data_ZNB
# 
_chem_comp.id                                    ZNB 
_chem_comp.name                                  "2-[6-azanyl-9-[(2R,3R,4S,5R)-5-[[(azanylidene-$l^{4}-azanylidene)amino]methyl]-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]sulfanyl-N-[[(2R,3S,4R,5R)-5-(6-azanyl-8-bromanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl]ethanamide" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C22 H25 Br N14 O7 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2012-01-06 
_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                        709.492 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     ZNB 
_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        3V8P 
_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 
ZNB N53   N53   N  -1 1 N N N N N N 15.068 5.644  11.321 -5.577 -5.648 3.031  N53   ZNB 1  
ZNB N52   N52   N  1  1 N N N N N N 15.974 6.304  11.950 -5.277 -4.665 2.577  N52   ZNB 2  
ZNB N51   N51   N  0  1 N N N N N N 16.866 6.997  12.529 -4.976 -3.681 2.123  N51   ZNB 3  
ZNB C5    C5    C  0  1 N N N N N N 17.460 6.610  13.808 -5.201 -3.435 0.696  C5    ZNB 4  
ZNB C4    C4    C  0  1 N N R N N N 18.613 7.523  14.092 -6.123 -2.226 0.526  C4    ZNB 5  
ZNB O4    O4    O  0  1 N N N N N N 18.307 8.649  13.363 -5.440 -1.014 0.913  O4    ZNB 6  
ZNB C2    C2    C  0  1 N N S N N N 18.498 7.973  15.535 -6.475 -2.023 -0.964 C2    ZNB 7  
ZNB O2    O2    O  0  1 N N N N N N 19.677 7.569  16.188 -7.755 -2.585 -1.258 O2    ZNB 8  
ZNB C3    C3    C  0  1 N N R N N N 18.506 9.488  15.482 -6.504 -0.488 -1.137 C3    ZNB 9  
ZNB O3    O3    O  0  1 N N N N N N 19.536 9.918  16.349 -7.804 -0.055 -1.543 O3    ZNB 10 
ZNB C1    C1    C  0  1 N N R N N N 18.979 9.667  14.071 -6.167 0.055  0.269  C1    ZNB 11 
ZNB N9A   N9A   N  0  1 Y N N N N N 19.005 10.967 13.377 -5.330 1.253  0.167  N9A   ZNB 12 
ZNB C4A   C4A   C  0  1 Y N N N N N 20.176 11.386 12.967 -5.721 2.545  0.429  C4A   ZNB 13 
ZNB N3A   N3A   N  0  1 Y N N N N N 21.391 10.854 13.080 -6.854 3.118  0.822  N3A   ZNB 14 
ZNB C2A   C2A   C  0  1 Y N N N N N 22.423 11.473 12.584 -6.923 4.422  0.993  C2A   ZNB 15 
ZNB N1A   N1A   N  0  1 Y N N N N N 22.302 12.618 11.965 -5.890 5.218  0.789  N1A   ZNB 16 
ZNB C6A   C6A   C  0  1 Y N N N N N 21.130 13.218 11.829 -4.716 4.735  0.394  C6A   ZNB 17 
ZNB N6A   N6A   N  0  1 N N N N N N 21.066 14.358 11.205 -3.638 5.579  0.182  N6A   ZNB 18 
ZNB C5A   C5A   C  0  1 Y N N N N N 19.999 12.589 12.343 -4.594 3.350  0.198  C5A   ZNB 19 
ZNB N7A   N7A   N  0  1 Y N N N N N 18.719 12.860 12.387 -3.585 2.529  -0.187 N7A   ZNB 20 
ZNB C8A   C8A   C  0  1 Y N N N N N 18.102 11.871 12.987 -4.013 1.291  -0.202 C8A   ZNB 21 
ZNB S81   S81   S  0  1 N N N N N N 16.358 12.005 13.223 -3.041 -0.112 -0.641 S81   ZNB 22 
ZNB C82   C82   C  0  1 N N N N N N 15.638 10.489 13.945 -1.465 0.699  -1.007 C82   ZNB 23 
ZNB C83   C83   C  0  1 N N N N N N 14.531 9.999  13.010 -0.451 -0.338 -1.417 C83   ZNB 24 
ZNB O83   O83   O  0  1 N N N N N N 13.461 9.557  13.387 -0.762 -1.509 -1.458 O83   ZNB 25 
ZNB "N5'" "N5'" N  0  1 N N N N N N 14.891 10.219 11.776 0.803  0.038  -1.739 "N5'" ZNB 26 
ZNB "C5'" "C5'" C  0  1 N N N N N N 14.286 9.872  10.511 1.790  -0.970 -2.137 "C5'" ZNB 27 
ZNB "C4'" "C4'" C  0  1 N N R N N N 15.598 9.718  9.726  3.122  -0.284 -2.447 "C4'" ZNB 28 
ZNB "O4'" "O4'" O  0  1 N N N N N N 16.035 8.387  9.721  3.674  0.277  -1.244 "O4'" ZNB 29 
ZNB "C3'" "C3'" C  0  1 N N S N N N 15.518 10.070 8.271  4.132  -1.319 -2.980 "C3'" ZNB 30 
ZNB "O3'" "O3'" O  0  1 N N N N N N 15.420 11.484 8.135  4.558  -0.969 -4.298 "O3'" ZNB 31 
ZNB "C2'" "C2'" C  0  1 N N R N N N 16.868 9.506  7.846  5.317  -1.239 -1.986 "C2'" ZNB 32 
ZNB "O2'" "O2'" O  0  1 N N N N N N 17.888 10.408 8.138  6.566  -1.307 -2.675 "O2'" ZNB 33 
ZNB "C1'" "C1'" C  0  1 N N R N N N 17.067 8.316  8.761  5.110  0.162  -1.346 "C1'" ZNB 34 
ZNB N9N   N9N   N  0  1 Y N N N N N 17.059 6.999  8.065  5.729  0.219  -0.020 N9N   ZNB 35 
ZNB C8N   C8N   C  0  1 Y N N N N N 16.133 6.450  7.279  5.251  -0.358 1.120  C8N   ZNB 36 
ZNB BR8   BR8   BR 0  0 N N N N N N 14.461 7.142  6.690  3.657  -1.368 1.238  BR8   ZNB 37 
ZNB N7N   N7N   N  0  1 Y N N N N N 16.528 5.263  6.882  6.055  -0.111 2.115  N7N   ZNB 38 
ZNB C5N   C5N   C  0  1 Y N N N N N 17.708 5.033  7.409  7.096  0.638  1.677  C5N   ZNB 39 
ZNB C4N   C4N   C  0  1 Y N N N N N 18.042 6.134  8.159  6.900  0.859  0.303  C4N   ZNB 40 
ZNB N3N   N3N   N  0  1 Y N N N N N 19.199 6.163  8.798  7.795  1.573  -0.371 N3N   ZNB 41 
ZNB C2N   C2N   C  0  1 Y N N N N N 19.997 5.141  8.705  8.851  2.072  0.238  C2N   ZNB 42 
ZNB N1N   N1N   N  0  1 Y N N N N N 19.719 4.074  7.997  9.076  1.895  1.527  N1N   ZNB 43 
ZNB C6N   C6N   C  0  1 Y N N N N N 18.597 3.973  7.331  8.238  1.190  2.281  C6N   ZNB 44 
ZNB N6N   N6N   N  0  1 N N N N N N 18.348 2.892  6.636  8.485  1.007  3.631  N6N   ZNB 45 
ZNB H2    H2    H  0  1 N N N N N N 16.710 6.700  14.608 -4.247 -3.236 0.207  H2    ZNB 46 
ZNB H3    H3    H  0  1 N N N N N N 17.815 5.570  13.753 -5.664 -4.312 0.244  H3    ZNB 47 
ZNB H4    H4    H  0  1 N N N N N N 19.588 7.068  13.865 -7.031 -2.356 1.116  H4    ZNB 48 
ZNB H5    H5    H  0  1 N N N N N N 17.582 7.588  16.008 -5.709 -2.466 -1.601 H5    ZNB 49 
ZNB H6    H6    H  0  1 N N N N N N 19.642 7.835  17.099 -7.810 -3.539 -1.108 H6    ZNB 50 
ZNB H7    H7    H  0  1 N N N N N N 17.519 9.934  15.674 -5.754 -0.170 -1.861 H7    ZNB 51 
ZNB H8    H8    H  0  1 N N N N N N 19.256 9.813  17.251 -8.092 -0.415 -2.393 H8    ZNB 52 
ZNB H9    H9    H  0  1 N N N N N N 20.032 9.350  14.098 -7.082 0.276  0.820  H9    ZNB 53 
ZNB H10   H10   H  0  1 N N N N N N 23.403 11.030 12.686 -7.859 4.855  1.313  H10   ZNB 54 
ZNB H11   H11   H  0  1 N N N N N N 21.981 14.624 10.902 -3.735 6.534  0.320  H11   ZNB 55 
ZNB H12   H12   H  0  1 N N N N N N 20.464 14.270 10.411 -2.786 5.215  -0.106 H12   ZNB 56 
ZNB H13   H13   H  0  1 N N N N N N 15.217 10.711 14.937 -1.604 1.413  -1.819 H13   ZNB 57 
ZNB H14   H14   H  0  1 N N N N N N 16.415 9.716  14.041 -1.111 1.222  -0.119 H14   ZNB 58 
ZNB H15   H15   H  0  1 N N N N N N 15.750 10.724 11.689 1.053  0.975  -1.706 H15   ZNB 59 
ZNB H16   H16   H  0  1 N N N N N N 13.647 10.675 10.114 1.929  -1.684 -1.326 H16   ZNB 60 
ZNB H17   H17   H  0  1 N N N N N N 13.710 8.936  10.560 1.436  -1.493 -3.025 H17   ZNB 61 
ZNB H18   H18   H  0  1 N N N N N N 16.356 10.359 10.200 2.971  0.502  -3.187 H18   ZNB 62 
ZNB H19   H19   H  0  1 N N N N N N 14.693 9.539  7.774  3.695  -2.317 -2.974 H19   ZNB 63 
ZNB H20   H20   H  0  1 N N N N N N 14.559 11.771 8.415  5.195  -1.586 -4.683 H20   ZNB 64 
ZNB H21   H21   H  0  1 N N N N N N 16.853 9.198  6.790  5.246  -2.025 -1.234 H21   ZNB 65 
ZNB H22   H22   H  0  1 N N N N N N 18.722 10.042 7.867  6.701  -2.129 -3.166 H22   ZNB 66 
ZNB H23   H23   H  0  1 N N N N N N 18.039 8.434  9.263  5.512  0.942  -1.992 H23   ZNB 67 
ZNB H24   H24   H  0  1 N N N N N N 20.936 5.173  9.238  9.560  2.647  -0.340 H24   ZNB 68 
ZNB H25   H25   H  0  1 N N N N N N 19.113 2.254  6.725  7.865  0.492  4.171  H25   ZNB 69 
ZNB H26   H26   H  0  1 N N N N N N 17.513 2.461  6.978  9.277  1.393  4.036  H26   ZNB 70 
# 
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 
ZNB N6N   C6N   SING N N 1  
ZNB BR8   C8N   SING N N 2  
ZNB N7N   C8N   DOUB Y N 3  
ZNB N7N   C5N   SING Y N 4  
ZNB C8N   N9N   SING Y N 5  
ZNB C6N   C5N   DOUB Y N 6  
ZNB C6N   N1N   SING Y N 7  
ZNB C5N   C4N   SING Y N 8  
ZNB "C2'" "O2'" SING N N 9  
ZNB "C2'" "C3'" SING N N 10 
ZNB "C2'" "C1'" SING N N 11 
ZNB N1N   C2N   DOUB Y N 12 
ZNB N9N   C4N   SING Y N 13 
ZNB N9N   "C1'" SING N N 14 
ZNB "O3'" "C3'" SING N N 15 
ZNB C4N   N3N   DOUB Y N 16 
ZNB "C3'" "C4'" SING N N 17 
ZNB C2N   N3N   SING Y N 18 
ZNB "C1'" "O4'" SING N N 19 
ZNB "O4'" "C4'" SING N N 20 
ZNB "C4'" "C5'" SING N N 21 
ZNB "C5'" "N5'" SING N N 22 
ZNB N6A   C6A   SING N N 23 
ZNB N53   N52   DOUB N N 24 
ZNB "N5'" C83   SING N N 25 
ZNB C6A   N1A   DOUB Y N 26 
ZNB C6A   C5A   SING Y N 27 
ZNB N52   N51   DOUB N N 28 
ZNB N1A   C2A   SING Y N 29 
ZNB C5A   N7A   SING Y N 30 
ZNB C5A   C4A   DOUB Y N 31 
ZNB N7A   C8A   DOUB Y N 32 
ZNB N51   C5    SING N N 33 
ZNB C2A   N3A   DOUB Y N 34 
ZNB C4A   N3A   SING Y N 35 
ZNB C4A   N9A   SING Y N 36 
ZNB C8A   S81   SING N N 37 
ZNB C8A   N9A   SING Y N 38 
ZNB C83   O83   DOUB N N 39 
ZNB C83   C82   SING N N 40 
ZNB S81   C82   SING N N 41 
ZNB O4    C1    SING N N 42 
ZNB O4    C4    SING N N 43 
ZNB N9A   C1    SING N N 44 
ZNB C5    C4    SING N N 45 
ZNB C1    C3    SING N N 46 
ZNB C4    C2    SING N N 47 
ZNB C3    C2    SING N N 48 
ZNB C3    O3    SING N N 49 
ZNB C2    O2    SING N N 50 
ZNB C5    H2    SING N N 51 
ZNB C5    H3    SING N N 52 
ZNB C4    H4    SING N N 53 
ZNB C2    H5    SING N N 54 
ZNB O2    H6    SING N N 55 
ZNB C3    H7    SING N N 56 
ZNB O3    H8    SING N N 57 
ZNB C1    H9    SING N N 58 
ZNB C2A   H10   SING N N 59 
ZNB N6A   H11   SING N N 60 
ZNB N6A   H12   SING N N 61 
ZNB C82   H13   SING N N 62 
ZNB C82   H14   SING N N 63 
ZNB "N5'" H15   SING N N 64 
ZNB "C5'" H16   SING N N 65 
ZNB "C5'" H17   SING N N 66 
ZNB "C4'" H18   SING N N 67 
ZNB "C3'" H19   SING N N 68 
ZNB "O3'" H20   SING N N 69 
ZNB "C2'" H21   SING N N 70 
ZNB "O2'" H22   SING N N 71 
ZNB "C1'" H23   SING N N 72 
ZNB C2N   H24   SING N N 73 
ZNB N6N   H25   SING N N 74 
ZNB N6N   H26   SING N N 75 
# 
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 
ZNB SMILES           ACDLabs              12.01 "OC1C(O)C(C\N=[N+]=[N-])OC1n1c2ncnc(N)c2nc1SCC(=O)NCC1OC(n2c(Br)nc3c(N)ncnc32)C(O)C1O"                                                                                                                                                                                           
ZNB InChI            InChI                1.06  "InChI=1S/C22H25BrN14O7S/c23-21-33-9-15(24)28-4-30-17(9)36(21)19-13(41)11(39)6(43-19)1-27-8(38)3-45-22-34-10-16(25)29-5-31-18(10)37(22)20-14(42)12(40)7(44-20)2-32-35-26/h4-7,11-14,19-20,39-42H,1-3H2,(H,27,38)(H2,24,28,30)(H2,25,29,31)/t6-,7-,11-,12-,13-,14-,19-,20-/m1/s1" 
ZNB InChIKey         InChI                1.06  WFFKQQMGOXMIGR-ZOUOOXKVSA-N                                                                                                                                                                                                                                                      
ZNB SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n([C@@H]3O[C@H](CNC(=O)CSc4nc5c(N)ncnc5n4[C@@H]6O[C@H](CN=[N+]=[N-])[C@@H](O)[C@H]6O)[C@@H](O)[C@H]3O)c(Br)nc12"                                                                                                                                                        
ZNB SMILES           CACTVS               3.385 "Nc1ncnc2n([CH]3O[CH](CNC(=O)CSc4nc5c(N)ncnc5n4[CH]6O[CH](CN=[N+]=[N-])[CH](O)[CH]6O)[CH](O)[CH]3O)c(Br)nc12"                                                                                                                                                                    
ZNB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(c(n2)SCC(=O)NC[C@@H]3[C@H]([C@H]([C@@H](O3)n4c5c(c(ncn5)N)nc4Br)O)O)[C@H]6[C@@H]([C@@H]([C@H](O6)CN=[N+]=[N-])O)O)N"                                                                                                                                              
ZNB SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(c(n2)SCC(=O)NCC3C(C(C(O3)n4c5c(c(ncn5)N)nc4Br)O)O)C6C(C(C(O6)CN=[N+]=[N-])O)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 
ZNB "SYSTEMATIC NAME" ACDLabs              12.01 "2-({6-amino-9-[(2R,3R,4S,5R)-5-(azidomethyl)-3,4-dihydroxyoxolan-2-yl]-9H-purin-8-yl}sulfanyl)-N-{[(2R,3S,4R,5R)-5-(6-amino-8-bromo-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}acetamide (non-preferred name)"            
ZNB "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[6-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(azidomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]sulfanyl-~{N}-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-8-bromanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl]ethanamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
ZNB "Create component"   2012-01-06 RCSB 
ZNB "Other modification" 2024-05-08 RCSB 
# 
