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 ##