data_VBL # _chem_comp.id VBL _chem_comp.name "(2~{S},3~{R})-2-pentyloctane-1,3-diol" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C13 H28 O2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-09-11 _chem_comp.pdbx_modified_date 2025-02-07 _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 216.360 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VBL _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 8QHF _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE _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 VBL C3 C1 C 0 1 N N S N N N 23.072 39.485 17.139 0.663 -0.209 -0.257 C3 VBL 1 VBL C4 C2 C 0 1 N N R N N N 24.221 40.566 17.204 -0.572 0.638 0.056 C4 VBL 2 VBL C5 C3 C 0 1 N N N N N N 24.121 41.395 18.499 -1.835 -0.169 -0.250 C5 VBL 3 VBL C6 C4 C 0 1 N N N N N N 25.251 42.429 18.623 -3.066 0.718 -0.056 C6 VBL 4 VBL C7 C5 C 0 1 N N N N N N 25.708 42.637 20.082 -4.330 -0.089 -0.363 C7 VBL 5 VBL C8 C6 C 0 1 N N N N N N 26.933 43.565 20.199 -5.561 0.798 -0.168 C8 VBL 6 VBL C9 C7 C 0 1 N N N N N N 26.890 44.812 19.310 -6.824 -0.009 -0.475 C9 VBL 7 VBL C1 C8 C 0 1 N N N N N N 20.622 39.114 17.888 3.159 -0.200 -0.381 C1 VBL 8 VBL C2 C9 C 0 1 N N N N N N 21.628 40.083 17.219 1.926 0.598 0.049 C2 VBL 9 VBL C10 C10 C 0 1 N N N N N N 23.228 38.471 15.948 0.645 -1.474 0.602 C10 VBL 10 VBL C12 C11 C 0 1 N N N N N N 20.921 39.619 21.263 6.917 0.615 -0.197 C12 VBL 11 VBL C11 C12 C 0 1 N N N N N N 19.856 39.028 20.337 5.654 -0.192 -0.504 C11 VBL 12 VBL C C13 C 0 1 N N N N N N 19.764 39.759 18.986 4.422 0.607 -0.074 C VBL 13 VBL O O1 O 0 1 N N N N N N 25.465 39.891 17.198 -0.562 1.001 1.439 O VBL 14 VBL O1 O2 O 0 1 N N N N N N 22.945 37.121 16.480 -0.472 -2.285 0.233 O1 VBL 15 VBL H1 H1 H 0 1 N N N N N N 23.190 38.882 18.052 0.656 -0.485 -1.312 H1 VBL 16 VBL H2 H2 H 0 1 N N N N N N 24.129 41.235 16.336 -0.559 1.540 -0.556 H2 VBL 17 VBL H3 H3 H 0 1 N N N N N N 23.156 41.924 18.506 -1.800 -0.521 -1.282 H3 VBL 18 VBL H4 H4 H 0 1 N N N N N N 24.171 40.712 19.360 -1.893 -1.023 0.423 H4 VBL 19 VBL H5 H5 H 0 1 N N N N N N 26.111 42.084 18.030 -3.102 1.070 0.975 H5 VBL 20 VBL H6 H6 H 0 1 N N N N N N 24.894 43.390 18.225 -3.009 1.573 -0.730 H6 VBL 21 VBL H7 H7 H 0 1 N N N N N N 24.877 43.079 20.651 -4.294 -0.441 -1.394 H7 VBL 22 VBL H8 H8 H 0 1 N N N N N N 25.967 41.658 20.512 -4.387 -0.944 0.311 H8 VBL 23 VBL H9 H9 H 0 1 N N N N N N 27.827 42.984 19.929 -5.596 1.150 0.863 H9 VBL 24 VBL H10 H10 H 0 1 N N N N N N 27.012 43.895 21.245 -5.503 1.653 -0.842 H10 VBL 25 VBL H11 H11 H 0 1 N N N N N N 27.803 45.405 19.465 -7.702 0.623 -0.336 H11 VBL 26 VBL H12 H12 H 0 1 N N N N N N 26.826 44.508 18.255 -6.789 -0.361 -1.506 H12 VBL 27 VBL H13 H13 H 0 1 N N N N N N 26.010 45.418 19.571 -6.882 -0.864 0.199 H13 VBL 28 VBL H14 H14 H 0 1 N N N N N N 19.950 38.723 17.110 3.189 -1.144 0.165 H14 VBL 29 VBL H15 H15 H 0 1 N N N N N N 21.188 38.284 18.335 3.107 -0.401 -1.451 H15 VBL 30 VBL H16 H16 H 0 1 N N N N N N 21.663 41.014 17.804 1.896 1.542 -0.496 H16 VBL 31 VBL H17 H17 H 0 1 N N N N N N 21.280 40.304 16.199 1.979 0.799 1.120 H17 VBL 32 VBL H18 H18 H 0 1 N N N N N N 24.253 38.512 15.551 1.567 -2.034 0.444 H18 VBL 33 VBL H19 H19 H 0 1 N N N N N N 22.515 38.717 15.148 0.563 -1.199 1.653 H19 VBL 34 VBL H20 H20 H 0 1 N N N N N N 20.939 39.057 22.208 7.795 0.046 -0.503 H20 VBL 35 VBL H21 H21 H 0 1 N N N N N N 21.906 39.552 20.778 6.887 1.559 -0.742 H21 VBL 36 VBL H22 H22 H 0 1 N N N N N N 20.684 40.673 21.468 6.969 0.815 0.873 H22 VBL 37 VBL H23 H23 H 0 1 N N N N N N 18.879 39.094 20.839 5.602 -0.392 -1.574 H23 VBL 38 VBL H24 H24 H 0 1 N N N N N N 20.101 37.972 20.149 5.684 -1.135 0.042 H24 VBL 39 VBL H25 H25 H 0 1 N N N N N N 20.099 40.797 19.127 4.392 1.550 -0.619 H25 VBL 40 VBL H26 H26 H 0 1 N N N N N N 18.714 39.754 18.657 4.474 0.807 0.997 H26 VBL 41 VBL H27 H27 H 0 1 N N N N N N 26.171 40.526 17.237 -0.572 0.246 2.043 H27 VBL 42 VBL H28 H28 H 0 1 N N N N N N 23.031 36.481 15.783 -0.547 -3.106 0.738 H28 VBL 43 # 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 VBL C10 O1 SING N N 1 VBL C10 C3 SING N N 2 VBL C3 C4 SING N N 3 VBL C3 C2 SING N N 4 VBL O C4 SING N N 5 VBL C4 C5 SING N N 6 VBL C2 C1 SING N N 7 VBL C1 C SING N N 8 VBL C5 C6 SING N N 9 VBL C6 C7 SING N N 10 VBL C C11 SING N N 11 VBL C9 C8 SING N N 12 VBL C7 C8 SING N N 13 VBL C11 C12 SING N N 14 VBL C3 H1 SING N N 15 VBL C4 H2 SING N N 16 VBL C5 H3 SING N N 17 VBL C5 H4 SING N N 18 VBL C6 H5 SING N N 19 VBL C6 H6 SING N N 20 VBL C7 H7 SING N N 21 VBL C7 H8 SING N N 22 VBL C8 H9 SING N N 23 VBL C8 H10 SING N N 24 VBL C9 H11 SING N N 25 VBL C9 H12 SING N N 26 VBL C9 H13 SING N N 27 VBL C1 H14 SING N N 28 VBL C1 H15 SING N N 29 VBL C2 H16 SING N N 30 VBL C2 H17 SING N N 31 VBL C10 H18 SING N N 32 VBL C10 H19 SING N N 33 VBL C12 H20 SING N N 34 VBL C12 H21 SING N N 35 VBL C12 H22 SING N N 36 VBL C11 H23 SING N N 37 VBL C11 H24 SING N N 38 VBL C H25 SING N N 39 VBL C H26 SING N N 40 VBL O H27 SING N N 41 VBL O1 H28 SING N N 42 # 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 VBL InChI InChI 1.06 "InChI=1S/C13H28O2/c1-3-5-7-9-12(11-14)13(15)10-8-6-4-2/h12-15H,3-11H2,1-2H3/t12-,13+/m0/s1" VBL InChIKey InChI 1.06 BPTAAAKIMVUYQK-QWHCGFSZSA-N VBL SMILES_CANONICAL CACTVS 3.385 "CCCCC[C@@H](O)[C@H](CO)CCCCC" VBL SMILES CACTVS 3.385 "CCCCC[CH](O)[CH](CO)CCCCC" VBL SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCCCC[C@@H](CO)[C@@H](CCCCC)O" VBL SMILES "OpenEye OEToolkits" 2.0.7 "CCCCCC(CO)C(CCCCC)O" # _pdbx_chem_comp_identifier.comp_id VBL _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~{S},3~{R})-2-pentyloctane-1,3-diol" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site VBL "Create component" 2023-09-11 PDBE VBL "Modify PCM" 2024-09-27 PDBE VBL "Initial release" 2025-02-12 RCSB # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id VBL _pdbx_chem_comp_pcm.modified_residue_id SER _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category Lipid/lipid-like _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom C10 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom OG _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #