data_D1J # _chem_comp.id D1J _chem_comp.name "1-(beta-D-glucopyranosyl)-5-(pent-1-yn-1-yl)pyrimidine-2,4(1H,3H)-dione" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H20 N2 O7" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-04-10 _chem_comp.pdbx_modified_date 2012-07-20 _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 340.329 _chem_comp.one_letter_code ? _chem_comp.three_letter_code D1J _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 ? _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # 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 D1J N1 N1 N 0 1 N N N 34.070 23.555 28.879 -0.014 0.532 -0.058 N1 D1J 1 D1J C2 C2 C 0 1 N N N 33.347 24.425 29.775 0.158 1.861 -0.132 C2 D1J 2 D1J O2 O2 O 0 1 N N N 32.106 24.528 29.721 1.287 2.308 -0.190 O2 D1J 3 D1J N3 N3 N 0 1 N N N 34.094 25.171 30.754 -0.882 2.713 -0.145 N3 D1J 4 D1J C4 C4 C 0 1 N N N 35.507 25.042 30.835 -2.147 2.245 -0.082 C4 D1J 5 D1J O4 O4 O 0 1 N N N 36.111 25.682 31.698 -3.093 3.011 -0.093 O4 D1J 6 D1J C5 C5 C 0 1 N N N 36.206 24.188 29.942 -2.358 0.793 0.000 C5 D1J 7 D1J C6 C6 C 0 1 N N N 35.496 23.467 28.962 -1.261 -0.021 0.009 C6 D1J 8 D1J C7 C7 C 0 1 N N N 37.514 24.031 30.006 -3.679 0.245 0.069 C7 D1J 9 D1J C8 C8 C 0 1 N N N 38.832 23.861 30.036 -4.762 -0.204 0.126 C8 D1J 10 D1J C9 C9 C 0 1 N N N 39.623 24.100 31.149 -6.121 -0.767 0.198 C9 D1J 11 D1J "C1'" "C1'" C 0 1 N N R 33.318 22.799 27.838 1.160 -0.344 -0.054 "C1'" D1J 12 D1J C10 C10 C 0 1 N N N 40.154 23.099 31.962 -6.037 -2.293 0.274 C10 D1J 13 D1J C11 C11 C 0 1 N N N 41.179 23.441 32.857 -7.449 -2.878 0.348 C11 D1J 14 D1J "C2'" "C2'" C 0 1 N N R 33.773 23.084 26.354 1.892 -0.223 -1.393 "C2'" D1J 15 D1J "O2'" "O2'" O 0 1 N N N 33.998 24.505 26.166 1.033 -0.661 -2.448 "O2'" D1J 16 D1J "C3'" "C3'" C 0 1 N N S 32.709 22.452 25.368 3.150 -1.095 -1.359 "C3'" D1J 17 D1J "O3'" "O3'" O 0 1 N N N 33.069 22.501 23.991 3.879 -0.931 -2.577 "O3'" D1J 18 D1J "C4'" "C4'" C 0 1 N N S 32.377 21.013 25.807 4.025 -0.665 -0.177 "C4'" D1J 19 D1J "O4'" "O4'" O 0 1 N N N 31.233 20.527 25.080 5.167 -1.520 -0.092 "O4'" D1J 20 D1J "C5'" "C5'" C 0 1 N N R 32.151 20.863 27.363 3.210 -0.770 1.115 "C5'" D1J 21 D1J "O5'" "O5'" O 0 1 N N N 33.272 21.392 28.056 2.039 0.041 1.005 "O5'" D1J 22 D1J "C6'" "C6'" C 0 1 N N N 32.125 19.374 27.854 4.057 -0.285 2.293 "C6'" D1J 23 D1J "O6'" "O6'" O 0 1 N N N 33.197 18.601 27.246 3.341 -0.491 3.512 "O6'" D1J 24 D1J HN3 HN3 H 0 1 N N N 33.615 25.785 31.382 -0.723 3.668 -0.199 HN3 D1J 25 D1J H6 H6 H 0 1 N N N 36.034 22.841 28.266 -1.379 -1.093 0.068 H6 D1J 26 D1J H19 H19 H 0 1 N N N 40.486 24.674 30.782 -6.626 -0.386 1.085 H19 D1J 27 D1J H29 H29 H 0 1 N N N 39.017 24.733 31.814 -6.681 -0.478 -0.692 H29 D1J 28 D1J "H1'" "H1'" H 0 1 N N N 32.281 23.161 27.892 0.842 -1.377 0.095 "H1'" D1J 29 D1J H110 H110 H 0 0 N N N 39.325 22.690 32.558 -5.532 -2.674 -0.614 H110 D1J 30 D1J H210 H210 H 0 0 N N N 40.550 22.316 31.298 -5.477 -2.582 1.163 H210 D1J 31 D1J H111 H111 H 0 0 N N N 41.487 22.548 33.421 -7.954 -2.497 1.235 H111 D1J 32 D1J H211 H211 H 0 0 N N N 42.039 23.835 32.296 -8.009 -2.589 -0.541 H211 D1J 33 D1J H311 H311 H 0 0 N N N 40.815 24.208 33.556 -7.389 -3.965 0.403 H311 D1J 34 D1J "H2'" "H2'" H 0 1 N N N 34.722 22.550 26.195 2.174 0.817 -1.561 "H2'" D1J 35 D1J "HO2'" "HO2'" H 0 0 N N N 34.646 24.809 26.791 1.434 -0.611 -3.327 "HO2'" D1J 36 D1J "H3'" "H3'" H 0 1 N N N 31.788 23.039 25.498 2.866 -2.141 -1.241 "H3'" D1J 37 D1J "HO3'" "HO3'" H 0 0 N N N 33.268 23.397 23.747 4.693 -1.451 -2.622 "HO3'" D1J 38 D1J "H4'" "H4'" H 0 1 N N N 33.244 20.387 25.551 4.350 0.366 -0.320 "H4'" D1J 39 D1J "HO4'" "HO4'" H 0 0 N N N 31.035 19.640 25.356 5.727 -1.507 -0.880 "HO4'" D1J 40 D1J "H5'" "H5'" H 0 1 N N N 31.216 21.366 27.650 2.920 -1.807 1.279 "H5'" D1J 41 D1J "H16'" "H16'" H 0 0 N N N 31.159 18.923 27.582 4.993 -0.844 2.322 "H16'" D1J 42 D1J "H26'" "H26'" H 0 0 N N N 32.244 19.355 28.947 4.273 0.777 2.173 "H26'" D1J 43 D1J "HO6'" "HO6'" H 0 0 N N N 33.159 17.705 27.559 3.819 -0.205 4.302 "HO6'" D1J 44 # 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 D1J "O3'" "C3'" SING N N 1 D1J "O4'" "C4'" SING N N 2 D1J "C3'" "C4'" SING N N 3 D1J "C3'" "C2'" SING N N 4 D1J "C4'" "C5'" SING N N 5 D1J "O2'" "C2'" SING N N 6 D1J "C2'" "C1'" SING N N 7 D1J "O6'" "C6'" SING N N 8 D1J "C5'" "C6'" SING N N 9 D1J "C5'" "O5'" SING N N 10 D1J "C1'" "O5'" SING N N 11 D1J "C1'" N1 SING N N 12 D1J N1 C6 SING N N 13 D1J N1 C2 SING N N 14 D1J C6 C5 DOUB N N 15 D1J O2 C2 DOUB N N 16 D1J C2 N3 SING N N 17 D1J C5 C7 SING N N 18 D1J C5 C4 SING N N 19 D1J C7 C8 TRIP N N 20 D1J C8 C9 SING N N 21 D1J N3 C4 SING N N 22 D1J C4 O4 DOUB N N 23 D1J C9 C10 SING N N 24 D1J C10 C11 SING N N 25 D1J N3 HN3 SING N N 26 D1J C6 H6 SING N N 27 D1J C9 H19 SING N N 28 D1J C9 H29 SING N N 29 D1J "C1'" "H1'" SING N N 30 D1J C10 H110 SING N N 31 D1J C10 H210 SING N N 32 D1J C11 H111 SING N N 33 D1J C11 H211 SING N N 34 D1J C11 H311 SING N N 35 D1J "C2'" "H2'" SING N N 36 D1J "O2'" "HO2'" SING N N 37 D1J "C3'" "H3'" SING N N 38 D1J "O3'" "HO3'" SING N N 39 D1J "C4'" "H4'" SING N N 40 D1J "O4'" "HO4'" SING N N 41 D1J "C5'" "H5'" SING N N 42 D1J "C6'" "H16'" SING N N 43 D1J "C6'" "H26'" SING N N 44 D1J "O6'" "HO6'" SING N N 45 # 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 D1J SMILES ACDLabs 12.01 "O=C1NC(=O)N(C=C1C#CCCC)C2OC(C(O)C(O)C2O)CO" D1J InChI InChI 1.03 "InChI=1S/C15H20N2O7/c1-2-3-4-5-8-6-17(15(23)16-13(8)22)14-12(21)11(20)10(19)9(7-18)24-14/h6,9-12,14,18-21H,2-3,7H2,1H3,(H,16,22,23)/t9-,10-,11+,12-,14-/m1/s1" D1J InChIKey InChI 1.03 XHEMRIMZCOFGEX-YGEZULPYSA-N D1J SMILES_CANONICAL CACTVS 3.370 "CCCC#CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)C(=O)NC1=O" D1J SMILES CACTVS 3.370 "CCCC#CC1=CN([CH]2O[CH](CO)[CH](O)[CH](O)[CH]2O)C(=O)NC1=O" D1J SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CCCC#CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O" D1J SMILES "OpenEye OEToolkits" 1.7.6 "CCCC#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 D1J "SYSTEMATIC NAME" ACDLabs 12.01 "1-(beta-D-glucopyranosyl)-5-(pent-1-yn-1-yl)pyrimidine-2,4(1H,3H)-dione" D1J "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "1-[(2R,3R,4S,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-5-pent-1-ynyl-pyrimidine-2,4-dione" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site D1J "Create component" 2012-04-10 RCSB #