data_CKB # _chem_comp.id CKB _chem_comp.name "1-beta-D-glucopyranosyl-5-methylpyrimidine-2,4(1H,3H)-dione" _chem_comp.type D-saccharide _chem_comp.pdbx_type ATOMS _chem_comp.formula "C11 H16 N2 O7" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;1-D-glucopyranosyl-thymine; 1-beta-D-glucosyl-5-methylpyrimidine-2,4(1H,3H)-dione; 1-D-glucosyl-5-methylpyrimidine-2,4(1H,3H)-dione; 1-glucosyl-5-methylpyrimidine-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 288.254 _chem_comp.one_letter_code ? _chem_comp.three_letter_code CKB _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 3BD7 _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 CKB 1-D-glucopyranosyl-thymine PDB ? 2 CKB "1-beta-D-glucosyl-5-methylpyrimidine-2,4(1H,3H)-dione" PDB ? 3 CKB "1-D-glucosyl-5-methylpyrimidine-2,4(1H,3H)-dione" PDB ? 4 CKB "1-glucosyl-5-methylpyrimidine-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 CKB C2A C2 C 0 1 N N N 38.516 36.823 30.391 1.498 -0.191 -1.064 C2A CKB 1 CKB C4A C4 C 0 1 N N N 37.145 35.569 31.982 3.760 -0.247 -0.484 C4A CKB 2 CKB C5A C5 C 0 1 N N N 37.531 36.445 33.154 3.406 -0.043 0.872 C5A CKB 3 CKB C6A C6 C 0 1 N N N 38.397 37.467 32.850 2.102 0.080 1.199 C6A CKB 4 CKB C7 C7 C 0 1 N N N 37.033 36.249 34.576 4.470 0.037 1.936 C7 CKB 5 CKB N1 N1 N 0 1 N N N 38.896 37.674 31.491 1.148 0.004 0.220 N1 CKB 6 CKB N3 N3 N 0 1 N N N 37.651 35.804 30.684 2.791 -0.316 -1.418 N3 CKB 7 CKB C1 "C1'" C 0 1 N N R 39.840 38.744 31.044 -0.267 0.136 0.575 C1 CKB 8 CKB C2 "C2'" C 0 1 N N R 39.428 40.134 31.715 -0.837 1.406 -0.063 C2 CKB 9 CKB C3 "C3'" C 0 1 N N S 40.474 41.175 31.211 -2.330 1.505 0.262 C3 CKB 10 CKB C4 "C4'" C 0 1 N N S 41.897 40.724 31.546 -3.035 0.239 -0.234 C4 CKB 11 CKB C5 "C5'" C 0 1 N N R 42.176 39.337 30.869 -2.381 -0.986 0.410 C5 CKB 12 CKB C6 "C6'" C 0 1 N N N 43.595 38.787 31.169 -3.040 -2.258 -0.126 C6 CKB 13 CKB O6 "O6'" O 0 1 N N N 43.697 38.544 32.624 -2.510 -3.395 0.559 O6 CKB 14 CKB O2 "O2'" O 0 1 N N N 38.077 40.519 31.416 -0.157 2.549 0.460 O2 CKB 15 CKB O3 "O3'" O 0 1 N N N 40.182 42.452 31.810 -2.886 2.648 -0.390 O3 CKB 16 CKB O4 "O4'" O 0 1 N N N 42.862 41.715 31.076 -4.417 0.288 0.128 O4 CKB 17 CKB O5 "O5'" O 0 1 N N N 41.215 38.288 31.306 -0.987 -1.001 0.094 O5 CKB 18 CKB O2A O2 O 0 1 N N N 38.890 36.916 29.214 0.634 -0.261 -1.917 O2A CKB 19 CKB O4A O4 O 0 1 N N N 36.372 34.607 32.118 4.930 -0.360 -0.803 O4A CKB 20 CKB H6 H6 H 0 1 N N N 38.718 38.135 33.635 1.812 0.236 2.227 H6 CKB 21 CKB H7 H7 H 0 1 N N N 37.891 36.202 35.262 5.452 -0.083 1.477 H7 CKB 22 CKB H7A H7A H 0 1 N N N 36.385 37.092 34.857 4.417 1.007 2.430 H7A CKB 23 CKB H7B H7B H 0 1 N N N 36.462 35.311 34.638 4.312 -0.754 2.668 H7B CKB 24 CKB HN3 HN3 H 0 1 N N N 37.363 35.196 29.944 3.026 -0.456 -2.349 HN3 CKB 25 CKB H1 "H1'" H 0 1 N N N 39.786 38.931 29.961 -0.366 0.197 1.658 H1 CKB 26 CKB H2 "H2'" H 0 1 N N N 39.442 40.058 32.812 -0.701 1.363 -1.144 H2 CKB 27 CKB H3 "H3'" H 0 1 N N N 40.409 41.262 30.116 -2.464 1.598 1.340 H3 CKB 28 CKB H4 "H4'" H 0 1 N N N 42.000 40.624 32.637 -2.944 0.172 -1.319 H4 CKB 29 CKB H5 "H5'" H 0 1 N N N 42.069 39.542 29.794 -2.508 -0.939 1.492 H5 CKB 30 CKB H61 "H6'" H 0 1 N N N 43.756 37.848 30.620 -4.116 -2.205 0.035 H61 CKB 31 CKB H62 "H6'A" H 0 1 N N N 44.359 39.512 30.851 -2.836 -2.351 -1.193 H62 CKB 32 CKB HO6 "HO6'" H 0 1 N Y N 43.719 37.609 32.789 -2.884 -4.238 0.270 HO6 CKB 33 CKB HO2 "HO2'" H 0 1 N Y N 37.585 40.604 32.224 -0.468 3.390 0.098 HO2 CKB 34 CKB HO3 "HO3'" H 0 1 N Y N 40.118 42.353 32.753 -3.832 2.773 -0.228 HO3 CKB 35 CKB HO4 "HO4'" H 0 1 N Y N 43.071 42.314 31.783 -4.894 1.043 -0.242 HO4 CKB 36 # # 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 CKB C2A N1 SING N N 1 CKB C2A N3 SING N N 2 CKB C2A O2A DOUB N N 3 CKB C4A C5A SING N N 4 CKB C4A N3 SING N N 5 CKB C4A O4A DOUB N N 6 CKB C5A C6A DOUB N N 7 CKB C5A C7 SING N N 8 CKB C6A N1 SING N N 9 CKB N1 C1 SING N N 10 CKB C1 C2 SING N N 11 CKB C1 O5 SING N N 12 CKB C2 C3 SING N N 13 CKB C2 O2 SING N N 14 CKB C3 C4 SING N N 15 CKB C3 O3 SING N N 16 CKB C4 C5 SING N N 17 CKB C4 O4 SING N N 18 CKB C5 C6 SING N N 19 CKB C5 O5 SING N N 20 CKB C6 O6 SING N N 21 CKB C6A H6 SING N N 22 CKB C7 H7 SING N N 23 CKB C7 H7A SING N N 24 CKB C7 H7B SING N N 25 CKB N3 HN3 SING N N 26 CKB C1 H1 SING N N 27 CKB C2 H2 SING N N 28 CKB C3 H3 SING N N 29 CKB C4 H4 SING N N 30 CKB C5 H5 SING N N 31 CKB C6 H61 SING N N 32 CKB C6 H62 SING N N 33 CKB O6 HO6 SING N N 34 CKB O2 HO2 SING N N 35 CKB O3 HO3 SING N N 36 CKB O4 HO4 SING N N 37 # # 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 CKB SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)C(O)C2O)CO" CKB SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)C(=O)NC1=O" CKB SMILES CACTVS 3.341 "CC1=CN([CH]2O[CH](CO)[CH](O)[CH](O)[CH]2O)C(=O)NC1=O" CKB SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O" CKB SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2C(C(C(C(O2)CO)O)O)O" CKB InChI InChI 1.03 "InChI=1S/C11H16N2O7/c1-4-2-13(11(19)12-9(4)18)10-8(17)7(16)6(15)5(3-14)20-10/h2,5-8,10,14-17H,3H2,1H3,(H,12,18,19)/t5-,6-,7+,8-,10-/m1/s1" CKB InChIKey InChI 1.03 RMXUFBPORJBBEZ-HPFNVAMJSA-N # # 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 CKB "SYSTEMATIC NAME" ACDLabs 10.04 "1-beta-D-glucopyranosyl-5-methylpyrimidine-2,4(1H,3H)-dione" CKB "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "5-methyl-1-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)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 CKB "CARBOHYDRATE ISOMER" D PDB ? CKB "CARBOHYDRATE RING" pyranose PDB ? CKB "CARBOHYDRATE ANOMER" beta PDB ? CKB "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 CKB "Create component" 2007-11-16 PDBJ CKB "Modify descriptor" 2011-06-04 RCSB CKB "Other modification" 2020-07-03 RCSB CKB "Modify synonyms" 2020-07-17 RCSB CKB "Modify internal type" 2020-07-17 RCSB CKB "Modify linking type" 2020-07-17 RCSB CKB "Modify atom id" 2020-07-17 RCSB CKB "Modify component atom id" 2020-07-17 RCSB CKB "Modify leaving atom flag" 2020-07-17 RCSB ##