data_U3S # _chem_comp.id U3S _chem_comp.name "1-(5-deoxy-5-piperidin-1-yl-alpha-L-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C14 H21 N3 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2008-06-10 _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 311.334 _chem_comp.one_letter_code ? _chem_comp.three_letter_code U3S _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 3D6Q _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 U3S C4 C4 C 0 1 N N N 34.834 -4.586 12.460 -3.977 1.891 -0.115 C4 U3S 1 U3S C5 C5 C 0 1 N N N 36.012 -4.501 13.197 -4.057 1.234 1.137 C5 U3S 2 U3S C6 C6 C 0 1 N N N 36.826 -3.376 13.062 -3.121 0.315 1.457 C6 U3S 3 U3S N1 N1 N 0 1 N N N 36.461 -2.309 12.202 -2.115 0.036 0.572 N1 U3S 4 U3S N3 N3 N 0 1 N N N 34.469 -3.552 11.598 -2.970 1.588 -0.958 N3 U3S 5 U3S CAV CAV C 0 1 N N N 43.496 -2.552 14.113 4.991 2.198 -0.086 CAV U3S 6 U3S CAK CAK C 0 1 N N N 42.291 -3.503 14.175 3.714 2.151 -0.930 CAK U3S 7 U3S CAM CAM C 0 1 N N N 40.941 -2.763 14.045 3.251 0.699 -1.065 CAM U3S 8 U3S CAJ CAJ C 0 1 N N N 43.407 -1.453 15.185 4.715 1.564 1.280 CAJ U3S 9 U3S CAL CAL C 0 1 N N N 41.951 -1.179 15.587 4.222 0.129 1.080 CAL U3S 10 U3S NBA NBA N 0 1 N N N 41.036 -1.337 14.435 2.999 0.138 0.268 NBA U3S 11 U3S "C5'" "C5'" C 0 1 N N N 39.765 -0.766 14.925 2.421 -1.209 0.172 "C5'" U3S 12 U3S "C4'" "C4'" C 0 1 N N S 38.533 -0.832 13.970 0.947 -1.104 -0.227 "C4'" U3S 13 U3S "O4'" "O4'" O 0 1 N N N 38.660 -1.368 12.615 0.208 -0.391 0.778 "O4'" U3S 14 U3S "C3'" "C3'" C 0 1 N N R 38.007 0.547 13.641 0.303 -2.512 -0.280 "C3'" U3S 15 U3S "O3'" "O3'" O 0 1 N N N 37.474 1.243 14.758 0.495 -3.118 -1.560 "O3'" U3S 16 U3S "C2'" "C2'" C 0 1 N N R 36.873 0.211 12.704 -1.191 -2.162 -0.045 "C2'" U3S 17 U3S "O2'" "O2'" O 0 1 N N N 36.875 1.295 11.773 -1.880 -3.254 0.567 "O2'" U3S 18 U3S "C1'" "C1'" C 0 1 N N R 37.343 -1.104 12.038 -1.099 -0.960 0.920 "C1'" U3S 19 U3S O4 O4 O 0 1 N N N 34.102 -5.569 12.556 -4.813 2.720 -0.428 O4 U3S 20 U3S C2 C2 C 0 1 N N N 35.270 -2.408 11.466 -2.050 0.668 -0.614 C2 U3S 21 U3S O2 O2 O 0 1 N N N 34.910 -1.512 10.708 -1.148 0.404 -1.385 O2 U3S 22 U3S H5 H5 H 0 1 N N N 36.293 -5.299 13.868 -4.856 1.464 1.826 H5 U3S 23 U3S H6 H6 H 0 1 N N N 37.748 -3.317 13.621 -3.165 -0.196 2.407 H6 U3S 24 U3S HN3 HN3 H 0 1 N N N 33.625 -3.627 11.067 -2.909 2.034 -1.818 HN3 U3S 25 U3S HAV HAV H 0 1 N N N 44.415 -3.134 14.279 5.782 1.644 -0.592 HAV U3S 26 U3S HAVA HAVA H 0 0 N N N 43.504 -2.070 13.124 5.301 3.234 0.049 HAVA U3S 27 U3S HAK HAK H 0 1 N N N 42.374 -4.223 13.348 2.935 2.738 -0.444 HAK U3S 28 U3S HAKA HAKA H 0 0 N N N 42.307 -3.999 15.157 3.916 2.562 -1.919 HAKA U3S 29 U3S HAM HAM H 0 1 N N N 40.614 -2.816 12.996 2.334 0.664 -1.653 HAM U3S 30 U3S HAMA HAMA H 0 0 N N N 40.224 -3.250 14.723 4.025 0.116 -1.564 HAMA U3S 31 U3S HAJ HAJ H 0 1 N N N 43.966 -1.779 16.075 5.631 1.556 1.869 HAJ U3S 32 U3S HAJA HAJA H 0 0 N N N 43.832 -0.528 14.770 3.951 2.142 1.801 HAJA U3S 33 U3S HAL HAL H 0 1 N N N 41.659 -1.891 16.373 4.992 -0.451 0.571 HAL U3S 34 U3S HALA HALA H 0 0 N N N 41.879 -0.143 15.949 4.011 -0.320 2.051 HALA U3S 35 U3S "H5'" "H5'" H 0 1 N N N 39.494 -1.321 15.835 2.961 -1.783 -0.581 "H5'" U3S 36 U3S "H5'A" "H5'A" H 0 0 N N N 39.966 0.307 15.059 2.501 -1.708 1.138 "H5'A" U3S 37 U3S "H4'" "H4'" H 0 1 N N N 37.923 -1.511 14.584 0.851 -0.605 -1.191 "H4'" U3S 38 U3S "H3'" "H3'" H 0 1 N N N 38.800 1.203 13.251 0.688 -3.150 0.516 "H3'" U3S 39 U3S "HO3'" "HO3'" H 0 0 N N N 37.355 0.638 15.481 0.108 -4.001 -1.639 "HO3'" U3S 40 U3S "H2'" "H2'" H 0 1 N N N 35.871 0.086 13.141 -1.675 -1.876 -0.979 "H2'" U3S 41 U3S "HO2'" "HO2'" H 0 0 N N N 36.875 2.119 12.246 -1.888 -4.062 0.036 "HO2'" U3S 42 U3S "H1'" "H1'" H 0 1 N N N 37.331 -0.949 10.949 -1.246 -1.296 1.946 "H1'" U3S 43 # 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 U3S C4 C5 SING N N 1 U3S C4 N3 SING N N 2 U3S C4 O4 DOUB N N 3 U3S C5 C6 DOUB N N 4 U3S C6 N1 SING N N 5 U3S N1 "C1'" SING N N 6 U3S N1 C2 SING N N 7 U3S N3 C2 SING N N 8 U3S CAV CAK SING N N 9 U3S CAV CAJ SING N N 10 U3S CAK CAM SING N N 11 U3S CAM NBA SING N N 12 U3S CAJ CAL SING N N 13 U3S CAL NBA SING N N 14 U3S NBA "C5'" SING N N 15 U3S "C5'" "C4'" SING N N 16 U3S "C4'" "O4'" SING N N 17 U3S "C4'" "C3'" SING N N 18 U3S "O4'" "C1'" SING N N 19 U3S "C3'" "O3'" SING N N 20 U3S "C3'" "C2'" SING N N 21 U3S "C2'" "O2'" SING N N 22 U3S "C2'" "C1'" SING N N 23 U3S C2 O2 DOUB N N 24 U3S C5 H5 SING N N 25 U3S C6 H6 SING N N 26 U3S N3 HN3 SING N N 27 U3S CAV HAV SING N N 28 U3S CAV HAVA SING N N 29 U3S CAK HAK SING N N 30 U3S CAK HAKA SING N N 31 U3S CAM HAM SING N N 32 U3S CAM HAMA SING N N 33 U3S CAJ HAJ SING N N 34 U3S CAJ HAJA SING N N 35 U3S CAL HAL SING N N 36 U3S CAL HALA SING N N 37 U3S "C5'" "H5'" SING N N 38 U3S "C5'" "H5'A" SING N N 39 U3S "C4'" "H4'" SING N N 40 U3S "C3'" "H3'" SING N N 41 U3S "O3'" "HO3'" SING N N 42 U3S "C2'" "H2'" SING N N 43 U3S "O2'" "HO2'" SING N N 44 U3S "C1'" "H1'" 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 U3S SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)CN3CCCCC3" U3S SMILES_CANONICAL CACTVS 3.341 "O[C@@H]1[C@@H](O)[C@@H](O[C@H]1CN2CCCCC2)N3C=CC(=O)NC3=O" U3S SMILES CACTVS 3.341 "O[CH]1[CH](O)[CH](O[CH]1CN2CCCCC2)N3C=CC(=O)NC3=O" U3S SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1CCN(CC1)C[C@H]2[C@@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O" U3S SMILES "OpenEye OEToolkits" 1.5.0 "C1CCN(CC1)CC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O" U3S InChI InChI 1.03 "InChI=1S/C14H21N3O5/c18-10-4-7-17(14(21)15-10)13-12(20)11(19)9(22-13)8-16-5-2-1-3-6-16/h4,7,9,11-13,19-20H,1-3,5-6,8H2,(H,15,18,21)/t9-,11-,12+,13+/m0/s1" U3S InChIKey InChI 1.03 PJCAMYRNNJAIMT-FTYKPCCVSA-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 U3S "SYSTEMATIC NAME" ACDLabs 10.04 "1-(5-deoxy-5-piperidin-1-yl-alpha-L-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione" U3S "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "1-[(2R,3R,4R,5S)-3,4-dihydroxy-5-(piperidin-1-ylmethyl)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 U3S "Create component" 2008-06-10 RCSB U3S "Modify descriptor" 2011-06-04 RCSB #