data_ZX4
# 
_chem_comp.id                                    ZX4 
_chem_comp.name                                  "5'-S-{(2R,4R)-1-[3-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)propyl]-2-carboxypiperidin-4-yl}-5'-thioadenosine" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C25 H32 N10 O6 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-04-17 
_chem_comp.pdbx_modified_date                    2024-06-28 
_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                        600.650 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     ZX4 
_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        8SIF 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
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 
ZX4 C1  C1  C 0 1 N N N N N N 18.960 9.777  2.820  2.128   -0.662 1.136  C1  ZX4 1  
ZX4 C10 C2  C 0 1 N N N N N N 13.945 5.717  6.272  -4.543  -0.121 -0.414 C10 ZX4 2  
ZX4 C11 C3  C 0 1 N N N N N N 12.722 6.083  7.142  -5.473  -0.416 -1.592 C11 ZX4 3  
ZX4 C12 C4  C 0 1 N N S N N N 20.458 9.947  2.915  3.168   -1.220 0.163  C12 ZX4 4  
ZX4 C13 C5  C 0 1 Y N N N N N 12.314 4.832  7.955  -6.643  -1.237 -1.115 C13 ZX4 5  
ZX4 C14 C6  C 0 1 Y N N N N N 13.132 3.761  8.166  -6.753  -2.576 -1.156 C14 ZX4 6  
ZX4 C15 C7  C 0 1 Y N N N N N 11.107 3.334  9.229  -8.666  -1.856 -0.232 C15 ZX4 7  
ZX4 C16 C8  C 0 1 Y N N N N N 10.967 4.651  8.611  -7.876  -0.733 -0.513 C16 ZX4 8  
ZX4 C17 C9  C 0 1 N N N N N N 9.713  5.298  8.802  -8.370  0.551  -0.194 C17 ZX4 9  
ZX4 C18 C10 C 0 1 N N N N N N 8.995  3.325  10.120 -10.319 -0.485 0.625  C18 ZX4 10 
ZX4 C19 C11 C 0 1 N N S N N N 21.388 8.988  2.226  3.868   -2.442 0.788  C19 ZX4 11 
ZX4 C2  C12 C 0 1 Y N N N N N 23.020 6.822  8.161  9.960   0.911  -0.284 C2  ZX4 12 
ZX4 C20 C13 C 0 1 N N R N N N 22.580 8.853  3.121  5.367   -2.052 0.805  C20 ZX4 13 
ZX4 C21 C14 C 0 1 N N R N N N 22.290 9.662  4.352  5.425   -0.938 -0.271 C21 ZX4 14 
ZX4 C22 C15 C 0 1 Y N N N N N 23.109 10.011 6.593  6.534   1.132  0.651  C22 ZX4 15 
ZX4 C23 C16 C 0 1 Y N N N N N 22.535 7.888  6.104  7.854   -0.249 -0.451 C23 ZX4 16 
ZX4 C24 C17 C 0 1 Y N N N N N 22.199 5.702  6.329  9.767   -1.101 -1.397 C24 ZX4 17 
ZX4 C25 C18 C 0 1 Y N N N N N 23.003 7.978  7.432  8.587   0.858  0.009  C25 ZX4 18 
ZX4 C3  C19 C 0 1 N N R N N N 18.732 7.406  4.788  0.056   1.216  1.631  C3  ZX4 19 
ZX4 C4  C20 C 0 1 N N N N N N 18.174 5.997  4.856  -0.933  0.082  1.915  C4  ZX4 20 
ZX4 C5  C21 C 0 1 N N N N N N 18.144 8.221  5.864  -0.717  2.448  1.153  C5  ZX4 21 
ZX4 C6  C22 C 0 1 N N R N N N 16.633 8.274  5.911  -1.530  2.084  -0.091 C6  ZX4 22 
ZX4 C7  C23 C 0 1 N N N N N N 16.238 9.056  7.187  -2.308  3.289  -0.553 C7  ZX4 23 
ZX4 C8  C24 C 0 1 N N N N N N 16.591 6.000  4.930  -1.740  -0.214 0.649  C8  ZX4 24 
ZX4 C9  C25 C 0 1 N N N N N N 14.638 7.043  5.845  -3.355  0.713  -0.898 C9  ZX4 25 
ZX4 N1  N1  N 0 1 Y N N N N N 22.638 9.174  5.665  6.563   -0.048 -0.031 N1  ZX4 26 
ZX4 N10 N2  N 0 1 N N N N N N 10.203 2.648  9.967  -9.870  -1.684 0.333  N10 ZX4 27 
ZX4 N2  N3  N 0 1 N N N N N N 7.944  2.717  10.888 -11.558 -0.363 1.203  N2  ZX4 28 
ZX4 N3  N4  N 0 1 Y N N N N N 23.370 9.362  7.761  7.723   1.661  0.674  N3  ZX4 29 
ZX4 N4  N5  N 0 1 Y N N N N N 22.133 6.787  5.507  8.479   -1.196 -1.142 N4  ZX4 30 
ZX4 N5  N6  N 0 1 Y N N N N N 22.622 5.673  7.613  10.498  -0.082 -0.985 N5  ZX4 31 
ZX4 N6  N7  N 0 1 N N N N N N 23.502 6.928  9.523  10.734  1.976  0.142  N6  ZX4 32 
ZX4 N7  N8  N 0 1 N N N N N N 16.059 6.951  6.009  -2.461  0.995  0.233  N7  ZX4 33 
ZX4 N8  N9  N 0 1 Y N N N N N 12.384 2.953  8.901  -7.962  -2.955 -0.631 N8  ZX4 34 
ZX4 N9  N10 N 0 1 N N N N N N 8.733  4.662  9.547  -9.594  0.642  0.374  N9  ZX4 35 
ZX4 O1  O1  O 0 1 N N N N N N 20.813 9.843  4.340  4.179   -0.231 -0.091 O1  ZX4 36 
ZX4 O2  O2  O 0 1 N N N N N N 21.784 9.550  0.953  3.663   -3.603 -0.019 O2  ZX4 37 
ZX4 O3  O3  O 0 1 N N N N N N 23.780 9.399  2.498  6.187   -3.162 0.434  O3  ZX4 38 
ZX4 O4  O4  O 0 1 N N N N N N 16.042 8.435  8.274  -1.754  4.155  -1.417 O4  ZX4 39 
ZX4 O5  O5  O 0 1 N N N N N N 16.123 10.308 7.159  -3.430  3.476  -0.146 O5  ZX4 40 
ZX4 O6  O6  O 0 1 N N N N N N 9.486  6.388  8.339  -7.711  1.551  -0.424 O6  ZX4 41 
ZX4 S1  S1  S 0 1 N N N N N N 18.312 8.077  3.093  1.222   0.695  0.343  S1  ZX4 42 
ZX4 H1  H1  H 0 1 N N N N N N 18.500 10.435 3.572  1.429   -1.452 1.413  H1  ZX4 43 
ZX4 H2  H2  H 0 1 N N N N N N 18.650 10.096 1.814  2.629   -0.291 2.030  H2  ZX4 44 
ZX4 H3  H3  H 0 1 N N N N N N 13.618 5.162  5.381  -5.088  0.433  0.350  H3  ZX4 45 
ZX4 H4  H4  H 0 1 N N N N N N 14.646 5.099  6.852  -4.180  -1.060 0.006  H4  ZX4 46 
ZX4 H5  H5  H 0 1 N N N N N N 12.984 6.903  7.827  -5.835  0.522  -2.013 H5  ZX4 47 
ZX4 H6  H6  H 0 1 N N N N N N 11.887 6.397  6.498  -4.928  -0.970 -2.356 H6  ZX4 48 
ZX4 H7  H7  H 0 1 N N N N N N 20.704 10.963 2.571  2.685   -1.505 -0.772 H7  ZX4 49 
ZX4 H8  H8  H 0 1 N N N N N N 14.143 3.609  7.818  -6.003  -3.250 -1.543 H8  ZX4 50 
ZX4 H9  H9  H 0 1 N N N N N N 20.898 8.012  2.092  3.507   -2.612 1.802  H9  ZX4 51 
ZX4 H10 H10 H 0 1 N N N N N N 22.731 7.798  3.392  5.657   -1.665 1.781  H10 ZX4 52 
ZX4 H11 H11 H 0 1 N N N N N N 22.751 10.652 4.217  5.482   -1.372 -1.270 H11 ZX4 53 
ZX4 H12 H12 H 0 1 N N N N N N 23.263 11.068 6.437  5.655   1.564  1.106  H12 ZX4 54 
ZX4 H13 H13 H 0 1 N N N N N N 21.878 4.761  5.908  10.244  -1.887 -1.964 H13 ZX4 55 
ZX4 H14 H14 H 0 1 N N N N N N 19.830 7.390  4.855  0.603   1.459  2.542  H14 ZX4 56 
ZX4 H15 H15 H 0 1 N N N N N N 18.488 5.445  3.958  -0.385  -0.812 2.214  H15 ZX4 57 
ZX4 H16 H16 H 0 1 N N N N N N 18.572 5.498  5.752  -1.609  0.380  2.716  H16 ZX4 58 
ZX4 H17 H17 H 0 1 N N N N N N 18.496 7.814  6.824  -1.390  2.784  1.942  H17 ZX4 59 
ZX4 H18 H18 H 0 1 N N N N N N 18.513 9.251  5.745  -0.015  3.245  0.908  H18 ZX4 60 
ZX4 H19 H19 H 0 1 N N N N N N 16.250 8.802  5.025  -0.856  1.761  -0.884 H19 ZX4 61 
ZX4 H20 H20 H 0 1 N N N N N N 16.192 6.314  3.954  -1.065  -0.526 -0.148 H20 ZX4 62 
ZX4 H21 H21 H 0 1 N N N N N N 16.246 4.980  5.156  -2.455  -1.012 0.852  H21 ZX4 63 
ZX4 H22 H22 H 0 1 N N N N N N 14.256 7.866  6.467  -2.809  0.159  -1.663 H22 ZX4 64 
ZX4 H23 H23 H 0 1 N N N N N N 14.409 7.245  4.788  -3.717  1.651  -1.319 H23 ZX4 65 
ZX4 H24 H24 H 0 1 N N N N N N 8.085  1.819  11.305 -12.087 -1.155 1.389  H24 ZX4 66 
ZX4 H25 H25 H 0 1 N N N N N N 7.072  3.192  11.006 -11.905 0.515  1.425  H25 ZX4 67 
ZX4 H26 H26 H 0 1 N N N N N N 23.482 6.026  9.955  10.330  2.697  0.650  H26 ZX4 68 
ZX4 H27 H27 H 0 1 N N N N N N 24.440 7.275  9.519  11.681  2.002  -0.066 H27 ZX4 69 
ZX4 H29 H29 H 0 1 N N N N N N 12.746 2.075  9.214  -8.271  -3.871 -0.552 H29 ZX4 70 
ZX4 H30 H30 H 0 1 N N N N N N 7.850  5.107  9.697  -9.957  1.512  0.603  H30 ZX4 71 
ZX4 H31 H31 H 0 1 N N N N N N 22.372 8.950  0.511  4.083   -4.402 0.328  H31 ZX4 72 
ZX4 H32 H32 H 0 1 N N N N N N 24.517 9.299  3.089  6.114   -3.921 1.030  H32 ZX4 73 
ZX4 H33 H33 H 0 1 N N N N N N 15.820 9.056  8.958  -2.292  4.912  -1.684 H33 ZX4 74 
# 
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 
ZX4 O2  C19 SING N N 1  
ZX4 C19 C12 SING N N 2  
ZX4 C19 C20 SING N N 3  
ZX4 O3  C20 SING N N 4  
ZX4 C1  C12 SING N N 5  
ZX4 C1  S1  SING N N 6  
ZX4 C12 O1  SING N N 7  
ZX4 S1  C3  SING N N 8  
ZX4 C20 C21 SING N N 9  
ZX4 O1  C21 SING N N 10 
ZX4 C21 N1  SING N N 11 
ZX4 C3  C4  SING N N 12 
ZX4 C3  C5  SING N N 13 
ZX4 C4  C8  SING N N 14 
ZX4 C8  N7  SING N N 15 
ZX4 N4  C23 DOUB Y N 16 
ZX4 N4  C24 SING Y N 17 
ZX4 N1  C23 SING Y N 18 
ZX4 N1  C22 SING Y N 19 
ZX4 C9  N7  SING N N 20 
ZX4 C9  C10 SING N N 21 
ZX4 C5  C6  SING N N 22 
ZX4 C6  N7  SING N N 23 
ZX4 C6  C7  SING N N 24 
ZX4 C23 C25 SING Y N 25 
ZX4 C10 C11 SING N N 26 
ZX4 C24 N5  DOUB Y N 27 
ZX4 C22 N3  DOUB Y N 28 
ZX4 C11 C13 SING N N 29 
ZX4 O5  C7  DOUB N N 30 
ZX4 C7  O4  SING N N 31 
ZX4 C25 N3  SING Y N 32 
ZX4 C25 C2  DOUB Y N 33 
ZX4 N5  C2  SING Y N 34 
ZX4 C13 C14 DOUB Y N 35 
ZX4 C13 C16 SING Y N 36 
ZX4 C2  N6  SING N N 37 
ZX4 C14 N8  SING Y N 38 
ZX4 O6  C17 DOUB N N 39 
ZX4 C16 C17 SING N N 40 
ZX4 C16 C15 DOUB Y N 41 
ZX4 C17 N9  SING N N 42 
ZX4 N8  C15 SING Y N 43 
ZX4 C15 N10 SING N N 44 
ZX4 N9  C18 SING N N 45 
ZX4 N10 C18 DOUB N N 46 
ZX4 C18 N2  SING N N 47 
ZX4 C1  H1  SING N N 48 
ZX4 C1  H2  SING N N 49 
ZX4 C10 H3  SING N N 50 
ZX4 C10 H4  SING N N 51 
ZX4 C11 H5  SING N N 52 
ZX4 C11 H6  SING N N 53 
ZX4 C12 H7  SING N N 54 
ZX4 C14 H8  SING N N 55 
ZX4 C19 H9  SING N N 56 
ZX4 C20 H10 SING N N 57 
ZX4 C21 H11 SING N N 58 
ZX4 C22 H12 SING N N 59 
ZX4 C24 H13 SING N N 60 
ZX4 C3  H14 SING N N 61 
ZX4 C4  H15 SING N N 62 
ZX4 C4  H16 SING N N 63 
ZX4 C5  H17 SING N N 64 
ZX4 C5  H18 SING N N 65 
ZX4 C6  H19 SING N N 66 
ZX4 C8  H20 SING N N 67 
ZX4 C8  H21 SING N N 68 
ZX4 C9  H22 SING N N 69 
ZX4 C9  H23 SING N N 70 
ZX4 N2  H24 SING N N 71 
ZX4 N2  H25 SING N N 72 
ZX4 N6  H26 SING N N 73 
ZX4 N6  H27 SING N N 74 
ZX4 N8  H29 SING N N 75 
ZX4 N9  H30 SING N N 76 
ZX4 O2  H31 SING N N 77 
ZX4 O3  H32 SING N N 78 
ZX4 O4  H33 SING N N 79 
# 
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 
ZX4 SMILES           ACDLabs              12.01 "O=C(O)C1CC(CCN1CCCc1c[NH]c2N=C(N)NC(=O)c21)SCC1OC(n2cnc3c(N)ncnc32)C(O)C1O"                                                                                                                                                                                                   
ZX4 InChI            InChI                1.06  "InChI=1S/C25H32N10O6S/c26-19-16-21(30-9-29-19)35(10-31-16)23-18(37)17(36)14(41-23)8-42-12-3-5-34(13(6-12)24(39)40)4-1-2-11-7-28-20-15(11)22(38)33-25(27)32-20/h7,9-10,12-14,17-18,23,36-37H,1-6,8H2,(H,39,40)(H2,26,29,30)(H4,27,28,32,33,38)/t12-,13-,14-,17-,18-,23-/m1/s1" 
ZX4 InChIKey         InChI                1.06  AOZGSZXCWJDLPF-LVEUASCASA-N                                                                                                                                                                                                                                                    
ZX4 SMILES_CANONICAL CACTVS               3.385 "NC1=Nc2[nH]cc(CCCN3CC[C@H](C[C@@H]3C(O)=O)SC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2C(=O)N1"                                                                                                                                                                         
ZX4 SMILES           CACTVS               3.385 "NC1=Nc2[nH]cc(CCCN3CC[CH](C[CH]3C(O)=O)SC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2C(=O)N1"                                                                                                                                                                                 
ZX4 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1c(c2c([nH]1)N=C(NC2=O)N)CCCN3CC[C@H](C[C@@H]3C(=O)O)SC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O"                                                                                                                                                                      
ZX4 SMILES           "OpenEye OEToolkits" 2.0.7 "c1c(c2c([nH]1)N=C(NC2=O)N)CCCN3CCC(CC3C(=O)O)SCC4C(C(C(O4)n5cnc6c5ncnc6N)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 
ZX4 "SYSTEMATIC NAME" ACDLabs              12.01 "5'-S-{(2R,4R)-1-[3-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)propyl]-2-carboxypiperidin-4-yl}-5'-thioadenosine"                                                                                           
ZX4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{R},4~{R})-4-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]-1-[3-(2-azanyl-4-oxidanylidene-3,7-dihydropyrrolo[2,3-d]pyrimidin-5-yl)propyl]piperidine-2-carboxylic 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 
ZX4 "Create component" 2023-04-17 RCSB 
ZX4 "Initial release"  2024-07-03 RCSB 
# 
