data_RP3
#

_chem_comp.id                                   RP3
_chem_comp.name                                 3-deoxy-5-O-phosphono-beta-D-ribofuranose
_chem_comp.type                                 "D-saccharide, beta linking"
_chem_comp.pdbx_type                            ATOMS
_chem_comp.formula                              "C5 H11 O7 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        
;3'-deoxy-D-ribofuranose-5'-phosphate; 3-deoxy-5-O-phosphono-beta-D-ribose; 3-deoxy-5-O-phosphono-D-ribose;
3-deoxy-5-O-phosphono-ribose
;

_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2015-07-28
_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                       214.110
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    RP3
_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       5CX8
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 RCSB
#   #
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  RP3  "3'-deoxy-D-ribofuranose-5'-phosphate"  PDB  ?  
2  RP3  3-deoxy-5-O-phosphono-beta-D-ribose     PDB  ?  
3  RP3  3-deoxy-5-O-phosphono-D-ribose          PDB  ?  
4  RP3  3-deoxy-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
RP3  O3X    O3X    O  0  1  N  N  N  26.566  23.161  95.939  -3.665   0.574  -1.316  O3X    RP3   1  
RP3  "P'"   "P'"   P  0  1  N  N  N  26.540  24.514  95.280  -2.854  -0.000  -0.049  "P'"   RP3   2  
RP3  O1X    O1X    O  0  1  N  N  N  26.760  25.693  96.184  -3.076   0.971   1.215  O1X    RP3   3  
RP3  O2X    O2X    O  0  1  N  N  N  25.411  24.623  94.306  -3.347  -1.357   0.278  O2X    RP3   4  
RP3  O5     "O5'"  O  0  1  N  N  N  27.843  24.564  94.332  -1.285  -0.071  -0.403  O5     RP3   5  
RP3  C5     "C5'"  C  0  1  N  N  N  27.863  25.463  93.216  -0.313  -0.635   0.480  C5     RP3   6  
RP3  C4     "C4'"  C  0  1  N  N  S  29.303  25.865  93.033   1.073  -0.542  -0.162  C4     RP3   7  
RP3  O4     "O1'"  O  0  1  N  N  N  30.064  24.743  92.596   1.506   0.834  -0.238  O4     RP3   8  
RP3  C3     "C3'"  C  0  1  N  N  N  29.576  27.008  92.068   2.139  -1.211   0.743  C3     RP3   9  
RP3  C2     "C2'"  C  0  1  N  N  R  30.696  26.470  91.192   3.437  -0.490   0.303  C2     RP3  10  
RP3  O2     "O2'"  O  0  1  N  N  N  31.777  27.371  91.118   4.154  -1.284  -0.644  O2     RP3  11  
RP3  C1     "C1'"  C  0  1  N  N  R  31.213  25.267  91.929   2.939   0.816  -0.354  C1     RP3  12  
RP3  O1     O1     O  0  1  N  Y  N  31.702  24.364  90.964   3.495   1.944   0.324  O1     RP3  13  
RP3  H1A    H1     H  0  1  N  N  N  25.852  22.632  95.605  -4.619   0.644  -1.174  H1A    RP3  14  
RP3  H2A    H2     H  0  1  N  N  N  26.116  26.365  95.991  -2.775   1.879   1.072  H2A    RP3  15  
RP3  H51    H3     H  0  1  N  N  N  27.243  26.347  93.426  -0.315  -0.086   1.422  H51    RP3  16  
RP3  H52    H4     H  0  1  N  N  N  27.489  24.959  92.313  -0.557  -1.681   0.668  H52    RP3  17  
RP3  H4     H5     H  0  1  N  N  N  29.682  26.176  94.018   1.068  -0.998  -1.151  H4     RP3  18  
RP3  H3     H6     H  0  1  N  N  N  29.898  27.911  92.608   1.928  -1.024   1.796  H3     RP3  19  
RP3  H7     H7     H  0  1  N  N  N  28.683  27.238  91.468   2.202  -2.281   0.544  H7     RP3  20  
RP3  H2     H8     H  0  1  N  N  N  30.314  26.190  90.199   4.062  -0.267   1.168  H2     RP3  21  
RP3  HO2    H9     H  0  1  N  Y  N  31.504  28.156  90.658   4.945  -0.856  -0.997  HO2    RP3  22  
RP3  H1     H10    H  0  1  N  N  N  31.994  25.563  92.645   3.226   0.835  -1.406  H1     RP3  23  
RP3  HO1    H11    H  0  1  N  Y  N  32.038  23.588  91.397   3.221   2.797  -0.041  HO1    RP3  24  
#   #
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
RP3  O1     C1     SING  N  N   1  
RP3  O2     C2     SING  N  N   2  
RP3  C2     C1     SING  N  N   3  
RP3  C2     C3     SING  N  N   4  
RP3  C1     O4     SING  N  N   5  
RP3  C3     C4     SING  N  N   6  
RP3  O4     C4     SING  N  N   7  
RP3  C4     C5     SING  N  N   8  
RP3  C5     O5     SING  N  N   9  
RP3  O2X    "P'"   DOUB  N  N  10  
RP3  O5     "P'"   SING  N  N  11  
RP3  "P'"   O3X    SING  N  N  12  
RP3  "P'"   O1X    SING  N  N  13  
RP3  O3X    H1A    SING  N  N  14  
RP3  O1X    H2A    SING  N  N  15  
RP3  C5     H51    SING  N  N  16  
RP3  C5     H52    SING  N  N  17  
RP3  C4     H4     SING  N  N  18  
RP3  C3     H3     SING  N  N  19  
RP3  C3     H7     SING  N  N  20  
RP3  C2     H2     SING  N  N  21  
RP3  O2     HO2    SING  N  N  22  
RP3  C1     H1     SING  N  N  23  
RP3  O1     HO1    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
RP3  SMILES            ACDLabs               12.01  "OP(O)(=O)OCC1OC(C(C1)O)O"  
RP3  InChI             InChI                 1.03   "InChI=1S/C5H11O7P/c6-4-1-3(12-5(4)7)2-11-13(8,9)10/h3-7H,1-2H2,(H2,8,9,10)/t3-,4+,5+/m0/s1"  
RP3  InChIKey          InChI                 1.03   OOLHLHJSMUTTHE-VPENINKCSA-N  
RP3  SMILES_CANONICAL  CACTVS                3.385  "O[C@@H]1C[C@@H](CO[P](O)(O)=O)O[C@H]1O"  
RP3  SMILES            CACTVS                3.385  "O[CH]1C[CH](CO[P](O)(O)=O)O[CH]1O"  
RP3  SMILES_CANONICAL  "OpenEye OEToolkits"  1.9.2  "C1[C@H](O[C@H]([C@@H]1O)O)COP(=O)(O)O"  
RP3  SMILES            "OpenEye OEToolkits"  1.9.2  "C1C(OC(C1O)O)COP(=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
RP3  "SYSTEMATIC NAME"            ACDLabs               12.01  3-deoxy-5-O-phosphono-beta-D-erythro-pentofuranose  
RP3  "SYSTEMATIC NAME"            "OpenEye OEToolkits"  1.9.2  "[(2S,4R,5R)-4,5-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate"  
RP3  "IUPAC CARBOHYDRATE SYMBOL"  PDB-CARE              1.0    b-D-3-deoxy-Ribf5PO3  
#   #
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
RP3  "CARBOHYDRATE ISOMER"                  D         PDB  ?  
RP3  "CARBOHYDRATE RING"                    furanose  PDB  ?  
RP3  "CARBOHYDRATE ANOMER"                  beta      PDB  ?  
RP3  "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
RP3  "Create component"          2015-07-28  EBI   
RP3  "Initial release"           2015-10-21  RCSB  
RP3  "Other modification"        2020-07-03  RCSB  
RP3  "Modify name"               2020-07-17  RCSB  
RP3  "Modify synonyms"           2020-07-17  RCSB  
RP3  "Modify internal type"      2020-07-17  RCSB  
RP3  "Modify linking type"       2020-07-17  RCSB  
RP3  "Modify atom id"            2020-07-17  RCSB  
RP3  "Modify component atom id"  2020-07-17  RCSB  
RP3  "Modify leaving atom flag"  2020-07-17  RCSB  
##
