I5M C1  C1  C 0 1 N N N 10.243 16.364 23.407 0.654   -6.101 -1.591 C1  I5M 3  
I5M N1  N2  N 0 1 N N N 6.903  17.405 27.266 4.238   -1.770 1.818  N1  I5M 4  
I5M O1  O1  O 0 1 N N N 6.592  14.929 27.742 2.154   -2.722 2.639  O1  I5M 5  
I5M C2  C2  C 0 1 N N N 10.291 16.528 21.891 1.099   -6.683 -2.949 C2  I5M 6  
I5M N2  N3  N 0 1 Y N N 9.834  21.034 26.698 7.204   1.949  -0.321 N2  I5M 7  
I5M O2  O2  O 0 1 N N N 8.241  19.730 27.833 5.850   0.545  1.063  O2  I5M 8  
I5M C3  C3  C 0 1 N N S 9.041  15.532 23.708 1.448   -4.786 -1.438 C3  I5M 9  
I5M N3  N4  N 0 1 Y N N 10.894 20.582 24.806 8.135   1.417  -2.223 N3  I5M 10 
I5M O3  O3  O 0 1 N N N 7.220  22.382 28.904 5.190   4.072  0.900  O3  I5M 11 
I5M C4  C4  C 0 1 N N S 8.512  15.838 25.113 1.866   -4.582 0.019  C4  I5M 12 
I5M C5  C5  C 0 1 N N N 7.018  15.506 25.298 2.775   -3.355 0.122  C5  I5M 13 
I5M C6  C6  C 0 1 N N N 6.435  18.636 26.686 3.676   -0.470 1.444  C6  I5M 14 
I5M N6  N5  N 0 1 Y N N 11.267 22.861 27.449 8.598   3.980  0.069  N6  I5M 15 
I5M N7  N6  N 0 1 N N N 10.958 12.373 28.014 -2.290  -1.348 0.426  N7  I5M 16 
I5M C8  C7  C 0 1 N N R 8.851  21.018 27.836 6.319   1.893  0.845  C8  I5M 17 
I5M O10 O4  O 0 1 N N N 15.508 10.714 36.338 -12.405 0.298  -0.237 O10 I5M 18 
I5M P   P1  P 0 1 N N N 16.356 9.344  36.469 -11.067 0.101  -1.300 P   I5M 19 
I5M O9  O5  O 0 1 N N N 15.701 7.894  36.950 -10.796 -1.413 -2.069 O9  I5M 20 
I5M O8  O6  O 0 1 N N N 17.229 8.979  35.087 -10.094 1.303  -1.567 O8  I5M 21 
I5M C26 C8  C 0 1 N N N 17.697 10.072 34.295 -9.397  1.855  -0.419 C26 I5M 22 
I5M C23 C9  C 0 1 N N N 17.150 9.933  32.846 -8.501  3.010  -0.873 C23 I5M 23 
I5M C24 C10 C 0 1 N N N 17.711 8.644  32.238 -7.480  2.494  -1.889 C24 I5M 24 
I5M C25 C11 C 0 1 N N N 17.740 11.081 32.054 -9.360  4.098  -1.520 C25 I5M 25 
I5M C22 C12 C 0 1 N N R 15.607 9.986  32.892 -7.767  3.592  0.337  C22 I5M 26 
I5M O7  O7  O 0 1 N N N 15.179 11.118 33.645 -8.713  4.189  1.226  O7  I5M 27 
I5M C21 C13 C 0 1 N N N 14.979 10.090 31.495 -7.030  2.490  1.055  C21 I5M 28 
I5M O6  O8  O 0 1 N N N 15.122 9.167  30.663 -7.426  2.098  2.132  O6  I5M 29 
I5M N8  N7  N 0 1 N N N 14.286 11.184 31.278 -5.931  1.942  0.500  N8  I5M 30 
I5M C20 C14 C 0 1 N N N 13.683 11.444 29.987 -5.277  0.801  1.145  C20 I5M 31 
I5M C19 C15 C 0 1 N N N 12.214 11.274 29.820 -4.063  0.374  0.317  C19 I5M 32 
I5M C18 C16 C 0 1 N N N 11.828 11.423 28.338 -3.389  -0.799 0.981  C18 I5M 33 
I5M O5  O9  O 0 1 N N N 12.420 10.724 27.471 -3.836  -1.250 2.014  O5  I5M 34 
I5M C17 C17 C 0 1 N N N 10.644 12.563 26.600 -1.636  -2.488 1.071  C17 I5M 35 
I5M C16 C18 C 0 1 N N N 9.363  13.366 26.332 -0.422  -2.915 0.243  C16 I5M 36 
I5M S1  S2  S 0 1 N N N 9.678  15.131 26.345 0.389   -4.327 1.042  S1  I5M 37 
I5M O   O10 O 0 1 N N N 4.910  16.168 26.458 4.135   -4.159 2.273  O   I5M 38 
I5M C7  C19 C 0 1 N N R 6.890  19.775 27.506 4.648   0.641  1.846  C7  I5M 39 
I5M C10 C20 C 0 1 N N S 6.682  21.142 26.887 4.020   2.017  1.554  C10 I5M 40 
I5M O4  O11 O 0 1 N N N 5.315  21.588 26.994 3.906   2.780  2.758  O4  I5M 41 
I5M C9  C21 C 0 1 N N R 7.687  21.952 27.630 5.016   2.690  0.579  C9  I5M 42 
I5M C15 C22 C 0 1 Y N N 10.870 21.867 26.617 8.164   2.898  -0.568 C15 I5M 43 
I5M C12 C23 C 0 1 Y N N 11.522 21.578 25.437 8.754   2.543  -1.793 C12 I5M 44 
I5M C11 C24 C 0 1 Y N N 9.848  20.278 25.621 7.229   1.063  -1.358 C11 I5M 45 
I5M C14 C25 C 0 1 Y N N 12.425 23.511 27.140 9.567   4.713  -0.438 C14 I5M 46 
I5M N5  N8  N 0 1 Y N N 13.071 23.268 25.989 10.149  4.422  -1.587 N5  I5M 47 
I5M C13 C26 C 0 1 Y N N 12.674 22.289 25.158 9.781   3.359  -2.295 C13 I5M 48 
I5M N4  N9  N 0 1 N N N 13.400 22.034 23.972 10.396  3.064  -3.500 N4  I5M 49 
I5M C27 C27 C 0 1 N N N 8.881  16.218 21.357 2.125   -5.670 -3.502 C27 I5M 50 
I5M H1  H1  H 0 1 N N N 7.622  16.799 22.893 3.345   -5.525 -1.831 H1  I5M 51 
I5M H3  H3  H 0 1 N N N 11.153 15.859 23.763 -0.417  -5.898 -1.600 H3  I5M 52 
I5M H4  H4  H 0 1 N N N 10.155 17.347 23.893 0.901   -6.789 -0.783 H4  I5M 53 
I5M H5  H5  H 0 1 N N N 7.889  17.367 27.101 5.178   -1.844 2.047  H5  I5M 54 
I5M H6  H6  H 0 1 N N N 11.021 15.827 21.459 1.567   -7.657 -2.808 H6  I5M 55 
I5M H7  H7  H 0 1 N N N 10.574 17.559 21.632 0.247   -6.767 -3.623 H7  I5M 56 
I5M H8  H8  H 0 1 N N N 9.275  14.461 23.616 0.855   -3.941 -1.787 H8  I5M 57 
I5M H9  H9  H 0 1 N N N 7.896  22.892 29.334 4.379   4.595  0.836  H9  I5M 58 
I5M H10 H10 H 0 1 N N N 8.609  16.924 25.255 2.403   -5.463 0.370  H10 I5M 59 
I5M H11 H11 H 0 1 N N N 6.461  15.979 24.476 2.237   -2.474 -0.229 H11 I5M 60 
I5M H12 H12 H 0 1 N N N 6.903  14.414 25.238 3.662   -3.508 -0.492 H12 I5M 61 
I5M H13 H13 H 0 1 N N N 6.836  18.736 25.667 3.516   -0.440 0.366  H13 I5M 62 
I5M H14 H14 H 0 1 N N N 5.336  18.628 26.649 2.725   -0.324 1.957  H14 I5M 63 
I5M H15 H15 H 0 1 N N N 10.531 12.941 28.717 -1.933  -0.987 -0.401 H15 I5M 64 
I5M H16 H16 H 0 1 N N N 9.356  21.231 28.790 6.829   2.271  1.731  H16 I5M 65 
I5M H19 H19 H 0 1 N N N 18.797 10.065 34.274 -10.124 2.223  0.305  H19 I5M 66 
I5M H20 H20 H 0 1 N N N 17.344 11.018 34.731 -8.785  1.080  0.042  H20 I5M 67 
I5M H21 H21 H 0 1 N N N 17.310 7.776  32.782 -6.958  1.632  -1.474 H21 I5M 68 
I5M H22 H22 H 0 1 N N N 17.418 8.580  31.180 -7.995  2.201  -2.804 H22 I5M 69 
I5M H23 H23 H 0 1 N N N 18.808 8.650  32.315 -6.761  3.281  -2.112 H23 I5M 70 
I5M H24 H24 H 0 1 N N N 17.365 12.034 32.455 -8.716  4.892  -1.898 H24 I5M 71 
I5M H25 H25 H 0 1 N N N 18.837 11.056 32.134 -9.930  3.669  -2.344 H25 I5M 72 
I5M H26 H26 H 0 1 N N N 17.447 10.987 30.998 -10.046 4.509  -0.779 H26 I5M 73 
I5M H27 H27 H 0 1 N N N 15.244 9.063  33.367 -7.056  4.346  0.002  H27 I5M 74 
I5M H28 H28 H 0 1 N N N 15.305 10.949 34.571 -9.378  3.575  1.564  H28 I5M 75 
I5M H29 H29 H 0 1 N N N 14.173 11.849 32.016 -5.574  2.302  -0.327 H29 I5M 76 
I5M H30 H30 H 0 1 N N N 14.168 10.770 29.265 -4.952  1.087  2.146  H30 I5M 77 
I5M H31 H31 H 0 1 N N N 13.916 12.487 29.728 -5.979  -0.030 1.215  H31 I5M 78 
I5M H32 H32 H 0 1 N N N 11.690 12.040 30.411 -4.388  0.089  -0.683 H32 I5M 79 
I5M H33 H33 H 0 1 N N N 11.921 10.274 30.173 -3.361  1.205  0.248  H33 I5M 80 
I5M H34 H34 H 0 1 N N N 10.530 11.571 26.138 -1.311  -2.203 2.071  H34 I5M 81 
I5M H35 H35 H 0 1 N N N 11.486 13.093 26.130 -2.338  -3.319 1.140  H35 I5M 82 
I5M H36 H36 H 0 1 N N N 8.623  13.129 27.111 -0.747  -3.201 -0.758 H36 I5M 83 
I5M H37 H37 H 0 1 N N N 8.962  13.082 25.348 0.281   -2.084 0.173  H37 I5M 84 
I5M H38 H38 H 0 1 N N N 6.308  19.758 28.439 4.888   0.557  2.906  H38 I5M 85 
I5M H39 H39 H 0 1 N N N 6.973  21.096 25.827 3.044   1.899  1.084  H39 I5M 86 
I5M H40 H40 H 0 1 N N N 5.229  22.446 26.595 3.516   3.656  2.633  H40 I5M 87 
I5M H41 H41 H 0 1 N N N 8.004  22.810 27.018 4.690   2.570  -0.454 H41 I5M 88 
I5M H42 H42 H 0 1 N N N 9.118  19.510 25.410 6.587   0.200  -1.451 H42 I5M 89 
I5M H43 H43 H 0 1 N N N 12.829 24.234 27.833 9.897   5.587  0.105  H43 I5M 90 
I5M H44 H44 H 0 1 N N N 14.171 22.668 23.910 10.118  2.285  -4.007 H44 I5M 91 
I5M H45 H45 H 0 1 N N N 13.742 21.094 23.986 11.104  3.635  -3.836 H45 I5M 92 
I5M H46 H46 H 0 1 N N N 8.471  17.074 20.801 1.638   -4.964 -4.173 H46 I5M 93 
I5M H47 H47 H 0 1 N N N 8.890  15.330 20.708 2.933   -6.191 -4.017 H47 I5M 94 
# 
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 
I5M C27 C2  SING N N 1  
I5M C27 N   SING N N 2  
I5M C2  C1  SING N N 3  
I5M N   C3  SING N N 4  
I5M C1  C3  SING N N 5  
I5M C3  C4  SING N N 6  
I5M N4  C13 SING N N 7  
I5M N3  C12 SING Y N 8  
I5M N3  C11 DOUB Y N 9  
I5M C4  C5  SING N N 10 
I5M C4  S1  SING N N 11 
I5M C13 C12 DOUB Y N 12 
I5M C13 N5  SING Y N 13 
I5M C5  S   SING N N 14 
I5M C12 C15 SING Y N 15 
I5M C11 N2  SING Y N 16 
I5M N5  C14 DOUB Y N 17 
I5M C16 S1  SING N N 18 
I5M C16 C17 SING N N 19 
I5M O   S   DOUB N N 20 
I5M C17 N7  SING N N 21 
I5M C15 N2  SING Y N 22 
I5M C15 N6  DOUB Y N 23 
I5M C6  N1  SING N N 24 
I5M C6  C7  SING N N 25 
I5M N2  C8  SING N N 26 
I5M S   N1  SING N N 27 
I5M S   O1  DOUB N N 28 
I5M C10 O4  SING N N 29 
I5M C10 C7  SING N N 30 
I5M C10 C9  SING N N 31 
I5M C14 N6  SING Y N 32 
I5M O5  C18 DOUB N N 33 
I5M C7  O2  SING N N 34 
I5M C9  C8  SING N N 35 
I5M C9  O3  SING N N 36 
I5M O2  C8  SING N N 37 
I5M N7  C18 SING N N 38 
I5M C18 C19 SING N N 39 
I5M C19 C20 SING N N 40 
I5M C20 N8  SING N N 41 
I5M O6  C21 DOUB N N 42 
I5M N8  C21 SING N N 43 
I5M C21 C22 SING N N 44 
I5M C25 C23 SING N N 45 
I5M C24 C23 SING N N 46 
I5M C23 C22 SING N N 47 
I5M C23 C26 SING N N 48 
I5M C22 O7  SING N N 49 
I5M C26 O8  SING N N 50 
I5M O8  P   SING N N 51 
I5M O10 P   DOUB N N 52 
I5M P   O9  DOUB N N 53 
I5M N   H1  SING N N 54 
I5M C1  H3  SING N N 55 
I5M C1  H4  SING N N 56 
I5M N1  H5  SING N N 57 
I5M C2  H6  SING N N 58 
I5M C2  H7  SING N N 59 
I5M C3  H8  SING N N 60 
I5M O3  H9  SING N N 61 
I5M C4  H10 SING N N 62 
I5M C5  H11 SING N N 63 
I5M C5  H12 SING N N 64 
I5M C6  H13 SING N N 65 
I5M C6  H14 SING N N 66 
I5M N7  H15 SING N N 67 
I5M C8  H16 SING N N 68 
I5M C26 H19 SING N N 69 
I5M C26 H20 SING N N 70 
I5M C24 H21 SING N N 71 
I5M C24 H22 SING N N 72 
I5M C24 H23 SING N N 73 
I5M C25 H24 SING N N 74 
I5M C25 H25 SING N N 75 
I5M C25 H26 SING N N 76 
I5M C22 H27 SING N N 77 
I5M O7  H28 SING N N 78 
I5M N8  H29 SING N N 79 
I5M C20 H30 SING N N 80 
I5M C20 H31 SING N N 81 
I5M C19 H32 SING N N 82 
I5M C19 H33 SING N N 83 
I5M C17 H34 SING N N 84 
I5M C17 H35 SING N N 85 
I5M C16 H36 SING N N 86 
I5M C16 H37 SING N N 87 
I5M C7  H38 SING N N 88 
I5M C10 H39 SING N N 89 
I5M O4  H40 SING N N 90 
I5M C9  H41 SING N N 91 
I5M C11 H42 SING N N 92 
I5M C14 H43 SING N N 93 
I5M N4  H44 SING N N 94 
I5M N4  H45 SING N N 95 
I5M C27 H46 SING N N 96 
I5M C27 H47 SING N N 97 
# 
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 
I5M SMILES           ACDLabs              12.01 "O=P(=O)OCC(C)(C)C(O)C(=O)NCCC(=O)NCCSC(CS(=O)(=O)NCC1OC(n2cnc3c(N)ncnc32)C(O)C1O)C1CCCN1"                                                                                                                                                                                                       
I5M InChI            InChI                1.03  "InChI=1S/C27H44N9O11PS2/c1-27(2,12-46-48(42)43)22(40)25(41)31-7-5-18(37)30-8-9-49-17(15-4-3-6-29-15)11-50(44,45)35-10-16-20(38)21(39)26(47-16)36-14-34-19-23(28)32-13-33-24(19)36/h13-17,20-22,26,29,35,38-40H,3-12H2,1-2H3,(H,30,37)(H,31,41)(H2,28,32,33)/t15-,16+,17+,20+,21+,22-,26+/m0/s1" 
I5M InChIKey         InChI                1.03  UUZQPBPCNSKBOR-LCZLERPASA-N                                                                                                                                                                                                                                                                      
I5M SMILES_CANONICAL CACTVS               3.385 "CC(C)(CO[P](=O)=O)[C@@H](O)C(=O)NCCC(=O)NCCS[C@H](C[S](=O)(=O)NC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)[C@@H]4CCCN4"                                                                                                                                                                    
I5M SMILES           CACTVS               3.385 "CC(C)(CO[P](=O)=O)[CH](O)C(=O)NCCC(=O)NCCS[CH](C[S](=O)(=O)NC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)[CH]4CCCN4"                                                                                                                                                                              
I5M SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)(COP(=O)=O)[C@H](C(=O)NCCC(=O)NCCS[C@H](CS(=O)(=O)NC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)[C@@H]4CCCN4)O"                                                                                                                                                                        
I5M SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)(COP(=O)=O)C(C(=O)NCCC(=O)NCCSC(CS(=O)(=O)NCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)C4CCCN4)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 
I5M "SYSTEMATIC NAME" ACDLabs              12.01 "5'-deoxy-5'-({(2S)-2-({2-[(N-{(2R)-4-[(dioxo-lambda~5~-phosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-beta-alanyl)amino]ethyl}sulfanyl)-2-[(2S)-pyrrolidin-2-yl]ethanesulfonyl}amino)adenosine"                                                            
I5M "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{R})-~{N}-[3-[2-[(1~{S})-2-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfamoyl]-1-[(2~{S})-pyrrolidin-2-yl]ethyl]sulfanylethylamino]-3-oxidanylidene-propyl]-3,3-dimethyl-2-oxidanyl-4-phosphooxy-butanamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
I5M "Create component" 2022-01-13 RCSB 
I5M "Modify formula"   2022-01-14 RCSB 
I5M "Initial release"  2022-07-20 RCSB 
# 
