data_A1EL3
# 
_chem_comp.id                                    A1EL3 
_chem_comp.name                                  "[(2~{S},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]methyl-[(3~{S})-3-azanyl-4-oxidanyl-4-oxidanylidene-butyl]-methyl-sulfanium" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C25 H35 N11 O11 P S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2025-02-14 
_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                        728.651 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1EL3 
_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        9LQA 
_chem_comp.pdbx_subcomponent_list                "SAM 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 
A1EL3 N23 N5  N 0 1 N N N N N N 35.755 6.496  7.066  -8.123  4.717  -0.649 N      SAM 1  
A1EL3 C22 C12 C 0 1 N N S N N N 34.981 7.427  6.226  -8.743  3.441  -0.266 CA     SAM 2  
A1EL3 C24 C13 C 0 1 N N N N N N 33.617 7.544  6.842  -9.973  3.709  0.562  C      SAM 3  
A1EL3 O25 O3  O 0 1 N N N N N N 33.527 7.439  8.046  -10.915 2.762  0.690  O      SAM 4  
A1EL3 O26 O4  O 0 1 N N N N N N 32.516 7.775  6.133  -10.112 4.777  1.110  OXT    SAM 5  
A1EL3 C21 C2  C 0 1 N N N N N N 35.043 6.941  4.772  -7.747  2.616  0.551  CB     SAM 6  
A1EL3 C20 C11 C 0 1 N N N N N N 34.596 7.925  3.680  -6.554  2.239  -0.329 CG     SAM 7  
A1EL3 S17 S1  S 1 1 N N R N N N 34.770 7.321  2.129  -5.374  1.260  0.641  SD     SAM 8  
A1EL3 C18 C10 C 0 1 N N N N N N 35.189 8.537  1.090  -6.208  -0.343 0.802  CE     SAM 9  
A1EL3 C16 C9  C 0 1 N N N N N N 36.069 6.338  2.452  -4.053  0.914  -0.553 "C5'"  SAM 10 
A1EL3 C14 C8  C 0 1 N N S N N N 36.741 5.685  1.267  -2.960  0.082  0.122  "C4'"  SAM 11 
A1EL3 O15 O1  O 0 1 N N N N N N 38.062 5.374  1.700  -3.473  -1.218 0.457  "O4'"  SAM 12 
A1EL3 C13 C7  C 0 1 N N S N N N 36.101 4.351  0.920  -1.784  -0.126 -0.851 "C3'"  SAM 13 
A1EL3 O27 O5  O 0 1 N N N N N N 36.348 4.175  -0.458 -0.582  0.425  -0.309 "O3'"  SAM 14 
A1EL3 C12 C6  C 0 1 N N R N N N 36.950 3.348  1.671  -1.665  -1.665 -0.979 "C2'"  SAM 15 
A1EL3 O19 O2  O 0 1 N N N N N N 36.991 2.058  1.081  -0.295  -2.071 -0.983 "O2'"  SAM 16 
A1EL3 C11 C5  C 0 1 N N R N N N 38.314 3.990  1.563  -2.384  -2.153 0.304  "C1'"  SAM 17 
A1EL3 N10 N4  N 0 1 Y N N N N N 39.212 3.452  2.598  -2.894  -3.515 0.123  N9     SAM 18 
A1EL3 C9  C25 C 0 1 Y N N N N N 40.359 2.800  2.373  -4.154  -3.859 -0.269 C8     SAM 19 
A1EL3 N8  N11 N 0 1 Y N N N N N 40.944 2.424  3.528  -4.263  -5.154 -0.326 N7     SAM 20 
A1EL3 C7  C24 C 0 1 Y N N N N N 40.152 2.842  4.517  -3.084  -5.722 0.024  C5     SAM 21 
A1EL3 C2  C1  C 0 1 Y N N N N N 40.182 2.780  5.985  -2.620  -7.043 0.142  C6     SAM 22 
A1EL3 N1  N3  N 0 1 N N N N N N 41.192 2.173  6.637  -3.453  -8.114 -0.133 N6     SAM 23 
A1EL3 N3  N1  N 0 1 Y N N N N N 39.159 3.346  6.638  -1.363  -7.241 0.523  N1     SAM 24 
A1EL3 C4  C3  C 0 1 Y N N N N N 38.145 3.951  5.999  -0.560  -6.226 0.788  C2     SAM 25 
A1EL3 N5  N2  N 0 1 Y N N N N N 38.056 4.047  4.675  -0.951  -4.973 0.691  N3     SAM 26 
A1EL3 C6  C4  C 0 1 Y N N N N N 39.011 3.519  3.898  -2.190  -4.677 0.311  C4     SAM 27 
A1EL3 P28 P1  P 0 1 N N N N N N 35.268 3.488  -1.393 0.253   1.593  -1.037 P      AMP 28 
A1EL3 O29 O6  O 0 1 N N N N N N 35.735 3.595  -2.769 0.589   1.174  -2.416 O1P    AMP 29 
A1EL3 O30 O7  O 0 1 N N N N N N 35.033 1.971  -0.958 -0.634  2.936  -1.086 O2P    AMP 30 
A1EL3 O31 O8  O 0 1 N N N N N N 33.889 4.273  -1.247 1.609   1.875  -0.216 "O5'"  AMP 31 
A1EL3 C32 C14 C 0 1 N N N N N N 33.783 5.615  -1.656 2.616   2.785  -0.665 "C5'"  AMP 32 
A1EL3 C33 C15 C 0 1 N N R N N N 32.558 6.196  -0.981 3.764   2.814  0.346  "C4'"  AMP 33 
A1EL3 O37 O9  O 0 1 N N N N N N 32.667 7.604  -0.991 4.435   1.543  0.361  "O4'"  AMP 34 
A1EL3 C34 C16 C 0 1 N N S N N N 31.302 5.847  -1.754 4.799   3.877  -0.067 "C3'"  AMP 35 
A1EL3 O49 O11 O 0 1 N N N N N N 30.237 5.820  -0.810 4.936   4.866  0.955  "O3'"  AMP 36 
A1EL3 C35 C17 C 0 1 N N R N N N 31.149 7.017  -2.708 6.117   3.081  -0.230 "C2'"  AMP 37 
A1EL3 O48 O10 O 0 1 N N N N N N 29.793 7.311  -3.040 7.224   3.809  0.305  "O2'"  AMP 38 
A1EL3 C36 C18 C 0 1 N N R N N N 31.743 8.156  -1.915 5.832   1.806  0.612  "C1'"  AMP 39 
A1EL3 N38 N6  N 0 1 Y N N N N N 32.501 9.070  -2.767 6.660   0.689  0.152  N9     AMP 40 
A1EL3 C39 C19 C 0 1 Y N N N N N 33.120 8.820  -3.925 6.294   -0.271 -0.744 C8     AMP 41 
A1EL3 N40 N7  N 0 1 Y N N N N N 33.721 9.938  -4.385 7.275   -1.106 -0.927 N7     AMP 42 
A1EL3 C41 C20 C 0 1 Y N N N N N 33.481 10.912 -3.498 8.330   -0.737 -0.161 C5     AMP 43 
A1EL3 C46 C23 C 0 1 Y N N N N N 33.801 12.339 -3.353 9.624   -1.244 0.050  C6     AMP 44 
A1EL3 N47 N10 N 0 1 N N N N N N 34.535 12.985 -4.278 10.056  -2.379 -0.613 N6     AMP 45 
A1EL3 N45 N9  N 0 1 Y N N N N N 33.336 12.969 -2.265 10.422  -0.607 0.901  N1     AMP 46 
A1EL3 C44 C22 C 0 1 Y N N N N N 32.602 12.352 -1.334 10.018  0.477  1.537  C2     AMP 47 
A1EL3 N43 N8  N 0 1 Y N N N N N 32.269 11.066 -1.393 8.816   0.987  1.371  N3     AMP 48 
A1EL3 C42 C21 C 0 1 Y N N N N N 32.676 10.322 -2.434 7.948   0.419  0.541  C4     AMP 49 
A1EL3 H27 H27 H 0 1 N N N N N N 35.724 6.800  8.018  -7.856  5.248  0.166  HN1    SAM 50 
A1EL3 H28 H28 H 0 1 N N N N N N 35.362 5.579  6.996  -7.333  4.567  -1.259 HN2    SAM 51 
A1EL3 H15 H15 H 0 1 N N N N N N 35.461 8.416  6.269  -9.022  2.889  -1.164 HA     SAM 52 
A1EL3 H1  H1  H 0 1 N N N N N N 34.404 6.049  4.694  -7.401  3.204  1.402  HB1    SAM 53 
A1EL3 H2  H2  H 0 1 N N N N N N 36.086 6.664  4.560  -8.235  1.710  0.911  HB2    SAM 54 
A1EL3 H13 H13 H 0 1 N N N N N N 35.200 8.840  3.767  -6.901  1.651  -1.179 HG1    SAM 55 
A1EL3 H14 H14 H 0 1 N N N N N N 33.536 8.168  3.843  -6.066  3.145  -0.688 HG2    SAM 56 
A1EL3 H10 H10 H 0 1 N N N N N N 34.312 9.171  0.894  -5.498  -1.086 1.166  HE1    SAM 57 
A1EL3 H11 H11 H 0 1 N N N N N N 35.988 9.145  1.540  -7.034  -0.253 1.508  HE2    SAM 58 
A1EL3 H12 H12 H 0 1 N N N N N N 35.547 8.104  0.144  -6.592  -0.652 -0.170 HE3    SAM 59 
A1EL3 H8  H8  H 0 1 N N N N N N 35.722 5.537  3.121  -4.462  0.360  -1.398 "H5'1" SAM 60 
A1EL3 H9  H9  H 0 1 N N N N N N 36.825 6.946  2.970  -3.627  1.854  -0.907 "H5'2" SAM 61 
A1EL3 H7  H7  H 0 1 N N N N N N 36.737 6.357  0.396  -2.614  0.587  1.023  "H4'"  SAM 62 
A1EL3 H6  H6  H 0 1 N N N N N N 35.039 4.305  1.202  -2.007  0.321  -1.820 "H3'"  SAM 63 
A1EL3 H5  H5  H 0 1 N N N N N N 36.636 3.300  2.724  -2.178  -2.022 -1.872 "H2'"  SAM 64 
A1EL3 H32 H32 H 0 1 N N N N N N 37.540 1.487  1.605  -0.169  -3.027 -1.061 "HO2'" SAM 65 
A1EL3 H4  H4  H 0 1 N N N N N N 38.732 3.775  0.568  -1.713  -2.105 1.162  "H1'"  SAM 66 
A1EL3 H24 H24 H 0 1 N N N N N N 40.764 2.601  1.392  -4.944  -3.159 -0.498 H8     SAM 67 
A1EL3 H25 H25 H 0 1 N N N N N N 41.034 2.228  7.623  -4.369  -7.956 -0.411 HN61   SAM 68 
A1EL3 H26 H26 H 0 1 N N N N N N 41.239 1.213  6.360  -3.121  -9.021 -0.049 HN62   SAM 69 
A1EL3 H3  H3  H 0 1 N N N N N N 37.355 4.385  6.595  0.454   -6.432 1.095  H2     SAM 70 
A1EL3 H33 H33 H 0 1 N N N N N N 32.620 7.546  8.307  -11.686 2.980  1.231  H33    SAM 71 
A1EL3 H34 H34 H 0 1 N N N N N N 35.243 1.397  -1.685 -0.891  3.270  -0.215 HOP2   AMP 72 
A1EL3 H16 H16 H 0 1 N N N N N N 34.681 6.173  -1.352 2.993   2.459  -1.634 "H5'1" AMP 73 
A1EL3 H17 H17 H 0 1 N N N N N N 33.671 5.668  -2.749 2.188   3.783  -0.758 "H5'2" AMP 74 
A1EL3 H18 H18 H 0 1 N N N N N N 32.481 5.810  0.046  3.377   3.040  1.340  "H4'"  AMP 75 
A1EL3 H19 H19 H 0 1 N N N N N N 31.416 4.898  -2.298 4.513   4.342  -1.011 "H3'"  AMP 76 
A1EL3 H36 H36 H 0 1 N N N N N N 30.352 5.082  -0.224 5.576   5.561  0.747  "HO3'" AMP 77 
A1EL3 H20 H20 H 0 1 N N N N N N 31.748 6.839  -3.613 6.289   2.826  -1.276 "H2'"  AMP 78 
A1EL3 H35 H35 H 0 1 N N N N N N 29.425 6.591  -3.539 7.441   4.613  -0.187 "HO2'" AMP 79 
A1EL3 H21 H21 H 0 1 N N N N N N 30.942 8.699  -1.392 6.001   2.000  1.671  "H1'"  AMP 80 
A1EL3 H22 H22 H 0 1 N N N N N N 33.137 7.861  -4.422 5.332   -0.329 -1.232 H8     AMP 81 
A1EL3 H30 H30 H 0 1 N N N N N N 34.648 13.941 -4.007 9.464   -2.835 -1.231 HN61   AMP 82 
A1EL3 H31 H31 H 0 1 N N N N N N 35.433 12.552 -4.353 10.952  -2.719 -0.459 HN62   AMP 83 
A1EL3 H23 H23 H 0 1 N N N N N N 32.261 12.929 -0.488 10.699  0.964  2.220  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 
A1EL3 N40 C39 DOUB Y N 1  
A1EL3 N40 C41 SING Y N 2  
A1EL3 N47 C46 SING N N 3  
A1EL3 C39 N38 SING Y N 4  
A1EL3 C41 C46 DOUB Y N 5  
A1EL3 C41 C42 SING Y N 6  
A1EL3 C46 N45 SING Y N 7  
A1EL3 O48 C35 SING N N 8  
A1EL3 O29 P28 DOUB N N 9  
A1EL3 N38 C42 SING Y N 10 
A1EL3 N38 C36 SING N N 11 
A1EL3 C35 C36 SING N N 12 
A1EL3 C35 C34 SING N N 13 
A1EL3 C42 N43 DOUB Y N 14 
A1EL3 N45 C44 DOUB Y N 15 
A1EL3 C36 O37 SING N N 16 
A1EL3 C34 C33 SING N N 17 
A1EL3 C34 O49 SING N N 18 
A1EL3 C32 O31 SING N N 19 
A1EL3 C32 C33 SING N N 20 
A1EL3 P28 O31 SING N N 21 
A1EL3 P28 O30 SING N N 22 
A1EL3 P28 O27 SING N N 23 
A1EL3 N43 C44 SING Y N 24 
A1EL3 O37 C33 SING N N 25 
A1EL3 O27 C13 SING N N 26 
A1EL3 C13 C14 SING N N 27 
A1EL3 C13 C12 SING N N 28 
A1EL3 O19 C12 SING N N 29 
A1EL3 C18 S17 SING N N 30 
A1EL3 C14 O15 SING N N 31 
A1EL3 C14 C16 SING N N 32 
A1EL3 C11 C12 SING N N 33 
A1EL3 C11 O15 SING N N 34 
A1EL3 C11 N10 SING N N 35 
A1EL3 S17 C16 SING N N 36 
A1EL3 S17 C20 SING N N 37 
A1EL3 C9  N10 SING Y N 38 
A1EL3 C9  N8  DOUB Y N 39 
A1EL3 N10 C6  SING Y N 40 
A1EL3 N8  C7  SING Y N 41 
A1EL3 C20 C21 SING N N 42 
A1EL3 C6  C7  DOUB Y N 43 
A1EL3 C6  N5  SING Y N 44 
A1EL3 C7  C2  SING Y N 45 
A1EL3 N5  C4  DOUB Y N 46 
A1EL3 C21 C22 SING N N 47 
A1EL3 C2  N1  SING N N 48 
A1EL3 C2  N3  DOUB Y N 49 
A1EL3 C4  N3  SING Y N 50 
A1EL3 O26 C24 DOUB N N 51 
A1EL3 C22 C24 SING N N 52 
A1EL3 C22 N23 SING N N 53 
A1EL3 C24 O25 SING N N 54 
A1EL3 C21 H1  SING N N 55 
A1EL3 C21 H2  SING N N 56 
A1EL3 C4  H3  SING N N 57 
A1EL3 C11 H4  SING N N 58 
A1EL3 C12 H5  SING N N 59 
A1EL3 C13 H6  SING N N 60 
A1EL3 C14 H7  SING N N 61 
A1EL3 C16 H8  SING N N 62 
A1EL3 C16 H9  SING N N 63 
A1EL3 C18 H10 SING N N 64 
A1EL3 C18 H11 SING N N 65 
A1EL3 C18 H12 SING N N 66 
A1EL3 C20 H13 SING N N 67 
A1EL3 C20 H14 SING N N 68 
A1EL3 C22 H15 SING N N 69 
A1EL3 C32 H16 SING N N 70 
A1EL3 C32 H17 SING N N 71 
A1EL3 C33 H18 SING N N 72 
A1EL3 C34 H19 SING N N 73 
A1EL3 C35 H20 SING N N 74 
A1EL3 C36 H21 SING N N 75 
A1EL3 C39 H22 SING N N 76 
A1EL3 C44 H23 SING N N 77 
A1EL3 C9  H24 SING N N 78 
A1EL3 N1  H25 SING N N 79 
A1EL3 N1  H26 SING N N 80 
A1EL3 N23 H27 SING N N 81 
A1EL3 N23 H28 SING N N 82 
A1EL3 N47 H30 SING N N 83 
A1EL3 N47 H31 SING N N 84 
A1EL3 O19 H32 SING N N 85 
A1EL3 O25 H33 SING N N 86 
A1EL3 O30 H34 SING N N 87 
A1EL3 O48 H35 SING N N 88 
A1EL3 O49 H36 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 
A1EL3 InChI            InChI                1.06  "InChI=1S/C25H34N11O11PS/c1-49(3-2-10(26)25(40)41)5-12-18(17(39)24(46-12)36-9-34-14-20(28)30-7-32-22(14)36)47-48(42,43)44-4-11-15(37)16(38)23(45-11)35-8-33-13-19(27)29-6-31-21(13)35/h6-12,15-18,23-24,37-39H,2-5,26H2,1H3,(H5-,27,28,29,30,31,32,40,41,42,43)/p+1/t10-,11+,12+,15+,16+,17+,18+,23+,24+,49+/m0/s1" 
A1EL3 InChIKey         InChI                1.06  AKDVTEPPXUCZRD-YBZFFHRHSA-O                                                                                                                                                                                                                                                                                         
A1EL3 SMILES_CANONICAL CACTVS               3.385 "C[S@+](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"                                                                                                                                                                                 
A1EL3 SMILES           CACTVS               3.385 "C[S+](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"                                                                                                                                                                                             
A1EL3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[S@+](CC[C@@H](C(=O)O)N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O"                                                                                                                                                                                
A1EL3 SMILES           "OpenEye OEToolkits" 2.0.7 "C[S+](CCC(C(=O)O)N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O"                                                                                                                                                                                                                          
# 
_pdbx_chem_comp_identifier.comp_id           A1EL3 
_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},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]methyl-[(3~{S})-3-azanyl-4-oxidanyl-4-oxidanylidene-butyl]-methyl-sulfanium" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1EL3 "Create component" 2025-02-14 PDBC 
A1EL3 "Initial release"  2025-11-26 RCSB 
# 
