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 ? ? 
# 
