data_D1M # _chem_comp.id D1M _chem_comp.name "5-ethynyl-1-(beta-D-glucopyranosyl)pyrimidine-2,4(1H,3H)-dione" _chem_comp.type D-saccharide _chem_comp.pdbx_type ATOMS _chem_comp.formula "C12 H14 N2 O7" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;5-ethynyl-1-(beta-D-glucosyl)pyrimidine-2,4(1H,3H)-dione; 5-ethynyl-1-(D-glucosyl)pyrimidine-2,4(1H,3H)-dione; 5-ethynyl-1-(glucosyl)pyrimidine-2,4(1H,3H)-dione ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-04-12 _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 298.249 _chem_comp.one_letter_code ? _chem_comp.three_letter_code D1M _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 4EL5 _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 D1M "5-ethynyl-1-(beta-D-glucosyl)pyrimidine-2,4(1H,3H)-dione" PDB ? 2 D1M "5-ethynyl-1-(D-glucosyl)pyrimidine-2,4(1H,3H)-dione" PDB ? 3 D1M "5-ethynyl-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 D1M N1 N1 N 0 1 N N N 34.097 23.508 28.807 0.974 0.008 -0.068 N1 D1M 1 D1M C2A C2 C 0 1 N N N 33.494 24.363 29.765 1.230 0.222 1.232 C2A D1M 2 D1M O2A O2 O 0 1 N N N 32.281 24.570 29.788 0.300 0.295 2.013 O2A D1M 3 D1M N3 N3 N 0 1 N N N 34.319 25.037 30.686 2.484 0.357 1.697 N3 D1M 4 D1M C4A C4 C 0 1 N N N 35.673 24.807 30.700 3.535 0.281 0.854 C4A D1M 5 D1M O4A O4 O 0 1 N N N 36.304 25.448 31.522 4.674 0.402 1.268 O4A D1M 6 D1M C5A C5 C 0 1 N N N 36.293 23.901 29.807 3.277 0.047 -0.575 C5A D1M 7 D1M C6A C6 C 0 1 N N N 35.509 23.279 28.838 1.981 -0.083 -0.985 C6A D1M 8 D1M C7 C7 C 0 1 N N N 37.709 23.693 29.916 4.357 -0.043 -1.511 C7 D1M 9 D1M C8 C8 C 0 1 N N N 38.877 23.561 30.059 5.242 -0.116 -2.279 C8 D1M 10 D1M C1 "C1'" C 0 1 N N R 33.213 22.851 27.851 -0.414 -0.138 -0.512 C1 D1M 11 D1M C2 "C2'" C 0 1 N N R 33.698 23.181 26.343 -1.017 -1.403 0.106 C2 D1M 12 D1M O2 "O2'" O 0 1 N N N 33.876 24.575 26.155 -0.299 -2.549 -0.355 O2 D1M 13 D1M C3 "C3'" C 0 1 N N S 32.653 22.576 25.422 -2.486 -1.516 -0.313 C3 D1M 14 D1M O3 "O3'" O 0 1 N N N 33.097 22.646 24.054 -3.077 -2.653 0.318 O3 D1M 15 D1M C4 "C4'" C 0 1 N N S 32.464 21.092 25.856 -3.228 -0.247 0.118 C4 D1M 16 D1M O4 "O4'" O 0 1 N N N 31.333 20.596 25.159 -4.583 -0.310 -0.332 O4 D1M 17 D1M C5 "C5'" C 0 1 N N R 32.231 20.862 27.418 -2.540 0.973 -0.500 C5 D1M 18 D1M O5 "O5'" O 0 1 N N N 33.281 21.431 28.141 -1.170 1.001 -0.095 O5 D1M 19 D1M C6 "C6'" C 0 1 N N N 32.109 19.283 27.746 -3.239 2.248 -0.026 C6 D1M 20 D1M O6 "O6'" O 0 1 N N N 33.319 18.699 27.236 -2.672 3.378 -0.692 O6 D1M 21 D1M HN3 HN3 H 0 1 N N N 33.917 25.686 31.332 2.635 0.512 2.643 HN3 D1M 22 D1M H6 H6 H 0 1 N N N 35.967 22.625 28.111 1.755 -0.256 -2.027 H6 D1M 23 D1M H8 H8 H 0 1 N N N 39.923 23.443 30.187 6.034 -0.182 -2.965 H8 D1M 24 D1M H1 "H1'" H 0 1 N N N 32.183 23.218 27.969 -0.443 -0.216 -1.598 H1 D1M 25 D1M H2 "H2'" H 0 1 N N N 34.651 22.656 26.183 -0.951 -1.344 1.193 H2 D1M 26 D1M HO2 "HO2'" H 0 1 N Y N 34.160 24.741 25.264 -0.628 -3.387 -0.002 HO2 D1M 27 D1M H3 "H3'" H 0 1 N N N 31.700 23.110 25.548 -2.549 -1.626 -1.396 H3 D1M 28 D1M HO3 "HO3'" H 0 1 N Y N 32.437 22.265 23.487 -4.009 -2.786 0.097 HO3 D1M 29 D1M H4 "H4'" H 0 1 N N N 33.364 20.531 25.564 -3.209 -0.165 1.205 H4 D1M 30 D1M HO4 "HO4'" H 0 1 N Y N 31.185 19.689 25.399 -5.079 -1.063 0.018 HO4 D1M 31 D1M H5 "H5'" H 0 1 N N N 31.275 21.334 27.690 -2.596 0.910 -1.587 H5 D1M 32 D1M H61 "H6'" H 0 1 N N N 32.029 19.119 28.831 -4.302 2.187 -0.256 H61 D1M 33 D1M H62 "H6'A" H 0 1 N N N 31.231 18.851 27.244 -3.105 2.357 1.051 H62 D1M 34 D1M HO6 "HO6'" H 0 1 N Y N 33.312 17.763 27.398 -3.068 4.223 -0.440 HO6 D1M 35 # # 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 D1M N1 C2A SING N N 1 D1M N1 C6A SING N N 2 D1M N1 C1 SING N N 3 D1M C2A O2A DOUB N N 4 D1M C2A N3 SING N N 5 D1M N3 C4A SING N N 6 D1M C4A O4A DOUB N N 7 D1M C4A C5A SING N N 8 D1M C5A C6A DOUB N N 9 D1M C5A C7 SING N N 10 D1M C7 C8 TRIP N N 11 D1M C1 C2 SING N N 12 D1M C1 O5 SING N N 13 D1M C2 O2 SING N N 14 D1M C2 C3 SING N N 15 D1M C3 O3 SING N N 16 D1M C3 C4 SING N N 17 D1M C4 O4 SING N N 18 D1M C4 C5 SING N N 19 D1M C5 O5 SING N N 20 D1M C5 C6 SING N N 21 D1M C6 O6 SING N N 22 D1M N3 HN3 SING N N 23 D1M C6A H6 SING N N 24 D1M C8 H8 SING N N 25 D1M C1 H1 SING N N 26 D1M C2 H2 SING N N 27 D1M O2 HO2 SING N N 28 D1M C3 H3 SING N N 29 D1M O3 HO3 SING N N 30 D1M C4 H4 SING N N 31 D1M O4 HO4 SING N N 32 D1M C5 H5 SING N N 33 D1M C6 H61 SING N N 34 D1M C6 H62 SING N N 35 D1M O6 HO6 SING N N 36 # # 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 D1M SMILES ACDLabs 12.01 "O=C1NC(=O)N(C=C1C#C)C2OC(C(O)C(O)C2O)CO" D1M InChI InChI 1.03 "InChI=1S/C12H14N2O7/c1-2-5-3-14(12(20)13-10(5)19)11-9(18)8(17)7(16)6(4-15)21-11/h1,3,6-9,11,15-18H,4H2,(H,13,19,20)/t6-,7-,8+,9-,11-/m1/s1" D1M InChIKey InChI 1.03 DSYJZEAWLKMMLW-ZBGLXGBJSA-N D1M SMILES_CANONICAL CACTVS 3.370 "OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)N2C=C(C#C)C(=O)NC2=O" D1M SMILES CACTVS 3.370 "OC[CH]1O[CH]([CH](O)[CH](O)[CH]1O)N2C=C(C#C)C(=O)NC2=O" D1M SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C#CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O" D1M SMILES "OpenEye OEToolkits" 1.7.6 "C#CC1=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 D1M "SYSTEMATIC NAME" ACDLabs 12.01 "5-ethynyl-1-(beta-D-glucopyranosyl)pyrimidine-2,4(1H,3H)-dione" D1M "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "5-ethynyl-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 D1M "CARBOHYDRATE ISOMER" D PDB ? D1M "CARBOHYDRATE RING" pyranose PDB ? D1M "CARBOHYDRATE ANOMER" beta PDB ? D1M "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 D1M "Create component" 2012-04-12 RCSB D1M "Other modification" 2020-07-03 RCSB D1M "Modify synonyms" 2020-07-17 RCSB D1M "Modify internal type" 2020-07-17 RCSB D1M "Modify linking type" 2020-07-17 RCSB D1M "Modify atom id" 2020-07-17 RCSB D1M "Modify component atom id" 2020-07-17 RCSB D1M "Modify leaving atom flag" 2020-07-17 RCSB ##