data_VZ6
# 
_chem_comp.id                                    VZ6 
_chem_comp.name                                  "9-[(1~{S},6~{R},8~{R},9~{R},10~{R},15~{R},17~{R},18~{R})-8-(6-aminopurin-9-yl)-9,18-bis(fluoranyl)-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13-pentaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{6,10}]octadecan-17-yl]-1~{H}-purin-6-one" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C21 H23 F2 N9 O10 P2" 
_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                    2023-12-15 
_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                        661.406 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VZ6 
_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        8ORW 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
# 
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 
VZ6 C18 C1  C 0 1 Y N N N N N 40.869 30.165 0.682  -6.796  -0.333 0.164  C18 VZ6 1  
VZ6 C13 C2  C 0 1 N N R N N N 40.981 27.652 0.992  -4.449  0.289  -0.550 C13 VZ6 2  
VZ6 C10 C3  C 0 1 N N N N N N 43.644 25.557 2.162  -1.293  -1.164 -0.433 C10 VZ6 3  
VZ6 C15 C4  C 0 1 Y N N N N N 42.581 29.432 1.829  -5.346  -1.990 0.056  C15 VZ6 4  
VZ6 C17 C5  C 0 1 Y N N N N N 41.683 31.207 1.093  -7.416  -1.541 0.523  C17 VZ6 5  
VZ6 C2  C6  C 0 1 N N R N N N 46.672 25.121 -0.540 2.174   0.447  0.615  C2  VZ6 6  
VZ6 C20 C7  C 0 1 Y N N N N N 39.467 31.536 -0.321 -8.788  0.766  0.495  C20 VZ6 7  
VZ6 C22 C8  C 0 1 Y N N N N N 41.287 32.508 0.724  -8.776  -1.511 0.873  C22 VZ6 8  
VZ6 C24 C9  C 0 1 N N R N N N 41.328 27.034 -0.359 -3.788  0.918  0.686  C24 VZ6 9  
VZ6 C28 C10 C 0 1 N N N N N N 47.913 26.376 -2.019 3.886   1.699  -0.580 C28 VZ6 10 
VZ6 C29 C11 C 0 1 N N R N N N 47.868 27.173 -0.711 4.330   0.223  -0.525 C29 VZ6 11 
VZ6 C3  C12 C 0 1 N N R N N N 46.650 25.507 -2.024 2.376   1.678  -0.295 C3  VZ6 12 
VZ6 C31 C13 C 0 1 Y N N N N N 46.620 29.263 -1.513 5.530   0.433  1.682  C31 VZ6 13 
VZ6 C33 C14 C 0 1 Y N N N N N 47.926 30.815 -0.857 7.490   -0.342 1.185  C33 VZ6 14 
VZ6 C34 C15 C 0 1 Y N N N N N 48.521 29.625 -0.482 6.713   -0.404 0.024  C34 VZ6 15 
VZ6 C36 C16 C 0 1 N N N N N N 50.269 30.606 0.449  8.484   -1.301 -1.146 C36 VZ6 16 
VZ6 C38 C17 C 0 1 N N N N N N 48.589 32.051 -0.535 8.831   -0.796 1.123  C38 VZ6 17 
VZ6 C4  C18 C 0 1 N N N N N N 45.409 26.251 -2.465 1.904   2.937  0.412  C4  VZ6 18 
VZ6 C40 C19 C 0 1 N N S N N N 46.722 26.519 0.062  3.149   -0.595 0.027  C40 VZ6 19 
VZ6 C8  C20 C 0 1 N N R N N N 42.630 26.301 -0.076 -2.296  1.020  0.301  C8  VZ6 20 
VZ6 C9  C21 C 0 1 N N R N N N 42.399 25.802 1.346  -2.136  0.041  -0.868 C9  VZ6 21 
VZ6 F1  F1  F 0 1 N N N N N N 47.793 24.398 -0.116 0.861   0.003  0.551  F1  VZ6 22 
VZ6 F25 F2  F 0 1 N N N N N N 40.342 26.102 -0.703 -4.304  2.187  0.944  F25 VZ6 23 
VZ6 N14 N1  N 0 1 Y N N N N N 41.456 29.020 1.163  -5.493  -0.647 -0.125 N14 VZ6 24 
VZ6 N16 N2  N 0 1 Y N N N N N 42.764 30.730 1.818  -6.476  -2.513 0.437  N16 VZ6 25 
VZ6 N19 N3  N 0 1 Y N N N N N 39.742 30.262 -0.030 -7.514  0.786  0.164  N19 VZ6 26 
VZ6 N21 N4  N 0 1 Y N N N N N 40.152 32.637 0.003  -9.411  -0.344 0.848  N21 VZ6 27 
VZ6 N23 N5  N 0 1 N N N N N N 41.969 33.613 1.043  -9.440  -2.670 1.236  N23 VZ6 28 
VZ6 N30 N6  N 0 1 Y N N N N N 47.674 28.628 -0.908 5.483   0.089  0.364  N30 VZ6 29 
VZ6 N32 N7  N 0 1 Y N N N N N 46.728 30.572 -1.507 6.713   0.178  2.162  N32 VZ6 30 
VZ6 N35 N8  N 0 1 N N N N N N 49.694 29.465 0.173  7.249   -0.887 -1.106 N35 VZ6 31 
VZ6 N37 N9  N 0 1 N N N N N N 49.779 31.827 0.132  9.293   -1.267 -0.056 N37 VZ6 32 
VZ6 O11 O1  O 0 1 N N N N N N 44.678 26.475 1.751  -0.119  -1.236 -1.242 O11 VZ6 33 
VZ6 O12 O2  O 0 1 N N N N N N 41.605 26.835 1.970  -3.431  -0.415 -1.263 O12 VZ6 34 
VZ6 O26 O3  O 0 1 N N N N N N 42.619 27.034 -2.884 -0.704  4.383  -1.144 O26 VZ6 35 
VZ6 O27 O4  O 0 1 N N N N N N 42.091 24.582 -3.371 -0.100  2.002  -1.702 O27 VZ6 36 
VZ6 O39 O5  O 0 1 N N N N N N 48.207 33.195 -0.781 9.550   -0.762 2.108  O39 VZ6 37 
VZ6 O41 O6  O 0 1 N N N N N N 47.107 26.432 1.450  2.505   -1.288 -1.038 O41 VZ6 38 
VZ6 O43 O7  O 0 1 N N N N N N 46.104 27.962 3.214  1.031   -2.633 0.515  O43 VZ6 39 
VZ6 O44 O8  O 0 1 N N N N N N 46.086 25.421 3.516  1.205   -3.413 -1.879 O44 VZ6 40 
VZ6 O5  O9  O 0 1 N N N N N N 44.421 25.300 -2.911 0.486   2.839  0.615  O5  VZ6 41 
VZ6 O7  O10 O 0 1 N N N N N N 42.813 25.245 -1.042 -2.005  2.360  -0.090 O7  VZ6 42 
VZ6 P42 P1  P 0 1 N N N N N N 46.003 26.603 2.631  1.157   -2.149 -0.878 P42 VZ6 43 
VZ6 P6  P2  P 0 1 N N N N N N 42.879 25.596 -2.638 -0.570  2.871  -0.601 P6  VZ6 44 
VZ6 H1  H1  H 0 1 N N N N N N 39.889 27.625 1.120  -4.874  1.057  -1.193 H1  VZ6 45 
VZ6 H2  H2  H 0 1 N N N N N N 43.420 25.711 3.228  -1.021  -1.063 0.615  H2  VZ6 46 
VZ6 H3  H3  H 0 1 N N N N N N 43.988 24.524 2.005  -1.886  -2.072 -0.564 H3  VZ6 47 
VZ6 H4  H4  H 0 1 N N N N N N 43.257 28.747 2.320  -4.428  -2.539 -0.094 H4  VZ6 48 
VZ6 H5  H5  H 0 1 N N N N N N 45.731 24.623 -0.266 2.460   0.689  1.635  H5  VZ6 49 
VZ6 H6  H6  H 0 1 N N N N N N 38.568 31.699 -0.897 -9.343  1.692  0.484  H6  VZ6 50 
VZ6 H7  H7  H 0 1 N N N N N N 41.470 27.812 -1.124 -3.908  0.268  1.551  H7  VZ6 51 
VZ6 H8  H8  H 0 1 N N N N N N 48.813 25.744 -2.051 4.403   2.275  0.182  H8  VZ6 52 
VZ6 H9  H9  H 0 1 N N N N N N 47.912 27.057 -2.883 4.074   2.102  -1.571 H9  VZ6 53 
VZ6 H10 H10 H 0 1 N N N N N N 48.806 27.002 -0.162 4.577   -0.119 -1.526 H10 VZ6 54 
VZ6 H11 H11 H 0 1 N N N N N N 46.806 24.616 -2.650 1.840   1.522  -1.227 H11 VZ6 55 
VZ6 H12 H12 H 0 1 N N N N N N 45.784 28.739 -1.951 4.710   0.857  2.242  H12 VZ6 56 
VZ6 H13 H13 H 0 1 N N N N N N 51.213 30.571 0.973  8.877   -1.683 -2.076 H13 VZ6 57 
VZ6 H14 H14 H 0 1 N N N N N N 45.662 26.933 -3.290 2.402   3.033  1.376  H14 VZ6 58 
VZ6 H15 H15 H 0 1 N N N N N N 45.007 26.830 -1.621 2.114   3.813  -0.201 H15 VZ6 59 
VZ6 H16 H16 H 0 1 N N N N N N 45.775 27.059 -0.086 3.485   -1.273 0.796  H16 VZ6 60 
VZ6 H17 H17 H 0 1 N N N N N N 43.473 27.008 -0.095 -1.677  0.719  1.147  H17 VZ6 61 
VZ6 H18 H18 H 0 1 N N N N N N 41.819 24.869 1.299  -1.654  0.534  -1.711 H18 VZ6 62 
VZ6 H19 H19 H 0 1 N N N N N N 41.499 34.414 0.672  -8.966  -3.516 1.250  H19 VZ6 63 
VZ6 H20 H20 H 0 1 N N N N N N 42.028 33.692 2.038  -10.380 -2.637 1.475  H20 VZ6 64 
VZ6 H21 H21 H 0 1 N N N N N N 50.317 32.626 0.400  10.207  -1.585 -0.125 H21 VZ6 65 
VZ6 H22 H22 H 0 1 N N N N N N 41.928 27.125 -3.529 0.124   4.757  -1.474 H22 VZ6 66 
VZ6 H23 H23 H 0 1 N N N N N N 46.202 25.705 4.415  0.423   -3.980 -1.835 H23 VZ6 67 
# 
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 
VZ6 O27 P6  DOUB N N 1  
VZ6 O5  P6  SING N N 2  
VZ6 O5  C4  SING N N 3  
VZ6 O26 P6  SING N N 4  
VZ6 P6  O7  SING N N 5  
VZ6 C4  C3  SING N N 6  
VZ6 C3  C28 SING N N 7  
VZ6 C3  C2  SING N N 8  
VZ6 C28 C29 SING N N 9  
VZ6 C31 N32 DOUB Y N 10 
VZ6 C31 N30 SING Y N 11 
VZ6 N32 C33 SING Y N 12 
VZ6 O7  C8  SING N N 13 
VZ6 N30 C29 SING N N 14 
VZ6 N30 C34 SING Y N 15 
VZ6 C33 C38 SING N N 16 
VZ6 C33 C34 DOUB Y N 17 
VZ6 O39 C38 DOUB N N 18 
VZ6 C29 C40 SING N N 19 
VZ6 F25 C24 SING N N 20 
VZ6 C2  F1  SING N N 21 
VZ6 C2  C40 SING N N 22 
VZ6 C38 N37 SING N N 23 
VZ6 C34 N35 SING N N 24 
VZ6 C24 C8  SING N N 25 
VZ6 C24 C13 SING N N 26 
VZ6 C20 N19 DOUB Y N 27 
VZ6 C20 N21 SING Y N 28 
VZ6 C8  C9  SING N N 29 
VZ6 N19 C18 SING Y N 30 
VZ6 N21 C22 DOUB Y N 31 
VZ6 C40 O41 SING N N 32 
VZ6 N37 C36 SING N N 33 
VZ6 N35 C36 DOUB N N 34 
VZ6 C18 C17 DOUB Y N 35 
VZ6 C18 N14 SING Y N 36 
VZ6 C22 N23 SING N N 37 
VZ6 C22 C17 SING Y N 38 
VZ6 C13 N14 SING N N 39 
VZ6 C13 O12 SING N N 40 
VZ6 C17 N16 SING Y N 41 
VZ6 N14 C15 SING Y N 42 
VZ6 C9  O12 SING N N 43 
VZ6 C9  C10 SING N N 44 
VZ6 O41 P42 SING N N 45 
VZ6 O11 C10 SING N N 46 
VZ6 O11 P42 SING N N 47 
VZ6 N16 C15 DOUB Y N 48 
VZ6 P42 O43 DOUB N N 49 
VZ6 P42 O44 SING N N 50 
VZ6 C13 H1  SING N N 51 
VZ6 C10 H2  SING N N 52 
VZ6 C10 H3  SING N N 53 
VZ6 C15 H4  SING N N 54 
VZ6 C2  H5  SING N N 55 
VZ6 C20 H6  SING N N 56 
VZ6 C24 H7  SING N N 57 
VZ6 C28 H8  SING N N 58 
VZ6 C28 H9  SING N N 59 
VZ6 C29 H10 SING N N 60 
VZ6 C3  H11 SING N N 61 
VZ6 C31 H12 SING N N 62 
VZ6 C36 H13 SING N N 63 
VZ6 C4  H14 SING N N 64 
VZ6 C4  H15 SING N N 65 
VZ6 C40 H16 SING N N 66 
VZ6 C8  H17 SING N N 67 
VZ6 C9  H18 SING N N 68 
VZ6 N23 H19 SING N N 69 
VZ6 N23 H20 SING N N 70 
VZ6 N37 H21 SING N N 71 
VZ6 O26 H22 SING N N 72 
VZ6 O44 H23 SING N N 73 
# 
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 
VZ6 InChI            InChI                1.06  "InChI=1S/C21H23F2N9O10P2/c22-11-8-1-9(31-6-30-14-19(31)27-5-28-20(14)33)15(11)41-44(36,37)39-3-10-16(42-43(34,35)38-2-8)12(23)21(40-10)32-7-29-13-17(24)25-4-26-18(13)32/h4-12,15-16,21H,1-3H2,(H,34,35)(H,36,37)(H2,24,25,26)(H,27,28,33)/t8-,9-,10-,11-,12-,15+,16-,21-/m1/s1" 
VZ6 InChIKey         InChI                1.06  QBIOYLVMQXGNNG-PKISWWTFSA-N                                                                                                                                                                                                                                                       
VZ6 SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@@H]4CO[P](O)(=O)O[C@@H]5[C@H](F)[C@@H](CO[P](O)(=O)O[C@H]4[C@H]3F)C[C@H]5n6cnc7C(=O)NC=Nc67"                                                                                                                                                          
VZ6 SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH]4CO[P](O)(=O)O[CH]5[CH](F)[CH](CO[P](O)(=O)O[CH]4[CH]3F)C[CH]5n6cnc7C(=O)NC=Nc67"                                                                                                                                                                      
VZ6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]4[C@H](O3)COP(=O)(O[C@H]5[C@@H](C[C@@H]([C@H]5F)COP(=O)(O4)O)n6cnc7c6N=CNC7=O)O)F)N"                                                                                                                                                         
VZ6 SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C4C(O3)COP(=O)(OC5C(CC(C5F)COP(=O)(O4)O)n6cnc7c6N=CNC7=O)O)F)N"                                                                                                                                                                                            
# 
_pdbx_chem_comp_identifier.comp_id           VZ6 
_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        "9-[(1~{S},6~{R},8~{R},9~{R},10~{R},15~{R},17~{R},18~{R})-8-(6-aminopurin-9-yl)-9,18-bis(fluoranyl)-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13-pentaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{6,10}]octadecan-17-yl]-1~{H}-purin-6-one" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
VZ6 "Create component" 2023-04-17 PDBE 
VZ6 "Initial release"  2023-12-20 RCSB 
# 
