data_VDF # _chem_comp.id VDF _chem_comp.name 2-O-phosphono-beta-L-arabinopyranose _chem_comp.type "L-saccharide, beta linking" _chem_comp.pdbx_type ATOMS _chem_comp.formula "C5 H11 O8 P" _chem_comp.mon_nstd_parent_comp_id ARB _chem_comp.pdbx_synonyms "2-O-phosphono-beta-L-arabinose; 2-O-phosphono-L-arabinose; 2-O-phosphono-arabinose; [(2S,3R,4S,5S)-2,4,5-tris(oxidanyl)oxan-3-yl] dihydrogen phosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-03-01 _chem_comp.pdbx_modified_date 2024-01-19 _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 230.110 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VDF _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 8CH2 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # 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 VDF OP2 O1 O 0 1 N N N N N N 15.236 -2.563 -13.927 2.414 -1.668 0.777 OP2 VDF 1 VDF P P1 P 0 1 N N N N N N 14.168 -2.532 -14.990 2.237 -0.325 -0.093 P VDF 2 VDF OP1 O2 O 0 1 N N N N N N 13.468 -3.759 -15.332 2.788 0.826 0.657 OP1 VDF 3 VDF OP3 O3 O 0 1 N Y N N N N 13.318 -1.373 -14.410 3.023 -0.482 -1.489 OP3 VDF 4 VDF O2 O4 O 0 1 N N N N N N 14.939 -1.972 -16.287 0.673 -0.076 -0.383 O2 VDF 5 VDF C2 C1 C 0 1 N N R N N N 15.779 -0.892 -16.314 -0.275 0.206 0.648 C2 VDF 6 VDF C3 C2 C 0 1 N N S N N N 15.008 0.340 -16.873 -1.361 -0.874 0.655 C3 VDF 7 VDF O3 O5 O 0 1 N N N N N N 14.110 0.843 -15.845 -2.273 -0.628 1.727 O3 VDF 8 VDF C4 C3 C 0 1 N N S N N N 15.963 1.496 -17.278 -2.115 -0.833 -0.678 C4 VDF 9 VDF O4 O6 O 0 1 N N N N N N 16.599 1.915 -16.136 -3.178 -1.788 -0.655 O4 VDF 10 VDF C5 C4 C 0 1 N N N N N N 17.023 0.984 -18.205 -2.692 0.570 -0.886 C5 VDF 11 VDF O5 O7 O 0 1 N N N N N N 17.705 -0.136 -17.624 -1.633 1.529 -0.851 O5 VDF 12 VDF C1 C5 C 0 1 N N S N N N 16.883 -1.276 -17.333 -0.922 1.570 0.389 C1 VDF 13 VDF O1 O8 O 0 1 N Y N N N N 16.351 -1.902 -18.437 0.091 2.575 0.325 O1 VDF 14 VDF H1A H1 H 0 1 N N N N N N 15.323 -3.447 -13.590 2.073 -2.463 0.346 H1A VDF 15 VDF H2A H2 H 0 1 N Y N N N N 12.409 -1.643 -14.357 3.973 -0.635 -1.390 H2A VDF 16 VDF H2 H3 H 0 1 N N N N N N 16.222 -0.657 -15.335 0.231 0.221 1.614 H2 VDF 17 VDF H3 H4 H 0 1 N N N N N N 14.434 0.027 -17.758 -0.900 -1.853 0.785 H3 VDF 18 VDF HO3 H5 H 0 1 N Y N N N N 13.514 0.153 -15.579 -2.989 -1.276 1.791 HO3 VDF 19 VDF H4 H6 H 0 1 N N N N N N 15.388 2.301 -17.758 -1.429 -1.070 -1.492 H4 VDF 20 VDF HO4 H7 H 0 1 N Y N N N N 15.957 2.248 -15.520 -3.698 -1.816 -1.469 HO4 VDF 21 VDF H51 H8 H 0 1 N N N N N N 17.749 1.787 -18.402 -3.193 0.617 -1.853 H51 VDF 22 VDF H52 H9 H 0 1 N N N N N N 16.556 0.672 -19.151 -3.408 0.789 -0.094 H52 VDF 23 VDF H1 H10 H 0 1 N N N N N N 17.522 -2.005 -16.814 -1.615 1.803 1.198 H1 VDF 24 VDF HO1 H11 H 0 1 N Y N N N N 15.823 -2.641 -18.159 -0.249 3.466 0.162 HO1 VDF 25 # 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 VDF O1 C1 SING N N 1 VDF C5 O5 SING N N 2 VDF C5 C4 SING N N 3 VDF O5 C1 SING N N 4 VDF C1 C2 SING N N 5 VDF C4 C3 SING N N 6 VDF C4 O4 SING N N 7 VDF C3 C2 SING N N 8 VDF C3 O3 SING N N 9 VDF C2 O2 SING N N 10 VDF O2 P SING N N 11 VDF OP1 P DOUB N N 12 VDF P OP3 SING N N 13 VDF P OP2 SING N N 14 VDF OP2 H1A SING N N 15 VDF OP3 H2A SING N N 16 VDF C2 H2 SING N N 17 VDF C3 H3 SING N N 18 VDF O3 HO3 SING N N 19 VDF C4 H4 SING N N 20 VDF O4 HO4 SING N N 21 VDF C5 H51 SING N N 22 VDF C5 H52 SING N N 23 VDF C1 H1 SING N N 24 VDF O1 HO1 SING N N 25 # 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 VDF InChI InChI 1.06 "InChI=1S/C5H11O8P/c6-2-1-12-5(8)4(3(2)7)13-14(9,10)11/h2-8H,1H2,(H2,9,10,11)/t2-,3-,4+,5-/m0/s1" VDF InChIKey InChI 1.06 QIAIUTJEZJIPSH-KLVWXMOXSA-N VDF SMILES_CANONICAL CACTVS 3.385 "O[C@H]1CO[C@H](O)[C@H](O[P](O)(O)=O)[C@H]1O" VDF SMILES CACTVS 3.385 "O[CH]1CO[CH](O)[CH](O[P](O)(O)=O)[CH]1O" VDF SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1[C@@H]([C@@H]([C@H]([C@H](O1)O)OP(=O)(O)O)O)O" VDF SMILES "OpenEye OEToolkits" 2.0.7 "C1C(C(C(C(O1)O)OP(=O)(O)O)O)O" # _pdbx_chem_comp_identifier.comp_id VDF _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},4~{S},5~{S})-2,4,5-tris(oxidanyl)oxan-3-yl] dihydrogen phosphate" # loop_ _pdbx_chem_comp_feature.comp_id _pdbx_chem_comp_feature.type _pdbx_chem_comp_feature.value _pdbx_chem_comp_feature.source _pdbx_chem_comp_feature.support VDF "CARBOHYDRATE ISOMER" L PDB ? VDF "CARBOHYDRATE RING" pyranose PDB ? VDF "CARBOHYDRATE ANOMER" beta PDB ? VDF "CARBOHYDRATE PRIMARY CARBONYL GROUP" aldose PDB ? # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 VDF 2-O-phosphono-beta-L-arabinose PDB ? 2 VDF 2-O-phosphono-L-arabinose PDB ? 3 VDF 2-O-phosphono-arabinose PDB ? 4 VDF "[(2S,3R,4S,5S)-2,4,5-tris(oxidanyl)oxan-3-yl] dihydrogen phosphate" PDB ? # _pdbx_chem_comp_related.comp_id VDF _pdbx_chem_comp_related.related_comp_id ARB _pdbx_chem_comp_related.relationship_type "Carbohydrate core" _pdbx_chem_comp_related.details ? # loop_ _pdbx_chem_comp_atom_related.ordinal _pdbx_chem_comp_atom_related.comp_id _pdbx_chem_comp_atom_related.atom_id _pdbx_chem_comp_atom_related.related_comp_id _pdbx_chem_comp_atom_related.related_atom_id _pdbx_chem_comp_atom_related.related_type 1 VDF O2 ARB O2 "Carbohydrate core" 2 VDF C2 ARB C2 "Carbohydrate core" 3 VDF C3 ARB C3 "Carbohydrate core" 4 VDF O3 ARB O3 "Carbohydrate core" 5 VDF C4 ARB C4 "Carbohydrate core" 6 VDF O4 ARB O4 "Carbohydrate core" 7 VDF C5 ARB C5 "Carbohydrate core" 8 VDF O5 ARB O5 "Carbohydrate core" 9 VDF C1 ARB C1 "Carbohydrate core" 10 VDF O1 ARB O1 "Carbohydrate core" 11 VDF H2 ARB H2 "Carbohydrate core" 12 VDF H3 ARB H3 "Carbohydrate core" 13 VDF HO3 ARB HO3 "Carbohydrate core" 14 VDF H4 ARB H4 "Carbohydrate core" 15 VDF HO4 ARB HO4 "Carbohydrate core" 16 VDF H51 ARB H51 "Carbohydrate core" 17 VDF H52 ARB H52 "Carbohydrate core" 18 VDF H1 ARB H1 "Carbohydrate core" 19 VDF HO1 ARB HO1 "Carbohydrate core" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site VDF "Create component" 2023-03-01 PDBE VDF "Modify internal type" 2023-05-17 PDBE VDF "Initial release" 2024-01-24 RCSB #