data_RP5 # _chem_comp.id RP5 _chem_comp.name 5-O-phosphono-beta-D-ribofuranose _chem_comp.type "D-saccharide, beta linking" _chem_comp.pdbx_type ATOMS _chem_comp.formula "C5 H11 O8 P" _chem_comp.mon_nstd_parent_comp_id BDR _chem_comp.pdbx_synonyms ;[(2R,3S,4S,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE; 5-O-phosphono-beta-D-ribose; 5-O-phosphono-D-ribose; 5-O-phosphono-ribose ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2003-04-30 _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 230.110 _chem_comp.one_letter_code ? _chem_comp.three_letter_code RP5 _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 1OGE _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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 RP5 "[(2R,3S,4S,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE" PDB ? 2 RP5 5-O-phosphono-beta-D-ribose PDB ? 3 RP5 5-O-phosphono-D-ribose PDB ? 4 RP5 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 RP5 C1 "C1'" C 0 1 N N R 51.204 4.561 26.399 2.674 -1.138 0.348 C1 RP5 1 RP5 O4 "O1'" O 0 1 N N N 50.599 3.388 26.893 1.240 -1.083 0.186 O4 RP5 2 RP5 C2 "C2'" C 0 1 N N R 52.159 5.032 27.495 3.207 0.083 -0.433 C2 RP5 3 RP5 O2 "O2'" O 0 1 N N N 53.384 4.323 27.398 4.317 0.670 0.250 O2 RP5 4 RP5 C3 "C3'" C 0 1 N N S 51.426 4.589 28.757 2.011 1.061 -0.462 C3 RP5 5 RP5 O3 "O3'" O 0 1 N N N 52.400 4.392 29.774 2.346 2.281 0.203 O3 RP5 6 RP5 C4 "C4'" C 0 1 N N R 50.697 3.314 28.306 0.897 0.315 0.305 C4 RP5 7 RP5 C5 "C5'" C 0 1 N N N 49.298 3.189 28.944 -0.465 0.586 -0.337 C5 RP5 8 RP5 O5 "O5'" O 0 1 N N N 48.622 1.993 28.494 -1.485 -0.078 0.412 O5 RP5 9 RP5 "P'" "P'" P 0 1 N N N 48.925 0.678 29.320 -3.045 -0.010 0.020 "P'" RP5 10 RP5 O1X O1X O 0 1 N N N 48.152 -0.448 28.755 -3.470 1.405 -0.072 O1X RP5 11 RP5 O2X O2X O 0 1 N N N 50.425 0.355 29.228 -3.274 -0.732 -1.401 O2X RP5 12 RP5 O3X O3X O 0 1 N N N 48.540 0.874 30.789 -3.915 -0.759 1.149 O3X RP5 13 RP5 O1 O1 O 0 1 N Y N 50.140 5.451 26.176 3.191 -2.349 -0.208 O1 RP5 14 RP5 H1 "H1'" H 0 1 N N N 51.779 4.449 25.468 2.940 -1.060 1.402 H1 RP5 15 RP5 H2 "H2'" H 0 1 N N N 52.396 6.105 27.454 3.492 -0.205 -1.445 H2 RP5 16 RP5 HO2 HA H 0 1 N Y N 53.976 4.618 28.080 5.075 0.077 0.350 HO2 RP5 17 RP5 H3 "H3'" H 0 1 N N N 50.702 5.299 29.182 1.704 1.259 -1.489 H3 RP5 18 RP5 HO3 HB H 0 1 N Y N 51.971 4.115 30.575 3.081 2.761 -0.203 HO3 RP5 19 RP5 H4 "H4'" H 0 1 N N N 51.255 2.422 28.628 0.891 0.616 1.352 H4 RP5 20 RP5 H51 "H5'1" H 0 1 N N N 49.408 3.146 30.038 -0.658 1.659 -0.342 H51 RP5 21 RP5 H52 "H5'2" H 0 1 N N N 48.697 4.066 28.660 -0.465 0.213 -1.361 H52 RP5 22 RP5 "HO'" "HO'" H 0 1 N N N 50.542 -0.499 28.828 -3.017 -1.664 -1.414 "HO'" RP5 23 RP5 HOA HOA H 0 1 N N N 47.884 0.232 31.033 -4.867 -0.757 0.978 HOA RP5 24 RP5 HO1 H1 H 0 1 N Y N 50.479 6.272 25.839 2.852 -3.151 0.212 HO1 RP5 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 RP5 C1 O4 SING N N 1 RP5 C1 C2 SING N N 2 RP5 C1 O1 SING N N 3 RP5 C1 H1 SING N N 4 RP5 O4 C4 SING N N 5 RP5 C2 O2 SING N N 6 RP5 C2 C3 SING N N 7 RP5 C2 H2 SING N N 8 RP5 O2 HO2 SING N N 9 RP5 C3 O3 SING N N 10 RP5 C3 C4 SING N N 11 RP5 C3 H3 SING N N 12 RP5 O3 HO3 SING N N 13 RP5 C4 C5 SING N N 14 RP5 C4 H4 SING N N 15 RP5 C5 O5 SING N N 16 RP5 C5 H51 SING N N 17 RP5 C5 H52 SING N N 18 RP5 O5 "P'" SING N N 19 RP5 "P'" O1X DOUB N N 20 RP5 "P'" O2X SING N N 21 RP5 "P'" O3X SING N N 22 RP5 O2X "HO'" SING N N 23 RP5 O3X HOA SING N N 24 RP5 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 RP5 SMILES ACDLabs 12.01 "O=P(O)(O)OCC1OC(O)C(O)C1O" RP5 SMILES_CANONICAL CACTVS 3.370 "O[C@@H]1O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]1O" RP5 SMILES CACTVS 3.370 "O[CH]1O[CH](CO[P](O)(O)=O)[CH](O)[CH]1O" RP5 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C([C@@H]1[C@H]([C@H]([C@@H](O1)O)O)O)OP(=O)(O)O" RP5 SMILES "OpenEye OEToolkits" 1.7.0 "C(C1C(C(C(O1)O)O)O)OP(=O)(O)O" RP5 InChI InChI 1.03 "InChI=1S/C5H11O8P/c6-3-2(1-12-14(9,10)11)13-5(8)4(3)7/h2-8H,1H2,(H2,9,10,11)/t2-,3-,4-,5-/m1/s1" RP5 InChIKey InChI 1.03 KTVPXOYAKDPRHY-TXICZTDVSA-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 RP5 "SYSTEMATIC NAME" ACDLabs 12.01 5-O-phosphono-beta-D-ribofuranose RP5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(2R,3S,4R,5R)-3,4,5-trihydroxyoxolan-2-yl]methyl dihydrogen phosphate" RP5 "IUPAC CARBOHYDRATE SYMBOL" PDB-CARE 1.0 b-D-Ribf5PO3 # _pdbx_chem_comp_related.comp_id RP5 _pdbx_chem_comp_related.related_comp_id BDR _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 RP5 C1 BDR C1 "Carbohydrate core" 2 RP5 C2 BDR C2 "Carbohydrate core" 3 RP5 C3 BDR C3 "Carbohydrate core" 4 RP5 C4 BDR C4 "Carbohydrate core" 5 RP5 C5 BDR C5 "Carbohydrate core" 6 RP5 O1 BDR O1 "Carbohydrate core" 7 RP5 O4 BDR O4 "Carbohydrate core" 8 RP5 O2 BDR O2 "Carbohydrate core" 9 RP5 O3 BDR O3 "Carbohydrate core" 10 RP5 O5 BDR O5 "Carbohydrate core" 11 RP5 HO1 BDR HO1 "Carbohydrate core" 12 RP5 H1 BDR H1 "Carbohydrate core" 13 RP5 H2 BDR H2 "Carbohydrate core" 14 RP5 H3 BDR H3 "Carbohydrate core" 15 RP5 H4 BDR H4 "Carbohydrate core" 16 RP5 H51 BDR H51 "Carbohydrate core" 17 RP5 H52 BDR H52 "Carbohydrate core" 18 RP5 HO2 BDR HO2 "Carbohydrate core" 19 RP5 HO3 BDR HO3 "Carbohydrate core" # # 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 RP5 "CARBOHYDRATE ISOMER" D PDB ? RP5 "CARBOHYDRATE RING" furanose PDB ? RP5 "CARBOHYDRATE ANOMER" beta PDB ? RP5 "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 RP5 "Create component" 2003-04-30 EBI RP5 "Modify name" 2011-02-21 RCSB RP5 "Modify descriptor" 2011-06-04 RCSB RP5 "Other modification" 2020-07-03 RCSB RP5 "Modify parent residue" 2020-07-17 RCSB RP5 "Modify synonyms" 2020-07-17 RCSB RP5 "Modify internal type" 2020-07-17 RCSB RP5 "Modify linking type" 2020-07-17 RCSB RP5 "Modify atom id" 2020-07-17 RCSB RP5 "Modify component atom id" 2020-07-17 RCSB RP5 "Modify leaving atom flag" 2020-07-17 RCSB ##