data_1X4 # _chem_comp.id 1X4 _chem_comp.name "2,3-dideoxy-5-O-phosphono-alpha-D-ribofuranose" _chem_comp.type "D-saccharide, alpha linking" _chem_comp.pdbx_type ATOMS _chem_comp.formula "C5 H11 O6 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;2,3-dideoxyribose-5-phosphate; 2,3-dideoxy-5-O-phosphono-alpha-D-ribose; 2,3-dideoxy-5-O-phosphono-D-ribose; 2,3-dideoxy-5-O-phosphono-ribose ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-07-22 _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 ? _chem_comp.formula_weight 198.111 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 1X4 _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 4LR9 _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 1X4 "2,3-dideoxyribose-5-phosphate" PDB ? 2 1X4 "2,3-dideoxy-5-O-phosphono-alpha-D-ribose" PDB ? 3 1X4 "2,3-dideoxy-5-O-phosphono-D-ribose" PDB ? 4 1X4 "2,3-dideoxy-5-O-phosphono-ribose" 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 1X4 O1P O1P O 0 1 N N N 20.252 6.836 8.475 -3.227 -1.309 0.766 O1P 1X4 1 1X4 P P P 0 1 N N N 19.116 5.768 8.080 -2.476 -0.148 -0.058 P 1X4 2 1X4 O2P O2P O 0 1 N N N 19.810 4.799 6.990 -2.508 -0.469 -1.503 O2P 1X4 3 1X4 O3P O3P O 0 1 N N N 18.624 5.037 9.266 -3.218 1.257 0.197 O3P 1X4 4 1X4 O5 "O5'" O 0 1 N N N 17.947 6.559 7.302 -0.946 -0.045 0.435 O5 1X4 5 1X4 C5 "C5'" C 0 1 N N N 17.813 7.966 7.499 0.012 0.821 -0.177 C5 1X4 6 1X4 C4 "C4'" C 0 1 N N S 16.612 8.511 6.755 1.359 0.673 0.532 C4 1X4 7 1X4 O4 "O1'" O 0 1 N N N 16.498 9.912 7.059 1.886 -0.640 0.305 O4 1X4 8 1X4 C3 "C3'" C 0 1 N N N 16.931 8.475 5.265 2.369 1.687 -0.046 C3 1X4 9 1X4 C2 "C2'" C 0 1 N N N 16.387 9.811 4.751 3.683 0.859 -0.084 C2 1X4 10 1X4 C1 "C1'" C 0 1 N N S 15.722 10.417 5.980 3.131 -0.553 -0.406 C1 1X4 11 1X4 O1 O1 O 0 1 N Y N 14.418 9.868 6.115 4.037 -1.557 0.055 O1 1X4 12 1X4 H1A H1 H 0 1 N N N 21.045 6.651 7.986 -4.155 -1.428 0.521 H1A 1X4 13 1X4 H2A H2 H 0 1 N N N 18.810 4.111 9.167 -3.234 1.531 1.124 H2A 1X4 14 1X4 H51 H3 H 0 1 N N N 18.720 8.468 7.132 0.123 0.555 -1.228 H51 1X4 15 1X4 H52 H4 H 0 1 N N N 17.691 8.168 8.573 -0.329 1.853 -0.097 H52 1X4 16 1X4 H4 H5 H 0 1 N N N 15.697 7.946 6.987 1.235 0.841 1.602 H4 1X4 17 1X4 H3 H6 H 0 1 N N N 16.425 7.630 4.775 2.077 1.997 -1.049 H3 1X4 18 1X4 H7 H7 H 0 1 N N N 18.016 8.401 5.097 2.471 2.551 0.611 H7 1X4 19 1X4 H2 H8 H 0 1 N N N 17.202 10.454 4.387 4.346 1.211 -0.874 H2 1X4 20 1X4 H9 H9 H 0 1 N N N 15.655 9.654 3.945 4.185 0.873 0.883 H9 1X4 21 1X4 H1 H10 H 0 1 N N N 15.721 11.516 5.932 2.964 -0.659 -1.478 H1 1X4 22 1X4 HO1 H11 H 0 1 N Y N 13.995 10.240 6.880 3.744 -2.461 -0.119 HO1 1X4 23 # # 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 1X4 C2 C3 SING N N 1 1X4 C2 C1 SING N N 2 1X4 C3 C4 SING N N 3 1X4 C1 O1 SING N N 4 1X4 C1 O4 SING N N 5 1X4 C4 O4 SING N N 6 1X4 C4 C5 SING N N 7 1X4 O2P P DOUB N N 8 1X4 O5 C5 SING N N 9 1X4 O5 P SING N N 10 1X4 P O1P SING N N 11 1X4 P O3P SING N N 12 1X4 O1P H1A SING N N 13 1X4 O3P H2A SING N N 14 1X4 C5 H51 SING N N 15 1X4 C5 H52 SING N N 16 1X4 C4 H4 SING N N 17 1X4 C3 H3 SING N N 18 1X4 C3 H7 SING N N 19 1X4 C2 H2 SING N N 20 1X4 C2 H9 SING N N 21 1X4 C1 H1 SING N N 22 1X4 O1 HO1 SING N N 23 # # 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 1X4 SMILES ACDLabs 12.01 "O=P(OCC1OC(O)CC1)(O)O" 1X4 InChI InChI 1.03 "InChI=1S/C5H11O6P/c6-5-2-1-4(11-5)3-10-12(7,8)9/h4-6H,1-3H2,(H2,7,8,9)/t4-,5-/m0/s1" 1X4 InChIKey InChI 1.03 DOJAXCJBQVATEM-WHFBIAKZSA-N 1X4 SMILES_CANONICAL CACTVS 3.385 "O[C@@H]1CC[C@@H](CO[P](O)(O)=O)O1" 1X4 SMILES CACTVS 3.385 "O[CH]1CC[CH](CO[P](O)(O)=O)O1" 1X4 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1C[C@H](O[C@@H]1COP(=O)(O)O)O" 1X4 SMILES "OpenEye OEToolkits" 1.7.6 "C1CC(OC1COP(=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 1X4 "SYSTEMATIC NAME" ACDLabs 12.01 "[(2S,5S)-5-hydroxytetrahydrofuran-2-yl]methyl dihydrogen phosphate" 1X4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2S,5S)-5-oxidanyloxolan-2-yl]methyl dihydrogen phosphate" 1X4 "IUPAC CARBOHYDRATE SYMBOL" PDB-CARE 1.0 "a-D-2,3-deoxy-Ribf5PO3" # # 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 1X4 "CARBOHYDRATE ISOMER" D PDB ? 1X4 "CARBOHYDRATE RING" furanose PDB ? 1X4 "CARBOHYDRATE ANOMER" alpha PDB ? 1X4 "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 1X4 "Create component" 2013-07-22 RCSB 1X4 "Initial release" 2013-07-31 RCSB 1X4 "Other modification" 2020-07-03 RCSB 1X4 "Modify name" 2020-07-17 RCSB 1X4 "Modify synonyms" 2020-07-17 RCSB 1X4 "Modify internal type" 2020-07-17 RCSB 1X4 "Modify linking type" 2020-07-17 RCSB 1X4 "Modify atom id" 2020-07-17 RCSB 1X4 "Modify component atom id" 2020-07-17 RCSB 1X4 "Modify leaving atom flag" 2020-07-17 RCSB ##