data_D1F # _chem_comp.id D1F _chem_comp.name "1-(beta-D-glucopyranosyl)-5-(hept-1-yn-1-yl)pyrimidine-2,4(1H,3H)-dione" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H24 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 368.382 _chem_comp.one_letter_code ? _chem_comp.three_letter_code D1F _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 4EJ2 _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 D1F N1 N1 N 0 1 N N N 34.060 23.776 28.953 -0.771 -0.761 -0.031 N1 D1F 1 D1F C2 C2 C 0 1 N N N 33.252 24.437 29.833 -1.205 -2.032 -0.021 C2 D1F 2 D1F O2 O2 O 0 1 N N N 32.017 24.421 29.703 -2.401 -2.247 -0.044 O2 D1F 3 D1F N3 N3 N 0 1 N N N 33.798 25.193 30.904 -0.355 -3.072 0.011 N3 D1F 4 D1F C4 C4 C 0 1 N N N 35.186 25.246 31.067 0.978 -2.863 0.036 C4 D1F 5 D1F O4 O4 O 0 1 N N N 35.738 25.874 31.977 1.754 -3.801 0.066 O4 D1F 6 D1F C5 C5 C 0 1 N N N 35.992 24.566 30.189 1.475 -1.479 0.027 C5 D1F 7 D1F C6 C6 C 0 1 N N N 35.494 23.815 29.110 0.561 -0.464 -0.007 C6 D1F 8 D1F C7 C7 C 0 1 N N N 37.395 24.824 30.652 2.880 -1.202 0.053 C7 D1F 9 D1F C8 C8 C 0 1 N N N 38.476 24.974 31.004 4.031 -0.976 0.074 C8 D1F 10 D1F C9 C9 C 0 1 N N N 39.868 25.270 31.533 5.475 -0.691 0.101 C9 D1F 11 D1F "C1'" "C1'" C 0 1 N N R 33.337 23.008 27.871 -1.747 0.330 -0.073 "C1'" D1F 12 D1F C10 C10 C 0 1 N N N 40.656 23.977 31.880 5.697 0.822 0.084 C10 D1F 13 D1F C11 C11 C 0 1 N N N 42.102 24.179 32.372 7.198 1.118 0.111 C11 D1F 14 D1F C12 C12 C 0 1 N N N 42.925 22.920 32.698 7.420 2.632 0.094 C12 D1F 15 D1F C13 C13 C 0 1 N N N 44.194 22.820 31.847 8.921 2.927 0.122 C13 D1F 16 D1F "C2'" "C2'" C 0 1 N N R 33.873 23.137 26.424 -2.509 0.282 -1.401 "C2'" D1F 17 D1F "O2'" "O2'" O 0 1 N N N 34.265 24.520 26.161 -1.596 0.484 -2.482 "O2'" D1F 18 D1F "C3'" "C3'" C 0 1 N N S 32.761 22.532 25.448 -3.568 1.388 -1.413 "C3'" D1F 19 D1F "O3'" "O3'" O 0 1 N N N 33.125 22.536 24.042 -4.332 1.305 -2.618 "O3'" D1F 20 D1F "C4'" "C4'" C 0 1 N N S 32.435 21.078 25.873 -4.494 1.207 -0.206 "C4'" D1F 21 D1F "O4'" "O4'" O 0 1 N N N 31.339 20.526 25.062 -5.442 2.275 -0.166 "O4'" D1F 22 D1F "C5'" "C5'" C 0 1 N N R 32.165 20.960 27.426 -3.656 1.219 1.076 "C5'" D1F 23 D1F "O5'" "O5'" O 0 1 N N N 33.199 21.602 28.204 -2.670 0.187 1.008 "O5'" D1F 24 D1F "C6'" "C6'" C 0 1 N N N 32.107 19.498 27.879 -4.565 0.979 2.282 "C6'" D1F 25 D1F "O6'" "O6'" O 0 1 N N N 33.209 18.762 27.334 -3.804 1.105 3.485 "O6'" D1F 26 D1F HN3 HN3 H 0 1 N N N 33.196 25.682 31.535 -0.701 -3.978 0.017 HN3 D1F 27 D1F H6 H6 H 0 1 N N N 36.152 23.293 28.432 0.891 0.564 -0.015 H6 D1F 28 D1F H9 H9 H 0 1 N N N 40.426 25.829 30.767 5.912 -1.112 1.006 H9 D1F 29 D1F H9A H9A H 0 1 N N N 39.778 25.883 32.442 5.950 -1.138 -0.773 H9A D1F 30 D1F "H1'" "H1'" H 0 1 N N N 32.318 23.422 27.842 -1.230 1.285 0.014 "H1'" D1F 31 D1F H10 H10 H 0 1 N N N 40.103 23.447 32.670 5.261 1.244 -0.822 H10 D1F 32 D1F H10A H10A H 0 0 N N N 40.692 23.352 30.975 5.223 1.269 0.958 H10A D1F 33 D1F H11 H11 H 0 1 N N N 42.642 24.732 31.589 7.635 0.697 1.017 H11 D1F 34 D1F H11A H11A H 0 0 N N N 42.057 24.789 33.286 7.673 0.672 -0.763 H11A D1F 35 D1F H12 H12 H 0 1 N N N 43.212 22.950 33.759 6.984 3.053 -0.811 H12 D1F 36 D1F H12A H12A H 0 0 N N N 42.303 22.032 32.511 6.946 3.078 0.968 H12A D1F 37 D1F H13 H13 H 0 1 N N N 44.746 21.907 32.116 9.358 2.506 1.027 H13 D1F 38 D1F H13A H13A H 0 0 N N N 43.919 22.782 30.783 9.396 2.481 -0.752 H13A D1F 39 D1F H13B H13B H 0 0 N N N 44.829 23.699 32.031 9.079 4.006 0.110 H13B D1F 40 D1F "H2'" "H2'" H 0 1 N N N 34.762 22.495 26.339 -2.993 -0.688 -1.509 "H2'" D1F 41 D1F "HO2'" "HO2'" H 0 0 N N N 34.593 24.593 25.272 -2.011 0.466 -3.355 "HO2'" D1F 42 D1F "H3'" "H3'" H 0 1 N N N 31.849 23.133 25.583 -3.080 2.362 -1.357 "H3'" D1F 43 D1F "HO3'" "HO3'" H 0 0 N N N 32.417 22.163 23.530 -5.024 1.977 -2.692 "HO3'" D1F 44 D1F "H4'" "H4'" H 0 1 N N N 33.335 20.479 25.668 -5.019 0.256 -0.289 "H4'" D1F 45 D1F "HO4'" "HO4'" H 0 0 N N N 31.157 19.636 25.339 -6.005 2.331 -0.951 "HO4'" D1F 46 D1F "H5'" "H5'" H 0 1 N N N 31.194 21.431 27.638 -3.163 2.186 1.179 "H5'" D1F 47 D1F "H6'" "H6'" H 0 1 N N N 32.151 19.457 28.977 -5.370 1.713 2.282 "H6'" D1F 48 D1F "H6'A" "H6'A" H 0 0 N N N 31.164 19.049 27.533 -4.989 -0.024 2.224 "H6'A" D1F 49 D1F "HO6'" "HO6'" H 0 0 N N N 33.160 17.858 27.623 -4.318 0.965 4.292 "HO6'" D1F 50 # 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 D1F N1 C2 SING N N 1 D1F N1 C6 SING N N 2 D1F N1 "C1'" SING N N 3 D1F C2 O2 DOUB N N 4 D1F C2 N3 SING N N 5 D1F N3 C4 SING N N 6 D1F C4 O4 DOUB N N 7 D1F C4 C5 SING N N 8 D1F C5 C6 DOUB N N 9 D1F C5 C7 SING N N 10 D1F C7 C8 TRIP N N 11 D1F C8 C9 SING N N 12 D1F C9 C10 SING N N 13 D1F "C1'" "C2'" SING N N 14 D1F "C1'" "O5'" SING N N 15 D1F C10 C11 SING N N 16 D1F C11 C12 SING N N 17 D1F C12 C13 SING N N 18 D1F "C2'" "O2'" SING N N 19 D1F "C2'" "C3'" SING N N 20 D1F "C3'" "O3'" SING N N 21 D1F "C3'" "C4'" SING N N 22 D1F "C4'" "O4'" SING N N 23 D1F "C4'" "C5'" SING N N 24 D1F "C5'" "O5'" SING N N 25 D1F "C5'" "C6'" SING N N 26 D1F "C6'" "O6'" SING N N 27 D1F N3 HN3 SING N N 28 D1F C6 H6 SING N N 29 D1F C9 H9 SING N N 30 D1F C9 H9A SING N N 31 D1F "C1'" "H1'" SING N N 32 D1F C10 H10 SING N N 33 D1F C10 H10A SING N N 34 D1F C11 H11 SING N N 35 D1F C11 H11A SING N N 36 D1F C12 H12 SING N N 37 D1F C12 H12A SING N N 38 D1F C13 H13 SING N N 39 D1F C13 H13A SING N N 40 D1F C13 H13B SING N N 41 D1F "C2'" "H2'" SING N N 42 D1F "O2'" "HO2'" SING N N 43 D1F "C3'" "H3'" SING N N 44 D1F "O3'" "HO3'" SING N N 45 D1F "C4'" "H4'" SING N N 46 D1F "O4'" "HO4'" SING N N 47 D1F "C5'" "H5'" SING N N 48 D1F "C6'" "H6'" SING N N 49 D1F "C6'" "H6'A" SING N N 50 D1F "O6'" "HO6'" SING N N 51 # 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 D1F SMILES ACDLabs 12.01 "O=C1NC(=O)N(C=C1C#CCCCCC)C2OC(C(O)C(O)C2O)CO" D1F InChI InChI 1.03 "InChI=1S/C17H24N2O7/c1-2-3-4-5-6-7-10-8-19(17(25)18-15(10)24)16-14(23)13(22)12(21)11(9-20)26-16/h8,11-14,16,20-23H,2-5,9H2,1H3,(H,18,24,25)/t11-,12-,13+,14-,16-/m1/s1" D1F InChIKey InChI 1.03 ZIAKFTYLGUACKB-XYFZXANASA-N D1F SMILES_CANONICAL CACTVS 3.370 "CCCCCC#CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)C(=O)NC1=O" D1F SMILES CACTVS 3.370 "CCCCCC#CC1=CN([CH]2O[CH](CO)[CH](O)[CH](O)[CH]2O)C(=O)NC1=O" D1F SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CCCCCC#CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O" D1F SMILES "OpenEye OEToolkits" 1.7.6 "CCCCCC#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 D1F "SYSTEMATIC NAME" ACDLabs 12.01 "1-(beta-D-glucopyranosyl)-5-(hept-1-yn-1-yl)pyrimidine-2,4(1H,3H)-dione" D1F "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "5-hept-1-ynyl-1-[(2R,3R,4S,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]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 D1F "Create component" 2012-04-10 RCSB #