data_A1D9C
# 
_chem_comp.id                                    A1D9C 
_chem_comp.name                                  "(2S)-2-[2-[[(2S,3S,4R,5R)-5-(6-azanyl-2-chloranyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]ethylamino]-3-(1H-imidazol-4-yl)propanoic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C18 H23 Cl N8 O5 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-06-18 
_chem_comp.pdbx_modified_date                    2024-11-01 
_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                        498.944 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1D9C 
_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        8ZX0 
_chem_comp.pdbx_subcomponent_list                ? 
_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 
A1D9C C4   C1  C  0 1 N N S N N N 13.838 12.391 16.486 -2.892 0.793  0.032  C4   A1D9C 1  
A1D9C C6   C2  C  0 1 Y N N N N N 13.037 12.860 14.106 -3.443 -1.391 1.170  C6   A1D9C 2  
A1D9C C8   C3  C  0 1 Y N N N N N 11.344 14.078 14.481 -5.508 -1.690 0.579  C8   A1D9C 3  
A1D9C C21  C4  C  0 1 N N N N N N 20.080 12.575 17.119 3.201  0.239  0.585  C21  A1D9C 4  
A1D9C C22  C5  C  0 1 N N N N N N 20.533 13.797 17.858 4.193  -0.522 -0.297 C22  A1D9C 5  
A1D9C C24  C6  C  0 1 N N R N N N 22.083 15.762 17.381 6.438  -1.427 -0.388 C24  A1D9C 6  
A1D9C C28  C7  C  0 1 N N N N N N 23.528 16.030 16.968 7.852  -1.071 0.073  C28  A1D9C 7  
A1D9C O1   O1  O  0 1 N N N N N N 15.553 10.273 18.223 -1.569 3.875  0.790  O1   A1D9C 8  
A1D9C C2   C8  C  0 1 N N S N N N 15.710 11.013 17.001 -1.617 2.507  1.202  C2   A1D9C 9  
A1D9C C3   C9  C  0 1 N N R N N N 14.441 11.057 16.117 -3.048 1.945  1.049  C3   A1D9C 10 
A1D9C N5   N1  N  0 1 Y N N N N N 12.962 12.972 15.472 -3.771 -0.324 0.387  N5   A1D9C 11 
A1D9C N7   N2  N  0 1 Y N N N N N 12.094 13.506 13.467 -4.462 -2.193 1.279  N7   A1D9C 12 
A1D9C C9   C10 C  0 1 Y N N N N N 10.170 14.849 14.477 -6.828 -2.107 0.340  C9   A1D9C 13 
A1D9C N10  N3  N  0 1 Y N N N N N 9.644  15.229 15.659 -7.607 -1.342 -0.418 N10  A1D9C 14 
A1D9C C11  C11 C  0 1 Y N N N N N 10.274 14.835 16.754 -7.158 -0.213 -0.940 C11  A1D9C 15 
A1D9C CL12 CL1 CL 0 0 N N N N N N 9.541  15.356 18.226 -8.228 0.738  -1.921 CL12 A1D9C 16 
A1D9C N13  N4  N  0 1 Y N N N N N 11.380 14.117 16.908 -5.923 0.208  -0.756 N13  A1D9C 17 
A1D9C C14  C12 C  0 1 Y N N N N N 11.870 13.760 15.720 -5.075 -0.488 -0.006 C14  A1D9C 18 
A1D9C N15  N5  N  0 1 N N N N N N 9.541  15.242 13.363 -7.307 -3.286 0.882  N15  A1D9C 19 
A1D9C O16  O2  O  0 1 N N N N N N 14.929 13.264 16.709 -1.507 0.395  0.134  O16  A1D9C 20 
A1D9C O17  O3  O  0 1 N N N N N N 13.513 10.055 16.487 -3.928 2.948  0.539  O17  A1D9C 21 
A1D9C C18  C13 C  0 1 N N R N N N 15.976 12.483 17.318 -0.765 1.628  0.259  C18  A1D9C 22 
A1D9C C19  C14 C  0 1 N N N N N N 17.341 12.886 16.797 0.610  1.362  0.875  C19  A1D9C 23 
A1D9C S20  S1  S  0 1 N N N N N N 18.540 11.937 17.765 1.639  0.456  -0.312 S20  A1D9C 24 
A1D9C N23  N6  N  0 1 N N N N N N 21.776 14.310 17.219 5.458  -0.698 0.430  N23  A1D9C 25 
A1D9C C25  C15 C  0 1 N N N N N N 21.102 16.549 16.527 6.217  -2.910 -0.233 C25  A1D9C 26 
A1D9C O26  O4  O  0 1 N N N N N N 21.052 17.792 16.725 7.001  -3.777 -0.892 O26  A1D9C 27 
A1D9C O27  O5  O  0 1 N N N N N N 20.490 15.908 15.649 5.335  -3.318 0.485  O27  A1D9C 28 
A1D9C C29  C16 C  0 1 Y N N N N N 23.778 15.682 15.538 8.116  0.389  -0.195 C29  A1D9C 29 
A1D9C C30  C17 C  0 1 Y N N N N N 23.864 16.490 14.448 8.513  1.301  0.712  C30  A1D9C 30 
A1D9C N31  N7  N  0 1 Y N N N N N 24.155 15.681 13.384 8.633  2.493  0.049  N31  A1D9C 31 
A1D9C C32  C18 C  0 1 Y N N N N N 24.234 14.433 13.850 8.304  2.267  -1.242 C32  A1D9C 32 
A1D9C N33  N8  N  0 1 Y N N N N N 24.010 14.381 15.157 8.001  1.005  -1.381 N33  A1D9C 33 
A1D9C H4   H1  H  0 1 N N N N N N 13.270 12.266 17.419 -3.113 1.142  -0.977 H4   A1D9C 34 
A1D9C H6   H2  H  0 1 N N N N N N 13.805 12.290 13.603 -2.478 -1.550 1.629  H6   A1D9C 35 
A1D9C H21A H3  H  0 0 N N N N N N 20.853 11.798 17.210 3.019  -0.326 1.499  H21A A1D9C 36 
A1D9C H21B H4  H  0 0 N N N N N N 19.941 12.832 16.058 3.614  1.215  0.837  H21B A1D9C 37 
A1D9C H22B H5  H  0 0 N N N N N N 19.749 14.568 17.814 3.780  -1.499 -0.549 H22B A1D9C 38 
A1D9C H22A H6  H  0 0 N N N N N N 20.736 13.540 18.908 4.375  0.043  -1.211 H22A A1D9C 39 
A1D9C H24  H7  H  0 1 N N N N N N 21.953 16.049 18.435 6.316  -1.149 -1.435 H24  A1D9C 40 
A1D9C H28A H8  H  0 0 N N N N N N 23.747 17.098 17.117 7.946  -1.266 1.141  H28A A1D9C 41 
A1D9C H28B H9  H  0 0 N N N N N N 24.195 15.427 17.601 8.576  -1.677 -0.472 H28B A1D9C 42 
A1D9C H1   H10 H  0 1 N N N N N N 16.368 10.290 18.711 -2.134 4.462  1.311  H1   A1D9C 43 
A1D9C H2   H11 H  0 1 N N N N N N 16.546 10.611 16.410 -1.275 2.407  2.232  H2   A1D9C 44 
A1D9C H3   H12 H  0 1 N N N N N N 14.707 11.020 15.050 -3.413 1.565  2.003  H3   A1D9C 45 
A1D9C H15A H13 H  0 0 N N N N N N 8.737  15.785 13.607 -6.729 -3.836 1.434  H15A A1D9C 46 
A1D9C H15B H14 H  0 0 N N N N N N 10.161 15.796 12.808 -8.221 -3.564 0.710  H15B A1D9C 47 
A1D9C H17  H15 H  0 1 N N N N N N 12.748 10.109 15.927 -4.015 3.723  1.111  H17  A1D9C 48 
A1D9C H18  H16 H  0 1 N N N N N N 15.957 12.618 18.410 -0.658 2.109  -0.714 H18  A1D9C 49 
A1D9C H19B H17 H  0 0 N N N N N N 17.431 12.640 15.729 1.087  2.311  1.120  H19B A1D9C 50 
A1D9C H19A H18 H  0 0 N N N N N N 17.502 13.965 16.940 0.493  0.769  1.782  H19A A1D9C 51 
A1D9C H23  H19 H  0 1 N N N N N N 22.544 13.797 17.602 5.829  0.190  0.731  H23  A1D9C 52 
A1D9C H5   H21 H  0 1 N N N N N N 20.465 18.190 16.093 6.822  -4.718 -0.761 H5   A1D9C 53 
A1D9C H30  H22 H  0 1 N N N N N N 23.729 17.561 14.426 8.700  1.127  1.761  H30  A1D9C 54 
A1D9C H31  H23 H  0 1 N N N N N N 24.284 15.970 12.436 8.903  3.341  0.434  H31  A1D9C 55 
A1D9C H32  H24 H  0 1 N N N N N N 24.453 13.571 13.238 8.298  3.006  -2.028 H32  A1D9C 56 
# 
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 
A1D9C O1  C2   SING N N 1  
A1D9C C2  C3   SING N N 2  
A1D9C C3  C4   SING N N 3  
A1D9C C4  N5   SING N N 4  
A1D9C N5  C6   SING Y N 5  
A1D9C C6  N7   DOUB Y N 6  
A1D9C N7  C8   SING Y N 7  
A1D9C C8  C9   DOUB Y N 8  
A1D9C C9  N10  SING Y N 9  
A1D9C N10 C11  DOUB Y N 10 
A1D9C C11 CL12 SING N N 11 
A1D9C C11 N13  SING Y N 12 
A1D9C N13 C14  DOUB Y N 13 
A1D9C C9  N15  SING N N 14 
A1D9C C4  O16  SING N N 15 
A1D9C C3  O17  SING N N 16 
A1D9C C2  C18  SING N N 17 
A1D9C C18 C19  SING N N 18 
A1D9C C19 S20  SING N N 19 
A1D9C S20 C21  SING N N 20 
A1D9C C21 C22  SING N N 21 
A1D9C C22 N23  SING N N 22 
A1D9C N23 C24  SING N N 23 
A1D9C C24 C25  SING N N 24 
A1D9C C25 O26  SING N N 25 
A1D9C C25 O27  DOUB N N 26 
A1D9C C24 C28  SING N N 27 
A1D9C C28 C29  SING N N 28 
A1D9C C29 C30  DOUB Y N 29 
A1D9C C30 N31  SING Y N 30 
A1D9C N31 C32  SING Y N 31 
A1D9C C32 N33  DOUB Y N 32 
A1D9C C14 N5   SING Y N 33 
A1D9C C14 C8   SING Y N 34 
A1D9C C18 O16  SING N N 35 
A1D9C N33 C29  SING Y N 36 
A1D9C C4  H4   SING N N 37 
A1D9C C6  H6   SING N N 38 
A1D9C C21 H21A SING N N 39 
A1D9C C21 H21B SING N N 40 
A1D9C C22 H22B SING N N 41 
A1D9C C22 H22A SING N N 42 
A1D9C C24 H24  SING N N 43 
A1D9C C28 H28A SING N N 44 
A1D9C C28 H28B SING N N 45 
A1D9C O1  H1   SING N N 46 
A1D9C C2  H2   SING N N 47 
A1D9C C3  H3   SING N N 48 
A1D9C N15 H15A SING N N 49 
A1D9C N15 H15B SING N N 50 
A1D9C O17 H17  SING N N 51 
A1D9C C18 H18  SING N N 52 
A1D9C C19 H19B SING N N 53 
A1D9C C19 H19A SING N N 54 
A1D9C N23 H23  SING N N 55 
A1D9C O26 H5   SING N N 56 
A1D9C C30 H30  SING N N 57 
A1D9C N31 H31  SING N N 58 
A1D9C C32 H32  SING N N 59 
# 
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 
A1D9C InChI            InChI                1.06  "InChI=1S/C18H23ClN8O5S/c19-18-25-14(20)11-15(26-18)27(7-24-11)16-13(29)12(28)10(32-16)5-33-2-1-22-9(17(30)31)3-8-4-21-6-23-8/h4,6-7,9-10,12-13,16,22,28-29H,1-3,5H2,(H,21,23)(H,30,31)(H2,20,25,26)/t9-,10+,12-,13-,16?/m1/s1" 
A1D9C InChIKey         InChI                1.06  JLQQSEYELKTFRD-DZTHZORUSA-N                                                                                                                                                                                                     
A1D9C SMILES_CANONICAL CACTVS               3.385 "Nc1nc(Cl)nc2n(cnc12)[C@H]3O[C@@H](CSCCN[C@H](Cc4c[nH]cn4)C(O)=O)[C@@H](O)[C@H]3O"                                                                                                                                              
A1D9C SMILES           CACTVS               3.385 "Nc1nc(Cl)nc2n(cnc12)[CH]3O[CH](CSCCN[CH](Cc4c[nH]cn4)C(O)=O)[CH](O)[CH]3O"                                                                                                                                                     
A1D9C SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1c(nc[nH]1)C[C@@H](C(=O)O)NCCSC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3nc(nc4N)Cl)O)O"                                                                                                                                           
A1D9C SMILES           "OpenEye OEToolkits" 2.0.7 "c1c(nc[nH]1)CC(C(=O)O)NCCSCC2C(C(C(O2)n3cnc4c3nc(nc4N)Cl)O)O"                                                                                                                                                                  
# 
_pdbx_chem_comp_identifier.comp_id           A1D9C 
_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})-2-[2-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-azanyl-2-chloranyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]ethylamino]-3-(1~{H}-imidazol-4-yl)propanoic 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 
A1D9C "Create component" 2024-06-18 PDBC 
A1D9C "Initial release"  2024-11-06 RCSB 
# 
