data_VPT
# 
_chem_comp.id                                    VPT 
_chem_comp.name                                  "[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-(3-prop-2-ynoxyphenyl)carbonylsulfamate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C20 H20 N6 O8 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-08-02 
_chem_comp.pdbx_modified_date                    2024-07-26 
_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                        504.473 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VPT 
_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        8K5S 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
# 
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 
VPT C2  C1  C 0 1 Y N N N N N 11.596 8.079  20.584 5.683  3.132  -0.415 C2  VPT 1  
VPT C4  C2  C 0 1 Y N N N N N 13.168 6.367  20.240 3.748  1.901  -0.267 C4  VPT 2  
VPT CBI C3  C 0 1 N N N N N N 21.351 0.156  17.610 -6.188 5.685  -1.087 CBI VPT 3  
VPT CBH C4  C 0 1 N N N N N N 21.121 0.680  16.630 -5.943 4.758  -0.410 CBH VPT 4  
VPT CBG C5  C 0 1 N N N N N N 20.933 1.208  15.510 -5.635 3.595  0.438  CBG VPT 5  
VPT OBF O1  O 0 1 N N N N N N 20.689 2.656  15.597 -4.890 2.638  -0.318 OBF VPT 6  
VPT CBB C6  C 0 1 Y N N N N N 20.023 3.375  16.562 -4.523 1.497  0.322  CBB VPT 7  
VPT CBA C7  C 0 1 Y N N N N N 19.363 2.739  17.595 -3.799 0.527  -0.352 CBA VPT 8  
VPT CBC C8  C 0 1 Y N N N N N 20.042 4.789  16.472 -4.869 1.305  1.653  CBC VPT 9  
VPT CBD C9  C 0 1 Y N N N N N 19.430 5.584  17.423 -4.498 0.146  2.309  CBD VPT 10 
VPT CBE C10 C 0 1 Y N N N N N 18.784 4.912  18.462 -3.781 -0.828 1.646  CBE VPT 11 
VPT CAY C11 C 0 1 Y N N N N N 18.720 3.500  18.566 -3.424 -0.643 0.310  CAY VPT 12 
VPT CAX C12 C 0 1 N N N N N N 18.082 2.864  19.652 -2.651 -1.683 -0.403 CAX VPT 13 
VPT OAZ O2  O 0 1 N N N N N N 17.608 3.532  20.582 -2.342 -1.519 -1.567 OAZ VPT 14 
VPT NAU N1  N 0 1 N N N N N N 18.132 1.504  19.630 -2.290 -2.812 0.238  NAU VPT 15 
VPT SAT S1  S 0 1 N N N N N N 17.580 0.602  20.854 -1.425 -3.977 -0.560 SAT VPT 16 
VPT OAV O3  O 0 1 N N N N N N 18.385 0.960  22.079 -1.176 -5.009 0.384  OAV VPT 17 
VPT OAW O4  O 0 1 N N N N N N 17.753 -0.875 20.444 -2.093 -4.198 -1.795 OAW VPT 18 
VPT O15 O5  O 0 1 N N N N N N 16.094 0.909  21.164 -0.071 -3.374 -0.906 O15 VPT 19 
VPT C15 C13 C 0 1 N N N N N N 15.118 0.981  20.144 0.817  -3.263 0.207  C15 VPT 20 
VPT C14 C14 C 0 1 N N R N N N 14.027 1.830  20.762 2.140  -2.648 -0.255 C14 VPT 21 
VPT O14 O6  O 0 1 N N N N N N 14.481 3.178  21.247 1.929  -1.287 -0.666 O14 VPT 22 
VPT C13 C15 C 0 1 N N S N N N 12.906 2.118  19.732 3.143  -2.623 0.915  C13 VPT 23 
VPT O13 O7  O 0 1 N N N N N N 12.100 0.925  19.605 4.307  -3.386 0.592  O13 VPT 24 
VPT C12 C16 C 0 1 N N R N N N 12.190 3.208  20.467 3.503  -1.125 1.073  C12 VPT 25 
VPT O12 O8  O 0 1 N N N N N N 11.496 2.539  21.540 4.900  -0.961 1.325  O12 VPT 26 
VPT C11 C17 C 0 1 N N R N N N 13.328 4.049  21.090 3.120  -0.551 -0.314 C11 VPT 27 
VPT N9  N2  N 0 1 Y N N N N N 13.800 5.195  20.312 2.831  0.882  -0.217 N9  VPT 28 
VPT C8  C18 C 0 1 Y N N N N N 14.922 5.266  19.587 1.600  1.448  -0.059 C8  VPT 29 
VPT N7  N3  N 0 1 Y N N N N N 15.003 6.464  19.052 1.710  2.744  -0.010 N7  VPT 30 
VPT C5  C19 C 0 1 Y N N N N N 13.912 7.170  19.435 3.015  3.090  -0.123 C5  VPT 31 
VPT N3  N4  N 0 1 Y N N N N N 12.014 6.782  20.817 5.069  1.969  -0.405 N3  VPT 32 
VPT N1  N5  N 0 1 Y N N N N N 12.375 8.921  19.750 5.036  4.277  -0.287 N1  VPT 33 
VPT C6  C20 C 0 1 Y N N N N N 13.517 8.446  19.185 3.716  4.308  -0.140 C6  VPT 34 
VPT N6  N6  N 0 1 N N N N N N 14.302 9.224  18.386 3.047  5.512  -0.003 N6  VPT 35 
VPT H1  H1  H 0 1 N N N N N N 10.685 8.447  21.033 6.757  3.152  -0.528 H1  VPT 36 
VPT H2  H2  H 0 1 N N N N N N 21.566 -0.333 18.525 -6.407 6.515  -1.692 H2  VPT 37 
VPT H3  H3  H 0 1 N N N N N N 20.060 0.732  15.039 -5.047 3.917  1.297  H3  VPT 38 
VPT H4  H4  H 0 1 N N N N N N 21.824 1.038  14.887 -6.564 3.141  0.783  H4  VPT 39 
VPT H5  H5  H 0 1 N N N N N N 19.346 1.660  17.649 -3.526 0.676  -1.386 H5  VPT 40 
VPT H6  H6  H 0 1 N N N N N N 20.547 5.257  15.640 -5.430 2.065  2.177  H6  VPT 41 
VPT H7  H7  H 0 1 N N N N N N 19.450 6.662  17.365 -4.770 0.004  3.345  H7  VPT 42 
VPT H8  H8  H 0 1 N N N N N N 18.306 5.502  19.230 -3.493 -1.732 2.162  H8  VPT 43 
VPT H9  H9  H 0 1 N N N N N N 18.523 1.047  18.831 -2.538 -2.942 1.167  H9  VPT 44 
VPT H10 H10 H 0 1 N N N N N N 14.741 -0.020 19.889 0.367  -2.626 0.969  H10 VPT 45 
VPT H11 H11 H 0 1 N N N N N N 15.526 1.460  19.242 1.003  -4.253 0.624  H11 VPT 46 
VPT H12 H12 H 0 1 N N N N N N 13.586 1.279  21.606 2.548  -3.227 -1.083 H12 VPT 47 
VPT H13 H13 H 0 1 N N N N N N 13.319 2.464  18.773 2.677  -3.001 1.825  H13 VPT 48 
VPT H14 H14 H 0 1 N N N N N N 12.589 0.260  19.134 4.997  -3.357 1.270  H14 VPT 49 
VPT H15 H15 H 0 1 N N N N N N 11.536 3.808  19.817 2.911  -0.664 1.863  H15 VPT 50 
VPT H16 H16 H 0 1 N N N N N N 11.015 3.178  22.053 5.206  -1.383 2.140  H16 VPT 51 
VPT H17 H17 H 0 1 N N N N N N 12.996 4.396  22.080 3.913  -0.735 -1.038 H17 VPT 52 
VPT H18 H18 H 0 1 N N N N N N 15.642 4.471  19.462 0.672  0.901  0.014  H18 VPT 53 
VPT H19 H19 H 0 1 N N N N N N 13.899 10.136 18.309 2.084  5.522  0.107  H19 VPT 54 
VPT H20 H20 H 0 1 N N N N N N 15.216 9.296  18.785 3.542  6.346  -0.016 H20 VPT 55 
# 
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 
VPT CBG OBF SING N N 1  
VPT CBG CBH SING N N 2  
VPT OBF CBB SING N N 3  
VPT CBC CBB DOUB Y N 4  
VPT CBC CBD SING Y N 5  
VPT CBB CBA SING Y N 6  
VPT CBH CBI TRIP N N 7  
VPT CBD CBE DOUB Y N 8  
VPT CBA CAY DOUB Y N 9  
VPT N6  C6  SING N N 10 
VPT CBE CAY SING Y N 11 
VPT CAY CAX SING N N 12 
VPT N7  C5  SING Y N 13 
VPT N7  C8  DOUB Y N 14 
VPT C6  C5  SING Y N 15 
VPT C6  N1  DOUB Y N 16 
VPT C5  C4  DOUB Y N 17 
VPT C8  N9  SING Y N 18 
VPT O13 C13 SING N N 19 
VPT NAU CAX SING N N 20 
VPT NAU SAT SING N N 21 
VPT CAX OAZ DOUB N N 22 
VPT C13 C12 SING N N 23 
VPT C13 C14 SING N N 24 
VPT N1  C2  SING Y N 25 
VPT C15 C14 SING N N 26 
VPT C15 O15 SING N N 27 
VPT C4  N9  SING Y N 28 
VPT C4  N3  SING Y N 29 
VPT N9  C11 SING N N 30 
VPT OAW SAT DOUB N N 31 
VPT C12 C11 SING N N 32 
VPT C12 O12 SING N N 33 
VPT C2  N3  DOUB Y N 34 
VPT C14 O14 SING N N 35 
VPT SAT O15 SING N N 36 
VPT SAT OAV DOUB N N 37 
VPT C11 O14 SING N N 38 
VPT C2  H1  SING N N 39 
VPT CBI H2  SING N N 40 
VPT CBG H3  SING N N 41 
VPT CBG H4  SING N N 42 
VPT CBA H5  SING N N 43 
VPT CBC H6  SING N N 44 
VPT CBD H7  SING N N 45 
VPT CBE H8  SING N N 46 
VPT NAU H9  SING N N 47 
VPT C15 H10 SING N N 48 
VPT C15 H11 SING N N 49 
VPT C14 H12 SING N N 50 
VPT C13 H13 SING N N 51 
VPT O13 H14 SING N N 52 
VPT C12 H15 SING N N 53 
VPT O12 H16 SING N N 54 
VPT C11 H17 SING N N 55 
VPT C8  H18 SING N N 56 
VPT N6  H19 SING N N 57 
VPT N6  H20 SING N N 58 
# 
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 
VPT InChI            InChI                1.06  "InChI=1S/C20H20N6O8S/c1-2-6-32-12-5-3-4-11(7-12)19(29)25-35(30,31)33-8-13-15(27)16(28)20(34-13)26-10-24-14-17(21)22-9-23-18(14)26/h1,3-5,7,9-10,13,15-16,20,27-28H,6,8H2,(H,25,29)(H2,21,22,23)/t13-,15-,16-,20-/m1/s1" 
VPT InChIKey         InChI                1.06  CEBNTACPQUEIBR-KHTYJDQRSA-N                                                                                                                                                                                              
VPT SMILES_CANONICAL CACTVS               3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[S](=O)(=O)NC(=O)c4cccc(OCC#C)c4)[C@@H](O)[C@H]3O"                                                                                                                                      
VPT SMILES           CACTVS               3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[S](=O)(=O)NC(=O)c4cccc(OCC#C)c4)[CH](O)[CH]3O"                                                                                                                                            
VPT SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C#CCOc1cccc(c1)C(=O)NS(=O)(=O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O"                                                                                                                                        
VPT SMILES           "OpenEye OEToolkits" 2.0.7 "C#CCOc1cccc(c1)C(=O)NS(=O)(=O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O"                                                                                                                                                          
# 
_pdbx_chem_comp_identifier.comp_id           VPT 
_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~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-(3-prop-2-ynoxyphenyl)carbonylsulfamate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
VPT "Create component" 2023-08-02 PDBJ 
VPT "Initial release"  2024-07-31 RCSB 
# 
