data_D3Z # _chem_comp.id D3Z _chem_comp.name "1-(5-deoxy-beta-L-xylofuranosyl)pyrimidine-2,4(1H,3H)-dione" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H12 N2 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2008-05-14 _chem_comp.pdbx_modified_date 2011-06-04 _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 228.202 _chem_comp.one_letter_code ? _chem_comp.three_letter_code D3Z _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 3D3Z _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 D3Z N1 N1 N 0 1 N N N 32.046 28.577 -6.031 0.793 0.223 -0.423 N1 D3Z 1 D3Z C2 C2 C 0 1 N N N 30.916 28.488 -5.195 1.307 -0.985 -0.129 C2 D3Z 2 D3Z N3 N3 N 0 1 N N N 30.343 29.601 -4.747 2.599 -1.120 0.224 N3 D3Z 3 D3Z C4 C4 C 0 1 N N N 30.814 30.810 -5.055 3.402 -0.038 0.287 C4 D3Z 4 D3Z C5 C5 C 0 1 N N N 31.914 30.903 -5.866 2.874 1.239 -0.020 C5 D3Z 5 D3Z C6 C6 C 0 1 N N N 32.534 29.763 -6.359 1.574 1.345 -0.371 C6 D3Z 6 D3Z O2 O2 O 0 1 N N N 30.433 27.384 -4.867 0.595 -1.969 -0.182 O2 D3Z 7 D3Z O4 O4 O 0 1 N N N 30.282 31.864 -4.649 4.571 -0.159 0.607 O4 D3Z 8 D3Z "C1'" "C1'" C 0 1 N N S 32.697 27.389 -6.522 -0.616 0.337 -0.810 "C1'" D3Z 9 D3Z "C2'" "C2'" C 0 1 N N S 32.362 26.298 -5.526 -1.371 1.254 0.178 "C2'" D3Z 10 D3Z "O2'" "O2'" O 0 1 N N N 31.487 25.331 -6.135 -1.493 2.573 -0.356 "O2'" D3Z 11 D3Z "C3'" "C3'" C 0 1 N N S 33.694 25.751 -5.044 -2.762 0.594 0.313 "C3'" D3Z 12 D3Z "C4'" "C4'" C 0 1 N N S 34.778 26.507 -5.791 -2.682 -0.643 -0.609 "C4'" D3Z 13 D3Z "O3'" "O3'" O 0 1 N N N 33.851 25.971 -3.652 -2.998 0.196 1.665 "O3'" D3Z 14 D3Z "O4'" "O4'" O 0 1 N N N 34.125 27.564 -6.521 -1.273 -0.944 -0.700 "O4'" D3Z 15 D3Z "C5'" "C5'" C 0 1 N N N 35.812 27.029 -4.800 -3.439 -1.819 0.011 "C5'" D3Z 16 D3Z HN3 HN3 H 0 1 N N N 29.535 29.529 -4.162 2.954 -1.998 0.434 HN3 D3Z 17 D3Z H5 H5 H 0 1 N N N 32.304 31.876 -6.125 3.502 2.116 0.025 H5 D3Z 18 D3Z H6 H6 H 0 1 N N N 33.400 29.842 -6.999 1.154 2.311 -0.609 H6 D3Z 19 D3Z "H1'" "H1'" H 0 1 N N N 32.369 27.157 -7.546 -0.700 0.723 -1.826 "H1'" D3Z 20 D3Z "H2'" "H2'" H 0 1 N N N 31.800 26.656 -4.651 -0.863 1.278 1.142 "H2'" D3Z 21 D3Z "HO2'" "HO2'" H 0 0 N N N 31.294 25.595 -7.027 -1.960 3.191 0.223 "HO2'" D3Z 22 D3Z "H3'" "H3'" H 0 1 N N N 33.750 24.668 -5.228 -3.542 1.275 -0.028 "H3'" D3Z 23 D3Z "H4'" "H4'" H 0 1 N N N 35.322 25.864 -6.498 -3.085 -0.408 -1.594 "H4'" D3Z 24 D3Z "HO3'" "HO3'" H 0 0 N N N 33.886 25.136 -3.201 -3.858 -0.224 1.807 "HO3'" D3Z 25 D3Z "H5'" "H5'" H 0 1 N N N 36.779 27.155 -5.310 -4.485 -1.546 0.148 "H5'" D3Z 26 D3Z "H5'A" "H5'A" H 0 0 N N N 35.480 27.998 -4.400 -3.373 -2.683 -0.651 "H5'A" D3Z 27 D3Z "H5'B" "H5'B" H 0 0 N N N 35.924 26.310 -3.975 -2.998 -2.067 0.976 "H5'B" D3Z 28 # 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 D3Z N1 C2 SING N N 1 D3Z N1 C6 SING N N 2 D3Z N1 "C1'" SING N N 3 D3Z C2 N3 SING N N 4 D3Z C2 O2 DOUB N N 5 D3Z N3 C4 SING N N 6 D3Z C4 C5 SING N N 7 D3Z C4 O4 DOUB N N 8 D3Z C5 C6 DOUB N N 9 D3Z "C1'" "C2'" SING N N 10 D3Z "C1'" "O4'" SING N N 11 D3Z "C2'" "O2'" SING N N 12 D3Z "C2'" "C3'" SING N N 13 D3Z "C3'" "C4'" SING N N 14 D3Z "C3'" "O3'" SING N N 15 D3Z "C4'" "O4'" SING N N 16 D3Z "C4'" "C5'" SING N N 17 D3Z N3 HN3 SING N N 18 D3Z C5 H5 SING N N 19 D3Z C6 H6 SING N N 20 D3Z "C1'" "H1'" SING N N 21 D3Z "C2'" "H2'" SING N N 22 D3Z "O2'" "HO2'" SING N N 23 D3Z "C3'" "H3'" SING N N 24 D3Z "C4'" "H4'" SING N N 25 D3Z "O3'" "HO3'" SING N N 26 D3Z "C5'" "H5'" SING N N 27 D3Z "C5'" "H5'A" SING N N 28 D3Z "C5'" "H5'B" SING N N 29 # 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 D3Z SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)C" D3Z SMILES_CANONICAL CACTVS 3.341 "C[C@@H]1O[C@@H]([C@@H](O)[C@@H]1O)N2C=CC(=O)NC2=O" D3Z SMILES CACTVS 3.341 "C[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=O)NC2=O" D3Z SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@H]1[C@H]([C@@H]([C@H](O1)N2C=CC(=O)NC2=O)O)O" D3Z SMILES "OpenEye OEToolkits" 1.5.0 "CC1C(C(C(O1)N2C=CC(=O)NC2=O)O)O" D3Z InChI InChI 1.03 "InChI=1S/C9H12N2O5/c1-4-6(13)7(14)8(16-4)11-3-2-5(12)10-9(11)15/h2-4,6-8,13-14H,1H3,(H,10,12,15)/t4-,6+,7-,8-/m0/s1" D3Z InChIKey InChI 1.03 WUBAOANSQGKRHF-UCVXFZOQSA-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 D3Z "SYSTEMATIC NAME" ACDLabs 10.04 "1-(5-deoxy-beta-L-xylofuranosyl)pyrimidine-2,4(1H,3H)-dione" D3Z "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "1-[(2S,3S,4S,5S)-3,4-dihydroxy-5-methyl-oxolan-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 D3Z "Create component" 2008-05-14 RCSB D3Z "Modify descriptor" 2011-06-04 RCSB #