data_A1EJT
# 
_chem_comp.id                                    A1EJT 
_chem_comp.name                                  "(2~{S})-6-[(~{E})-[(2~{S},3~{S},4~{R})-5-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-2,3,4-tris(oxidanyl)pentylidene]amino]-2-azanyl-hexanoic acid" 
_chem_comp.type                                  "L-peptide linking" 
_chem_comp.pdbx_type                             ATOMP 
_chem_comp.formula                               "C21 H35 N7 O15 P2" 
_chem_comp.mon_nstd_parent_comp_id               LYS 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-01-17 
_chem_comp.pdbx_modified_date                    2025-11-07 
_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                        687.488 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1EJT 
_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        9LDC 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBC 
_chem_comp.pdbx_pcm                              Y 
# 
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 
A1EJT C1  C1  C 0 1 N N N N N N -2.788 14.597 0.856   -6.998  0.212  0.449  C1  A1EJT 1  
A1EJT C2  C2  C 0 1 N N S N N N -3.206 14.996 -0.547  -5.631  0.107  -0.177 C2  A1EJT 2  
A1EJT C4  C3  C 0 1 N N S N N N -2.826 16.440 -0.884  -4.683  -0.611 0.786  C4  A1EJT 3  
A1EJT C6  C4  C 0 1 N N R N N N -3.929 17.123 -1.698  -3.295  -0.717 0.151  C6  A1EJT 4  
A1EJT C8  C5  C 0 1 N N N N N N -3.460 18.395 -2.348  -2.347  -1.435 1.113  C8  A1EJT 5  
A1EJT N   N1  N 0 1 N N N Y Y N -5.353 8.934  5.770   -14.556 0.293  0.013  N   A1EJT 6  
A1EJT CA  C6  C 0 1 N N S N Y N -4.764 10.277 5.764   -13.944 1.628  -0.044 CA  A1EJT 7  
A1EJT C   C7  C 0 1 N N N N Y Y -5.456 11.256 6.703   -14.812 2.543  -0.869 C   A1EJT 8  
A1EJT O   O1  O 0 1 N N N N Y Y -4.920 12.366 6.894   -15.614 2.078  -1.644 O   A1EJT 9  
A1EJT CB  C8  C 0 1 N N N N N N -4.760 10.880 4.343   -12.558 1.527  -0.682 CB  A1EJT 10 
A1EJT CG  C9  C 0 1 N N N N N N -3.659 10.319 3.424   -11.640 0.700  0.221  CG  A1EJT 11 
A1EJT CD  C10 C 0 1 N N N N N N -3.631 10.987 2.013   -10.253 0.599  -0.418 CD  A1EJT 12 
A1EJT CE  C11 C 0 1 N N N N N N -2.709 12.248 1.996   -9.335  -0.228 0.484  CE  A1EJT 13 
A1EJT NZ  N2  N 0 1 N N N N N N -3.128 13.206 0.894   -8.007  -0.324 -0.127 NZ  A1EJT 14 
A1EJT C21 C12 C 0 1 N N R N N N 1.443  22.806 -8.038  7.458   0.535  -1.130 C21 A1EJT 15 
A1EJT C26 C13 C 0 1 Y N N N N N 2.927  27.386 -8.861  9.713   4.282  1.078  C26 A1EJT 16 
A1EJT C18 C14 C 0 1 N N N N N N -1.768 21.718 -7.333  5.372   -2.354 -0.649 C18 A1EJT 17 
A1EJT C19 C15 C 0 1 N N R N N N -0.466 21.510 -8.055  6.116   -1.317 -1.493 C19 A1EJT 18 
A1EJT C23 C16 C 0 1 Y N N N N N 1.859  24.870 -6.648  7.398   1.581  1.166  C23 A1EJT 19 
A1EJT C25 C17 C 0 1 Y N N N N N 2.518  26.272 -8.104  8.839   3.188  0.959  C25 A1EJT 20 
A1EJT C29 C18 C 0 1 Y N N N N N 2.774  26.026 -10.741 10.354  3.965  -1.117 C29 A1EJT 21 
A1EJT C31 C19 C 0 1 Y N N N N N 2.271  25.097 -8.783  8.780   2.517  -0.275 C31 A1EJT 22 
A1EJT C32 C20 C 0 1 N N R N N N 1.524  21.916 -6.793  8.441   -0.664 -1.159 C32 A1EJT 23 
A1EJT C34 C21 C 0 1 N N S N N N 0.591  20.776 -7.208  7.560   -1.791 -1.751 C34 A1EJT 24 
A1EJT N22 N3  N 0 1 Y N N N N N 1.845  24.196 -7.836  7.863   1.509  -0.114 N22 A1EJT 25 
A1EJT N24 N4  N 0 1 Y N N N N N 2.251  26.118 -6.738  7.971   2.566  1.793  N24 A1EJT 26 
A1EJT N27 N5  N 0 1 N N N N N N 3.199  28.588 -8.326  9.814   4.981  2.268  N27 A1EJT 27 
A1EJT N28 N6  N 0 1 Y N N N N N 3.050  27.226 -10.213 10.444  4.626  0.023  N28 A1EJT 28 
A1EJT N30 N7  N 0 1 Y N N N N N 2.380  24.908 -10.109 9.545   2.938  -1.276 N30 A1EJT 29 
A1EJT O11 O2  O 0 1 N N N N N N -0.797 18.292 -5.082  -0.074  -3.518 1.627  O11 A1EJT 30 
A1EJT O12 O3  O 0 1 N N N N N N -0.881 19.634 -2.861  0.526   -1.309 2.691  O12 A1EJT 31 
A1EJT O13 O4  O 0 1 N N N N N N -2.468 20.096 -4.688  1.528   -2.027 0.369  O13 A1EJT 32 
A1EJT O15 O5  O 0 1 N N N N N N -4.228 21.276 -5.948  2.704   -4.246 -0.407 O15 A1EJT 33 
A1EJT O16 O6  O 0 1 N N N N N N -3.922 18.741 -6.227  3.421   -3.044 1.693  O16 A1EJT 34 
A1EJT O17 O7  O 0 1 N N N N N N -2.356 20.405 -7.200  4.004   -1.964 -0.512 O17 A1EJT 35 
A1EJT O20 O8  O 0 1 N N N N N N 0.075  22.813 -8.379  6.196   -0.072 -0.779 O20 A1EJT 36 
A1EJT O3  O9  O 0 1 N N N N N N -2.704 14.113 -1.540  -5.720  -0.632 -1.397 O3  A1EJT 37 
A1EJT O33 O10 O 0 1 N N N N N N 2.856  21.530 -6.439  9.556   -0.388 -2.009 O33 A1EJT 38 
A1EJT O35 O11 O 0 1 N N N N N N 1.209  19.748 -7.989  7.798   -1.927 -3.154 O35 A1EJT 39 
A1EJT O5  O12 O 0 1 N N N N N N -2.694 17.090 0.379   -4.593  0.128  2.006  O5  A1EJT 40 
A1EJT O7  O13 O 0 1 N N N N N N -4.450 16.266 -2.717  -3.385  -1.456 -1.069 O7  A1EJT 41 
A1EJT O9  O14 O 0 1 N N N N N N -2.678 17.976 -3.474  -1.025  -1.431 0.571  O9  A1EJT 42 
A1EJT P10 P1  P 0 1 N N N N N N -1.555 18.969 -4.007  0.232   -2.102 1.321  P10 A1EJT 43 
A1EJT P14 P2  P 0 1 N N N N N N -3.349 20.089 -6.017  2.925   -2.825 0.316  P14 A1EJT 44 
A1EJT H1  H1  H 0 1 N N N N N N -2.346 15.207 1.630   -7.125  0.735  1.385  H1  A1EJT 45 
A1EJT H3  H3  H 0 1 N N N N N N -4.305 14.946 -0.576  -5.249  1.107  -0.385 H3  A1EJT 46 
A1EJT H4  H4  H 0 1 N N N N N N -1.881 16.457 -1.446  -5.065  -1.610 0.994  H4  A1EJT 47 
A1EJT H5  H5  H 0 1 N N N N N N -4.742 17.380 -1.003  -2.913  0.283  -0.057 H5  A1EJT 48 
A1EJT H6  H6  H 0 1 N N N N N N -2.846 18.982 -1.649  -2.347  -0.920 2.075  H6  A1EJT 49 
A1EJT H7  H7  H 0 1 N N N N N N -4.318 18.999 -2.678  -2.680  -2.463 1.252  H7  A1EJT 50 
A1EJT H   H8  H 0 1 N N N Y Y N -5.342 8.569  6.701   -14.652 -0.100 -0.911 H   A1EJT 51 
A1EJT HXT H9  H 0 1 N Y N Y Y N -6.296 8.982  5.442   -14.026 -0.322 0.614  HXT A1EJT 52 
A1EJT HA  H11 H 0 1 N N N N Y N -3.716 10.194 6.086   -13.852 2.028  0.966  HA  A1EJT 53 
A1EJT HB2 H13 H 0 1 N N N N N N -4.617 11.967 4.430   -12.640 1.045  -1.656 HB2 A1EJT 54 
A1EJT HB3 H14 H 0 1 N N N N N N -5.736 10.675 3.878   -12.141 2.527  -0.805 HB3 A1EJT 55 
A1EJT HG2 H15 H 0 1 N N N N N N -3.828 9.240  3.296   -11.557 1.182  1.195  HG2 A1EJT 56 
A1EJT HG3 H16 H 0 1 N N N N N N -2.684 10.483 3.907   -12.056 -0.300 0.344  HG3 A1EJT 57 
A1EJT HD2 H17 H 0 1 N N N N N N -4.653 11.288 1.739   -10.335 0.117  -1.392 HD2 A1EJT 58 
A1EJT HD3 H18 H 0 1 N N N N N N -3.254 10.259 1.280   -9.836  1.599  -0.541 HD3 A1EJT 59 
A1EJT HE2 H19 H 0 1 N N N N N N -1.669 11.933 1.824   -9.253  0.254  1.459  HE2 A1EJT 60 
A1EJT HE3 H20 H 0 1 N N N N N N -2.781 12.761 2.967   -9.752  -1.228 0.608  HE3 A1EJT 61 
A1EJT H23 H23 H 0 1 N N N N N N 2.043  22.354 -8.842  7.400   1.007  -2.111 H23 A1EJT 62 
A1EJT H24 H24 H 0 1 N N N N N N -1.590 22.161 -6.342  5.425   -3.326 -1.138 H24 A1EJT 63 
A1EJT H25 H25 H 0 1 N N N N N N -2.429 22.377 -7.916  5.832   -2.417 0.337  H25 A1EJT 64 
A1EJT H26 H26 H 0 1 N N N N N N -0.647 20.935 -8.975  5.599   -1.171 -2.441 H26 A1EJT 65 
A1EJT H27 H27 H 0 1 N N N N N N 1.571  24.413 -5.713  6.661   0.918  1.595  H27 A1EJT 66 
A1EJT H28 H28 H 0 1 N N N N N N 2.882  25.947 -11.813 10.966  4.278  -1.949 H28 A1EJT 67 
A1EJT H29 H29 H 0 1 N N N N N N 1.060  22.454 -5.953  8.774   -0.918 -0.153 H29 A1EJT 68 
A1EJT H30 H30 H 0 1 N N N N N N 0.110  20.353 -6.314  7.750   -2.733 -1.238 H30 A1EJT 69 
A1EJT H31 H31 H 0 1 N N N N N N 3.468  29.223 -9.050  9.278   4.717  3.032  H31 A1EJT 70 
A1EJT H32 H32 H 0 1 N N N N N N 2.385  28.938 -7.861  10.421  5.734  2.338  H32 A1EJT 71 
A1EJT H33 H33 H 0 1 N N N N N N 0.060  19.544 -2.951  0.734   -0.373 2.567  H33 A1EJT 72 
A1EJT H34 H34 H 0 1 N N N N N N -5.133 21.007 -6.056  2.379   -4.179 -1.316 H34 A1EJT 73 
A1EJT H35 H35 H 0 1 N N N N N N -2.945 13.220 -1.322  -6.054  -1.533 -1.287 H35 A1EJT 74 
A1EJT H36 H36 H 0 1 N N N N N N 2.832  20.983 -5.663  10.199  -1.109 -2.059 H36 A1EJT 75 
A1EJT H37 H37 H 0 1 N N N N N N 1.860  19.298 -7.463  8.692   -2.223 -3.374 H37 A1EJT 76 
A1EJT H38 H38 H 0 1 N N N N N N -2.010 16.666 0.884   -4.260  1.029  1.896  H38 A1EJT 77 
A1EJT H39 H39 H 0 1 N N N N N N -4.752 15.455 -2.325  -3.718  -2.357 -0.960 H39 A1EJT 78 
A1EJT OXT O15 O 0 1 N Y N N Y Y -6.592 10.866 7.295   -14.694 3.874  -0.743 OXT A1EJT 79 
A1EJT H8  H2  H 0 1 N Y N N Y Y -6.906 11.558 7.865   -15.272 4.420  -1.293 H8  A1EJT 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 
A1EJT C29 N28 DOUB Y N 1  
A1EJT C29 N30 SING Y N 2  
A1EJT N28 C26 SING Y N 3  
A1EJT N30 C31 DOUB Y N 4  
A1EJT C26 N27 SING N N 5  
A1EJT C26 C25 DOUB Y N 6  
A1EJT C31 C25 SING Y N 7  
A1EJT C31 N22 SING Y N 8  
A1EJT O20 C19 SING N N 9  
A1EJT O20 C21 SING N N 10 
A1EJT C25 N24 SING Y N 11 
A1EJT C19 C18 SING N N 12 
A1EJT C19 C34 SING N N 13 
A1EJT C21 N22 SING N N 14 
A1EJT C21 C32 SING N N 15 
A1EJT O35 C34 SING N N 16 
A1EJT N22 C23 SING Y N 17 
A1EJT C18 O17 SING N N 18 
A1EJT C34 C32 SING N N 19 
A1EJT O17 P14 SING N N 20 
A1EJT C32 O33 SING N N 21 
A1EJT N24 C23 DOUB Y N 22 
A1EJT O16 P14 DOUB N N 23 
A1EJT P14 O15 SING N N 24 
A1EJT P14 O13 SING N N 25 
A1EJT O11 P10 DOUB N N 26 
A1EJT O13 P10 SING N N 27 
A1EJT P10 O9  SING N N 28 
A1EJT P10 O12 SING N N 29 
A1EJT O9  C8  SING N N 30 
A1EJT O7  C6  SING N N 31 
A1EJT C8  C6  SING N N 32 
A1EJT C6  C4  SING N N 33 
A1EJT O3  C2  SING N N 34 
A1EJT C4  C2  SING N N 35 
A1EJT C4  O5  SING N N 36 
A1EJT C2  C1  SING N N 37 
A1EJT C1  NZ  DOUB N N 38 
A1EJT NZ  CE  SING N N 39 
A1EJT CE  CD  SING N N 40 
A1EJT CD  CG  SING N N 41 
A1EJT CG  CB  SING N N 42 
A1EJT CB  CA  SING N N 43 
A1EJT CA  N   SING N N 44 
A1EJT CA  C   SING N N 45 
A1EJT C   O   DOUB N N 46 
A1EJT C1  H1  SING N N 47 
A1EJT C2  H3  SING N N 48 
A1EJT C4  H4  SING N N 49 
A1EJT C6  H5  SING N N 50 
A1EJT C8  H6  SING N N 51 
A1EJT C8  H7  SING N N 52 
A1EJT N   H   SING N N 53 
A1EJT N   HXT SING N N 54 
A1EJT CA  HA  SING N N 55 
A1EJT CB  HB2 SING N N 56 
A1EJT CB  HB3 SING N N 57 
A1EJT CG  HG2 SING N N 58 
A1EJT CG  HG3 SING N N 59 
A1EJT CD  HD2 SING N N 60 
A1EJT CD  HD3 SING N N 61 
A1EJT CE  HE2 SING N N 62 
A1EJT CE  HE3 SING N N 63 
A1EJT C21 H23 SING N N 64 
A1EJT C18 H24 SING N N 65 
A1EJT C18 H25 SING N N 66 
A1EJT C19 H26 SING N N 67 
A1EJT C23 H27 SING N N 68 
A1EJT C29 H28 SING N N 69 
A1EJT C32 H29 SING N N 70 
A1EJT C34 H30 SING N N 71 
A1EJT N27 H31 SING N N 72 
A1EJT N27 H32 SING N N 73 
A1EJT O12 H33 SING N N 74 
A1EJT O15 H34 SING N N 75 
A1EJT O3  H35 SING N N 76 
A1EJT O33 H36 SING N N 77 
A1EJT O35 H37 SING N N 78 
A1EJT O5  H38 SING N N 79 
A1EJT O7  H39 SING N N 80 
A1EJT C   OXT SING N N 81 
A1EJT OXT H8  SING N N 82 
# 
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 
A1EJT InChI            InChI                1.06  "InChI=1S/C21H35N7O15P2/c22-10(21(34)35)3-1-2-4-24-5-11(29)15(31)12(30)6-40-44(36,37)43-45(38,39)41-7-13-16(32)17(33)20(42-13)28-9-27-14-18(23)25-8-26-19(14)28/h5,8-13,15-17,20,29-33H,1-4,6-7,22H2,(H,34,35)(H,36,37)(H,38,39)(H2,23,25,26)/b24-5+/t10-,11-,12+,13+,15-,16+,17+,20+/m0/s1" 
A1EJT InChIKey         InChI                1.06  TWCZUHNBLKYDPP-OMGOSZEYSA-N                                                                                                                                                                                                                                                                  
A1EJT SMILES_CANONICAL CACTVS               3.385 "N[C@@H](CCCCN=C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O"                                                                                                                                                                      
A1EJT SMILES           CACTVS               3.385 "N[CH](CCCCN=C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O"                                                                                                                                                                                
A1EJT 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)OP(=O)(O)OC[C@H]([C@H]([C@H](/C=N/CCCC[C@@H](C(=O)O)N)O)O)O)O)O)N"                                                                                                                                                                 
A1EJT SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC(C(C(C=NCCCCC(C(=O)O)N)O)O)O)O)O)N"                                                                                                                                                                                                      
# 
_pdbx_chem_comp_identifier.comp_id           A1EJT 
_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})-6-[(~{E})-[(2~{S},3~{S},4~{R})-5-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-2,3,4-tris(oxidanyl)pentylidene]amino]-2-azanyl-hexanoic acid" 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            A1EJT 
_pdbx_chem_comp_pcm.modified_residue_id                LYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Non-standard residue" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               ? 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   ? 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1EJT "Create component" 2025-01-17 PDBC 
A1EJT "Initial release"  2025-11-12 RCSB 
# 
