data_1XE
# 
_chem_comp.id                                    1XE 
_chem_comp.name                                  "[5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)furan-2-yl]methyl (3R)-4-{[3-({(E)-2-[(2,2-dihydroxyethyl)sulfanyl]ethenyl}amino)-3-oxopropyl]amino}-3-hydroxy-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C23 H34 N7 O18 P3 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2013-07-25 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        821.538 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     1XE 
_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        4KVM 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_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_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_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 
1XE N1A N1A N 0 1 Y N N N N N -63.863 -12.746 -75.279 10.846  1.621  -0.621 N1A 1XE 1  
1XE C2A C2A C 0 1 Y N N N N N -64.479 -11.617 -74.906 9.690   1.554  -1.255 C2A 1XE 2  
1XE N3A N3A N 0 1 Y N N N N N -64.005 -10.400 -75.239 8.783   0.640  -0.977 N3A 1XE 3  
1XE C4A C4A C 0 1 Y N N N N N -62.869 -10.276 -75.979 9.003   -0.265 -0.029 C4A 1XE 4  
1XE C5A C5A C 0 1 Y N N N N N -62.216 -11.420 -76.379 10.219  -0.236 0.675  C5A 1XE 5  
1XE C6A C6A C 0 1 Y N N N N N -62.743 -12.687 -76.008 11.155  0.758  0.341  C6A 1XE 6  
1XE N6A N6A N 0 1 N N N N N N -62.063 -13.893 -76.423 12.370  0.836  1.000  N6A 1XE 7  
1XE N7A N7A N 0 1 Y N N N N N -61.138 -11.027 -77.087 10.187  -1.252 1.570  N7A 1XE 8  
1XE C8A C8A C 0 1 Y N N N N N -61.092 -9.698  -77.148 9.056   -1.889 1.464  C8A 1XE 9  
1XE N9A N9A N 0 1 Y N N N N N -62.140 -9.222  -76.485 8.290   -1.318 0.490  N9A 1XE 10 
1XE C1B C1B C 0 1 Y N N N N N -62.392 -7.857  -76.346 7.012   -1.729 0.094  C1B 1XE 11 
1XE C2B C2B C 0 1 Y N N N N N -63.535 -7.241  -75.839 6.318   -2.770 0.613  C2B 1XE 12 
1XE O2B O2B O 0 1 N N N N N N -64.744 -7.833  -75.336 6.727   -3.604 1.610  O2B 1XE 13 
1XE C3B C3B C 0 1 Y N N N N N -63.247 -5.834  -75.917 5.082   -2.823 -0.080 C3B 1XE 14 
1XE O3B O3B O 0 1 N N N N N N -64.037 -4.792  -75.566 4.076   -3.719 0.122  O3B 1XE 15 
1XE P3B P3B P 0 1 N N N N N N -65.304 -4.550  -76.435 2.994   -3.251 1.219  P3B 1XE 16 
1XE O7A O7A O 0 1 N N N N N N -65.673 -5.914  -77.168 2.220   -1.943 0.685  O7A 1XE 17 
1XE O8A O8A O 0 1 N N N N N N -66.441 -4.087  -75.573 1.934   -4.437 1.467  O8A 1XE 18 
1XE O9A O9A O 0 1 N N N N N N -64.990 -3.544  -77.455 3.684   -2.932 2.488  O9A 1XE 19 
1XE C4B C4B C 0 1 Y N N N N N -61.983 -5.733  -76.465 5.094   -1.817 -0.978 C4B 1XE 20 
1XE O4B O4B O 0 1 Y N N N N N -61.516 -6.935  -76.699 6.262   -1.155 -0.865 O4B 1XE 21 
1XE C5B C5B C 0 1 N N N N N N -61.286 -4.449  -76.723 3.984   -1.486 -1.943 C5B 1XE 22 
1XE O5B O5B O 0 1 N N N N N N -59.949 -4.295  -76.164 3.084   -0.558 -1.333 O5B 1XE 23 
1XE P1A P1A P 0 1 N N N N N N -59.624 -4.589  -74.599 1.778   0.016  -2.079 P1A 1XE 24 
1XE O1A O1A O 0 1 N N N N N N -60.909 -4.835  -73.783 0.744   -1.187 -2.352 O1A 1XE 25 
1XE O2A O2A O 0 1 N N N N N N -58.924 -3.436  -74.070 2.175   0.628  -3.368 O2A 1XE 26 
1XE O3A O3A O 0 1 N N N N N N -58.697 -5.862  -74.485 1.075   1.128  -1.151 O3A 1XE 27 
1XE P2A P2A P 0 1 N N N N N N -58.021 -6.214  -73.113 -0.035  2.264  -1.413 P2A 1XE 28 
1XE O4A O4A O 0 1 N N N N N N -58.901 -7.233  -72.275 -1.146  1.693  -2.208 O4A 1XE 29 
1XE O5A O5A O 0 1 N N N N N N -57.798 -4.924  -72.275 0.629   3.488  -2.221 O5A 1XE 30 
1XE O6A O6A O 0 1 N N N N N N -56.616 -6.874  -73.483 -0.602  2.796  -0.003 O6A 1XE 31 
1XE CBP CBP C 0 1 N N N N N N -55.391 -8.386  -75.123 -1.960  4.021  1.576  CBP 1XE 32 
1XE CCP CCP C 0 1 N N N N N N -56.459 -7.321  -74.860 -1.676  3.733  0.101  CCP 1XE 33 
1XE CDP CDP C 0 1 N N N N N N -55.689 -9.165  -76.331 -2.348  2.721  2.284  CDP 1XE 34 
1XE CEP CEP C 0 1 N N N N N N -54.045 -7.717  -75.278 -0.708  4.605  2.233  CEP 1XE 35 
1XE CAP CAP C 0 1 N N R N N N -55.317 -9.288  -73.864 -3.110  5.025  1.687  CAP 1XE 36 
1XE OAP OAP O 0 1 N N N N N N -56.524 -10.023 -73.848 -2.700  6.280  1.141  OAP 1XE 37 
1XE C9P C9P C 0 1 N N N N N N -54.197 -10.276 -73.804 -4.302  4.510  0.923  C9P 1XE 38 
1XE O9P O9P O 0 1 N N N N N N -54.420 -11.473 -74.134 -4.661  5.071  -0.090 O9P 1XE 39 
1XE N8P N8P N 0 1 N N N N N N -52.839 -9.911  -73.360 -4.969  3.425  1.365  N8P 1XE 40 
1XE C7P C7P C 0 1 N N N N N N -51.972 -11.122 -73.435 -6.066  2.867  0.572  C7P 1XE 41 
1XE C6P C6P C 0 1 N N N N N N -51.685 -11.921 -74.697 -6.649  1.649  1.293  C6P 1XE 42 
1XE C5P C5P C 0 1 N N N N N N -51.953 -11.454 -76.132 -7.778  1.075  0.477  C5P 1XE 43 
1XE O5P O5P O 0 1 N N N N N N -52.582 -12.201 -76.956 -8.086  1.588  -0.578 O5P 1XE 44 
1XE N4P N4P N 0 1 N N N N N N -51.506 -10.144 -76.658 -8.444  -0.010 0.919  N4P 1XE 45 
1XE C3P C3P C 0 1 N N N N N N -51.808 -9.773  -78.083 -9.494  -0.544 0.161  C3P 1XE 46 
1XE C2P C2P C 0 1 N N N N N N -50.784 -10.186 -79.091 -10.150 -1.611 0.596  C2P 1XE 47 
1XE S1P S1P S 0 1 N N N N N N -51.156 -10.089 -80.776 -11.470 -2.283 -0.358 S1P 1XE 48 
1XE C1  C1  C 0 1 N N N N N N -50.402 -8.657  -81.472 -12.021 -3.692 0.643  C1  1XE 49 
1XE C2  C2  C 0 1 N N N N N N -48.889 -8.476  -81.309 -13.184 -4.394 -0.061 C2  1XE 50 
1XE O21 O21 O 0 1 N N N N N N -48.489 -8.078  -80.076 -14.266 -3.475 -0.226 O21 1XE 51 
1XE O1  O1  O 0 1 N Y N N N N -47.941 -9.501  -81.620 -12.755 -4.859 -1.342 O1  1XE 52 
1XE H1  H1  H 0 1 N N N N N N -65.384 -11.684 -74.320 9.479   2.275  -2.030 H1  1XE 53 
1XE H2  H2  H 0 1 N N N N N N -62.560 -14.691 -76.082 12.583  0.200  1.701  H2  1XE 54 
1XE H3  H3  H 0 1 N N N N N N -62.024 -13.927 -77.422 13.007  1.527  0.761  H3  1XE 55 
1XE H4  H4  H 0 1 N N N N N N -60.336 -9.111  -77.648 8.768   -2.743 2.059  H4  1XE 56 
1XE H5  H5  H 0 1 N N N N N N -65.342 -7.148  -75.061 6.486   -3.306 2.497  H5  1XE 57 
1XE H6  H6  H 0 1 N N N N N N -65.614 -5.795  -78.109 1.745   -2.079 -0.146 H6  1XE 58 
1XE H7  H7  H 0 1 N N N N N N -66.730 -3.230  -75.863 1.251   -4.225 2.117  H7  1XE 59 
1XE H8  H8  H 0 1 N N N N N N -61.205 -4.329  -77.813 4.407   -1.043 -2.845 H8  1XE 60 
1XE H9  H9  H 0 1 N N N N N N -61.912 -3.644  -76.311 3.445   -2.397 -2.204 H9  1XE 61 
1XE H10 H10 H 0 1 N N N N N N -60.980 -4.180  -73.099 0.440   -1.635 -1.551 H10 1XE 62 
1XE H11 H11 H 0 1 N N N N N N -58.234 -5.012  -71.436 1.365   3.911  -1.758 H11 1XE 63 
1XE H12 H12 H 0 1 N N N N N N -56.208 -6.440  -75.469 -1.399  4.659  -0.404 H12 1XE 64 
1XE H13 H13 H 0 1 N N N N N N -57.425 -7.731  -75.189 -2.568  3.317  -0.367 H13 1XE 65 
1XE H14 H14 H 0 1 N N N N N N -56.669 -9.653  -76.221 -1.491  2.049  2.303  H14 1XE 66 
1XE H15 H15 H 0 1 N N N N N N -55.709 -8.495  -77.203 -2.660  2.943  3.305  H15 1XE 67 
1XE H16 H16 H 0 1 N N N N N N -54.912 -9.930  -76.474 -3.170  2.247  1.748  H16 1XE 68 
1XE H17 H17 H 0 1 N N N N N N -53.819 -7.132  -74.374 -0.479  5.571  1.783  H17 1XE 69 
1XE H18 H18 H 0 1 N N N N N N -53.269 -8.483  -75.422 -0.884  4.734  3.300  H18 1XE 70 
1XE H19 H19 H 0 1 N N N N N N -54.066 -7.048  -76.151 0.132   3.926  2.082  H19 1XE 71 
1XE H20 H20 H 0 1 N N N N N N -55.263 -8.636  -72.979 -3.379  5.155  2.735  H20 1XE 72 
1XE H21 H21 H 0 1 N N N N N N -56.333 -10.948 -73.949 -2.445  6.240  0.209  H21 1XE 73 
1XE H22 H22 H 0 1 N N N N N N -52.548 -9.003  -73.059 -4.722  3.015  2.208  H22 1XE 74 
1XE H23 H23 H 0 1 N N N N N N -52.413 -11.841 -72.729 -6.844  3.620  0.445  H23 1XE 75 
1XE H24 H24 H 0 1 N N N N N N -50.988 -10.800 -73.064 -5.691  2.564  -0.406 H24 1XE 76 
1XE H25 H25 H 0 1 N N N N N N -52.256 -12.855 -74.585 -5.871  0.896  1.419  H25 1XE 77 
1XE H26 H26 H 0 1 N N N N N N -50.608 -12.143 -74.661 -7.024  1.952  2.270  H26 1XE 78 
1XE H27 H27 H 0 1 N N N N N N -51.006 -9.510  -76.068 -8.198  -0.421 1.763  H27 1XE 79 
1XE H28 H28 H 0 1 N N N N N N -52.707 -9.242  -78.361 -9.769  -0.087 -0.778 H28 1XE 80 
1XE H29 H29 H 0 1 N N N N N N -49.817 -10.543 -78.768 -9.875  -2.069 1.535  H29 1XE 81 
1XE H30 H30 H 0 1 N N N N N N -50.885 -7.781  -81.015 -11.196 -4.393 0.769  H30 1XE 82 
1XE H31 H31 H 0 1 N N N N N N -50.613 -8.671  -82.551 -12.349 -3.338 1.620  H31 1XE 83 
1XE H32 H32 H 0 1 N N N N N N -47.543 -7.991  -80.062 -14.042 -2.695 -0.752 H32 1XE 84 
1XE H33 H33 H 0 1 N N N N N N -47.062 -9.183  -81.448 -13.442 -5.316 -1.846 H33 1XE 85 
1XE H34 H34 H 0 1 N N N N N N -48.645 -7.646  -81.988 -13.515 -5.241 0.541  H34 1XE 86 
# 
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 
1XE C1  C2  SING N N 1  
1XE C1  S1P SING N N 2  
1XE C2  O21 SING N N 3  
1XE S1P C2P SING N N 4  
1XE C2P C3P DOUB N E 5  
1XE C3P N4P SING N N 6  
1XE O9A P3B DOUB N N 7  
1XE O7A P3B SING N N 8  
1XE C8A N7A DOUB Y N 9  
1XE C8A N9A SING Y N 10 
1XE N7A C5A SING Y N 11 
1XE O5P C5P DOUB N N 12 
1XE C5B C4B SING N N 13 
1XE C5B O5B SING N N 14 
1XE O4B C4B SING Y N 15 
1XE O4B C1B SING Y N 16 
1XE N4P C5P SING N N 17 
1XE N9A C1B SING N N 18 
1XE N9A C4A SING Y N 19 
1XE C4B C3B DOUB Y N 20 
1XE P3B O8A SING N N 21 
1XE P3B O3B SING N N 22 
1XE N6A C6A SING N N 23 
1XE C5A C6A DOUB Y N 24 
1XE C5A C4A SING Y N 25 
1XE C1B C2B DOUB Y N 26 
1XE CDP CBP SING N N 27 
1XE O5B P1A SING N N 28 
1XE C5P C6P SING N N 29 
1XE C6A N1A SING Y N 30 
1XE C4A N3A DOUB Y N 31 
1XE C3B C2B SING Y N 32 
1XE C3B O3B SING N N 33 
1XE C2B O2B SING N N 34 
1XE N1A C2A DOUB Y N 35 
1XE CEP CBP SING N N 36 
1XE N3A C2A SING Y N 37 
1XE CBP CCP SING N N 38 
1XE CBP CAP SING N N 39 
1XE CCP O6A SING N N 40 
1XE C6P C7P SING N N 41 
1XE P1A O3A SING N N 42 
1XE P1A O2A DOUB N N 43 
1XE P1A O1A SING N N 44 
1XE O3A P2A SING N N 45 
1XE O9P C9P DOUB N N 46 
1XE CAP OAP SING N N 47 
1XE CAP C9P SING N N 48 
1XE C9P N8P SING N N 49 
1XE O6A P2A SING N N 50 
1XE C7P N8P SING N N 51 
1XE P2A O4A DOUB N N 52 
1XE P2A O5A SING N N 53 
1XE C2  O1  SING N N 54 
1XE C2A H1  SING N N 55 
1XE N6A H2  SING N N 56 
1XE N6A H3  SING N N 57 
1XE C8A H4  SING N N 58 
1XE O2B H5  SING N N 59 
1XE O7A H6  SING N N 60 
1XE O8A H7  SING N N 61 
1XE C5B H8  SING N N 62 
1XE C5B H9  SING N N 63 
1XE O1A H10 SING N N 64 
1XE O5A H11 SING N N 65 
1XE CCP H12 SING N N 66 
1XE CCP H13 SING N N 67 
1XE CDP H14 SING N N 68 
1XE CDP H15 SING N N 69 
1XE CDP H16 SING N N 70 
1XE CEP H17 SING N N 71 
1XE CEP H18 SING N N 72 
1XE CEP H19 SING N N 73 
1XE CAP H20 SING N N 74 
1XE OAP H21 SING N N 75 
1XE N8P H22 SING N N 76 
1XE C7P H23 SING N N 77 
1XE C7P H24 SING N N 78 
1XE C6P H25 SING N N 79 
1XE C6P H26 SING N N 80 
1XE N4P H27 SING N N 81 
1XE C3P H28 SING N N 82 
1XE C2P H29 SING N N 83 
1XE C1  H30 SING N N 84 
1XE C1  H31 SING N N 85 
1XE O21 H32 SING N N 86 
1XE O1  H33 SING N N 87 
1XE C2  H34 SING N N 88 
# 
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 
1XE SMILES           ACDLabs              12.01 "O=C(N\C=C\SCC(O)O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCc3oc(n2cnc1c(ncnc12)N)c(O)c3OP(=O)(O)O"                                                                                                                                                                                                             
1XE InChI            InChI                1.03  "InChI=1S/C23H34N7O18P3S/c1-23(2,18(35)21(36)26-4-3-13(31)25-5-6-52-8-14(32)33)9-45-51(42,43)48-50(40,41)44-7-12-17(47-49(37,38)39)16(34)22(46-12)30-11-29-15-19(24)27-10-28-20(15)30/h5-6,10-11,14,18,32-35H,3-4,7-9H2,1-2H3,(H,25,31)(H,26,36)(H,40,41)(H,42,43)(H2,24,27,28)(H2,37,38,39)/b6-5+/t18-/m0/s1" 
1XE InChIKey         InChI                1.03  IWZWXZGRAJOFTE-QWNKOJSDSA-N                                                                                                                                                                                                                                                                                    
1XE SMILES_CANONICAL CACTVS               3.385 "CC(C)(CO[P](O)(=O)O[P](O)(=O)OCc1oc(n2cnc3c(N)ncnc23)c(O)c1O[P](O)(O)=O)[C@@H](O)C(=O)NCCC(=O)N/C=C/SCC(O)O"                                                                                                                                                                                                  
1XE SMILES           CACTVS               3.385 "CC(C)(CO[P](O)(=O)O[P](O)(=O)OCc1oc(n2cnc3c(N)ncnc23)c(O)c1O[P](O)(O)=O)[CH](O)C(=O)NCCC(=O)NC=CSCC(O)O"                                                                                                                                                                                                      
1XE SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC(C)(COP(=O)(O)OP(=O)(O)OCc1c(c(c(o1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)N/C=C/SCC(O)O)O"                                                                                                                                                                                                         
1XE SMILES           "OpenEye OEToolkits" 1.7.6 "CC(C)(COP(=O)(O)OP(=O)(O)OCc1c(c(c(o1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NC=CSCC(O)O)O"                                                                                                                                                                                                               
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
1XE "SYSTEMATIC NAME" ACDLabs              12.01 "[5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)furan-2-yl]methyl (3R)-4-{[3-({(E)-2-[(2,2-dihydroxyethyl)sulfanyl]ethenyl}amino)-3-oxopropyl]amino}-3-hydroxy-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate"                                           
1XE "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[[5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-furan-2-yl]methoxy-oxidanyl-phosphoryl] [(3R)-4-[[3-[[(E)-2-[2,2-bis(oxidanyl)ethylsulfanyl]ethenyl]amino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
1XE "Create component" 2013-07-25 RCSB 
1XE "Initial release"  2013-07-31 RCSB 
1XE "Modify PCM"       2024-09-27 PDBE 
# 
loop_
_pdbx_chem_comp_pcm.pcm_id 
_pdbx_chem_comp_pcm.comp_id 
_pdbx_chem_comp_pcm.modified_residue_id 
_pdbx_chem_comp_pcm.type 
_pdbx_chem_comp_pcm.category 
_pdbx_chem_comp_pcm.position 
_pdbx_chem_comp_pcm.polypeptide_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 
1 1XE MET None "Covalent chemical modification" "Amino-acid backbone" N-terminal C2 N ? ? 
2 1XE SER None "Covalent chemical modification" "Amino-acid backbone" N-terminal C2 N ? ? 
# 
