data_RP3 # _chem_comp.id RP3 _chem_comp.name 3-deoxy-5-O-phosphono-beta-D-ribofuranose _chem_comp.type "D-saccharide, beta linking" _chem_comp.pdbx_type ATOMS _chem_comp.formula "C5 H11 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;3'-deoxy-D-ribofuranose-5'-phosphate; 3-deoxy-5-O-phosphono-beta-D-ribose; 3-deoxy-5-O-phosphono-D-ribose; 3-deoxy-5-O-phosphono-ribose ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-07-28 _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 214.110 _chem_comp.one_letter_code ? _chem_comp.three_letter_code RP3 _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 5CX8 _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 RP3 "3'-deoxy-D-ribofuranose-5'-phosphate" PDB ? 2 RP3 3-deoxy-5-O-phosphono-beta-D-ribose PDB ? 3 RP3 3-deoxy-5-O-phosphono-D-ribose PDB ? 4 RP3 3-deoxy-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 RP3 O3X O3X O 0 1 N N N 26.566 23.161 95.939 -3.665 0.574 -1.316 O3X RP3 1 RP3 "P'" "P'" P 0 1 N N N 26.540 24.514 95.280 -2.854 -0.000 -0.049 "P'" RP3 2 RP3 O1X O1X O 0 1 N N N 26.760 25.693 96.184 -3.076 0.971 1.215 O1X RP3 3 RP3 O2X O2X O 0 1 N N N 25.411 24.623 94.306 -3.347 -1.357 0.278 O2X RP3 4 RP3 O5 "O5'" O 0 1 N N N 27.843 24.564 94.332 -1.285 -0.071 -0.403 O5 RP3 5 RP3 C5 "C5'" C 0 1 N N N 27.863 25.463 93.216 -0.313 -0.635 0.480 C5 RP3 6 RP3 C4 "C4'" C 0 1 N N S 29.303 25.865 93.033 1.073 -0.542 -0.162 C4 RP3 7 RP3 O4 "O1'" O 0 1 N N N 30.064 24.743 92.596 1.506 0.834 -0.238 O4 RP3 8 RP3 C3 "C3'" C 0 1 N N N 29.576 27.008 92.068 2.139 -1.211 0.743 C3 RP3 9 RP3 C2 "C2'" C 0 1 N N R 30.696 26.470 91.192 3.437 -0.490 0.303 C2 RP3 10 RP3 O2 "O2'" O 0 1 N N N 31.777 27.371 91.118 4.154 -1.284 -0.644 O2 RP3 11 RP3 C1 "C1'" C 0 1 N N R 31.213 25.267 91.929 2.939 0.816 -0.354 C1 RP3 12 RP3 O1 O1 O 0 1 N Y N 31.702 24.364 90.964 3.495 1.944 0.324 O1 RP3 13 RP3 H1A H1 H 0 1 N N N 25.852 22.632 95.605 -4.619 0.644 -1.174 H1A RP3 14 RP3 H2A H2 H 0 1 N N N 26.116 26.365 95.991 -2.775 1.879 1.072 H2A RP3 15 RP3 H51 H3 H 0 1 N N N 27.243 26.347 93.426 -0.315 -0.086 1.422 H51 RP3 16 RP3 H52 H4 H 0 1 N N N 27.489 24.959 92.313 -0.557 -1.681 0.668 H52 RP3 17 RP3 H4 H5 H 0 1 N N N 29.682 26.176 94.018 1.068 -0.998 -1.151 H4 RP3 18 RP3 H3 H6 H 0 1 N N N 29.898 27.911 92.608 1.928 -1.024 1.796 H3 RP3 19 RP3 H7 H7 H 0 1 N N N 28.683 27.238 91.468 2.202 -2.281 0.544 H7 RP3 20 RP3 H2 H8 H 0 1 N N N 30.314 26.190 90.199 4.062 -0.267 1.168 H2 RP3 21 RP3 HO2 H9 H 0 1 N Y N 31.504 28.156 90.658 4.945 -0.856 -0.997 HO2 RP3 22 RP3 H1 H10 H 0 1 N N N 31.994 25.563 92.645 3.226 0.835 -1.406 H1 RP3 23 RP3 HO1 H11 H 0 1 N Y N 32.038 23.588 91.397 3.221 2.797 -0.041 HO1 RP3 24 # # 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 RP3 O1 C1 SING N N 1 RP3 O2 C2 SING N N 2 RP3 C2 C1 SING N N 3 RP3 C2 C3 SING N N 4 RP3 C1 O4 SING N N 5 RP3 C3 C4 SING N N 6 RP3 O4 C4 SING N N 7 RP3 C4 C5 SING N N 8 RP3 C5 O5 SING N N 9 RP3 O2X "P'" DOUB N N 10 RP3 O5 "P'" SING N N 11 RP3 "P'" O3X SING N N 12 RP3 "P'" O1X SING N N 13 RP3 O3X H1A SING N N 14 RP3 O1X H2A SING N N 15 RP3 C5 H51 SING N N 16 RP3 C5 H52 SING N N 17 RP3 C4 H4 SING N N 18 RP3 C3 H3 SING N N 19 RP3 C3 H7 SING N N 20 RP3 C2 H2 SING N N 21 RP3 O2 HO2 SING N N 22 RP3 C1 H1 SING N N 23 RP3 O1 HO1 SING N N 24 # # 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 RP3 SMILES ACDLabs 12.01 "OP(O)(=O)OCC1OC(C(C1)O)O" RP3 InChI InChI 1.03 "InChI=1S/C5H11O7P/c6-4-1-3(12-5(4)7)2-11-13(8,9)10/h3-7H,1-2H2,(H2,8,9,10)/t3-,4+,5+/m0/s1" RP3 InChIKey InChI 1.03 OOLHLHJSMUTTHE-VPENINKCSA-N RP3 SMILES_CANONICAL CACTVS 3.385 "O[C@@H]1C[C@@H](CO[P](O)(O)=O)O[C@H]1O" RP3 SMILES CACTVS 3.385 "O[CH]1C[CH](CO[P](O)(O)=O)O[CH]1O" RP3 SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "C1[C@H](O[C@H]([C@@H]1O)O)COP(=O)(O)O" RP3 SMILES "OpenEye OEToolkits" 1.9.2 "C1C(OC(C1O)O)COP(=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 RP3 "SYSTEMATIC NAME" ACDLabs 12.01 3-deoxy-5-O-phosphono-beta-D-erythro-pentofuranose RP3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(2S,4R,5R)-4,5-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" RP3 "IUPAC CARBOHYDRATE SYMBOL" PDB-CARE 1.0 b-D-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 RP3 "CARBOHYDRATE ISOMER" D PDB ? RP3 "CARBOHYDRATE RING" furanose PDB ? RP3 "CARBOHYDRATE ANOMER" beta PDB ? RP3 "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 RP3 "Create component" 2015-07-28 EBI RP3 "Initial release" 2015-10-21 RCSB RP3 "Other modification" 2020-07-03 RCSB RP3 "Modify name" 2020-07-17 RCSB RP3 "Modify synonyms" 2020-07-17 RCSB RP3 "Modify internal type" 2020-07-17 RCSB RP3 "Modify linking type" 2020-07-17 RCSB RP3 "Modify atom id" 2020-07-17 RCSB RP3 "Modify component atom id" 2020-07-17 RCSB RP3 "Modify leaving atom flag" 2020-07-17 RCSB ##