data_ZNA
# 
_chem_comp.id                                    ZNA 
_chem_comp.name                                  "[[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonylpyridin-1-ium-1-yl)-3,4-bis(oxidanyl)thiolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C21 H28 N7 O13 P2 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2018-08-15 
_chem_comp.pdbx_modified_date                    2024-05-08 
_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                        680.499 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     ZNA 
_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        6EDR 
_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_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 
ZNA N01 N1  N 0 1 N N N N N N -17.634 -0.787 -1.646 -2.871 -7.199 0.981  N01 ZNA 1  
ZNA C02 C1  C 0 1 N N N N N N -16.549 -0.012 -1.822 -3.758 -6.280 0.550  C02 ZNA 2  
ZNA O03 O1  O 0 1 N N N N N N -16.462 1.083  -1.260 -4.813 -6.636 0.062  O03 ZNA 3  
ZNA C04 C2  C 0 1 Y N N N N N -15.493 -0.477 -2.644 -3.448 -4.840 0.672  C04 ZNA 4  
ZNA C44 C3  C 0 1 Y N N N N N -15.331 -1.827 -3.004 -4.358 -3.878 0.229  C44 ZNA 5  
ZNA C05 C4  C 0 1 Y N N N N N -14.533 0.431  -3.130 -2.240 -4.417 1.238  C05 ZNA 6  
ZNA C06 C5  C 0 1 Y N N N N N -13.466 0.008  -3.931 -1.998 -3.057 1.328  C06 ZNA 7  
ZNA C07 C6  C 0 1 Y N N N N N -13.323 -1.332 -4.284 -2.949 -2.168 0.861  C07 ZNA 8  
ZNA N08 N2  N 1 1 Y N N N N N -14.268 -2.256 -3.832 -4.082 -2.596 0.337  N08 ZNA 9  
ZNA C09 C7  C 0 1 N N R N N N -14.204 -3.716 -4.127 -5.058 -1.615 -0.144 C09 ZNA 10 
ZNA S10 S1  S 0 1 N N N N N N -13.417 -4.399 -2.643 -4.319 -0.540 -1.441 S10 ZNA 11 
ZNA C42 C8  C 0 1 N N R N N N -13.289 -4.268 -5.274 -5.413 -0.605 0.967  C42 ZNA 12 
ZNA O43 O2  O 0 1 N N N N N N -13.908 -5.453 -5.793 -6.615 -1.030 1.612  O43 ZNA 13 
ZNA C40 C9  C 0 1 N N S N N N -11.903 -4.676 -4.705 -5.614 0.807  0.432  C40 ZNA 14 
ZNA O41 O3  O 0 1 N N N N N N -11.194 -5.499 -5.658 -6.938 1.238  0.752  O41 ZNA 15 
ZNA C11 C10 C 0 1 N N R N N N -12.208 -5.496 -3.449 -5.416 0.896  -1.095 C11 ZNA 16 
ZNA C12 C11 C 0 1 N N N N N N -10.982 -5.704 -2.555 -4.730 2.208  -1.479 C12 ZNA 17 
ZNA O13 O4  O 0 1 N N N N N N -11.049 -4.944 -1.333 -3.505 2.334  -0.754 O13 ZNA 18 
ZNA P14 P1  P 0 1 N N N N N N -11.447 -5.586 0.108  -2.520 3.598  -0.910 P14 ZNA 19 
ZNA O15 O5  O 0 1 N N N N N N -10.420 -5.151 1.075  -3.260 4.924  -0.375 O15 ZNA 20 
ZNA O16 O6  O 0 1 N N N N N N -11.764 -7.032 -0.014 -2.164 3.773  -2.336 O16 ZNA 21 
ZNA O17 O7  O 0 1 N N N N N N -12.852 -4.831 0.415  -1.182 3.346  -0.050 O17 ZNA 22 
ZNA P18 P2  P 0 1 N N N N N N -13.044 -3.502 1.308  0.273  4.035  -0.017 P18 ZNA 23 
ZNA O19 O8  O 0 1 N N N N N N -12.361 -3.688 2.604  0.201  5.398  0.836  O19 ZNA 24 
ZNA O20 O9  O 0 1 N N N N N N -14.489 -3.194 1.299  0.706  4.339  -1.399 O20 ZNA 25 
ZNA O21 O10 O 0 1 N N N N N N -12.224 -2.326 0.498  1.327  3.028  0.667  O21 ZNA 26 
ZNA C22 C12 C 0 1 N N N N N N -12.795 -1.529 -0.561 2.726  3.306  0.751  C22 ZNA 27 
ZNA C23 C13 C 0 1 N N R N N N -12.435 -0.029 -0.435 3.435  2.148  1.456  C23 ZNA 28 
ZNA O24 O11 O 0 1 N N N N N N -12.544 0.527  0.894  3.365  0.965  0.643  O24 ZNA 29 
ZNA C38 C14 C 0 1 N N S N N N -10.975 0.228  -0.776 4.926  2.485  1.647  C38 ZNA 30 
ZNA O39 O12 O 0 1 N N N N N N -10.710 0.046  -2.188 5.265  2.485  3.035  O39 ZNA 31 
ZNA C36 C15 C 0 1 N N R N N N -10.869 1.688  -0.370 5.671  1.347  0.908  C36 ZNA 32 
ZNA O37 O13 O 0 1 N N N N N N -11.315 2.544  -1.442 6.812  0.916  1.652  O37 ZNA 33 
ZNA C25 C16 C 0 1 N N R N N N -11.829 1.800  0.836  4.592  0.234  0.855  C25 ZNA 34 
ZNA N26 N3  N 0 1 Y N N N N N -11.085 2.046  2.118  4.848  -0.680 -0.261 N26 ZNA 35 
ZNA C27 C17 C 0 1 Y N N N N N -10.391 1.107  2.757  4.297  -0.608 -1.505 C27 ZNA 36 
ZNA N28 N4  N 0 1 Y N N N N N -9.858  1.649  3.848  4.746  -1.578 -2.247 N28 ZNA 37 
ZNA C29 C18 C 0 1 Y N N N N N -10.215 2.931  3.900  5.610  -2.333 -1.528 C29 ZNA 38 
ZNA C35 C19 C 0 1 Y N N N N N -10.982 3.180  2.821  5.691  -1.763 -0.246 C35 ZNA 39 
ZNA N34 N5  N 0 1 Y N N N N N -11.490 4.415  2.614  6.487  -2.320 0.660  N34 ZNA 40 
ZNA C33 C20 C 0 1 Y N N N N N -11.217 5.448  3.533  7.194  -3.391 0.365  C33 ZNA 41 
ZNA N32 N6  N 0 1 Y N N N N N -10.412 5.154  4.649  7.154  -3.960 -0.826 N32 ZNA 42 
ZNA C30 C21 C 0 1 Y N N N N N -9.939  3.900  4.793  6.381  -3.478 -1.794 C30 ZNA 43 
ZNA N31 N7  N 0 1 N N N N N N -9.171  3.564  5.831  6.347  -4.081 -3.039 N31 ZNA 44 
ZNA H1  H1  H 0 1 N N N N N N -18.379 -0.477 -1.055 -3.075 -8.144 0.901  H1  ZNA 45 
ZNA H2  H2  H 0 1 N N N N N N -17.696 -1.673 -2.106 -2.028 -6.915 1.367  H2  ZNA 46 
ZNA H3  H3  H 0 1 N N N N N N -16.038 -2.556 -2.638 -5.297 -4.189 -0.205 H3  ZNA 47 
ZNA H4  H4  H 0 1 N N N N N N -14.622 1.478  -2.879 -1.515 -5.134 1.595  H4  ZNA 48 
ZNA H5  H5  H 0 1 N N N N N N -12.743 0.731  -4.280 -1.077 -2.694 1.759  H5  ZNA 49 
ZNA H6  H6  H 0 1 N N N N N N -12.494 -1.652 -4.898 -2.763 -1.107 0.931  H6  ZNA 50 
ZNA H7  H7  H 0 1 N N N N N N -15.210 -4.155 -4.198 -5.953 -2.113 -0.517 H7  ZNA 51 
ZNA H8  H8  H 0 1 N N N N N N -13.164 -3.500 -6.052 -4.608 -0.592 1.702  H8  ZNA 52 
ZNA H9  H9  H 0 1 N N N N N N -14.761 -5.235 -6.150 -6.869 -0.486 2.370  H9  ZNA 53 
ZNA H10 H10 H 0 1 N N N N N N -11.326 -3.777 -4.442 -4.902 1.473  0.919  H10 ZNA 54 
ZNA H11 H11 H 0 1 N N N N N N -10.348 -5.742 -5.300 -7.120 1.278  1.701  H11 ZNA 55 
ZNA H12 H12 H 0 1 N N N N N N -12.708 -6.446 -3.689 -6.368 0.789  -1.615 H12 ZNA 56 
ZNA H13 H13 H 0 1 N N N N N N -10.908 -6.772 -2.302 -4.521 2.210  -2.548 H13 ZNA 57 
ZNA H14 H14 H 0 1 N N N N N N -10.084 -5.397 -3.112 -5.384 3.045  -1.235 H14 ZNA 58 
ZNA H15 H15 H 0 1 N N N N N N -10.069 -5.909 1.527  -3.522 4.881  0.554  H15 ZNA 59 
ZNA H16 H16 H 0 1 N N N N N N -12.986 -3.577 3.311  -0.076 5.274  1.754  H16 ZNA 60 
ZNA H17 H17 H 0 1 N N N N N N -13.890 -1.633 -0.529 3.134  3.424  -0.253 H17 ZNA 61 
ZNA H18 H18 H 0 1 N N N N N N -12.419 -1.902 -1.525 2.881  4.225  1.316  H18 ZNA 62 
ZNA H19 H19 H 0 1 N N N N N N -13.068 0.541  -1.131 2.968  1.961  2.423  H19 ZNA 63 
ZNA H20 H20 H 0 1 N N N N N N -10.316 -0.396 -0.154 5.161  3.449  1.196  H20 ZNA 64 
ZNA H21 H21 H 0 1 N N N N N N -9.791  0.214  -2.363 6.193  2.691  3.214  H21 ZNA 65 
ZNA H22 H22 H 0 1 N N N N N N -9.841  1.928  -0.060 5.958  1.658  -0.097 H22 ZNA 66 
ZNA H23 H23 H 0 1 N N N N N N -11.243 3.452  -1.173 7.476  1.606  1.789  H23 ZNA 67 
ZNA H24 H24 H 0 1 N N N N N N -12.536 2.624  0.656  4.557  -0.310 1.799  H24 ZNA 68 
ZNA H25 H25 H 0 1 N N N N N N -10.280 0.080  2.443  3.593  0.144  -1.828 H25 ZNA 69 
ZNA H26 H26 H 0 1 N N N N N N -11.616 6.441  3.384  7.831  -3.819 1.124  H26 ZNA 70 
ZNA H27 H27 H 0 1 N N N N N N -9.036  4.362  6.419  5.786  -3.713 -3.740 H27 ZNA 71 
ZNA H28 H28 H 0 1 N N N N N N -9.616  2.837  6.353  6.883  -4.870 -3.211 H28 ZNA 72 
# 
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 
ZNA O43 C42 SING N N 1  
ZNA O41 C40 SING N N 2  
ZNA C42 C40 SING N N 3  
ZNA C42 C09 SING N N 4  
ZNA C40 C11 SING N N 5  
ZNA C07 C06 DOUB Y N 6  
ZNA C07 N08 SING Y N 7  
ZNA C09 N08 SING N N 8  
ZNA C09 S10 SING N N 9  
ZNA C06 C05 SING Y N 10 
ZNA N08 C44 DOUB Y N 11 
ZNA C11 S10 SING N N 12 
ZNA C11 C12 SING N N 13 
ZNA C05 C04 DOUB Y N 14 
ZNA C44 C04 SING Y N 15 
ZNA C04 C02 SING N N 16 
ZNA C12 O13 SING N N 17 
ZNA O39 C38 SING N N 18 
ZNA C02 N01 SING N N 19 
ZNA C02 O03 DOUB N N 20 
ZNA O37 C36 SING N N 21 
ZNA O13 P14 SING N N 22 
ZNA C38 C23 SING N N 23 
ZNA C38 C36 SING N N 24 
ZNA C22 C23 SING N N 25 
ZNA C22 O21 SING N N 26 
ZNA C23 O24 SING N N 27 
ZNA C36 C25 SING N N 28 
ZNA O16 P14 DOUB N N 29 
ZNA P14 O17 SING N N 30 
ZNA P14 O15 SING N N 31 
ZNA O17 P18 SING N N 32 
ZNA O21 P18 SING N N 33 
ZNA C25 O24 SING N N 34 
ZNA C25 N26 SING N N 35 
ZNA O20 P18 DOUB N N 36 
ZNA P18 O19 SING N N 37 
ZNA N26 C27 SING Y N 38 
ZNA N26 C35 SING Y N 39 
ZNA N34 C35 DOUB Y N 40 
ZNA N34 C33 SING Y N 41 
ZNA C27 N28 DOUB Y N 42 
ZNA C35 C29 SING Y N 43 
ZNA C33 N32 DOUB Y N 44 
ZNA N28 C29 SING Y N 45 
ZNA C29 C30 DOUB Y N 46 
ZNA N32 C30 SING Y N 47 
ZNA C30 N31 SING N N 48 
ZNA N01 H1  SING N N 49 
ZNA N01 H2  SING N N 50 
ZNA C44 H3  SING N N 51 
ZNA C05 H4  SING N N 52 
ZNA C06 H5  SING N N 53 
ZNA C07 H6  SING N N 54 
ZNA C09 H7  SING N N 55 
ZNA C42 H8  SING N N 56 
ZNA O43 H9  SING N N 57 
ZNA C40 H10 SING N N 58 
ZNA O41 H11 SING N N 59 
ZNA C11 H12 SING N N 60 
ZNA C12 H13 SING N N 61 
ZNA C12 H14 SING N N 62 
ZNA O15 H15 SING N N 63 
ZNA O19 H16 SING N N 64 
ZNA C22 H17 SING N N 65 
ZNA C22 H18 SING N N 66 
ZNA C23 H19 SING N N 67 
ZNA C38 H20 SING N N 68 
ZNA O39 H21 SING N N 69 
ZNA C36 H22 SING N N 70 
ZNA O37 H23 SING N N 71 
ZNA C25 H24 SING N N 72 
ZNA C27 H25 SING N N 73 
ZNA C33 H26 SING N N 74 
ZNA N31 H27 SING N N 75 
ZNA N31 H28 SING N N 76 
# 
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 
ZNA SMILES           ACDLabs              12.01 "Nc1ncnc2c1ncn2C1OC(COP(=O)(O)OP(=O)(O)OCC2SC([n+]3cc(ccc3)C(N)=O)C(O)C2O)C(O)C1O"                                                                                                                                                                                                       
ZNA InChI            InChI                1.06  "InChI=1S/C21H27N7O13P2S/c22-17-12-19(25-7-24-17)28(8-26-12)20-15(31)13(29)10(40-20)5-38-42(34,35)41-43(36,37)39-6-11-14(30)16(32)21(44-11)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/p+1/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1" 
ZNA InChIKey         InChI                1.06  YLEHCOOOOOOSDX-NNYOXOHSSA-O                                                                                                                                                                                                                                                              
ZNA SMILES_CANONICAL CACTVS               3.385 "NC(=O)c1ccc[n+](c1)[C@@H]2S[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O"                                                                                                                                                              
ZNA SMILES           CACTVS               3.385 "NC(=O)c1ccc[n+](c1)[CH]2S[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O"                                                                                                                                                                         
ZNA SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](S2)COP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N"                                                                                                                                                             
ZNA SMILES           "OpenEye OEToolkits" 2.0.7 "c1cc(c[n+](c1)C2C(C(C(S2)COP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N"                                                                                                                                                                                                 
# 
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 
ZNA "SYSTEMATIC NAME" ACDLabs              12.01 "1-[(2R,3R,4S,5R)-5-({[(R)-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxythiolan-2-yl]-3-carbamoylpyridin-1-ium (non-preferred name)" 
ZNA "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonylpyridin-1-ium-1-yl)-3,4-bis(oxidanyl)thiolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl 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 
ZNA "Create component" 2018-08-15 RCSB 
ZNA "Initial release"  2018-11-21 RCSB 
ZNA "Modify charge"    2024-05-08 RCSB 
# 
