data_GPK
#

_chem_comp.id                                   GPK
_chem_comp.name                                 "5-fluoro-1-(beta-D-glucopyranosyl)pyrimidine-2,4(1H,3H)-dione"
_chem_comp.type                                 D-saccharide
_chem_comp.pdbx_type                            ATOMS
_chem_comp.formula                              "C10 H13 F N2 O7"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        
;5-fluoro-1-(beta-D-glucosyl)pyrimidine-2,4(1H,3H)-dione; 5-fluoro-1-(D-glucosyl)pyrimidine-2,4(1H,3H)-dione;
5-fluoro-1-(glucosyl)pyrimidine-2,4(1H,3H)-dione
;

_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2011-08-10
_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                       292.218
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    GPK
_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       3SYR
_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  GPK  "5-fluoro-1-(beta-D-glucosyl)pyrimidine-2,4(1H,3H)-dione"  PDB  ?  
2  GPK  "5-fluoro-1-(D-glucosyl)pyrimidine-2,4(1H,3H)-dione"       PDB  ?  
3  GPK  "5-fluoro-1-(glucosyl)pyrimidine-2,4(1H,3H)-dione"         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
GPK  C1A    C1      C  0  1  N  N  N  35.503  23.491  28.595  -2.062   0.079  -1.168  C1A    GPK   1  
GPK  F1     F1      F  0  1  N  N  N  37.610  24.155  29.411  -4.326   0.029  -1.775  F1     GPK   2  
GPK  C2A    C2      C  0  1  N  N  N  36.275  24.181  29.518  -3.363  -0.042  -0.829  C2A    GPK   3  
GPK  C3A    C3      C  0  1  N  N  N  35.649  24.904  30.535  -3.706  -0.246   0.531  C3A    GPK   4  
GPK  O3A    O3      O  0  1  N  N  N  36.347  25.543  31.344  -4.873  -0.359   0.860  O3A    GPK   5  
GPK  N4     N4      N  0  1  N  N  N  34.298  24.935  30.635  -2.728  -0.315   1.456  N4     GPK   6  
GPK  C5A    C5      C  0  1  N  N  N  33.512  24.265  29.758  -1.438  -0.190   1.092  C5A    GPK   7  
GPK  O5A    O5      O  0  1  N  N  N  32.262  24.254  29.874  -0.568  -0.253   1.939  O5A    GPK   8  
GPK  C1     "C1'"   C  0  1  N  N  R  33.227  22.796  27.745   0.314   0.135  -0.561  C1     GPK   9  
GPK  "N1'"  "N1'"   N  0  1  N  N  N  34.099  23.454  28.771  -1.098   0.004  -0.195  "N1'"  GPK  10  
GPK  C2     "C2'"   C  0  1  N  N  R  33.657  23.040  26.293   0.889   1.406   0.071  C2     GPK  11  
GPK  O2     "O2'"   O  0  1  N  N  N  33.760  24.449  26.045   0.206   2.549  -0.447  O2     GPK  12  
GPK  C3     "C3'"   C  0  1  N  N  S  32.613  22.381  25.376   2.380   1.504  -0.266  C3     GPK  13  
GPK  O3     "O3'"   O  0  1  N  N  N  33.022  22.450  24.024   2.942   2.648   0.381  O3     GPK  14  
GPK  C4     "C4'"   C  0  1  N  N  S  32.364  20.929  25.760   3.089   0.238   0.226  C4     GPK  15  
GPK  O4     "O4'"   O  0  1  N  N  N  31.255  20.457  24.976   4.467   0.287  -0.147  O4     GPK  16  
GPK  C5     "C5'"   C  0  1  N  N  R  32.113  20.760  27.272   2.428  -0.987  -0.412  C5     GPK  17  
GPK  O5     "O5'"   O  0  1  N  N  N  33.168  21.378  27.998   1.037  -1.002  -0.085  O5     GPK  18  
GPK  C6     "C6'"   C  0  1  N  N  N  32.085  19.307  27.768   3.091  -2.259   0.120  C6     GPK  19  
GPK  O6     "O6'"   O  0  1  N  N  N  33.175  18.551  27.212   2.556  -3.396  -0.561  O6     GPK  20  
GPK  H1A    H1      H  0  1  N  N  N  35.965  22.991  27.757  -1.781   0.231  -2.199  H1A    GPK  21  
GPK  HN4    HN4     H  0  1  N  N  N  33.873  25.463  31.370  -2.955  -0.454   2.389  HN4    GPK  22  
GPK  H1     "H1'"   H  0  1  N  N  N  32.236  23.261  27.849   0.405   0.196  -1.645  H1     GPK  23  
GPK  H2     "H2'"   H  0  1  N  N  N  34.646  22.600  26.095   0.761   1.364   1.153  H2     GPK  24  
GPK  HO2    "HO2'"  H  0  1  N  Y  N  34.026  24.594  25.145   0.520   3.390  -0.089  HO2    GPK  25  
GPK  H3     "H3'"   H  0  1  N  N  N  31.673  22.938  25.502   2.505   1.598  -1.345  H3     GPK  26  
GPK  HO3    "HO3'"  H  0  1  N  Y  N  32.366  22.039  23.473   3.886   2.772   0.211  HO3    GPK  27  
GPK  H4     "H4'"   H  0  1  N  N  N  33.261  20.329  25.547   3.007   0.173   1.311  H4     GPK  28  
GPK  HO4    "HO4'"  H  0  1  N  Y  N  31.075  19.550  25.195   4.947   1.042   0.219  HO4    GPK  29  
GPK  H5     "H5'"   H  0  1  N  N  N  31.122  21.209  27.436   2.547  -0.941  -1.495  H5     GPK  30  
GPK  H61    "H6'"   H  0  1  N  N  N  32.169  19.302  28.865   4.167  -2.207  -0.050  H61    GPK  31  
GPK  H62    "H6'A"  H  0  1  N  N  N  31.136  18.843  27.462   2.896  -2.350   1.189  H62    GPK  32  
GPK  HO6    "HO6'"  H  0  1  N  Y  N  33.137  17.657  27.532   2.931  -4.239  -0.273  HO6    GPK  33  
#   #
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
GPK  C1A  C2A    DOUB  N  N   1  
GPK  C1A  "N1'"  SING  N  N   2  
GPK  F1   C2A    SING  N  N   3  
GPK  C2A  C3A    SING  N  N   4  
GPK  C3A  O3A    DOUB  N  N   5  
GPK  C3A  N4     SING  N  N   6  
GPK  N4   C5A    SING  N  N   7  
GPK  C5A  O5A    DOUB  N  N   8  
GPK  C5A  "N1'"  SING  N  N   9  
GPK  C1   "N1'"  SING  N  N  10  
GPK  C1   C2     SING  N  N  11  
GPK  C1   O5     SING  N  N  12  
GPK  C2   O2     SING  N  N  13  
GPK  C2   C3     SING  N  N  14  
GPK  C3   O3     SING  N  N  15  
GPK  C3   C4     SING  N  N  16  
GPK  C4   O4     SING  N  N  17  
GPK  C4   C5     SING  N  N  18  
GPK  C5   O5     SING  N  N  19  
GPK  C5   C6     SING  N  N  20  
GPK  C6   O6     SING  N  N  21  
GPK  C1A  H1A    SING  N  N  22  
GPK  N4   HN4    SING  N  N  23  
GPK  C1   H1     SING  N  N  24  
GPK  C2   H2     SING  N  N  25  
GPK  O2   HO2    SING  N  N  26  
GPK  C3   H3     SING  N  N  27  
GPK  O3   HO3    SING  N  N  28  
GPK  C4   H4     SING  N  N  29  
GPK  O4   HO4    SING  N  N  30  
GPK  C5   H5     SING  N  N  31  
GPK  C6   H61    SING  N  N  32  
GPK  C6   H62    SING  N  N  33  
GPK  O6   HO6    SING  N  N  34  
#   #
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
GPK  SMILES            ACDLabs               12.01  "FC1=CN(C(=O)NC1=O)C2OC(C(O)C(O)C2O)CO"  
GPK  InChI             InChI                 1.03   "InChI=1S/C10H13FN2O7/c11-3-1-13(10(19)12-8(3)18)9-7(17)6(16)5(15)4(2-14)20-9/h1,4-7,9,14-17H,2H2,(H,12,18,19)/t4-,5-,6+,7-,9-/m1/s1"  
GPK  InChIKey          InChI                 1.03   YHWGRVDTEORPPJ-XSEHCYKFSA-N  
GPK  SMILES_CANONICAL  CACTVS                3.370  "OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)N2C=C(F)C(=O)NC2=O"  
GPK  SMILES            CACTVS                3.370  "OC[CH]1O[CH]([CH](O)[CH](O)[CH]1O)N2C=C(F)C(=O)NC2=O"  
GPK  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.2  "C1=C(C(=O)NC(=O)N1[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O)F"  
GPK  SMILES            "OpenEye OEToolkits"  1.7.2  "C1=C(C(=O)NC(=O)N1C2C(C(C(C(O2)CO)O)O)O)F"  
#   #
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
GPK  "SYSTEMATIC NAME"  ACDLabs               12.01  "5-fluoro-1-(beta-D-glucopyranosyl)pyrimidine-2,4(1H,3H)-dione"  
GPK  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.2  "5-fluoranyl-1-[(2R,3R,4S,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]pyrimidine-2,4-dione"  
#   #
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
GPK  "CARBOHYDRATE ISOMER"                  D         PDB  ?  
GPK  "CARBOHYDRATE RING"                    pyranose  PDB  ?  
GPK  "CARBOHYDRATE ANOMER"                  beta      PDB  ?  
GPK  "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
GPK  "Create component"          2011-08-10  RCSB  
GPK  "Other modification"        2020-07-03  RCSB  
GPK  "Modify synonyms"           2020-07-17  RCSB  
GPK  "Modify internal type"      2020-07-17  RCSB  
GPK  "Modify linking type"       2020-07-17  RCSB  
GPK  "Modify atom id"            2020-07-17  RCSB  
GPK  "Modify component atom id"  2020-07-17  RCSB  
GPK  "Modify leaving atom flag"  2020-07-17  RCSB  
##
