data_A1IF6
# 
_chem_comp.id                                    A1IF6 
_chem_comp.name                                  "(2~{R},4~{S},5~{S},6~{S})-5-acetamido-6-[(1~{S},2~{S})-1-acetamido-2-oxidanyl-propyl]-2-[[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-oxane-2-carboxylic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C22 H34 N5 O15 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-06-27 
_chem_comp.pdbx_modified_date                    2024-10-04 
_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                        639.504 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1IF6 
_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        9FTC 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_chem_comp.pdbx_pcm                              ? 
# 
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_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_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 
A1IF6 C1     C1  C 0 1 N N N N N N 9.677  41.713 8.857  -6.164 -3.718 -1.820 C1     A1IF6 1  
A1IF6 N1     N1  N 0 1 N N N N N N 2.831  39.878 14.540 6.383  -0.005 -0.903 N1     A1IF6 2  
A1IF6 O1     O1  O 0 1 N N N N N N 8.755  43.277 7.326  -6.579 -2.655 0.246  O1     A1IF6 3  
A1IF6 C2     C2  C 0 1 N N N N N N 2.792  39.954 15.932 6.694  0.452  0.324  C2     A1IF6 4  
A1IF6 C3     C3  C 0 1 N N S N N N 6.265  41.909 7.174  -4.321 -1.189 0.386  C3     A1IF6 5  
A1IF6 C4     C4  C 0 1 N N N N N N 2.997  42.266 15.786 8.443  1.704  -0.520 C4     A1IF6 6  
A1IF6 C5     C5  C 0 1 N N N N N N 3.059  42.227 14.383 8.144  1.243  -1.819 C5     A1IF6 7  
A1IF6 C6     C6  C 0 1 N N N N N N 3.004  41.020 13.804 7.108  0.388  -1.988 C6     A1IF6 8  
A1IF6 C7     C7  C 0 1 N N R N N N 2.815  42.427 8.228  -2.164 1.847  0.580  C7     A1IF6 9  
A1IF6 C8     C8  C 0 1 N N N N N N 1.854  43.114 7.268  -1.922 2.736  1.772  C8     A1IF6 10 
A1IF6 C9     C9  C 0 1 N N N N N N 2.996  43.163 9.545  -2.758 2.675  -0.563 C9     A1IF6 11 
A1IF6 C10    C10 C 0 1 N N S N N N 4.199  42.636 10.310 -3.058 1.754  -1.749 C10    A1IF6 12 
A1IF6 C11    C11 C 0 1 N N S N N N 5.423  42.714 9.457  -4.001 0.638  -1.289 C11    A1IF6 13 
A1IF6 C12    C12 C 0 1 N N N N N N 6.790  44.721 9.696  -6.236 1.482  -1.766 C12    A1IF6 14 
A1IF6 C13    C13 C 0 1 N N N N N N 7.185  46.056 9.117  -7.547 2.080  -1.323 C13    A1IF6 15 
A1IF6 O3P    O2  O 0 1 N N N N N N 2.456  41.074 8.470  -0.928 1.269  0.157  O3P    A1IF6 16 
A1IF6 P      P1  P 0 1 N N N N N N 1.281  40.461 9.387  -0.027 0.332  1.108  P      A1IF6 17 
A1IF6 O1P    O3  O 0 1 N N N N N N 0.749  39.372 8.584  -0.847 -0.793 1.610  O1P    A1IF6 18 
A1IF6 O2P    O4  O 0 1 N N N N N N 0.406  41.506 9.954  0.518  1.196  2.352  O2P    A1IF6 19 
A1IF6 "O5'"  O5  O 0 1 N N N N N N 2.071  39.861 10.633 1.219  -0.245 0.267  "O5'"  A1IF6 20 
A1IF6 "C5'"  C14 C 0 1 N N N N N N 2.997  38.746 10.414 2.146  -1.192 0.802  "C5'"  A1IF6 21 
A1IF6 "C4'"  C15 C 0 1 N N R N N N 3.035  37.879 11.649 3.201  -1.525 -0.256 "C4'"  A1IF6 22 
A1IF6 "O4'"  O6  O 0 1 N N N N N N 3.605  38.588 12.782 4.064  -0.389 -0.480 "O4'"  A1IF6 23 
A1IF6 "C3'"  C16 C 0 1 N N S N N N 1.659  37.402 12.105 4.140  -2.640 0.255  "C3'"  A1IF6 24 
A1IF6 "O3'"  O7  O 0 1 N N N N N N 1.765  36.051 12.547 3.740  -3.909 -0.266 "O3'"  A1IF6 25 
A1IF6 "C2'"  C17 C 0 1 N N R N N N 1.344  38.330 13.267 5.528  -2.243 -0.295 "C2'"  A1IF6 26 
A1IF6 "O2'"  O8  O 0 1 N N N N N N 0.383  37.828 14.173 6.028  -3.254 -1.172 "O2'"  A1IF6 27 
A1IF6 "C1'"  C18 C 0 1 N N R N N N 2.723  38.548 13.887 5.263  -0.934 -1.072 "C1'"  A1IF6 28 
A1IF6 N3     N2  N 0 1 N N N N N N 2.855  41.158 16.530 7.710  1.294  0.507  N3     A1IF6 29 
A1IF6 O2     O9  O 0 1 N N N N N N 2.655  38.907 16.586 6.034  0.090  1.284  O2     A1IF6 30 
A1IF6 N4     N3  N 0 1 N N N N N N 3.074  43.415 16.418 9.491  2.572  -0.319 N4     A1IF6 31 
A1IF6 C21    C19 C 0 1 N N N N N N 8.600  42.210 7.935  -5.817 -2.785 -0.688 C21    A1IF6 32 
A1IF6 N11    N4  N 0 1 N N N N N N 7.510  41.449 7.830  -4.659 -2.096 -0.714 N11    A1IF6 33 
A1IF6 C41    C20 C 0 1 N N S N N N 6.006  41.109 5.898  -3.655 -1.981 1.513  C41    A1IF6 34 
A1IF6 C51    C21 C 0 1 N N N N N N 5.796  39.614 6.113  -4.559 -3.145 1.923  C51    A1IF6 35 
A1IF6 O21    O10 O 0 1 N N N N N N 7.088  41.282 4.963  -3.442 -1.124 2.636  O21    A1IF6 36 
A1IF6 C61    C22 C 0 1 N N S N N N 5.151  41.884 8.204  -3.359 -0.112 -0.119 C61    A1IF6 37 
A1IF6 O3     O11 O 0 1 N N N N N N 4.024  42.402 7.484  -3.078 0.808  0.938  O3     A1IF6 38 
A1IF6 O5     O12 O 0 1 N N N N N N 2.092  44.265 6.865  -2.402 2.454  2.844  O5     A1IF6 39 
A1IF6 O6     O13 O 0 1 N N N N N N 0.851  42.495 6.891  -1.173 3.843  1.643  O6     A1IF6 40 
A1IF6 O7     O14 O 0 1 N N N N N N 4.434  43.351 11.527 -3.680 2.505  -2.793 O7     A1IF6 41 
A1IF6 N2     N5  N 0 1 N N N N N N 5.830  44.063 9.101  -5.274 1.220  -0.859 N2     A1IF6 42 
A1IF6 O8     O15 O 0 1 N N N N N N 7.381  44.268 10.675 -6.048 1.235  -2.938 O8     A1IF6 43 
A1IF6 H1     H1  H 0 1 N N N N N N 10.516 42.425 8.859  -5.365 -3.703 -2.561 H1     A1IF6 44 
A1IF6 H2     H2  H 0 1 N N N N N N 9.273  41.619 9.876  -6.282 -4.730 -1.434 H2     A1IF6 45 
A1IF6 H3     H3  H 0 1 N N N N N N 10.031 40.731 8.511  -7.096 -3.395 -2.284 H3     A1IF6 46 
A1IF6 H51    H4  H 0 1 N N N N N N 6.411  42.958 6.876  -5.230 -0.719 0.761  H51    A1IF6 47 
A1IF6 H5     H5  H 0 1 N N N N N N 3.147  43.130 13.797 8.732  1.567  -2.665 H5     A1IF6 48 
A1IF6 H6     H6  H 0 1 N N N N N N 3.098  40.946 12.731 6.859  0.021  -2.973 H6     A1IF6 49 
A1IF6 H13    H7  H 0 1 N N N N N N 3.142  44.234 9.340  -3.681 3.149  -0.228 H13    A1IF6 50 
A1IF6 H14    H8  H 0 1 N N N N N N 2.093  43.027 10.159 -2.044 3.441  -0.867 H14    A1IF6 51 
A1IF6 H15    H9  H 0 1 N N N N N N 4.012  41.578 10.546 -2.128 1.318  -2.116 H15    A1IF6 52 
A1IF6 H17    H10 H 0 1 N N N N N N 6.248  42.232 10.002 -4.176 -0.054 -2.113 H17    A1IF6 53 
A1IF6 H21    H11 H 0 1 N N N N N N 8.018  46.477 9.699  -8.194 2.219  -2.189 H21    A1IF6 54 
A1IF6 H19    H12 H 0 1 N N N N N N 7.499  45.923 8.071  -8.030 1.410  -0.612 H19    A1IF6 55 
A1IF6 H20    H13 H 0 1 N N N N N N 6.326  46.742 9.158  -7.364 3.044  -0.848 H20    A1IF6 56 
A1IF6 H12    H14 H 0 1 N N N N N N -0.495 41.334 9.707  1.064  1.952  2.096  H12    A1IF6 57 
A1IF6 "H5'1" H15 H 0 0 N N N N N N 2.656  38.148 9.556  2.633  -0.768 1.680  "H5'1" A1IF6 58 
A1IF6 "H5'2" H16 H 0 0 N N N N N N 4.004  39.139 10.210 1.614  -2.101 1.084  "H5'2" A1IF6 59 
A1IF6 "H4'"  H17 H 0 1 N N N N N N 3.650  36.993 11.432 2.721  -1.829 -1.186 "H4'"  A1IF6 60 
A1IF6 "H3'"  H18 H 0 1 N N N N N N 0.919  37.520 11.299 4.150  -2.662 1.345  "H3'"  A1IF6 61 
A1IF6 "HO3'" H19 H 0 0 N N N N N N 0.913  35.743 12.834 4.296  -4.646 0.023  "HO3'" A1IF6 62 
A1IF6 "H2'1" H20 H 0 0 N N N N N N 0.998  39.290 12.856 6.227  -2.068 0.523  "H2'1" A1IF6 63 
A1IF6 "HO2'" H21 H 0 0 N N N N N N 0.241  38.461 14.867 6.155  -4.114 -0.749 "HO2'" A1IF6 64 
A1IF6 "H1'"  H22 H 0 1 N N N N N N 2.966  37.737 14.589 5.102  -1.147 -2.129 "H1'"  A1IF6 65 
A1IF6 HN41   H23 H 0 0 N N N N N N 3.026  43.441 17.417 10.026 2.870  -1.071 HN41   A1IF6 66 
A1IF6 HN42   H24 H 0 0 N N N N N N 3.180  44.264 15.901 9.694  2.888  0.576  HN42   A1IF6 67 
A1IF6 H4     H25 H 0 1 N N N N N N 7.535  40.525 8.212  -4.049 -2.200 -1.462 H4     A1IF6 68 
A1IF6 H61    H26 H 0 1 N N N N N N 5.087  41.507 5.443  -2.697 -2.370 1.166  H61    A1IF6 69 
A1IF6 H9     H27 H 0 1 N N N N N N 5.618  39.125 5.144  -4.721 -3.799 1.066  H9     A1IF6 70 
A1IF6 H7     H28 H 0 1 N N N N N N 6.692  39.182 6.582  -4.085 -3.709 2.726  H7     A1IF6 71 
A1IF6 H8     H29 H 0 1 N N N N N N 4.927  39.456 6.768  -5.517 -2.756 2.269  H8     A1IF6 72 
A1IF6 H10    H30 H 0 1 N N N N N N 6.911  40.779 4.177  -2.800 -0.419 2.477  H10    A1IF6 73 
A1IF6 H11    H31 H 0 1 N N N N N N 4.963  40.842 8.502  -2.432 -0.579 -0.450 H11    A1IF6 74 
A1IF6 H22    H32 H 0 1 N N N N N N 0.353  43.035 6.288  -1.046 4.382  2.435  H22    A1IF6 75 
A1IF6 H16    H33 H 0 1 N N N N N N 3.660  43.306 12.076 -3.140 3.234  -3.128 H16    A1IF6 76 
A1IF6 H18    H34 H 0 1 N N N N N N 5.345  44.517 8.353  -5.425 1.417  0.079  H18    A1IF6 77 
# 
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 
A1IF6 O3P   P      SING N N 1  
A1IF6 O3P   C7     SING N N 2  
A1IF6 P     O2P    SING N N 3  
A1IF6 P     "O5'"  SING N N 4  
A1IF6 P     O1P    DOUB N N 5  
A1IF6 "O5'" "C5'"  SING N N 6  
A1IF6 "C5'" "C4'"  SING N N 7  
A1IF6 "C4'" "C3'"  SING N N 8  
A1IF6 "O4'" "C1'"  SING N N 9  
A1IF6 "C4'" "O4'"  SING N N 10 
A1IF6 "C3'" "O3'"  SING N N 11 
A1IF6 "C3'" "C2'"  SING N N 12 
A1IF6 "C2'" "O2'"  SING N N 13 
A1IF6 "C2'" "C1'"  SING N N 14 
A1IF6 "C1'" N1     SING N N 15 
A1IF6 C2    O2     DOUB N N 16 
A1IF6 N1    C2     SING N N 17 
A1IF6 C2    N3     SING N N 18 
A1IF6 C4    C5     SING N N 19 
A1IF6 N3    C4     DOUB N N 20 
A1IF6 C5    C6     DOUB N N 21 
A1IF6 N1    C6     SING N N 22 
A1IF6 C4    N4     SING N N 23 
A1IF6 C1    C21    SING N N 24 
A1IF6 C21   N11    SING N N 25 
A1IF6 C21   O1     DOUB N N 26 
A1IF6 N11   C3     SING N N 27 
A1IF6 C3    C41    SING N N 28 
A1IF6 C41   C51    SING N N 29 
A1IF6 C41   O21    SING N N 30 
A1IF6 C3    C61    SING N N 31 
A1IF6 C61   O3     SING N N 32 
A1IF6 O3    C7     SING N N 33 
A1IF6 C7    C8     SING N N 34 
A1IF6 C8    O6     SING N N 35 
A1IF6 C8    O5     DOUB N N 36 
A1IF6 C7    C9     SING N N 37 
A1IF6 C10   C11    SING N N 38 
A1IF6 C9    C10    SING N N 39 
A1IF6 C10   O7     SING N N 40 
A1IF6 C61   C11    SING N N 41 
A1IF6 C11   N2     SING N N 42 
A1IF6 N2    C12    SING N N 43 
A1IF6 C12   C13    SING N N 44 
A1IF6 C12   O8     DOUB N N 45 
A1IF6 C1    H1     SING N N 46 
A1IF6 C1    H2     SING N N 47 
A1IF6 C1    H3     SING N N 48 
A1IF6 C3    H51    SING N N 49 
A1IF6 C5    H5     SING N N 50 
A1IF6 C6    H6     SING N N 51 
A1IF6 C9    H13    SING N N 52 
A1IF6 C9    H14    SING N N 53 
A1IF6 C10   H15    SING N N 54 
A1IF6 C11   H17    SING N N 55 
A1IF6 C13   H21    SING N N 56 
A1IF6 C13   H19    SING N N 57 
A1IF6 C13   H20    SING N N 58 
A1IF6 O2P   H12    SING N N 59 
A1IF6 "C5'" "H5'1" SING N N 60 
A1IF6 "C5'" "H5'2" SING N N 61 
A1IF6 "C4'" "H4'"  SING N N 62 
A1IF6 "C3'" "H3'"  SING N N 63 
A1IF6 "O3'" "HO3'" SING N N 64 
A1IF6 "C2'" "H2'1" SING N N 65 
A1IF6 "O2'" "HO2'" SING N N 66 
A1IF6 "C1'" "H1'"  SING N N 67 
A1IF6 N4    HN41   SING N N 68 
A1IF6 N4    HN42   SING N N 69 
A1IF6 N11   H4     SING N N 70 
A1IF6 C41   H61    SING N N 71 
A1IF6 C51   H9     SING N N 72 
A1IF6 C51   H7     SING N N 73 
A1IF6 C51   H8     SING N N 74 
A1IF6 O21   H10    SING N N 75 
A1IF6 C61   H11    SING N N 76 
A1IF6 O6    H22    SING N N 77 
A1IF6 O7    H16    SING N N 78 
A1IF6 N2    H18    SING N N 79 
# 
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 
A1IF6 InChI            InChI                1.06  "InChI=1S/C22H34N5O15P/c1-8(28)14(24-9(2)29)18-15(25-10(3)30)11(31)6-22(41-18,20(34)35)42-43(37,38)39-7-12-16(32)17(33)19(40-12)27-5-4-13(23)26-21(27)36/h4-5,8,11-12,14-19,28,31-33H,6-7H2,1-3H3,(H,24,29)(H,25,30)(H,34,35)(H,37,38)(H2,23,26,36)/t8-,11-,12+,14-,15-,16+,17+,18-,19+,22+/m0/s1" 
A1IF6 InChIKey         InChI                1.06  XTZJKGIMUFZFBV-STPXTTIVSA-N                                                                                                                                                                                                                                                                        
A1IF6 SMILES_CANONICAL CACTVS               3.385 "C[C@H](O)[C@H](NC(C)=O)[C@@H]1O[C@](C[C@H](O)[C@@H]1NC(C)=O)(O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=NC3=O)N)C(O)=O"                                                                                                                                                                   
A1IF6 SMILES           CACTVS               3.385 "C[CH](O)[CH](NC(C)=O)[CH]1O[C](C[CH](O)[CH]1NC(C)=O)(O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=NC3=O)N)C(O)=O"                                                                                                                                                                                
A1IF6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H]([C@@H]([C@H]1[C@H]([C@H](C[C@](O1)(C(=O)O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=NC3=O)N)O)O)O)NC(=O)C)NC(=O)C)O"                                                                                                                                                                
A1IF6 SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C(C1C(C(CC(O1)(C(=O)O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=NC3=O)N)O)O)O)NC(=O)C)NC(=O)C)O"                                                                                                                                                                                                           
# 
_pdbx_chem_comp_identifier.comp_id           A1IF6 
_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~{R},4~{S},5~{S},6~{S})-5-acetamido-6-[(1~{S},2~{S})-1-acetamido-2-oxidanyl-propyl]-2-[[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-oxane-2-carboxylic 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 
A1IF6 "Create component" 2024-06-27 PDBE 
A1IF6 "Initial release"  2024-10-09 RCSB 
# 
