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 _pdbx_chem_comp_pcm.first_instance_model_db_code 1 VPI CYS None Crosslinker "Amino-acid side chain" "Any position" C15 SG ? ? 8K4R 2 VPI SER None Crosslinker "Amino-acid side chain" "Any position" P OG ? ? 8K4R #