data_DU2 # _chem_comp.id DU2 _chem_comp.name "2',5'-dideoxy-5'-{[(R)-(1-methyl-1H-imidazol-2-yl)(phenyl)methyl]amino}uridine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H23 N5 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2011-11-10 _chem_comp.pdbx_modified_date 2012-08-24 _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 397.428 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DU2 _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 3T6Y _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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 DU2 N1 N1 N 0 1 N N N 17.713 21.750 -0.341 -3.648 -0.360 0.283 N1 DU2 1 DU2 C2 C2 C 0 1 N N N 18.465 22.717 -0.838 -4.596 -0.402 1.237 C2 DU2 2 DU2 O2 O2 O 0 1 N N N 19.675 22.573 -0.786 -4.636 -1.347 2.001 O2 DU2 3 DU2 N3 N3 N 0 1 N N N 17.922 23.820 -1.428 -5.500 0.587 1.357 N3 DU2 4 DU2 C4 C4 C 0 1 N N N 16.581 23.892 -1.507 -5.469 1.643 0.518 C4 DU2 5 DU2 O4 O4 O 0 1 N N N 16.070 24.859 -2.069 -6.286 2.539 0.627 O4 DU2 6 DU2 C5 C5 C 0 1 N N N 15.791 22.902 -0.951 -4.477 1.699 -0.490 C5 DU2 7 DU2 C6 C6 C 0 1 N N N 16.353 21.823 -0.358 -3.582 0.693 -0.589 C6 DU2 8 DU2 "C1'" "C1'" C 0 1 N N R 18.409 20.651 0.280 -2.674 -1.449 0.180 "C1'" DU2 9 DU2 C17 C17 C 0 1 N N R 18.240 18.516 -4.104 2.849 -0.130 -0.455 C17 DU2 10 DU2 C18 C18 C 0 1 Y N N 17.684 19.738 -4.469 3.991 -0.489 0.461 C18 DU2 11 DU2 C19 C19 C 0 1 Y N N 18.131 20.903 -3.876 5.256 -0.693 -0.059 C19 DU2 12 DU2 "C2'" "C2'" C 0 1 N N N 17.518 19.961 1.351 -2.861 -2.196 -1.155 "C2'" DU2 13 DU2 C20 C20 C 0 1 Y N N 17.595 22.145 -4.257 6.303 -1.022 0.781 C20 DU2 14 DU2 C21 C21 C 0 1 Y N N 16.599 22.256 -5.244 6.086 -1.147 2.140 C21 DU2 15 DU2 C22 C22 C 0 1 Y N N 16.170 21.061 -5.831 4.822 -0.943 2.660 C22 DU2 16 DU2 C23 C23 C 0 1 Y N N 16.689 19.808 -5.464 3.775 -0.609 1.821 C23 DU2 17 DU2 C24 C24 C 0 1 Y N N 19.149 17.910 -5.002 2.605 1.356 -0.395 C24 DU2 18 DU2 N25 N25 N 0 1 Y N N 19.760 16.741 -4.801 2.026 1.992 0.586 N25 DU2 19 DU2 C26 C26 C 0 1 Y N N 20.686 16.362 -5.908 1.980 3.302 0.298 C26 DU2 20 DU2 C27 C27 C 0 1 Y N N 20.552 17.505 -6.872 2.553 3.483 -0.907 C27 DU2 21 DU2 N28 N28 N 0 1 Y N N 19.593 18.357 -6.171 2.954 2.250 -1.345 N28 DU2 22 DU2 C29 C29 C 0 1 N N N 19.168 19.579 -6.748 3.633 1.954 -2.609 C29 DU2 23 DU2 "C3'" "C3'" C 0 1 N N S 16.734 19.018 0.489 -1.488 -2.065 -1.859 "C3'" DU2 24 DU2 "C4'" "C4'" C 0 1 N N R 17.730 18.586 -0.589 -0.542 -1.759 -0.670 "C4'" DU2 25 DU2 "O4'" "O4'" O 0 1 N N N 18.636 19.737 -0.788 -1.339 -0.914 0.187 "O4'" DU2 26 DU2 O41 O41 O 0 1 N N N 16.487 17.958 1.331 -1.124 -3.290 -2.498 O41 DU2 27 DU2 "C5'" "C5'" C 0 1 N N N 17.009 18.352 -1.929 0.705 -1.014 -1.151 "C5'" DU2 28 DU2 "N5'" "N5'" N 0 1 N N N 17.965 17.849 -2.948 1.637 -0.843 -0.029 "N5'" DU2 29 DU2 HN3 HN3 H 0 1 N N N 18.501 24.551 -1.790 -6.177 0.541 2.050 HN3 DU2 30 DU2 H5 H5 H 0 1 N N N 14.715 22.991 -0.990 -4.436 2.536 -1.172 H5 DU2 31 DU2 H6 H6 H 0 1 N N N 15.745 21.048 0.086 -2.818 0.719 -1.352 H6 DU2 32 DU2 "H1'" "H1'" H 0 1 N N N 19.328 20.983 0.785 -2.802 -2.141 1.012 "H1'" DU2 33 DU2 H17 H17 H 0 1 N N N 17.637 19.095 -3.389 3.099 -0.416 -1.477 H17 DU2 34 DU2 H19 H19 H 0 1 N N N 18.897 20.859 -3.115 5.425 -0.595 -1.121 H19 DU2 35 DU2 "H2'" "H2'" H 0 1 N N N 18.108 19.439 2.119 -3.099 -3.244 -0.976 "H2'" DU2 36 DU2 "H2'A" "H2'A" H 0 0 N N N 16.876 20.674 1.889 -3.641 -1.722 -1.751 "H2'A" DU2 37 DU2 H20 H20 H 0 1 N N N 17.959 23.042 -3.777 7.291 -1.182 0.375 H20 DU2 38 DU2 H21 H21 H 0 1 N N N 16.188 23.212 -5.533 6.904 -1.405 2.796 H21 DU2 39 DU2 H22 H22 H 0 1 N N N 15.410 21.103 -6.597 4.652 -1.041 3.722 H22 DU2 40 DU2 H23 H23 H 0 1 N N N 16.329 18.908 -5.940 2.788 -0.445 2.227 H23 DU2 41 DU2 H26 H26 H 0 1 N N N 21.303 15.480 -5.995 1.558 4.075 0.923 H26 DU2 42 DU2 H27 H27 H 0 1 N N N 21.034 17.657 -7.826 2.675 4.422 -1.427 H27 DU2 43 DU2 H29 H29 H 0 1 N N N 19.677 19.726 -7.712 2.891 1.750 -3.381 H29 DU2 44 DU2 H29A H29A H 0 0 N N N 18.080 19.550 -6.908 4.239 2.811 -2.905 H29A DU2 45 DU2 H29B H29B H 0 0 N N N 19.417 20.410 -6.072 4.274 1.082 -2.482 H29B DU2 46 DU2 "H3'" "H3'" H 0 1 N N N 15.810 19.412 0.041 -1.493 -1.242 -2.573 "H3'" DU2 47 DU2 "H4'" "H4'" H 0 1 N N N 18.244 17.663 -0.284 -0.265 -2.678 -0.153 "H4'" DU2 48 DU2 HO41 HO41 H 0 0 N N N 15.987 17.296 0.869 -1.738 -3.570 -3.190 HO41 DU2 49 DU2 "H5'" "H5'" H 0 1 N N N 16.210 17.610 -1.785 1.189 -1.589 -1.941 "H5'" DU2 50 DU2 "H5'A" "H5'A" H 0 0 N N N 16.576 19.301 -2.277 0.418 -0.036 -1.538 "H5'A" DU2 51 DU2 "HN5'" "HN5'" H 0 0 N N N 17.598 16.965 -3.237 1.869 -1.732 0.388 "HN5'" DU2 52 # 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 DU2 N1 C2 SING N N 1 DU2 N1 C6 SING N N 2 DU2 N1 "C1'" SING N N 3 DU2 C2 O2 DOUB N N 4 DU2 C2 N3 SING N N 5 DU2 N3 C4 SING N N 6 DU2 C4 O4 DOUB N N 7 DU2 C4 C5 SING N N 8 DU2 C5 C6 DOUB N N 9 DU2 "C1'" "C2'" SING N N 10 DU2 "C1'" "O4'" SING N N 11 DU2 C17 C18 SING N N 12 DU2 C17 C24 SING N N 13 DU2 C17 "N5'" SING N N 14 DU2 C18 C19 DOUB Y N 15 DU2 C18 C23 SING Y N 16 DU2 C19 C20 SING Y N 17 DU2 "C2'" "C3'" SING N N 18 DU2 C20 C21 DOUB Y N 19 DU2 C21 C22 SING Y N 20 DU2 C22 C23 DOUB Y N 21 DU2 C24 N25 DOUB Y N 22 DU2 C24 N28 SING Y N 23 DU2 N25 C26 SING Y N 24 DU2 C26 C27 DOUB Y N 25 DU2 C27 N28 SING Y N 26 DU2 N28 C29 SING N N 27 DU2 "C3'" "C4'" SING N N 28 DU2 "C3'" O41 SING N N 29 DU2 "C4'" "O4'" SING N N 30 DU2 "C4'" "C5'" SING N N 31 DU2 "C5'" "N5'" SING N N 32 DU2 N3 HN3 SING N N 33 DU2 C5 H5 SING N N 34 DU2 C6 H6 SING N N 35 DU2 "C1'" "H1'" SING N N 36 DU2 C17 H17 SING N N 37 DU2 C19 H19 SING N N 38 DU2 "C2'" "H2'" SING N N 39 DU2 "C2'" "H2'A" SING N N 40 DU2 C20 H20 SING N N 41 DU2 C21 H21 SING N N 42 DU2 C22 H22 SING N N 43 DU2 C23 H23 SING N N 44 DU2 C26 H26 SING N N 45 DU2 C27 H27 SING N N 46 DU2 C29 H29 SING N N 47 DU2 C29 H29A SING N N 48 DU2 C29 H29B SING N N 49 DU2 "C3'" "H3'" SING N N 50 DU2 "C4'" "H4'" SING N N 51 DU2 O41 HO41 SING N N 52 DU2 "C5'" "H5'" SING N N 53 DU2 "C5'" "H5'A" SING N N 54 DU2 "N5'" "HN5'" SING N N 55 # 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 DU2 SMILES ACDLabs 12.01 "O=C1NC(=O)N(C=C1)C2OC(C(O)C2)CNC(c3ccccc3)c4nccn4C" DU2 InChI InChI 1.03 "InChI=1S/C20H23N5O4/c1-24-10-8-21-19(24)18(13-5-3-2-4-6-13)22-12-15-14(26)11-17(29-15)25-9-7-16(27)23-20(25)28/h2-10,14-15,17-18,22,26H,11-12H2,1H3,(H,23,27,28)/t14-,15+,17+,18?/m0/s1" DU2 InChIKey InChI 1.03 KPWKGDCQLFIJMC-URHIDPGUSA-N DU2 SMILES_CANONICAL CACTVS 3.370 "Cn1ccnc1[C@H](NC[C@H]2O[C@H](C[C@@H]2O)N3C=CC(=O)NC3=O)c4ccccc4" DU2 SMILES CACTVS 3.370 "Cn1ccnc1[CH](NC[CH]2O[CH](C[CH]2O)N3C=CC(=O)NC3=O)c4ccccc4" DU2 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "Cn1ccnc1C(c2ccccc2)NC[C@@H]3[C@H](C[C@@H](O3)N4C=CC(=O)NC4=O)O" DU2 SMILES "OpenEye OEToolkits" 1.7.2 "Cn1ccnc1C(c2ccccc2)NCC3C(CC(O3)N4C=CC(=O)NC4=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 DU2 "SYSTEMATIC NAME" ACDLabs 12.01 "2',5'-dideoxy-5'-{[(R)-(1-methyl-1H-imidazol-2-yl)(phenyl)methyl]amino}uridine" DU2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "1-[(2R,4S,5R)-5-[[[(1-methylimidazol-2-yl)-phenyl-methyl]amino]methyl]-4-oxidanyl-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 DU2 "Create component" 2011-11-10 PDBJ DU2 "Modify name" 2012-08-20 PDBJ DU2 "Modify formula" 2012-08-20 PDBJ DU2 "Modify name" 2012-08-21 PDBJ DU2 "Modify formula" 2012-08-21 PDBJ DU2 "Initial release" 2012-08-24 RCSB #