data_RIP # _chem_comp.id RIP _chem_comp.name beta-D-ribopyranose _chem_comp.type "D-saccharide, beta linking" _chem_comp.pdbx_type ATOMS _chem_comp.formula "C5 H10 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "beta-D-ribose; D-ribose; ribose; RIBOSE(PYRANOSE FORM)" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _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 150.130 _chem_comp.one_letter_code ? _chem_comp.three_letter_code RIP _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 1DRK _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm Y # 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 RIP beta-D-ribose PDB ? 2 RIP D-ribose PDB ? 3 RIP ribose PDB ? 4 RIP "RIBOSE(PYRANOSE FORM)" 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.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 RIP C1 C1 C 0 1 N N R N N N 49.732 33.632 43.618 0.538 0.292 -1.219 C1 RIP 1 RIP C2 C2 C 0 1 N N R N N N 49.036 33.099 44.894 -0.651 -0.575 -0.803 C2 RIP 2 RIP C3 C3 C 0 1 N N R N N N 48.701 34.269 45.823 -0.960 -0.326 0.677 C3 RIP 3 RIP C4 C4 C 0 1 N N R N N N 49.947 35.132 46.049 0.322 -0.541 1.489 C4 RIP 4 RIP C5 C5 C 0 1 N N N N N N 50.577 35.563 44.747 1.438 0.324 0.899 C5 RIP 5 RIP O1 O1 O 0 1 N Y N N N N 50.148 32.576 42.779 0.812 0.086 -2.606 O1 RIP 6 RIP O2 O2 O 0 1 N N N N N N 47.840 32.383 44.582 -1.791 -0.235 -1.595 O2 RIP 7 RIP O3 O3 O 0 1 N N N N N N 47.653 35.053 45.273 -1.419 1.015 0.852 O3 RIP 8 RIP O4 O4 O 0 1 N N N N N N 49.611 36.278 46.764 0.095 -0.167 2.849 O4 RIP 9 RIP O5 O5 O 0 1 N N N N N N 50.878 34.425 43.967 1.686 -0.061 -0.450 O5 RIP 10 RIP H1 H1 H 0 1 N N N N N N 48.988 34.257 43.071 0.298 1.342 -1.049 H1 RIP 11 RIP H2 H2 H 0 1 N N N N N N 49.738 32.395 45.398 -0.405 -1.627 -0.950 H2 RIP 12 RIP H3 H3 H 0 1 N N N N N N 48.360 33.862 46.803 -1.729 -1.022 1.013 H3 RIP 13 RIP H4 H4 H 0 1 N N N N N N 50.675 34.507 46.616 0.611 -1.591 1.442 H4 RIP 14 RIP H51 H51 H 0 1 N N N N N N 49.942 36.295 44.195 1.138 1.371 0.927 H51 RIP 15 RIP H52 H52 H 0 1 N N N N N N 51.469 36.211 44.906 2.347 0.192 1.486 H52 RIP 16 RIP HO1 HO1 H 0 1 N Y N N N N 50.575 32.903 41.996 1.563 0.653 -2.829 HO1 RIP 17 RIP HO2 HO2 H 0 1 N Y N N N N 47.412 32.055 45.365 -1.551 -0.402 -2.516 HO2 RIP 18 RIP HO3 HO3 H 0 1 N Y N N N N 47.445 35.779 45.849 -1.601 1.128 1.795 HO3 RIP 19 RIP HO4 HO4 H 0 1 N Y N N N N 50.383 36.813 46.904 0.926 -0.315 3.322 HO4 RIP 20 # 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 RIP C1 C2 SING N N 1 RIP C1 O1 SING N N 2 RIP C1 O5 SING N N 3 RIP C1 H1 SING N N 4 RIP C2 C3 SING N N 5 RIP C2 O2 SING N N 6 RIP C2 H2 SING N N 7 RIP C3 C4 SING N N 8 RIP C3 O3 SING N N 9 RIP C3 H3 SING N N 10 RIP C4 C5 SING N N 11 RIP C4 O4 SING N N 12 RIP C4 H4 SING N N 13 RIP C5 O5 SING N N 14 RIP C5 H51 SING N N 15 RIP C5 H52 SING N N 16 RIP O1 HO1 SING N N 17 RIP O2 HO2 SING N N 18 RIP O3 HO3 SING N N 19 RIP O4 HO4 SING N N 20 # 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 RIP SMILES ACDLabs 10.04 "OC1C(O)COC(O)C1O" RIP SMILES_CANONICAL CACTVS 3.341 "O[C@@H]1CO[C@@H](O)[C@H](O)[C@@H]1O" RIP SMILES CACTVS 3.341 "O[CH]1CO[CH](O)[CH](O)[CH]1O" RIP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@H]([C@H]([C@H]([C@@H](O1)O)O)O)O" RIP SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(C(C(O1)O)O)O)O" RIP InChI InChI 1.03 "InChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3-,4-,5-/m1/s1" RIP InChIKey InChI 1.03 SRBFZHDQGSBBOR-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 RIP "SYSTEMATIC NAME" ACDLabs 10.04 beta-D-ribopyranose RIP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R,3R,4R,5R)-oxane-2,3,4,5-tetrol" RIP "CONDENSED IUPAC CARBOHYDRATE SYMBOL" GMML 1.0 DRibpb RIP "COMMON NAME" GMML 1.0 b-D-ribopyranose RIP "IUPAC CARBOHYDRATE SYMBOL" PDB-CARE 1.0 b-D-Ribp RIP "SNFG CARBOHYDRATE SYMBOL" GMML 1.0 Rib # 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 RIP "CARBOHYDRATE ISOMER" D PDB ? RIP "CARBOHYDRATE RING" pyranose PDB ? RIP "CARBOHYDRATE ANOMER" beta PDB ? RIP "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 RIP "Create component" 1999-07-08 RCSB RIP "Modify descriptor" 2011-06-04 RCSB RIP "Other modification" 2019-08-12 RCSB RIP "Other modification" 2019-12-19 RCSB RIP "Other modification" 2020-07-03 RCSB RIP "Modify name" 2020-07-17 RCSB RIP "Modify synonyms" 2020-07-17 RCSB RIP "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 RIP SER None Carbohydrate "Amino-acid side chain" "Any position" C1 OG ? ? 2 RIP SER None Carbohydrate "Amino-acid side chain" "Any position" C5 OG ? ? 3 RIP SER None Carbohydrate "Amino-acid side chain" "Any position" O5 CB ? ? 4 RIP THR None Carbohydrate "Amino-acid side chain" "Any position" C1 OG1 ? ? #