data_A1EL0
# 
_chem_comp.id                                    A1EL0 
_chem_comp.name                                  "(2~{S})-4-[[(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]methylsulfanyl]-2-azanyl-butanoic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C24 H32 N11 O11 P S" 
_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                        713.617 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1EL0 
_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        9LQC 
_chem_comp.pdbx_subcomponent_list                "SAH 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 
A1EL0 N23 N2  N 0 1 N N N N N N -0.011 -9.980  29.485 -8.225  4.750  -0.437 N      SAH 1  
A1EL0 C22 C8  C 0 1 N N S N N N 0.695  -8.774  29.017 -8.842  3.479  -0.034 CA     SAH 2  
A1EL0 C21 C7  C 0 1 N N N N N N -0.044 -7.526  29.482 -7.822  2.639  0.737  CB     SAH 3  
A1EL0 C20 C6  C 0 1 N N N N N N -0.154 -6.533  28.329 -6.670  2.253  -0.194 CG     SAH 4  
A1EL0 S19 S1  S 0 1 N N N N N N -0.987 -5.076  28.869 -5.461  1.257  0.720  SD     SAH 5  
A1EL0 C24 C9  C 0 1 N N N N N N 2.101  -8.775  29.547 -10.033 3.755  0.846  C      SAH 6  
A1EL0 O26 O5  O 0 1 N N N N N N 3.007  -7.943  29.039 -10.137 4.821  1.405  O      SAH 7  
A1EL0 O25 O4  O 0 1 N N N N N N 2.439  -9.539  30.439 -10.979 2.817  1.009  OXT    SAH 8  
A1EL0 C18 C5  C 0 1 N N N N N N -0.388 -4.594  30.459 -4.195  0.904  -0.530 "C5'"  SAH 9  
A1EL0 C16 C4  C 0 1 N N S N N N -1.074 -3.286  30.843 -3.084  0.056  0.094  "C4'"  SAH 10 
A1EL0 O17 O3  O 0 1 N N N N N N -2.472 -3.531  31.050 -3.597  -1.240 0.444  "O4'"  SAH 11 
A1EL0 C14 C3  C 0 1 N N S N N N -0.535 -2.686  32.129 -1.952  -0.159 -0.928 "C3'"  SAH 12 
A1EL0 O15 O2  O 0 1 N N N N N N -0.744 -1.284  32.039 -0.723  0.376  -0.434 "O3'"  SAH 13 
A1EL0 C12 C2  C 0 1 N N R N N N -1.514 -3.186  33.157 -1.855  -1.698 -1.068 "C2'"  SAH 14 
A1EL0 O13 O1  O 0 1 N N N N N N -1.588 -2.286  34.262 -0.491  -2.119 -1.131 "O2'"  SAH 15 
A1EL0 C11 C1  C 0 1 N N R N N N -2.826 -3.192  32.395 -2.525  -2.186 0.241  "C1'"  SAH 16 
A1EL0 N10 N1  N 0 1 Y N N N N N -3.758 -4.180  32.982 -3.057  -3.541 0.075  N9     SAH 17 
A1EL0 C68 C20 C 0 1 Y N N N N N -4.924 -3.895  33.582 -4.311  -3.869 -0.348 C8     SAH 18 
A1EL0 N69 N8  N 0 1 Y N N N N N -5.534 -5.024  34.014 -4.445  -5.163 -0.380 N7     SAH 19 
A1EL0 C70 C21 C 0 1 Y N N N N N -4.747 -6.064  33.689 -3.289  -5.746 0.020  C5     SAH 20 
A1EL0 C75 C24 C 0 1 Y N N N N N -4.789 -7.532  33.848 -2.856  -7.073 0.181  C6     SAH 21 
A1EL0 N76 N11 N 0 1 N N N N N N -5.825 -8.146  34.460 -3.701  -8.133 -0.096 N6     SAH 22 
A1EL0 N74 N10 N 0 1 Y N N N N N -3.755 -8.249  33.361 -1.615  -7.287 0.606  N1     SAH 23 
A1EL0 C73 C23 C 0 1 Y N N N N N -2.717 -7.655  32.750 -0.800  -6.282 0.872  C2     SAH 24 
A1EL0 N72 N9  N 0 1 Y N N N N N -2.612 -6.331  32.570 -1.162  -5.024 0.735  N3     SAH 25 
A1EL0 C71 C22 C 0 1 Y N N N N N -3.578 -5.496  33.011 -2.383  -4.712 0.310  C4     SAH 26 
A1EL0 P27 P1  P 0 1 N N N N N N 0.295  -0.193  32.614 0.094   1.540  -1.191 P      AMP 27 
A1EL0 O28 O6  O 0 1 N N N N N N -0.300 1.152   32.497 0.367   1.124  -2.584 O1P    AMP 28 
A1EL0 O29 O7  O 0 1 N N N N N N 0.673  -0.527  34.145 -0.780  2.892  -1.196 O2P    AMP 29 
A1EL0 O30 O8  O 0 1 N N N N N N 1.628  -0.220  31.718 1.486   1.802  -0.426 "O5'"  AMP 30 
A1EL0 C31 C10 C 0 1 N N N N N N 1.545  -0.160  30.299 2.483   2.704  -0.912 "C5'"  AMP 31 
A1EL0 C32 C11 C 0 1 N N R N N N 2.851  -0.716  29.758 3.672   2.715  0.051  "C4'"  AMP 32 
A1EL0 O38 O11 O 0 1 N N N N N N 2.745  -0.901  28.345 4.381   1.459  -0.011 "O4'"  AMP 33 
A1EL0 C33 C12 C 0 1 N N S N N N 3.984  0.273   30.001 4.708   3.775  -0.387 "C3'"  AMP 34 
A1EL0 O34 O9  O 0 1 N N N N N N 5.179  -0.419  30.381 4.547   4.975  0.371  "O3'"  AMP 35 
A1EL0 C35 C13 C 0 1 N N R N N N 4.205  0.931   28.655 6.071   3.118  -0.077 "C2'"  AMP 36 
A1EL0 O36 O10 O 0 1 N N N N N N 5.596  1.207   28.463 6.795   3.894  0.879  "O2'"  AMP 37 
A1EL0 C37 C14 C 0 1 N N R N N N 3.718  -0.111  27.661 5.698   1.739  0.511  "C1'"  AMP 38 
A1EL0 N39 N3  N 0 1 Y N N N N N 3.079  0.511   26.481 6.651   0.719  0.065  N9     AMP 39 
A1EL0 C40 C15 C 0 1 Y N N N N N 2.276  1.589   26.485 6.530   -0.070 -1.040 C8     AMP 40 
A1EL0 N41 N4  N 0 1 Y N N N N N 1.865  1.877   25.226 7.557   -0.863 -1.134 N7     AMP 41 
A1EL0 C42 C16 C 0 1 Y N N N N N 2.404  0.963   24.398 8.401   -0.634 -0.099 C5     AMP 42 
A1EL0 C47 C19 C 0 1 Y N N N N N 2.385  0.685   22.947 9.633   -1.172 0.309  C6     AMP 43 
A1EL0 N48 N7  N 0 1 N N N N N N 1.680  1.458   22.095 10.244  -2.177 -0.421 N6     AMP 44 
A1EL0 N46 N6  N 0 1 Y N N N N N 3.095  -0.372  22.502 10.198  -0.694 1.413  N1     AMP 45 
A1EL0 C45 C18 C 0 1 Y N N N N N 3.804  -1.152  23.337 9.623   0.265  2.115  C2     AMP 46 
A1EL0 N44 N5  N 0 1 Y N N N N N 3.867  -0.957  24.661 8.469   0.798  1.771  N3     AMP 47 
A1EL0 C43 C17 C 0 1 Y N N N N N 3.201  0.065   25.237 7.832   0.388  0.679  C4     AMP 48 
A1EL0 H22 H22 H 0 1 N N N N N N 0.480  -10.795 29.176 -7.918  5.274  0.369  HN1    SAH 49 
A1EL0 H23 H23 H 0 1 N N N N N N -0.053 -9.975  30.484 -7.463  4.595  -1.080 HN2    SAH 50 
A1EL0 H11 H11 H 0 1 N N N N N N 0.728  -8.775  27.917 -9.164  2.934  -0.922 HA     SAH 51 
A1EL0 H9  H9  H 0 1 N N N N N N 0.509  -7.062  30.312 -7.433  3.218  1.574  HB1    SAH 52 
A1EL0 H10 H10 H 0 1 N N N N N N -1.052 -7.804  29.822 -8.304  1.736  1.112  HB2    SAH 53 
A1EL0 H7  H7  H 0 1 N N N N N N -0.720 -6.992  27.505 -7.059  1.674  -1.032 HG1    SAH 54 
A1EL0 H8  H8  H 0 1 N N N N N N 0.854  -6.268  27.979 -6.188  3.156  -0.569 HG2    SAH 55 
A1EL0 H30 H30 H 0 1 N N N N N N 3.358  -9.406  30.639 -11.725 3.040  1.583  HXT    SAH 56 
A1EL0 H5  H5  H 0 1 N N N N N N -0.626 -5.372  31.199 -4.645  0.359  -1.359 "H5'1" SAH 57 
A1EL0 H6  H6  H 0 1 N N N N N N 0.701  -4.447  30.419 -3.775  1.840  -0.896 "H5'2" SAH 58 
A1EL0 H4  H4  H 0 1 N N N N N N -0.936 -2.561  30.027 -2.695  0.553  0.983  "H4'"  SAH 59 
A1EL0 H3  H3  H 0 1 N N N N N N 0.503  -2.983  32.339 -2.210  0.295  -1.885 "H3'"  SAH 60 
A1EL0 H2  H2  H 0 1 N N N N N N -1.252 -4.205  33.478 -2.408  -2.045 -1.941 "H2'"  SAH 61 
A1EL0 H29 H29 H 0 1 N N N N N N -2.210 -2.617  34.900 -0.379  -3.076 -1.219 "HO2'" SAH 62 
A1EL0 H1  H1  H 0 1 N N N N N N -3.274 -2.188  32.434 -1.820  -2.151 1.072  "H1'"  SAH 63 
A1EL0 H20 H20 H 0 1 N N N N N N -5.322 -2.899  33.704 -5.080  -3.159 -0.617 H8     SAH 64 
A1EL0 H27 H27 H 0 1 N N N N N N -5.670 -9.134  34.469 -4.605  -7.964 -0.405 HN61   SAH 65 
A1EL0 H28 H28 H 0 1 N N N N N N -5.902 -7.812  35.400 -3.391  -9.044 0.020  HN62   SAH 66 
A1EL0 H21 H21 H 0 1 N N N N N N -1.919 -8.282  32.381 0.200   -6.500 1.215  H2     SAH 67 
A1EL0 H31 H31 H 0 1 N N N N N N 0.441  0.211   34.697 -0.997  3.223  -0.313 HOP2   AMP 68 
A1EL0 H12 H12 H 0 1 N N N N N N 1.412  0.882   29.971 2.816   2.380  -1.898 "H5'1" AMP 69 
A1EL0 H13 H13 H 0 1 N N N N N N 0.699  -0.767  29.943 2.062   3.707  -0.982 "H5'2" AMP 70 
A1EL0 H14 H14 H 0 1 N N N N N N 3.081  -1.667  30.260 3.334   2.913  1.068  "H4'"  AMP 71 
A1EL0 H15 H15 H 0 1 N N N N N N 3.688  1.020   30.752 4.615   3.982  -1.453 "H3'"  AMP 72 
A1EL0 H32 H32 H 0 1 N N N N N N 5.050  -0.835  31.225 5.172   5.675  0.137  "HO3'" AMP 73 
A1EL0 H16 H16 H 0 1 N N N N N N 3.598  1.845   28.574 6.654   2.998  -0.991 "H2'"  AMP 74 
A1EL0 H33 H33 H 0 1 N N N N N N 5.880  1.859   29.093 7.003   4.790  0.582  "HO2'" AMP 75 
A1EL0 H17 H17 H 0 1 N N N N N N 4.567  -0.733  27.342 5.673   1.785  1.600  "H1'"  AMP 76 
A1EL0 H18 H18 H 0 1 N N N N N N 1.998  2.147   27.367 5.703   -0.042 -1.734 H8     AMP 77 
A1EL0 H25 H25 H 0 1 N N N N N N 1.788  1.112   21.163 9.821   -2.517 -1.225 HN61   AMP 78 
A1EL0 H26 H26 H 0 1 N N N N N N 0.713  1.437   22.348 11.094  -2.540 -0.128 HN62   AMP 79 
A1EL0 H19 H19 H 0 1 N N N N N N 4.353  -1.982  22.917 10.116  0.624  3.006  H2     AMP 80 
# 
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 
A1EL0 N48 C47 SING N N 1  
A1EL0 N46 C47 DOUB Y N 2  
A1EL0 N46 C45 SING Y N 3  
A1EL0 C47 C42 SING Y N 4  
A1EL0 C45 N44 DOUB Y N 5  
A1EL0 C42 N41 SING Y N 6  
A1EL0 C42 C43 DOUB Y N 7  
A1EL0 N44 C43 SING Y N 8  
A1EL0 N41 C40 DOUB Y N 9  
A1EL0 C43 N39 SING Y N 10 
A1EL0 N39 C40 SING Y N 11 
A1EL0 N39 C37 SING N N 12 
A1EL0 C37 O38 SING N N 13 
A1EL0 C37 C35 SING N N 14 
A1EL0 C20 S19 SING N N 15 
A1EL0 C20 C21 SING N N 16 
A1EL0 O38 C32 SING N N 17 
A1EL0 O36 C35 SING N N 18 
A1EL0 C35 C33 SING N N 19 
A1EL0 S19 C18 SING N N 20 
A1EL0 C22 C21 SING N N 21 
A1EL0 C22 N23 SING N N 22 
A1EL0 C22 C24 SING N N 23 
A1EL0 O26 C24 DOUB N N 24 
A1EL0 C24 O25 SING N N 25 
A1EL0 C32 C33 SING N N 26 
A1EL0 C32 C31 SING N N 27 
A1EL0 C33 O34 SING N N 28 
A1EL0 C31 O30 SING N N 29 
A1EL0 C18 C16 SING N N 30 
A1EL0 C16 O17 SING N N 31 
A1EL0 C16 C14 SING N N 32 
A1EL0 O17 C11 SING N N 33 
A1EL0 O30 P27 SING N N 34 
A1EL0 O15 C14 SING N N 35 
A1EL0 O15 P27 SING N N 36 
A1EL0 C14 C12 SING N N 37 
A1EL0 C11 N10 SING N N 38 
A1EL0 C11 C12 SING N N 39 
A1EL0 O28 P27 DOUB N N 40 
A1EL0 N72 C73 DOUB Y N 41 
A1EL0 N72 C71 SING Y N 42 
A1EL0 P27 O29 SING N N 43 
A1EL0 C73 N74 SING Y N 44 
A1EL0 N10 C71 SING Y N 45 
A1EL0 N10 C68 SING Y N 46 
A1EL0 C71 C70 DOUB Y N 47 
A1EL0 C12 O13 SING N N 48 
A1EL0 N74 C75 DOUB Y N 49 
A1EL0 C68 N69 DOUB Y N 50 
A1EL0 C70 C75 SING Y N 51 
A1EL0 C70 N69 SING Y N 52 
A1EL0 C75 N76 SING N N 53 
A1EL0 C11 H1  SING N N 54 
A1EL0 C12 H2  SING N N 55 
A1EL0 C14 H3  SING N N 56 
A1EL0 C16 H4  SING N N 57 
A1EL0 C18 H5  SING N N 58 
A1EL0 C18 H6  SING N N 59 
A1EL0 C20 H7  SING N N 60 
A1EL0 C20 H8  SING N N 61 
A1EL0 C21 H9  SING N N 62 
A1EL0 C21 H10 SING N N 63 
A1EL0 C22 H11 SING N N 64 
A1EL0 C31 H12 SING N N 65 
A1EL0 C31 H13 SING N N 66 
A1EL0 C32 H14 SING N N 67 
A1EL0 C33 H15 SING N N 68 
A1EL0 C35 H16 SING N N 69 
A1EL0 C37 H17 SING N N 70 
A1EL0 C40 H18 SING N N 71 
A1EL0 C45 H19 SING N N 72 
A1EL0 C68 H20 SING N N 73 
A1EL0 C73 H21 SING N N 74 
A1EL0 N23 H22 SING N N 75 
A1EL0 N23 H23 SING N N 76 
A1EL0 N48 H25 SING N N 77 
A1EL0 N48 H26 SING N N 78 
A1EL0 N76 H27 SING N N 79 
A1EL0 N76 H28 SING N N 80 
A1EL0 O13 H29 SING N N 81 
A1EL0 O25 H30 SING N N 82 
A1EL0 O29 H31 SING N N 83 
A1EL0 O34 H32 SING N N 84 
A1EL0 O36 H33 SING N N 85 
# 
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 
A1EL0 InChI            InChI                1.06  "InChI=1S/C24H32N11O11PS/c25-9(24(39)40)1-2-48-4-11-17(16(38)23(45-11)35-8-33-13-19(27)29-6-31-21(13)35)46-47(41,42)43-3-10-14(36)15(37)22(44-10)34-7-32-12-18(26)28-5-30-20(12)34/h5-11,14-17,22-23,36-38H,1-4,25H2,(H,39,40)(H,41,42)(H2,26,28,30)(H2,27,29,31)/t9-,10+,11+,14+,15+,16+,17+,22+,23+/m0/s1" 
A1EL0 InChIKey         InChI                1.06  QBCXMARFZQJLMA-XPJWLEQASA-N                                                                                                                                                                                                                                                                                  
A1EL0 SMILES_CANONICAL CACTVS               3.385 "N[C@@H](CCSC[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)C(O)=O"                                                                                                                                                                                
A1EL0 SMILES           CACTVS               3.385 "N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34)n5cnc6c(N)ncnc56)C(O)=O"                                                                                                                                                                                            
A1EL0 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)CSCC[C@@H](C(=O)O)N)O)O)N"                                                                                                                                                                            
A1EL0 SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OC4C(OC(C4O)n5cnc6c5ncnc6N)CSCCC(C(=O)O)N)O)O)N"                                                                                                                                                                                                                     
# 
_pdbx_chem_comp_identifier.comp_id           A1EL0 
_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})-4-[[(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]methylsulfanyl]-2-azanyl-butanoic 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 
A1EL0 "Create component" 2025-02-13 PDBC 
A1EL0 "Initial release"  2025-11-26 RCSB 
# 
