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  
##
