data_VPH # _chem_comp.id VPH _chem_comp.name "methyl (2S,3R,4S,5R,6R)-6-(hydroxymethyl)-4,5-bis(oxidanyl)-3-sulfanyl-oxane-2-carboxylate" _chem_comp.type saccharide _chem_comp.pdbx_type ATOMS _chem_comp.formula "C8 H14 O6 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-03-24 _chem_comp.pdbx_modified_date 2026-06-22 _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 238.258 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VPH _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 8OJI _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE _chem_comp.pdbx_pcm ? # 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_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_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 VPH "C5'" C1 C 0 1 N N R N N N 24.467 40.618 32.579 -1.978 0.407 -0.517 "C5'" VPH 1 VPH "C4'" C2 C 0 1 N N R N N N 23.774 40.271 31.270 -2.017 -1.019 0.038 "C4'" VPH 2 VPH "C3'" C3 C 0 1 N N S N N N 23.443 38.787 31.259 -0.741 -1.757 -0.381 "C3'" VPH 3 VPH "C2'" C4 C 0 1 N N R N N N 22.653 38.417 32.497 0.476 -0.972 0.118 "C2'" VPH 4 VPH "C1'" C5 C 0 1 N N S N N N 23.388 38.869 33.760 0.419 0.452 -0.440 "C1'" VPH 5 VPH "O5'" O1 O 0 1 N N N N N N 23.621 40.277 33.687 -0.805 1.071 -0.039 "O5'" VPH 6 VPH "C6'" C6 C 0 1 N N N N N N 24.828 42.074 32.708 -3.220 1.170 -0.053 "C6'" VPH 7 VPH "O6'" O2 O 0 1 N N N N N N 25.849 42.223 33.681 -3.242 2.462 -0.663 "O6'" VPH 8 VPH "O4'" O3 O 0 1 N N N N N N 22.582 41.024 31.155 -2.098 -0.975 1.464 "O4'" VPH 9 VPH "O3'" O4 O 0 1 N N N N N N 22.693 38.443 30.100 -0.735 -3.065 0.193 "O3'" VPH 10 VPH C7 C7 C 0 1 N N N N N N 22.628 38.506 35.028 1.582 1.248 0.094 C7 VPH 11 VPH O8 O5 O 0 1 N N N N N N 22.205 39.593 35.656 2.837 0.910 -0.241 O8 VPH 12 VPH C9 C8 C 0 1 N N N N N N 20.925 39.478 36.318 3.908 1.721 0.311 C9 VPH 13 VPH O7 O6 O 0 1 N N N N N N 22.440 37.382 35.400 1.385 2.191 0.825 O7 VPH 14 VPH "H5'" H1 H 0 1 N N N N N N 25.394 40.028 32.639 -1.958 0.374 -1.606 "H5'" VPH 15 VPH "H4'" H2 H 0 1 N N N N N N 24.453 40.494 30.434 -2.887 -1.541 -0.361 "H4'" VPH 16 VPH "H3'" H3 H 0 1 N N N N N N 24.387 38.223 31.269 -0.705 -1.834 -1.468 "H3'" VPH 17 VPH "H2'" H4 H 0 1 N N N N N N 21.727 39.009 32.457 0.465 -0.938 1.207 "H2'" VPH 18 VPH "H1'" H6 H 0 1 N N N N N N 24.356 38.347 33.788 0.471 0.419 -1.528 "H1'" VPH 19 VPH "H61'" H7 H 0 0 N N N N N N 25.187 42.450 31.739 -4.114 0.617 -0.341 "H61'" VPH 20 VPH "H62'" H8 H 0 0 N N N N N N 23.941 42.646 33.017 -3.195 1.280 1.031 "H62'" VPH 21 VPH "HO6'" H9 H 0 0 N Y N N N N 26.077 43.141 33.763 -4.004 3.002 -0.413 "HO6'" VPH 22 VPH "HO4'" H10 H 0 0 N Y N N N N 22.790 41.951 31.162 -2.127 -1.846 1.883 "HO4'" VPH 23 VPH "HO3'" H11 H 0 0 N Y N N N N 22.497 37.513 30.113 0.046 -3.589 -0.031 "HO3'" VPH 24 VPH H12 H12 H 0 1 N N N N N N 20.675 40.433 36.803 4.868 1.341 -0.038 H12 VPH 25 VPH H13 H13 H 0 1 N N N N N N 20.150 39.229 35.578 3.786 2.754 -0.015 H13 VPH 26 VPH H14 H14 H 0 1 N N N N N N 20.975 38.684 37.077 3.873 1.676 1.399 H14 VPH 27 VPH S1 S1 S 0 1 N N N N N N ? ? ? 1.995 -1.785 -0.450 S1 VPH 28 VPH "HS1'" H5 H 0 0 N Y N N N N ? ? ? 2.964 -1.000 0.054 "HS1'" VPH 29 # 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 VPH "O3'" "C3'" SING N N 1 VPH "O4'" "C4'" SING N N 2 VPH "C3'" "C4'" SING N N 3 VPH "C3'" "C2'" SING N N 4 VPH "C4'" "C5'" SING N N 5 VPH "C2'" "C1'" SING N N 6 VPH "C5'" "C6'" SING N N 7 VPH "C5'" "O5'" SING N N 8 VPH "C6'" "O6'" SING N N 9 VPH "O5'" "C1'" SING N N 10 VPH "C1'" C7 SING N N 11 VPH C7 O7 DOUB N N 12 VPH C7 O8 SING N N 13 VPH O8 C9 SING N N 14 VPH "C5'" "H5'" SING N N 15 VPH "C4'" "H4'" SING N N 16 VPH "C3'" "H3'" SING N N 17 VPH "C2'" "H2'" SING N N 18 VPH "C1'" "H1'" SING N N 19 VPH "C6'" "H61'" SING N N 20 VPH "C6'" "H62'" SING N N 21 VPH "O6'" "HO6'" SING N N 22 VPH "O4'" "HO4'" SING N N 23 VPH "O3'" "HO3'" SING N N 24 VPH C9 H12 SING N N 25 VPH C9 H13 SING N N 26 VPH C9 H14 SING N N 27 VPH "C2'" S1 SING N N 28 VPH S1 "HS1'" SING N N 29 # 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 VPH InChI InChI 1.06 "InChI=1S/C8H14O6S/c1-13-8(12)6-7(15)5(11)4(10)3(2-9)14-6/h3-7,9-11,15H,2H2,1H3/t3-,4+,5+,6-,7?/m1/s1" VPH InChIKey InChI 1.06 UYGITGUNLYPQLW-TVPFVARWSA-N VPH SMILES_CANONICAL CACTVS 3.385 "COC(=O)[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1S" VPH SMILES CACTVS 3.385 "COC(=O)[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1S" VPH SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "COC(=O)[C@H]1[C@@H]([C@H]([C@H]([C@H](O1)CO)O)O)S" VPH SMILES "OpenEye OEToolkits" 2.0.7 "COC(=O)C1C(C(C(C(O1)CO)O)O)S" # _pdbx_chem_comp_identifier.comp_id VPH _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 "methyl (2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-4,5-bis(oxidanyl)-3-sulfanyl-oxane-2-carboxylate" # _pdbx_chem_comp_feature.comp_id VPH _pdbx_chem_comp_feature.type "CARBOHYDRATE RING" _pdbx_chem_comp_feature.value pyranose _pdbx_chem_comp_feature.source PDB _pdbx_chem_comp_feature.support ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site VPH "Create component" 2023-03-24 PDBE VPH "Initial release" 2023-09-13 RCSB VPH "Modify internal type" 2026-06-18 PDBE VPH "Modify linking type" 2026-06-18 PDBE VPH "Modify atom id" 2026-06-18 PDBE VPH "Modify leaving atom flag" 2026-06-22 PDBE #