data_ZDC # _chem_comp.id ZDC _chem_comp.name "3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid" _chem_comp.type D-saccharide _chem_comp.pdbx_type ATOMS _chem_comp.formula "C8 H14 O6" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-12-17 _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 206.193 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ZDC _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 3DCQ _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _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 ZDC C1 C1 C 0 1 N N S N N N 13.263 47.159 9.319 -1.065 1.087 0.817 C1 ZDC 1 ZDC C1M C1M C 0 1 N N N N N N 13.959 47.845 10.483 -1.132 2.005 -0.405 C1M ZDC 2 ZDC C2 C2 C 0 1 N N S N N N 14.167 47.088 8.096 -2.141 0.003 0.701 C2 ZDC 3 ZDC C3 C3 C 0 1 N N R N N N 13.517 46.301 6.993 -1.862 -0.852 -0.539 C3 ZDC 4 ZDC C4 C4 C 0 1 N N S N N N 13.092 44.916 7.506 -0.453 -1.441 -0.433 C4 ZDC 5 ZDC C5 C5 C 0 1 N N S N N N 12.166 45.109 8.721 0.558 -0.303 -0.274 C5 ZDC 6 ZDC C6 C6 C 0 1 N N N N N N 10.831 45.770 8.324 1.962 -0.886 -0.107 C6 ZDC 7 ZDC C7 C7 C 0 1 N N N N N N 10.238 46.093 9.693 2.971 0.233 -0.074 C7 ZDC 8 ZDC O2 O2 O 0 1 N N N N N N 15.393 46.478 8.447 -3.425 0.617 0.581 O2 ZDC 9 ZDC O3 O3 O 0 1 N N N N N N 14.443 46.183 5.923 -1.956 -0.039 -1.711 O3 ZDC 10 ZDC O4 O4 O 0 1 N N N N N N 12.411 44.212 6.483 -0.381 -2.307 0.702 O4 ZDC 11 ZDC O5 O5 O 0 1 N N N N N N 12.899 45.822 9.741 0.224 0.472 0.880 O5 ZDC 12 ZDC O7A O7A O 0 1 N N N N N N 9.927 45.192 10.470 2.604 1.380 -0.173 O7A ZDC 13 ZDC O7B O7B O 0 1 N Y N N N N 10.016 47.354 10.010 4.277 -0.044 0.066 O7B ZDC 14 ZDC H1 H1 H 0 1 N N N N N N 12.358 47.728 9.060 -1.233 1.671 1.721 H1 ZDC 15 ZDC H1M1 H1M1 H 0 0 N N N N N N 14.247 48.865 10.189 -0.805 1.458 -1.289 H1M1 ZDC 16 ZDC H1M2 H1M2 H 0 0 N N N N N N 13.275 47.891 11.343 -2.158 2.345 -0.548 H1M2 ZDC 17 ZDC H1M3 H1M3 H 0 0 N N N N N N 14.859 47.275 10.759 -0.482 2.866 -0.249 H1M3 ZDC 18 ZDC H2 H2 H 0 1 N N N N N N 14.348 48.112 7.738 -2.120 -0.627 1.590 H2 ZDC 19 ZDC H2O H2O H 0 1 N N N N N N 15.956 46.435 7.683 -3.665 1.178 1.332 H2O ZDC 20 ZDC H3 H3 H 0 1 N N N N N N 12.618 46.838 6.655 -2.592 -1.659 -0.596 H3 ZDC 21 ZDC H3O H3O H 0 1 N N N N N N 14.048 45.687 5.215 -2.822 0.372 -1.836 H3O ZDC 22 ZDC H4 H4 H 0 1 N N N N N N 13.988 44.364 7.825 -0.225 -2.007 -1.337 H4 ZDC 23 ZDC H4O H4O H 0 1 N N N N N N 12.151 43.357 6.805 -0.999 -3.050 0.669 H4O ZDC 24 ZDC H5 H5 H 0 1 N N N N N N 11.927 44.107 9.107 0.531 0.333 -1.158 H5 ZDC 25 ZDC H61 H61 H 0 1 N N N N N N 10.994 46.682 7.731 2.014 -1.450 0.824 H61 ZDC 26 ZDC H62 H62 H 0 1 N N N N N N 10.190 45.076 7.761 2.182 -1.548 -0.945 H62 ZDC 27 ZDC H7OB H7OB H 0 0 N N N N N N 9.612 47.399 10.868 4.886 0.707 0.082 H7OB ZDC 28 # 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 ZDC C1 C1M SING N N 1 ZDC C1M H1M1 SING N N 2 ZDC C1M H1M2 SING N N 3 ZDC C1M H1M3 SING N N 4 ZDC C1 H1 SING N N 5 ZDC C1 O5 SING N N 6 ZDC C1 C2 SING N N 7 ZDC C2 H2 SING N N 8 ZDC C2 O2 SING N N 9 ZDC O2 H2O SING N N 10 ZDC C2 C3 SING N N 11 ZDC C3 H3 SING N N 12 ZDC C3 O3 SING N N 13 ZDC O3 H3O SING N N 14 ZDC C3 C4 SING N N 15 ZDC C4 H4 SING N N 16 ZDC C4 O4 SING N N 17 ZDC O4 H4O SING N N 18 ZDC C4 C5 SING N N 19 ZDC C5 H5 SING N N 20 ZDC C5 O5 SING N N 21 ZDC C5 C6 SING N N 22 ZDC C6 H61 SING N N 23 ZDC C6 H62 SING N N 24 ZDC C6 C7 SING N N 25 ZDC C7 O7A DOUB N N 26 ZDC C7 O7B SING N N 27 ZDC O7B H7OB SING N N 28 # 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 ZDC SMILES ACDLabs 12.01 "O=C(O)CC1OC(C(O)C(O)C1O)C" ZDC InChI InChI 1.03 "InChI=1S/C8H14O6/c1-3-6(11)8(13)7(12)4(14-3)2-5(9)10/h3-4,6-8,11-13H,2H2,1H3,(H,9,10)/t3-,4-,6+,7+,8+/m0/s1" ZDC InChIKey InChI 1.03 YTZUDUWVQZSKNN-OASCRQMUSA-N ZDC SMILES_CANONICAL CACTVS 3.370 "C[C@@H]1O[C@@H](CC(O)=O)[C@@H](O)[C@H](O)[C@@H]1O" ZDC SMILES CACTVS 3.370 "C[CH]1O[CH](CC(O)=O)[CH](O)[CH](O)[CH]1O" ZDC SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C[C@H]1[C@H]([C@H]([C@@H]([C@@H](O1)CC(=O)O)O)O)O" ZDC SMILES "OpenEye OEToolkits" 1.7.6 "CC1C(C(C(C(O1)CC(=O)O)O)O)O" # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier ZDC "SYSTEMATIC NAME" ACDLabs 12.01 "3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid" ZDC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "2-[(2S,3S,4R,5S,6S)-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]ethanoic acid" # 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 ZDC "CARBOHYDRATE ISOMER" D PDB ? ZDC "CARBOHYDRATE RING" pyranose PDB ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site ZDC "Create component" 2012-12-17 RCSB ZDC "Modify atom id" 2013-01-02 RCSB ZDC "Initial release" 2016-02-10 RCSB ZDC "Other modification" 2020-07-03 RCSB ZDC "Modify linking type" 2020-07-17 RCSB ZDC "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 ZDC ALA None Carbohydrate "Amino-acid backbone" N-terminal C7 N ? ? 2 ZDC CYS None Carbohydrate "Amino-acid backbone" N-terminal C7 N ? ? 3 ZDC DCY None Carbohydrate "Amino-acid backbone" N-terminal C7 N ? ? 4 ZDC DLE None Carbohydrate "Amino-acid backbone" N-terminal C7 N ? ? 5 ZDC DLY None Carbohydrate "Amino-acid backbone" N-terminal C7 N ? ? 6 ZDC DTY None Carbohydrate "Amino-acid backbone" N-terminal C7 N ? ? 7 ZDC LYS None Carbohydrate "Amino-acid backbone" N-terminal C7 N ? ? 8 ZDC DPP None Carbohydrate "Amino-acid side chain" "Any position" C7 NG ? ? 9 ZDC LYS None Carbohydrate "Amino-acid side chain" "Any position" C7 NZ ? ? #