data_R5P # _chem_comp.id R5P _chem_comp.name RIBOSE-5-PHOSPHATE _chem_comp.type SACCHARIDE _chem_comp.pdbx_type ATOMS _chem_comp.formula "C5 H11 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2001-06-19 _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 OR5 _chem_comp.formula_weight 230.110 _chem_comp.one_letter_code ? _chem_comp.three_letter_code R5P _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 1JCY _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm Y # 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 R5P C1 C1 C 0 1 N N N N N N 35.417 51.390 17.968 -4.409 -0.681 -0.022 C1 R5P 1 R5P O1 O1 O 0 1 N Y N N N N 35.199 50.436 18.671 -5.279 -0.086 -0.612 O1 R5P 2 R5P C2 C2 C 0 1 N N R N N N 34.794 52.742 18.326 -3.211 0.066 0.507 C2 R5P 3 R5P O2 O2 O 0 1 N Y N N N N 33.370 52.746 18.226 -3.336 1.453 0.188 O2 R5P 4 R5P C3 C3 C 0 1 N N R N N N 35.213 53.741 17.270 -1.939 -0.493 -0.132 C3 R5P 5 R5P O3 O3 O 0 1 N N N N N N 34.413 53.714 16.067 -1.814 -1.880 0.187 O3 R5P 6 R5P C4 C4 C 0 1 N N R N N N 36.725 53.720 17.532 -0.723 0.265 0.405 C4 R5P 7 R5P O4 O4 O 0 1 N N N N N N 37.465 53.834 18.760 -0.847 1.653 0.086 O4 R5P 8 R5P C5 C5 C 0 1 N N N N N N 37.114 54.723 16.486 0.550 -0.293 -0.234 C5 R5P 9 R5P O5 O5 O 0 1 N N N N N N 38.528 54.676 16.380 1.692 0.334 0.352 O5 R5P 10 R5P P P P 0 1 N N N N N N 39.428 55.624 15.505 3.203 -0.014 -0.082 P R5P 11 R5P O1P O1P O 0 1 N N N N N N 40.780 55.502 16.113 3.350 0.168 -1.544 O1P R5P 12 R5P O2P O2P O 0 1 N N N N N N 39.336 55.030 14.148 4.222 0.968 0.686 O2P R5P 13 R5P O3P O3P O 0 1 N N N N N N 38.865 57.005 15.590 3.535 -1.541 0.304 O3P R5P 14 R5P H11 H11 H 0 1 N N N N N N 36.045 51.292 17.095 -4.491 -1.747 0.130 H11 R5P 15 R5P HC2 HC2 H 0 1 N N N N N N 35.134 53.067 19.320 -3.157 -0.055 1.589 HC2 R5P 16 R5P HO2 HO2 H 0 1 N Y N N N N 33.043 51.860 18.325 -3.389 1.635 -0.760 HO2 R5P 17 R5P HC3 HC3 H 0 1 N N N N N N 34.919 54.696 17.730 -1.993 -0.372 -1.214 HC3 R5P 18 R5P HO3 HO3 H 0 1 N N N N N N 34.737 54.366 15.456 -1.761 -2.062 1.135 HO3 R5P 19 R5P HC4 HC4 H 0 1 N N N N N N 37.046 52.758 17.106 -0.669 0.145 1.487 HC4 R5P 20 R5P HO4 HO4 H 0 1 N N N N N N 38.395 53.782 18.576 -0.901 1.835 -0.862 HO4 R5P 21 R5P H51 H51 H 0 1 N N N N N N 36.653 54.463 15.522 0.599 -1.369 -0.066 H51 R5P 22 R5P H52 H52 H 0 1 N N N N N N 36.790 55.730 16.788 0.536 -0.093 -1.306 H52 R5P 23 R5P HOP2 HOP2 H 0 0 N N N N N N 40.179 54.668 13.902 5.152 0.815 0.472 HOP2 R5P 24 R5P HOP3 HOP3 H 0 0 N N N N N N 39.486 57.574 16.028 3.458 -1.733 1.249 HOP3 R5P 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 R5P C1 O1 DOUB N N 1 R5P C1 C2 SING N N 2 R5P C2 O2 SING N N 3 R5P C2 C3 SING N N 4 R5P C3 O3 SING N N 5 R5P C3 C4 SING N N 6 R5P C4 O4 SING N N 7 R5P C4 C5 SING N N 8 R5P C5 O5 SING N N 9 R5P O5 P SING N N 10 R5P P O1P DOUB N N 11 R5P P O2P SING N N 12 R5P P O3P SING N N 13 R5P C1 H11 SING N N 14 R5P C2 HC2 SING N N 15 R5P O2 HO2 SING N N 16 R5P C3 HC3 SING N N 17 R5P O3 HO3 SING N N 18 R5P C4 HC4 SING N N 19 R5P O4 HO4 SING N N 20 R5P C5 H51 SING N N 21 R5P C5 H52 SING N N 22 R5P O2P HOP2 SING N N 23 R5P O3P HOP3 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 R5P SMILES ACDLabs 12.01 "O=P(OCC(O)C(O)C(O)C=O)(O)O" R5P InChI InChI 1.03 "InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h1,3-5,7-9H,2H2,(H2,10,11,12)/t3-,4+,5-/m0/s1" R5P InChIKey InChI 1.03 PPQRONHOSHZGFQ-LMVFSUKVSA-N R5P SMILES_CANONICAL CACTVS 3.370 "O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@@H](O)C=O" R5P SMILES CACTVS 3.370 "O[CH](CO[P](O)(O)=O)[CH](O)[CH](O)C=O" R5P SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C(C(C(C(C=O)O)O)O)OP(=O)(O)O" R5P SMILES "OpenEye OEToolkits" 1.7.6 "C(C(C(C(C=O)O)O)O)OP(=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 R5P "SYSTEMATIC NAME" ACDLabs 12.01 5-O-phosphono-D-ribose R5P "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[2,3,4-tris(oxidanyl)-5-oxidanylidene-pentyl] dihydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site R5P "Create component" 2001-06-19 RCSB R5P "Other modification" 2012-01-03 RCSB R5P "Modify leaving atom flag" 2024-04-30 PDBE R5P "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 R5P LYS None Carbohydrate "Amino-acid side chain" "Any position" C2 NZ ? ? 2 R5P LYS None Carbohydrate "Amino-acid side chain" "Any position" C1 NZ ? ? #