data_CJB # _chem_comp.id CJB _chem_comp.name "1-beta-D-glucopyranosylpyrimidine-2,4(1H,3H)-dione" _chem_comp.type D-saccharide _chem_comp.pdbx_type ATOMS _chem_comp.formula "C10 H14 N2 O7" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;1-D-glucopyranosyl-uracil; 1-beta-D-glucosylpyrimidine-2,4(1H,3H)-dione; 1-D-glucosylpyrimidine-2,4(1H,3H)-dione; 1-glucosylpyrimidine-2,4(1H,3H)-dione ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2007-11-16 _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 274.227 _chem_comp.one_letter_code ? _chem_comp.three_letter_code CJB _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 3BCS _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # 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 CJB 1-D-glucopyranosyl-uracil PDB ? 2 CJB "1-beta-D-glucosylpyrimidine-2,4(1H,3H)-dione" PDB ? 3 CJB "1-D-glucosylpyrimidine-2,4(1H,3H)-dione" PDB ? 4 CJB "1-glucosylpyrimidine-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 CJB N1 N1 N 0 1 N N N 34.211 23.606 28.783 1.312 -0.031 0.072 N1 CJB 1 CJB O2A O2 O 0 1 N N N 32.389 24.257 29.995 1.897 0.206 2.194 O2A CJB 2 CJB C2A C2 C 0 1 N N N 33.617 24.261 29.863 2.243 0.031 1.041 C2A CJB 3 CJB N3 N3 N 0 1 N N N 34.434 24.932 30.780 3.551 -0.098 0.753 N3 CJB 4 CJB C4A C4 C 0 1 N N N 35.825 24.944 30.624 3.951 -0.293 -0.519 C4A CJB 5 CJB O4A O4 O 0 1 N N N 36.502 25.548 31.448 5.135 -0.411 -0.781 O4A CJB 6 CJB C5A C5 C 0 1 N N N 36.430 24.278 29.556 2.982 -0.361 -1.549 C5A CJB 7 CJB C6A C6 C 0 1 N N N 35.615 23.610 28.638 1.676 -0.228 -1.233 C6A CJB 8 CJB C1 "C1'" C 0 1 N N R 33.326 22.902 27.818 -0.105 0.107 0.416 C1 CJB 9 CJB O5 "O5'" O 0 1 N N N 33.312 21.481 28.106 -0.828 -1.023 -0.077 O5 CJB 10 CJB C5 "C5'" C 0 1 N N R 32.236 20.851 27.361 -2.224 -1.002 0.229 C5 CJB 11 CJB C6 "C6'" C 0 1 N N N 32.166 19.384 27.802 -2.886 -2.267 -0.320 C6 CJB 12 CJB O6 "O6'" O 0 1 N N N 33.299 18.675 27.301 -2.367 -3.411 0.362 O6 CJB 13 CJB C4 "C4'" C 0 1 N N S 32.409 21.004 25.827 -2.867 0.231 -0.413 C4 CJB 14 CJB O4 "O4'" O 0 1 N N N 31.251 20.490 25.155 -4.250 0.286 -0.061 O4 CJB 15 CJB C3 "C3'" C 0 1 N N S 32.649 22.466 25.417 -2.158 1.490 0.097 C3 CJB 16 CJB O3 "O3'" O 0 1 N N N 33.094 22.516 24.062 -2.703 2.640 -0.553 O3 CJB 17 CJB C2 "C2'" C 0 1 N N R 33.699 23.126 26.335 -0.663 1.384 -0.218 C2 CJB 18 CJB O2 "O2'" O 0 1 N N N 33.833 24.527 26.052 0.019 2.520 0.317 O2 CJB 19 CJB HN3 HN3 H 0 1 N N N 34.019 25.408 31.555 4.209 -0.051 1.465 HN3 CJB 20 CJB H5A H5 H 0 1 N N N 37.504 24.279 29.442 3.283 -0.516 -2.575 H5A CJB 21 CJB H6 H6 H 0 1 N N N 36.066 23.090 27.806 0.923 -0.277 -2.005 H6 CJB 22 CJB H1 "H1'" H 0 1 N N N 32.306 23.290 27.955 -0.212 0.162 1.500 H1 CJB 23 CJB H5 "H5'" H 0 1 N N N 31.285 21.330 27.637 -2.359 -0.961 1.310 H5 CJB 24 CJB H61 "H6'" H 0 1 N N N 32.159 19.333 28.901 -3.963 -2.210 -0.166 H61 CJB 25 CJB H62 "H6'A" H 0 1 N N N 31.246 18.928 27.408 -2.676 -2.353 -1.386 H62 CJB 26 CJB HO6 "HO6'" H 0 1 N Y N 33.252 17.767 27.576 -2.743 -4.250 0.064 HO6 CJB 27 CJB H4 "H4'" H 0 1 N N N 33.292 20.419 25.529 -2.769 0.170 -1.497 H4 CJB 28 CJB HO4 "HO4'" H 0 1 N Y N 31.361 20.585 24.216 -4.721 1.043 -0.434 HO4 CJB 29 CJB H3 "H3'" H 0 1 N N N 31.702 23.017 25.521 -2.300 1.578 1.174 H3 CJB 30 CJB HO3 "HO3'" H 0 1 N Y N 33.242 23.420 23.810 -3.650 2.766 -0.402 HO3 CJB 31 CJB H2 "H2'" H 0 1 N N N 34.663 22.628 26.154 -0.520 1.347 -1.298 H2 CJB 32 CJB HO2 "HO2'" H 0 1 N Y N 34.062 24.645 25.138 -0.284 3.365 -0.042 HO2 CJB 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 CJB N1 C2A SING N N 1 CJB N1 C6A SING N N 2 CJB N1 C1 SING N N 3 CJB O2A C2A DOUB N N 4 CJB C2A N3 SING N N 5 CJB N3 C4A SING N N 6 CJB C4A O4A DOUB N N 7 CJB C4A C5A SING N N 8 CJB C5A C6A DOUB N N 9 CJB C1 O5 SING N N 10 CJB C1 C2 SING N N 11 CJB O5 C5 SING N N 12 CJB C5 C6 SING N N 13 CJB C5 C4 SING N N 14 CJB C6 O6 SING N N 15 CJB C4 O4 SING N N 16 CJB C4 C3 SING N N 17 CJB C3 O3 SING N N 18 CJB C3 C2 SING N N 19 CJB C2 O2 SING N N 20 CJB N3 HN3 SING N N 21 CJB C5A H5A SING N N 22 CJB C6A H6 SING N N 23 CJB C1 H1 SING N N 24 CJB C5 H5 SING N N 25 CJB C6 H61 SING N N 26 CJB C6 H62 SING N N 27 CJB O6 HO6 SING N N 28 CJB C4 H4 SING N N 29 CJB O4 HO4 SING N N 30 CJB C3 H3 SING N N 31 CJB O3 HO3 SING N N 32 CJB C2 H2 SING N N 33 CJB O2 HO2 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 CJB SMILES ACDLabs 12.01 "O=C1NC(=O)N(C=C1)C2OC(C(O)C(O)C2O)CO" CJB InChI InChI 1.03 "InChI=1S/C10H14N2O7/c13-3-4-6(15)7(16)8(17)9(19-4)12-2-1-5(14)11-10(12)18/h1-2,4,6-9,13,15-17H,3H2,(H,11,14,18)/t4-,6-,7+,8-,9-/m1/s1" CJB InChIKey InChI 1.03 PBGBADORVLQASN-DDIGBBAMSA-N CJB SMILES_CANONICAL CACTVS 3.370 "OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)N2C=CC(=O)NC2=O" CJB SMILES CACTVS 3.370 "OC[CH]1O[CH]([CH](O)[CH](O)[CH]1O)N2C=CC(=O)NC2=O" CJB SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O" CJB SMILES "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=O)NC1=O)C2C(C(C(C(O2)CO)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 CJB "SYSTEMATIC NAME" ACDLabs 12.01 "1-(beta-D-glucopyranosyl)pyrimidine-2,4(1H,3H)-dione" CJB "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "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 CJB "CARBOHYDRATE ISOMER" D PDB ? CJB "CARBOHYDRATE RING" pyranose PDB ? CJB "CARBOHYDRATE ANOMER" beta PDB ? CJB "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 CJB "Create component" 2007-11-16 PDBJ CJB "Modify descriptor" 2011-06-04 RCSB CJB "Modify atom id" 2013-06-20 RCSB CJB "Other modification" 2020-07-03 RCSB CJB "Modify synonyms" 2020-07-17 RCSB CJB "Modify internal type" 2020-07-17 RCSB CJB "Modify linking type" 2020-07-17 RCSB CJB "Modify atom id" 2020-07-17 RCSB CJB "Modify component atom id" 2020-07-17 RCSB CJB "Modify leaving atom flag" 2020-07-17 RCSB ##