data_A1EL1
# 
_chem_comp.id                                    A1EL1 
_chem_comp.name                                  "(2~{S},5~{S})-6-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-oxolan-2-yl]-2,5-bis(azanyl)hexanoic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C25 H35 N12 O11 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-02-13 
_chem_comp.pdbx_modified_date                    2025-11-21 
_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                        710.593 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1EL1 
_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        9LQH 
_chem_comp.pdbx_subcomponent_list                "SFG AMP" 
_chem_comp.pdbx_processing_site                  PDBC 
_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 
A1EL1 N26 N4  N 0 1 N N N N N N 8.758  -19.725 -37.854 -6.285  -5.966 0.223  N      SFG 1  
A1EL1 C22 C12 C 0 1 N N S N N N 7.721  -20.775 -37.872 -7.221  -4.857 -0.003 CA     SFG 2  
A1EL1 C23 C13 C 0 1 N N N N N N 6.391  -20.125 -38.136 -8.351  -5.326 -0.884 C      SFG 3  
A1EL1 O24 O4  O 0 1 N N N N N N 5.339  -20.891 -38.408 -8.214  -6.311 -1.569 O      SFG 4  
A1EL1 O25 O5  O 0 1 N N N N N N 6.270  -18.903 -38.129 -9.509  -4.648 -0.906 OXT    SFG 5  
A1EL1 C21 C11 C 0 1 N N N N N N 7.712  -21.622 -36.584 -6.487  -3.702 -0.687 CB     SFG 6  
A1EL1 C20 C10 C 0 1 N N N N N N 7.192  -20.879 -35.347 -5.421  -3.145 0.259  CG     SFG 7  
A1EL1 C19 C9  C 0 1 N N S N N N 7.472  -21.641 -34.040 -4.687  -1.989 -0.425 CD     SFG 8  
A1EL1 N49 N10 N 0 1 N N N N N N 8.899  -21.502 -33.665 -3.948  -2.497 -1.588 NE     SFG 9  
A1EL1 C18 C8  C 0 1 N N N N N N 7.092  -23.115 -34.176 -3.708  -1.351 0.563  "C5'"  SFG 10 
A1EL1 C16 C7  C 0 1 N N R N N N 7.035  -23.897 -32.858 -3.066  -0.120 -0.079 "C4'"  SFG 11 
A1EL1 O17 O3  O 0 1 N N N N N N 8.082  -23.538 -31.951 -4.039  0.937  -0.224 "O4'"  SFG 12 
A1EL1 C14 C6  C 0 1 N N S N N N 5.791  -23.658 -32.035 -1.982  0.468  0.852  "C3'"  SFG 13 
A1EL1 O15 O2  O 0 1 N N N N N N 4.656  -24.292 -32.606 -0.683  0.028  0.448  "O3'"  SFG 14 
A1EL1 C12 C5  C 0 1 N N R N N N 6.191  -24.205 -30.684 -2.117  1.996  0.669  "C2'"  SFG 15 
A1EL1 O13 O1  O 0 1 N N N N N N 6.118  -25.636 -30.677 -0.907  2.547  0.146  "O2'"  SFG 16 
A1EL1 C11 C4  C 0 1 N N R N N N 7.657  -23.808 -30.619 -3.267  2.151  -0.351 "C1'"  SFG 17 
A1EL1 N10 N3  N 0 1 Y N N N N N 7.772  -22.578 -29.801 -4.091  3.316  -0.019 N9     SFG 18 
A1EL1 C9  C25 C 0 1 Y N N N N N 7.484  -21.325 -30.198 -5.203  3.319  0.770  C8     SFG 19 
A1EL1 N8  N12 N 0 1 Y N N N N N 7.683  -20.439 -29.186 -5.686  4.525  0.852  N7     SFG 20 
A1EL1 C7  C24 C 0 1 Y N N N N N 8.111  -21.147 -28.125 -4.916  5.370  0.125  C5     SFG 21 
A1EL1 C2  C1  C 0 1 Y N N N N N 8.506  -20.844 -26.751 -4.948  6.748  -0.149 C6     SFG 22 
A1EL1 N1  N2  N 0 1 N N N N N N 8.477  -19.571 -26.292 -5.941  7.552  0.382  N6     SFG 23 
A1EL1 N3  N1  N 0 1 Y N N N N N 8.893  -21.862 -25.958 -4.002  7.260  -0.930 N1     SFG 24 
A1EL1 C4  C2  C 0 1 Y N N N N N 8.914  -23.133 -26.408 -3.051  6.500  -1.441 C2     SFG 25 
A1EL1 N5  N11 N 0 1 Y N N N N N 8.574  -23.488 -27.655 -2.981  5.206  -1.211 N3     SFG 26 
A1EL1 C6  C3  C 0 1 Y N N N N N 8.166  -22.549 -28.531 -3.880  4.605  -0.438 C4     SFG 27 
A1EL1 P27 P1  P 0 1 N N N N N N 3.425  -23.353 -33.037 0.293   -0.820 1.407  P      AMP 28 
A1EL1 O29 O7  O 0 1 N N N N N N 3.821  -22.457 -34.286 -0.413  -2.032 1.881  O1P    AMP 29 
A1EL1 O28 O6  O 0 1 N N N N N N 2.927  -22.592 -31.873 0.720   0.081  2.671  O2P    AMP 30 
A1EL1 O30 O8  O 0 1 N N N N N N 2.271  -24.380 -33.479 1.609   -1.252 0.586  "O5'"  AMP 31 
A1EL1 C31 C14 C 0 1 N N N N N N 2.165  -24.782 -34.845 2.620   -2.104 1.129  "C5'"  AMP 32 
A1EL1 C32 C15 C 0 1 N N R N N N 1.340  -26.062 -34.898 3.724   -2.311 0.090  "C4'"  AMP 33 
A1EL1 O38 O11 O 0 1 N N N N N N 2.176  -27.167 -34.535 4.408   -1.070 -0.150 "O4'"  AMP 34 
A1EL1 C33 C16 C 0 1 N N S N N N 0.196  -26.083 -33.893 4.766   -3.312 0.625  "C3'"  AMP 35 
A1EL1 O34 O9  O 0 1 N N N N N N -1.023 -25.576 -34.439 4.849   -4.453 -0.232 "O3'"  AMP 36 
A1EL1 C35 C17 C 0 1 N N R N N N 0.071  -27.547 -33.544 6.096   -2.522 0.606  "C2'"  AMP 37 
A1EL1 O36 O10 O 0 1 N N N N N N -0.668 -28.232 -34.559 7.172   -3.345 0.150  "O2'"  AMP 38 
A1EL1 C37 C18 C 0 1 N N R N N N 1.504  -28.013 -33.604 5.790   -1.395 -0.412 "C1'"  AMP 39 
A1EL1 N39 N5  N 0 1 Y N N N N N 2.170  -27.861 -32.290 6.648   -0.232 -0.169 N9     AMP 40 
A1EL1 C40 C19 C 0 1 Y N N N N N 3.201  -27.032 -32.045 6.363   0.826  0.641  C8     AMP 41 
A1EL1 N41 N6  N 0 1 Y N N N N N 3.603  -27.145 -30.755 7.346   1.677  0.624  N7     AMP 42 
A1EL1 C42 C20 C 0 1 Y N N N N N 2.822  -28.061 -30.164 8.323   1.221  -0.196 C5     AMP 43 
A1EL1 C47 C23 C 0 1 Y N N N N N 2.721  -28.655 -28.817 9.583   1.701  -0.595 C6     AMP 44 
A1EL1 N48 N9  N 0 1 N N N N N N 3.555  -28.267 -27.818 10.065  2.906  -0.117 N6     AMP 45 
A1EL1 N46 N8  N 0 1 Y N N N N N 1.767  -29.596 -28.622 10.299  0.969  -1.442 N1     AMP 46 
A1EL1 C45 C22 C 0 1 Y N N N N N 0.941  -29.984 -29.610 9.847   -0.183 -1.903 C2     AMP 47 
A1EL1 N44 N7  N 0 1 Y N N N N N 0.976  -29.491 -30.856 8.674   -0.671 -1.558 N3     AMP 48 
A1EL1 C43 C21 C 0 1 Y N N N N N 1.880  -28.539 -31.185 7.890   -0.012 -0.711 C4     AMP 49 
A1EL1 H25 H25 H 0 1 N N N N N N 9.651  -20.140 -37.679 -6.728  -6.717 0.731  HN1    SFG 50 
A1EL1 H26 H26 H 0 1 N N N N N N 8.775  -19.258 -38.738 -5.899  -6.298 -0.649 HN2    SFG 51 
A1EL1 H13 H13 H 0 1 N N N N N N 7.936  -21.454 -38.710 -7.621  -4.519 0.953  HA     SFG 52 
A1EL1 H34 H34 H 0 1 N N N N N N 5.372  -18.672 -38.335 -10.205 -4.986 -1.487 HXT    SFG 53 
A1EL1 H11 H11 H 0 1 N N N N N N 7.072  -22.500 -36.753 -6.012  -4.062 -1.599 HB1    SFG 54 
A1EL1 H12 H12 H 0 1 N N N N N N 8.741  -21.952 -36.381 -7.200  -2.915 -0.934 HB2    SFG 55 
A1EL1 H9  H9  H 0 1 N N N N N N 7.683  -19.896 -35.294 -5.896  -2.784 1.171  HG1    SFG 56 
A1EL1 H10 H10 H 0 1 N N N N N N 6.105  -20.741 -35.449 -4.708  -3.931 0.507  HG2    SFG 57 
A1EL1 H8  H8  H 0 1 N N N N N N 6.852  -21.198 -33.247 -5.411  -1.242 -0.752 HD     SFG 58 
A1EL1 H30 H30 H 0 1 N N N N N N 9.071  -22.000 -32.815 -3.271  -3.192 -1.310 HNE1   SFG 59 
A1EL1 H31 H31 H 0 1 N N N N N N 9.473  -21.877 -34.393 -4.579  -2.866 -2.284 HNE2   SFG 60 
A1EL1 H6  H6  H 0 1 N N N N N N 6.100  -23.169 -34.647 -4.243  -1.054 1.465  "H5'1" SFG 61 
A1EL1 H7  H7  H 0 1 N N N N N N 7.834  -23.599 -34.828 -2.932  -2.072 0.822  "H5'2" SFG 62 
A1EL1 H5  H5  H 0 1 N N N N N N 7.100  -24.970 -33.091 -2.636  -0.378 -1.046 "H4'"  SFG 63 
A1EL1 H4  H4  H 0 1 N N N N N N 5.620  -22.575 -31.948 -2.175  0.189  1.888  "H3'"  SFG 64 
A1EL1 H3  H3  H 0 1 N N N N N N 5.611  -23.743 -29.871 -2.376  2.473  1.614  "H2'"  SFG 65 
A1EL1 H33 H33 H 0 1 N N N N N N 6.372  -25.962 -29.822 -0.937  3.504  0.011  "HO2'" SFG 66 
A1EL1 H2  H2  H 0 1 N N N N N N 8.245  -24.623 -30.171 -2.869  2.243  -1.362 "H1'"  SFG 67 
A1EL1 H22 H22 H 0 1 N N N N N N 7.141  -21.059 -31.187 -5.622  2.449  1.253  H8     SFG 68 
A1EL1 H23 H23 H 0 1 N N N N N N 8.774  -19.554 -25.337 -6.625  7.167  0.950  HN61   SFG 69 
A1EL1 H24 H24 H 0 1 N N N N N N 9.090  -19.004 -26.842 -5.952  8.502  0.185  HN62   SFG 70 
A1EL1 H1  H1  H 0 1 N N N N N N 9.223  -23.910 -25.724 -2.302  6.957  -2.070 H2     SFG 71 
A1EL1 H35 H35 H 0 1 N N N N N N 2.928  -21.664 -32.077 1.189   0.893  2.434  HOP2   AMP 72 
A1EL1 H14 H14 H 0 1 N N N N N N 3.167  -24.967 -35.258 3.043   -1.642 2.021  "H5'1" AMP 73 
A1EL1 H15 H15 H 0 1 N N N N N N 1.668  -23.993 -35.428 2.182   -3.067 1.391  "H5'2" AMP 74 
A1EL1 H16 H16 H 0 1 N N N N N N 0.938  -26.196 -35.913 3.293   -2.682 -0.840 "H4'"  AMP 75 
A1EL1 H17 H17 H 0 1 N N N N N N 0.487  -25.515 -32.997 4.516   -3.616 1.642  "H3'"  AMP 76 
A1EL1 H36 H36 H 0 1 N N N N N N -1.704 -25.609 -33.778 5.491   -5.116 0.057  "HO3'" AMP 77 
A1EL1 H18 H18 H 0 1 N N N N N N -0.356 -27.686 -32.540 6.317   -2.108 1.590  "H2'"  AMP 78 
A1EL1 H37 H37 H 0 1 N N N N N N -0.742 -29.151 -34.332 7.342   -4.115 0.709  "HO2'" AMP 79 
A1EL1 H19 H19 H 0 1 N N N N N N 1.541  -29.063 -33.929 5.913   -1.757 -1.434 "H1'"  AMP 80 
A1EL1 H20 H20 H 0 1 N N N N N N 3.646  -26.370 -32.773 5.454   0.940  1.214  H8     AMP 81 
A1EL1 H28 H28 H 0 1 N N N N N N 3.337  -28.775 -26.985 9.533   3.431  0.501  HN61   AMP 82 
A1EL1 H29 H29 H 0 1 N N N N N N 4.501  -28.452 -28.083 10.936  3.227  -0.400 HN62   AMP 83 
A1EL1 H21 H21 H 0 1 N N N N N N 0.203  -30.740 -29.385 10.462  -0.745 -2.590 H2     AMP 84 
# 
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 
A1EL1 O24 C23 DOUB N N 1  
A1EL1 C23 O25 SING N N 2  
A1EL1 C23 C22 SING N N 3  
A1EL1 C22 N26 SING N N 4  
A1EL1 C22 C21 SING N N 5  
A1EL1 C21 C20 SING N N 6  
A1EL1 C20 C19 SING N N 7  
A1EL1 C32 C31 SING N N 8  
A1EL1 C32 O38 SING N N 9  
A1EL1 C32 C33 SING N N 10 
A1EL1 C31 O30 SING N N 11 
A1EL1 O36 C35 SING N N 12 
A1EL1 O38 C37 SING N N 13 
A1EL1 O34 C33 SING N N 14 
A1EL1 O29 P27 DOUB N N 15 
A1EL1 C18 C19 SING N N 16 
A1EL1 C18 C16 SING N N 17 
A1EL1 C19 N49 SING N N 18 
A1EL1 C33 C35 SING N N 19 
A1EL1 C37 C35 SING N N 20 
A1EL1 C37 N39 SING N N 21 
A1EL1 O30 P27 SING N N 22 
A1EL1 P27 O15 SING N N 23 
A1EL1 P27 O28 SING N N 24 
A1EL1 C16 C14 SING N N 25 
A1EL1 C16 O17 SING N N 26 
A1EL1 O15 C14 SING N N 27 
A1EL1 N39 C40 SING Y N 28 
A1EL1 N39 C43 SING Y N 29 
A1EL1 C40 N41 DOUB Y N 30 
A1EL1 C14 C12 SING N N 31 
A1EL1 O17 C11 SING N N 32 
A1EL1 C43 N44 DOUB Y N 33 
A1EL1 C43 C42 SING Y N 34 
A1EL1 N44 C45 SING Y N 35 
A1EL1 N41 C42 SING Y N 36 
A1EL1 C12 O13 SING N N 37 
A1EL1 C12 C11 SING N N 38 
A1EL1 C11 N10 SING N N 39 
A1EL1 C9  N10 SING Y N 40 
A1EL1 C9  N8  DOUB Y N 41 
A1EL1 C42 C47 DOUB Y N 42 
A1EL1 N10 C6  SING Y N 43 
A1EL1 C45 N46 DOUB Y N 44 
A1EL1 N8  C7  SING Y N 45 
A1EL1 C47 N46 SING Y N 46 
A1EL1 C47 N48 SING N N 47 
A1EL1 C6  C7  DOUB Y N 48 
A1EL1 C6  N5  SING Y N 49 
A1EL1 C7  C2  SING Y N 50 
A1EL1 N5  C4  DOUB Y N 51 
A1EL1 C2  N1  SING N N 52 
A1EL1 C2  N3  DOUB Y N 53 
A1EL1 C4  N3  SING Y N 54 
A1EL1 C4  H1  SING N N 55 
A1EL1 C11 H2  SING N N 56 
A1EL1 C12 H3  SING N N 57 
A1EL1 C14 H4  SING N N 58 
A1EL1 C16 H5  SING N N 59 
A1EL1 C18 H6  SING N N 60 
A1EL1 C18 H7  SING N N 61 
A1EL1 C19 H8  SING N N 62 
A1EL1 C20 H9  SING N N 63 
A1EL1 C20 H10 SING N N 64 
A1EL1 C21 H11 SING N N 65 
A1EL1 C21 H12 SING N N 66 
A1EL1 C22 H13 SING N N 67 
A1EL1 C31 H14 SING N N 68 
A1EL1 C31 H15 SING N N 69 
A1EL1 C32 H16 SING N N 70 
A1EL1 C33 H17 SING N N 71 
A1EL1 C35 H18 SING N N 72 
A1EL1 C37 H19 SING N N 73 
A1EL1 C40 H20 SING N N 74 
A1EL1 C45 H21 SING N N 75 
A1EL1 C9  H22 SING N N 76 
A1EL1 N1  H23 SING N N 77 
A1EL1 N1  H24 SING N N 78 
A1EL1 N26 H25 SING N N 79 
A1EL1 N26 H26 SING N N 80 
A1EL1 N48 H28 SING N N 81 
A1EL1 N48 H29 SING N N 82 
A1EL1 N49 H30 SING N N 83 
A1EL1 N49 H31 SING N N 84 
A1EL1 O13 H33 SING N N 85 
A1EL1 O25 H34 SING N N 86 
A1EL1 O28 H35 SING N N 87 
A1EL1 O34 H36 SING N N 88 
A1EL1 O36 H37 SING N N 89 
# 
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 
A1EL1 InChI            InChI                1.06  "InChI=1S/C25H35N12O11P/c26-9(1-2-10(27)25(41)42)3-11-18(17(40)24(46-11)37-8-35-14-20(29)31-6-33-22(14)37)48-49(43,44)45-4-12-15(38)16(39)23(47-12)36-7-34-13-19(28)30-5-32-21(13)36/h5-12,15-18,23-24,38-40H,1-4,26-27H2,(H,41,42)(H,43,44)(H2,28,30,32)(H2,29,31,33)/t9-,10-,11+,12+,15+,16+,17+,18+,23+,24+/m0/s1" 
A1EL1 InChIKey         InChI                1.06  XNBPELUUEBZQEC-PYTRVWNWSA-N                                                                                                                                                                                                                                                                                           
A1EL1 SMILES_CANONICAL CACTVS               3.385 "N[C@@H](CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34)n5cnc6c(N)ncnc56"                                                                                                                                                                                  
A1EL1 SMILES           CACTVS               3.385 "N[CH](CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34)n5cnc6c(N)ncnc56"                                                                                                                                                                                               
A1EL1 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O[C@@H]4[C@H](O[C@H]([C@@H]4O)n5cnc6c5ncnc6N)C[C@H](CC[C@@H](C(=O)O)N)N)O)O)N"                                                                                                                                                                              
A1EL1 SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OC4C(OC(C4O)n5cnc6c5ncnc6N)CC(CCC(C(=O)O)N)N)O)O)N"                                                                                                                                                                                                                           
# 
_pdbx_chem_comp_identifier.comp_id           A1EL1 
_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~{S},5~{S})-6-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-oxolan-2-yl]-2,5-bis(azanyl)hexanoic 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 
A1EL1 "Create component" 2025-02-13 PDBC 
A1EL1 "Initial release"  2025-11-26 RCSB 
# 
