data_MDA # _chem_comp.id MDA _chem_comp.name "2,6-dideoxy-3-C-methyl-beta-D-ribo-hexopyranose" _chem_comp.type "D-saccharide, beta linking" _chem_comp.pdbx_type ATOMS _chem_comp.formula "C7 H14 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;2,6-DIDEOXY-3 C-METHYL-D-RIBOPYRANOSIDE; 2,6-dideoxy-3-C-methyl-beta-D-ribo-hexose; 2,6-dideoxy-3-C-methyl-D-ribo-hexose; 2,6-dideoxy-3-C-methyl-ribo-hexose ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2020-07-17 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces DDB _chem_comp.formula_weight 162.184 _chem_comp.one_letter_code ? _chem_comp.three_letter_code MDA _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 146D _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # 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 MDA "2,6-DIDEOXY-3 C-METHYL-D-RIBOPYRANOSIDE" PDB ? 2 MDA "2,6-dideoxy-3-C-methyl-beta-D-ribo-hexose" PDB ? 3 MDA "2,6-dideoxy-3-C-methyl-D-ribo-hexose" PDB ? 4 MDA "2,6-dideoxy-3-C-methyl-ribo-hexose" PDB ? # # 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.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 MDA C1 C1 C 0 1 N N R 6.275 6.378 16.542 -0.263 -0.237 1.663 C1 MDA 1 MDA C2 C2 C 0 1 N N N 6.252 7.703 15.769 -1.316 0.420 0.767 C2 MDA 2 MDA C3 C3 C 0 1 N N S 6.493 7.499 14.255 -1.034 0.045 -0.691 C3 MDA 3 MDA C4 C4 C 0 1 N N R 7.845 6.775 14.102 0.418 0.407 -1.018 C4 MDA 4 MDA C5 C5 C 0 1 N N R 7.804 5.456 14.900 1.339 -0.250 0.011 C5 MDA 5 MDA C6 C6 C 0 1 N N N 9.188 4.736 14.785 2.795 0.076 -0.326 C6 MDA 6 MDA "C3'" "C3'" C 0 1 N N N 6.520 8.838 13.483 -1.977 0.823 -1.612 "C3'" MDA 7 MDA O1 O1 O 0 1 N Y N 6.078 6.631 17.942 -0.537 0.082 3.029 O1 MDA 8 MDA O5 O5 O 0 1 N N N 7.526 5.720 16.284 1.033 0.241 1.315 O5 MDA 9 MDA O3 O3 O 0 1 N N N 5.488 6.661 13.712 -1.236 -1.357 -0.873 O3 MDA 10 MDA O4 O4 O 0 1 N N N 8.088 6.485 12.738 0.747 -0.066 -2.325 O4 MDA 11 MDA H1 H1 H 0 1 N N N 5.445 5.739 16.208 -0.299 -1.318 1.530 H1 MDA 12 MDA H2 H21 H 0 1 N N N 7.046 8.351 16.165 -2.307 0.066 1.050 H2 MDA 13 MDA H22 H22 H 0 1 N N N 5.261 8.147 15.936 -1.267 1.502 0.882 H22 MDA 14 MDA H4 H4 H 0 1 N N N 8.662 7.415 14.462 0.541 1.489 -0.981 H4 MDA 15 MDA H5 H5 H 0 1 N N N 6.951 4.870 14.528 1.196 -1.330 -0.011 H5 MDA 16 MDA H61 H61 H 0 1 N N N 9.230 3.797 15.355 3.452 -0.393 0.405 H61 MDA 17 MDA H62 H62 H 0 1 N N N 9.469 4.523 13.744 3.031 -0.301 -1.321 H62 MDA 18 MDA H63 H63 H 0 1 N N N 9.975 5.385 15.194 2.940 1.156 -0.303 H63 MDA 19 MDA "H3'1" "H3'1" H 0 0 N N N 6.742 8.661 12.421 -3.010 0.576 -1.367 "H3'1" MDA 20 MDA "H3'2" "H3'2" H 0 0 N N N 5.555 9.362 13.528 -1.817 1.892 -1.476 "H3'2" MDA 21 MDA "H3'3" "H3'3" H 0 0 N N N 7.304 9.493 13.890 -1.775 0.554 -2.649 "H3'3" MDA 22 MDA HO1 HO1 H 0 1 N Y N 6.092 5.810 18.420 0.143 -0.353 3.559 HO1 MDA 23 MDA HO3 HO3 H 0 1 N Y N 4.646 7.104 13.610 -2.158 -1.539 -0.645 HO3 MDA 24 MDA HO4 HO4 H 0 1 N Y N 8.093 7.300 12.231 1.667 0.181 -2.489 HO4 MDA 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 MDA C1 C2 SING N N 1 MDA C1 O1 SING N N 2 MDA C1 O5 SING N N 3 MDA C1 H1 SING N N 4 MDA C2 C3 SING N N 5 MDA C2 H2 SING N N 6 MDA C2 H22 SING N N 7 MDA C3 C4 SING N N 8 MDA C3 "C3'" SING N N 9 MDA C3 O3 SING N N 10 MDA C4 C5 SING N N 11 MDA C4 O4 SING N N 12 MDA C4 H4 SING N N 13 MDA C5 C6 SING N N 14 MDA C5 O5 SING N N 15 MDA C5 H5 SING N N 16 MDA C6 H61 SING N N 17 MDA C6 H62 SING N N 18 MDA C6 H63 SING N N 19 MDA "C3'" "H3'1" SING N N 20 MDA "C3'" "H3'2" SING N N 21 MDA "C3'" "H3'3" SING N N 22 MDA O1 HO1 SING N N 23 MDA O3 HO3 SING N N 24 MDA O4 HO4 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 MDA SMILES ACDLabs 10.04 "OC1(C)C(O)C(OC(O)C1)C" MDA SMILES_CANONICAL CACTVS 3.341 "C[C@H]1O[C@@H](O)C[C@](C)(O)[C@@H]1O" MDA SMILES CACTVS 3.341 "C[CH]1O[CH](O)C[C](C)(O)[CH]1O" MDA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@@H]1[C@H]([C@@](C[C@@H](O1)O)(C)O)O" MDA SMILES "OpenEye OEToolkits" 1.5.0 "CC1C(C(CC(O1)O)(C)O)O" MDA InChI InChI 1.03 "InChI=1S/C7H14O4/c1-4-6(9)7(2,10)3-5(8)11-4/h4-6,8-10H,3H2,1-2H3/t4-,5-,6-,7+/m1/s1" MDA InChIKey InChI 1.03 YQLFLCVNXSPEKQ-GBNDHIKLSA-N # # 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 MDA "SYSTEMATIC NAME" ACDLabs 10.04 "2,6-dideoxy-3-C-methyl-beta-D-ribo-hexopyranose" MDA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R,4S,5R,6R)-4,6-dimethyloxane-2,4,5-triol" # # 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 MDA "CARBOHYDRATE ISOMER" D PDB ? MDA "CARBOHYDRATE RING" pyranose PDB ? MDA "CARBOHYDRATE ANOMER" beta PDB ? MDA "CARBOHYDRATE PRIMARY CARBONYL GROUP" aldose 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 MDA "Create component" 1999-07-08 RCSB MDA "Modify descriptor" 2011-06-04 RCSB MDA "Other modification" 2020-07-03 RCSB MDA "Modify name" 2020-07-17 RCSB MDA "Modify synonyms" 2020-07-17 RCSB MDA "Modify internal type" 2020-07-17 RCSB MDA "Modify linking type" 2020-07-17 RCSB MDA "Modify atom id" 2020-07-17 RCSB MDA "Modify component atom id" 2020-07-17 RCSB MDA "Modify leaving atom flag" 2020-07-17 RCSB ##