data_VPI
# 
_chem_comp.id                                    VPI 
_chem_comp.name                                  "[(3~{R})-4-[[3-(6-acetamidohexylamino)-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C17 H34 N3 O8 P" 
_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                    2024-09-27 
_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                        439.441 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VPI 
_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        8K4R 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
_chem_comp.pdbx_pcm                              Y 
# 
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 
VPI O7  O1  O 0 1 N N N N N N 3.297  2.192  -3.162 12.501  -1.949 0.791  O7  VPI 1  
VPI C14 C1  C 0 1 N N N N N N 3.254  3.239  -3.800 12.515  -1.102 -0.077 C14 VPI 2  
VPI C15 C2  C 0 1 N N N N N N 3.599  3.301  -5.240 13.813  -0.729 -0.744 C15 VPI 3  
VPI N3  N1  N 0 1 N N N N N N 2.978  4.424  -3.276 11.368  -0.499 -0.449 N3  VPI 4  
VPI C13 C3  C 0 1 N N N N N N 2.845  4.605  -1.842 10.105  -0.866 0.196  C13 VPI 5  
VPI C12 C4  C 0 1 N N N N N N 1.370  4.706  -1.493 8.967   -0.040 -0.405 C12 VPI 6  
VPI C16 C5  C 0 1 N N N N N N 1.172  4.348  -0.031 7.647   -0.423 0.268  C16 VPI 7  
VPI C17 C6  C 0 1 N N N N N N -0.327 4.307  0.243  6.509   0.404  -0.333 C17 VPI 8  
VPI C11 C7  C 0 1 N N N N N N -0.647 3.755  1.606  5.189   0.020  0.340  C11 VPI 9  
VPI C10 C8  C 0 1 N N N N N N -1.203 2.375  1.400  4.051   0.847  -0.261 C10 VPI 10 
VPI N2  N2  N 0 1 N N N N N N -1.404 1.743  2.660  2.788   0.479  0.383  N2  VPI 11 
VPI C9  C9  C 0 1 N N N N N N -1.142 0.480  2.921  1.641   1.083  0.012  C9  VPI 12 
VPI O6  O2  O 0 1 N N N N N N -0.654 -0.303 2.148  1.655   1.930  -0.856 O6  VPI 13 
VPI C8  C10 C 0 1 N N N N N N -1.563 0.006  4.282  0.342   0.705  0.675  C8  VPI 14 
VPI C7  C11 C 0 1 N N N N N N -0.732 0.665  5.342  -0.797  1.531  0.074  C7  VPI 15 
VPI N1  N3  N 0 1 N N N N N N -1.515 0.823  6.551  -2.060  1.164  0.718  N1  VPI 16 
VPI C6  C12 C 0 1 N N N N N N -0.955 0.995  7.742  -3.207  1.767  0.347  C6  VPI 17 
VPI O5  O3  O 0 1 N N N N N N 0.236  0.972  7.825  -3.181  2.679  -0.453 O5  VPI 18 
VPI C1  C13 C 0 1 N N R N N N -1.884 1.188  8.917  -4.521  1.310  0.925  C1  VPI 19 
VPI O8  O4  O 0 1 N N N N N N -1.350 1.821  10.113 -4.277  0.432  2.026  O8  VPI 20 
VPI C2  C14 C 0 1 N N N N N N -2.435 -0.185 9.311  -5.321  0.571  -0.148 C2  VPI 21 
VPI C4  C15 C 0 1 N N N N N N -1.469 -1.337 9.103  -5.710  1.549  -1.258 C4  VPI 22 
VPI C5  C16 C 0 1 N N N N N N -2.961 -0.065 10.773 -4.468  -0.555 -0.737 C5  VPI 23 
VPI C3  C17 C 0 1 N N N N N N -3.592 -0.512 8.395  -6.586  -0.022 0.476  C3  VPI 24 
VPI O1  O5  O 0 1 N N N N N N -4.263 0.733  8.308  -7.334  -0.712 -0.528 O1  VPI 25 
VPI P   P1  P 0 1 N N N N N N -5.181 1.057  7.084  -8.727  -1.460 -0.224 P   VPI 26 
VPI O3  O6  O 0 1 N N N N N N -4.510 2.110  6.300  -9.351  -2.013 -1.601 O3  VPI 27 
VPI O4  O7  O 0 1 N N N N N N -5.354 -0.383 6.422  -8.467  -2.691 0.780  O4  VPI 28 
VPI H1  H1  H 0 1 N N N N N N 3.879  2.298  -5.594 13.628  0.040  -1.495 H1  VPI 29 
VPI H2  H2  H 0 1 N N N N N N 2.730  3.661  -5.810 14.509  -0.347 0.003  H2  VPI 30 
VPI H3  H3  H 0 1 N N N N N N 4.444  3.990  -5.385 14.242  -1.609 -1.224 H3  VPI 31 
VPI H4  H4  H 0 1 N N N N N N 2.859  5.211  -3.882 11.380  0.179  -1.143 H4  VPI 32 
VPI H5  H5  H 0 1 N N N N N N 3.290  3.746  -1.319 9.909   -1.926 0.034  H5  VPI 33 
VPI H6  H6  H 0 1 N N N N N N 3.361  5.528  -1.537 10.172  -0.669 1.266  H6  VPI 34 
VPI H7  H7  H 0 1 N N N N N N 1.021  5.734  -1.670 9.162   1.020  -0.243 H7  VPI 35 
VPI H8  H8  H 0 1 N N N N N N 0.796  4.010  -2.122 8.900   -0.237 -1.475 H8  VPI 36 
VPI H9  H9  H 0 1 N N N N N N 1.617  3.363  0.176  7.451   -1.483 0.106  H9  VPI 37 
VPI H10 H10 H 0 1 N N N N N N 1.648  5.107  0.607  7.714   -0.226 1.338  H10 VPI 38 
VPI H11 H11 H 0 1 N N N N N N -0.727 5.329  0.173  6.705   1.464  -0.171 H11 VPI 39 
VPI H12 H12 H 0 1 N N N N N N -0.808 3.673  -0.517 6.442   0.206  -1.403 H12 VPI 40 
VPI H13 H13 H 0 1 N N N N N N 0.266  3.707  2.218  4.994   -1.040 0.178  H13 VPI 41 
VPI H14 H14 H 0 1 N N N N N N -1.391 4.392  2.106  5.256   0.217  1.410  H14 VPI 42 
VPI H15 H15 H 0 1 N N N N N N -2.164 2.444  0.869  4.247   1.906  -0.099 H15 VPI 43 
VPI H16 H16 H 0 1 N N N N N N -0.495 1.782  0.803  3.984   0.649  -1.331 H16 VPI 44 
VPI H17 H17 H 0 1 N N N N N N -1.772 2.301  3.403  2.776   -0.198 1.077  H17 VPI 45 
VPI H18 H18 H 0 1 N N N N N N -2.622 0.257  4.442  0.146   -0.355 0.513  H18 VPI 46 
VPI H19 H19 H 0 1 N N N N N N -1.432 -1.084 4.343  0.409   0.902  1.745  H19 VPI 47 
VPI H20 H20 H 0 1 N N N N N N 0.149  0.042  5.556  -0.601  2.591  0.236  H20 VPI 48 
VPI H21 H21 H 0 1 N N N N N N -0.404 1.653  4.987  -0.864  1.334  -0.996 H21 VPI 49 
VPI H22 H22 H 0 1 N N N N N N -2.513 0.802  6.486  -2.072  0.486  1.412  H22 VPI 50 
VPI H23 H23 H 0 1 N N N N N N -2.736 1.789  8.566  -5.087  2.175  1.270  H23 VPI 51 
VPI H24 H24 H 0 1 N N N N N N -0.408 1.913  10.030 -3.776  -0.362 1.793  H24 VPI 52 
VPI H25 H25 H 0 1 N N N N N N -0.581 -1.190 9.735  -4.810  1.912  -1.755 H25 VPI 53 
VPI H26 H26 H 0 1 N N N N N N -1.961 -2.282 9.376  -6.346  1.041  -1.984 H26 VPI 54 
VPI H27 H27 H 0 1 N N N N N N -1.165 -1.374 8.047  -6.252  2.391  -0.827 H27 VPI 55 
VPI H28 H28 H 0 1 N N N N N N -2.124 0.173  11.446 -4.190  -1.252 0.054  H28 VPI 56 
VPI H29 H29 H 0 1 N N N N N N -3.714 0.735  10.827 -5.038  -1.081 -1.502 H29 VPI 57 
VPI H30 H30 H 0 1 N N N N N N -3.417 -1.019 11.078 -3.566  -0.132 -1.181 H30 VPI 58 
VPI H31 H31 H 0 1 N N N N N N -4.241 -1.286 8.832  -6.309  -0.719 1.266  H31 VPI 59 
VPI H32 H32 H 0 1 N N N N N N -3.238 -0.845 7.408  -7.194  0.780  0.895  H32 VPI 60 
VPI H33 H33 H 0 1 N N N N N N -5.069 2.877  6.256  -10.193 -2.476 -1.494 H33 VPI 61 
VPI H34 H34 H 0 1 N N N N N N -6.176 -0.765 6.705  -7.856  -3.357 0.437  H34 VPI 62 
VPI O2  O8  O 0 1 N N N N N N -6.561 0.929  7.832  -9.673  -0.507 0.398  O2  VPI 63 
# 
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 
VPI C15 C14 SING N N 1  
VPI C14 N3  SING N N 2  
VPI C14 O7  DOUB N N 3  
VPI N3  C13 SING N N 4  
VPI C13 C12 SING N N 5  
VPI C12 C16 SING N N 6  
VPI C16 C17 SING N N 7  
VPI C17 C11 SING N N 8  
VPI C10 C11 SING N N 9  
VPI C10 N2  SING N N 10 
VPI O6  C9  DOUB N N 11 
VPI N2  C9  SING N N 12 
VPI C9  C8  SING N N 13 
VPI C8  C7  SING N N 14 
VPI C7  N1  SING N N 15 
VPI O3  P   SING N N 16 
VPI O4  P   SING N N 17 
VPI N1  C6  SING N N 18 
VPI P   O1  SING N N 19 
VPI C6  O5  DOUB N N 20 
VPI C6  C1  SING N N 21 
VPI O1  C3  SING N N 22 
VPI C3  C2  SING N N 23 
VPI C1  C2  SING N N 24 
VPI C1  O8  SING N N 25 
VPI C4  C2  SING N N 26 
VPI C2  C5  SING N N 27 
VPI C15 H1  SING N N 28 
VPI C15 H2  SING N N 29 
VPI C15 H3  SING N N 30 
VPI N3  H4  SING N N 31 
VPI C13 H5  SING N N 32 
VPI C13 H6  SING N N 33 
VPI C12 H7  SING N N 34 
VPI C12 H8  SING N N 35 
VPI C16 H9  SING N N 36 
VPI C16 H10 SING N N 37 
VPI C17 H11 SING N N 38 
VPI C17 H12 SING N N 39 
VPI C11 H13 SING N N 40 
VPI C11 H14 SING N N 41 
VPI C10 H15 SING N N 42 
VPI C10 H16 SING N N 43 
VPI N2  H17 SING N N 44 
VPI C8  H18 SING N N 45 
VPI C8  H19 SING N N 46 
VPI C7  H20 SING N N 47 
VPI C7  H21 SING N N 48 
VPI N1  H22 SING N N 49 
VPI C1  H23 SING N N 50 
VPI O8  H24 SING N N 51 
VPI C4  H25 SING N N 52 
VPI C4  H26 SING N N 53 
VPI C4  H27 SING N N 54 
VPI C5  H28 SING N N 55 
VPI C5  H29 SING N N 56 
VPI C5  H30 SING N N 57 
VPI C3  H31 SING N N 58 
VPI C3  H32 SING N N 59 
VPI O3  H33 SING N N 60 
VPI O4  H34 SING N N 61 
VPI P   O2  DOUB N N 62 
# 
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 
VPI InChI            InChI                1.06  "InChI=1S/C17H34N3O8P/c1-13(21)18-9-6-4-5-7-10-19-14(22)8-11-20-16(24)15(23)17(2,3)12-28-29(25,26)27/h15,23H,4-12H2,1-3H3,(H,18,21)(H,19,22)(H,20,24)(H2,25,26,27)/t15-/m0/s1" 
VPI InChIKey         InChI                1.06  KSMJRHVJQGTOAX-HNNXBMFYSA-N                                                                                                                                                    
VPI SMILES_CANONICAL CACTVS               3.385 "CC(=O)NCCCCCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(O)=O"                                                                                                                      
VPI SMILES           CACTVS               3.385 "CC(=O)NCCCCCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(O)=O"                                                                                                                       
VPI SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(=O)NCCCCCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)O)O"                                                                                                                       
VPI SMILES           "OpenEye OEToolkits" 2.0.7 "CC(=O)NCCCCCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)O)O"                                                                                                                            
# 
_pdbx_chem_comp_identifier.comp_id           VPI 
_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        "[(3~{R})-4-[[3-(6-acetamidohexylamino)-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen 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 
VPI "Create component" 2023-08-02 PDBJ 
VPI "Initial release"  2023-11-01 RCSB 
VPI "Modify PCM"       2024-09-27 PDBE 
# 
loop_
_pdbx_chem_comp_pcm.pcm_id 
_pdbx_chem_comp_pcm.comp_id 
_pdbx_chem_comp_pcm.modified_residue_id 
_pdbx_chem_comp_pcm.type 
_pdbx_chem_comp_pcm.category 
_pdbx_chem_comp_pcm.position 
_pdbx_chem_comp_pcm.polypeptide_position 
_pdbx_chem_comp_pcm.comp_id_linking_atom 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession 
1 VPI CYS None Crosslinker "Amino-acid side chain" "Any position" C15 SG ? ? 
2 VPI SER None Crosslinker "Amino-acid side chain" "Any position" P   OG ? ? 
# 
