data_GPV
#

_chem_comp.id                                   GPV
_chem_comp.name                                 "1-(beta-D-glucopyranosyl)-5-iodopyrimidine-2,4(1H,3H)-dione"
_chem_comp.type                                 D-saccharide
_chem_comp.pdbx_type                            ATOMS
_chem_comp.formula                              "C10 H13 I N2 O7"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        
;1-(beta-D-glucosyl)-5-iodopyrimidine-2,4(1H,3H)-dione; 1-(D-glucosyl)-5-iodopyrimidine-2,4(1H,3H)-dione;
1-(glucosyl)-5-iodopyrimidine-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                       400.124
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    GPV
_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       3T3H
_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  GPV  "1-(beta-D-glucosyl)-5-iodopyrimidine-2,4(1H,3H)-dione"  PDB  ?  
2  GPV  "1-(D-glucosyl)-5-iodopyrimidine-2,4(1H,3H)-dione"       PDB  ?  
3  GPV  "1-(glucosyl)-5-iodopyrimidine-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
GPV  I    I       I  0  1  N  N  N  38.154  23.560  30.155   3.271   1.106   0.354  I    GPV   1  
GPV  N1   N1      N  0  1  N  N  N  33.957  23.442  28.909  -0.350  -1.104  -0.368  N1   GPV   2  
GPV  C2A  C2      C  0  1  N  N  N  33.299  24.350  29.732   0.072  -2.296  -0.829  C2A  GPV   3  
GPV  O2A  O2      O  0  1  N  N  N  32.087  24.535  29.610  -0.745  -3.147  -1.124  O2A  GPV   4  
GPV  N3   N3      N  0  1  N  N  N  34.029  25.086  30.681   1.384  -2.559  -0.967  N3   GPV   5  
GPV  C4A  C4      C  0  1  N  N  N  35.410  24.885  30.816   2.303  -1.626  -0.644  C4A  GPV   6  
GPV  O4A  O4      O  0  1  N  N  N  36.010  25.532  31.660   3.490  -1.863  -0.770  O4A  GPV   7  
GPV  C5A  C5      C  0  1  N  N  N  36.070  23.976  29.992   1.873  -0.367  -0.158  C5A  GPV   8  
GPV  C6A  C6      C  0  1  N  N  N  35.323  23.264  29.043   0.550  -0.130  -0.029  C6A  GPV   9  
GPV  C1   "C1'"   C  0  1  N  N  R  33.189  22.702  27.867  -1.785  -0.845  -0.234  C1   GPV  10  
GPV  C2   "C2'"   C  0  1  N  N  R  33.651  23.025  26.416  -2.134  -0.656   1.245  C2   GPV  11  
GPV  O2   "O2'"   O  0  1  N  N  N  33.692  24.460  26.184  -1.849  -1.860   1.960  O2   GPV  12  
GPV  C3   "C3'"   C  0  1  N  N  S  32.646  22.338  25.478  -3.624  -0.326   1.372  C3   GPV  13  
GPV  O3   "O3'"   O  0  1  N  N  N  32.963  22.494  24.116  -3.943  -0.076   2.742  O3   GPV  14  
GPV  C4   "C4'"   C  0  1  N  N  S  32.399  20.890  25.826  -3.933   0.922   0.538  C4   GPV  15  
GPV  O4   "O4'"   O  0  1  N  N  N  31.228  20.507  25.100  -5.334   1.197   0.591  O4   GPV  16  
GPV  C5   "C5'"   C  0  1  N  N  R  32.126  20.719  27.329  -3.514   0.672  -0.913  C5   GPV  17  
GPV  O5   "O5'"   O  0  1  N  N  N  33.228  21.273  27.959  -2.125   0.340  -0.957  O5   GPV  18  
GPV  C6   "C6'"   C  0  1  N  N  N  32.155  19.283  27.909  -3.764   1.935  -1.740  C6   GPV  19  
GPV  O6   "O6'"   O  0  1  N  N  N  33.089  18.473  27.203  -3.484   1.666  -3.116  O6   GPV  20  
GPV  HN3  HN3     H  0  1  N  N  N  33.563  25.754  31.261   1.671  -3.424  -1.301  HN3  GPV  21  
GPV  H6   H6      H  0  1  N  N  N  35.827  22.558  28.399   0.203   0.824   0.340  H6   GPV  22  
GPV  H1   "H1'"   H  0  1  N  N  N  32.169  23.059  28.072  -2.346  -1.689  -0.635  H1   GPV  23  
GPV  H2   "H2'"   H  0  1  N  N  N  34.672  22.657  26.236  -1.542   0.162   1.657  H2   GPV  24  
GPV  HO2  "HO2'"  H  0  1  N  Y  N  33.976  24.629  25.293  -2.046  -1.812   2.906  HO2  GPV  25  
GPV  H3   "H3'"   H  0  1  N  N  N  31.698  22.870  25.646  -4.216  -1.165   1.007  H3   GPV  26  
GPV  HO3  "HO3'"  H  0  1  N  Y  N  32.311  22.051  23.586  -4.873   0.140   2.897  HO3  GPV  27  
GPV  H4   "H4'"   H  0  1  N  N  N  33.277  20.278  25.573  -3.379   1.772   0.937  H4   GPV  28  
GPV  HO4  "HO4'"  H  0  1  N  Y  N  31.025  19.597  25.283  -5.669   1.361   1.483  HO4  GPV  29  
GPV  H5   "H5'"   H  0  1  N  N  N  31.121  21.140  27.479  -4.098  -0.152  -1.323  H5   GPV  30  
GPV  H61  "H6'"   H  0  1  N  N  N  32.448  19.329  28.968  -4.805   2.239  -1.634  H61  GPV  31  
GPV  H62  "H6'A"  H  0  1  N  N  N  31.153  18.838  27.817  -3.114   2.735  -1.387  H62  GPV  32  
GPV  HO6  "HO6'"  H  0  1  N  Y  N  33.093  17.598  27.572  -3.620   2.424  -3.700  HO6  GPV  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
GPV  I    C5A  SING  N  N   1  
GPV  N1   C2A  SING  N  N   2  
GPV  N1   C6A  SING  N  N   3  
GPV  N1   C1   SING  N  N   4  
GPV  C2A  O2A  DOUB  N  N   5  
GPV  C2A  N3   SING  N  N   6  
GPV  N3   C4A  SING  N  N   7  
GPV  C4A  O4A  DOUB  N  N   8  
GPV  C4A  C5A  SING  N  N   9  
GPV  C5A  C6A  DOUB  N  N  10  
GPV  C1   C2   SING  N  N  11  
GPV  C1   O5   SING  N  N  12  
GPV  C2   O2   SING  N  N  13  
GPV  C2   C3   SING  N  N  14  
GPV  C3   O3   SING  N  N  15  
GPV  C3   C4   SING  N  N  16  
GPV  C4   O4   SING  N  N  17  
GPV  C4   C5   SING  N  N  18  
GPV  C5   O5   SING  N  N  19  
GPV  C5   C6   SING  N  N  20  
GPV  C6   O6   SING  N  N  21  
GPV  N3   HN3  SING  N  N  22  
GPV  C6A  H6   SING  N  N  23  
GPV  C1   H1   SING  N  N  24  
GPV  C2   H2   SING  N  N  25  
GPV  O2   HO2  SING  N  N  26  
GPV  C3   H3   SING  N  N  27  
GPV  O3   HO3  SING  N  N  28  
GPV  C4   H4   SING  N  N  29  
GPV  O4   HO4  SING  N  N  30  
GPV  C5   H5   SING  N  N  31  
GPV  C6   H61  SING  N  N  32  
GPV  C6   H62  SING  N  N  33  
GPV  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
GPV  SMILES            ACDLabs               12.01  "IC1=CN(C(=O)NC1=O)C2OC(C(O)C(O)C2O)CO"  
GPV  InChI             InChI                 1.03   "InChI=1S/C10H13IN2O7/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"  
GPV  InChIKey          InChI                 1.03   NKQVRMXGIOZKRJ-XSEHCYKFSA-N  
GPV  SMILES_CANONICAL  CACTVS                3.370  "OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)N2C=C(I)C(=O)NC2=O"  
GPV  SMILES            CACTVS                3.370  "OC[CH]1O[CH]([CH](O)[CH](O)[CH]1O)N2C=C(I)C(=O)NC2=O"  
GPV  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)I"  
GPV  SMILES            "OpenEye OEToolkits"  1.7.2  "C1=C(C(=O)NC(=O)N1C2C(C(C(C(O2)CO)O)O)O)I"  
#   #
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
GPV  "SYSTEMATIC NAME"  ACDLabs               12.01  "1-(beta-D-glucopyranosyl)-5-iodopyrimidine-2,4(1H,3H)-dione"  
GPV  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.2  "1-[(2R,3R,4S,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-5-iodanyl-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
GPV  "CARBOHYDRATE ISOMER"                  D         PDB  ?  
GPV  "CARBOHYDRATE RING"                    pyranose  PDB  ?  
GPV  "CARBOHYDRATE ANOMER"                  beta      PDB  ?  
GPV  "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
GPV  "Create component"          2011-08-10  RCSB  
GPV  "Other modification"        2020-07-03  RCSB  
GPV  "Modify synonyms"           2020-07-17  RCSB  
GPV  "Modify internal type"      2020-07-17  RCSB  
GPV  "Modify linking type"       2020-07-17  RCSB  
GPV  "Modify atom id"            2020-07-17  RCSB  
GPV  "Modify component atom id"  2020-07-17  RCSB  
GPV  "Modify leaving atom flag"  2020-07-17  RCSB  
##
