data_DU4 # _chem_comp.id DU4 _chem_comp.name "2',5'-dideoxy-5'-[(diphenylmethyl)(methyl)amino]uridine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C23 H25 N3 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 407.462 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DU4 _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 3T70 _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 DU4 N1 N1 N 0 1 N N N 17.504 21.747 -0.241 3.408 -0.315 -0.404 N1 DU4 1 DU4 C2 C2 C 0 1 N N N 18.329 22.730 -0.831 4.306 -0.265 -1.404 C2 DU4 2 DU4 O2 O2 O 0 1 N N N 19.561 22.661 -0.823 4.369 -1.181 -2.200 O2 DU4 3 DU4 N3 N3 N 0 1 N N N 17.731 23.819 -1.452 5.137 0.786 -1.536 N3 DU4 4 DU4 C4 C4 C 0 1 N N N 16.335 23.943 -1.507 5.081 1.811 -0.661 C4 DU4 5 DU4 O4 O4 O 0 1 N N N 15.852 24.925 -2.066 5.831 2.762 -0.780 O4 DU4 6 DU4 C5 C5 C 0 1 N N N 15.510 22.973 -0.927 4.140 1.771 0.396 C5 DU4 7 DU4 C6 C6 C 0 1 N N N 16.098 21.881 -0.288 3.318 0.705 0.505 C6 DU4 8 DU4 "C1'" "C1'" C 0 1 N N R 18.139 20.573 0.408 2.513 -1.469 -0.290 "C1'" DU4 9 DU4 C17 C17 C 0 1 N N N 18.031 18.244 -4.406 -2.944 -0.333 0.593 C17 DU4 10 DU4 C18 C18 C 0 1 Y N N 19.188 17.939 -5.397 -2.443 1.024 1.014 C18 DU4 11 DU4 C19 C19 C 0 1 Y N N 19.011 16.949 -6.366 -2.909 1.602 2.180 C19 DU4 12 DU4 "C2'" "C2'" C 0 1 N N N 17.284 19.723 1.354 2.816 -2.241 1.009 "C2'" DU4 13 DU4 C20 C20 C 0 1 Y N N 20.035 16.651 -7.271 -2.449 2.847 2.566 C20 DU4 14 DU4 C21 C21 C 0 1 Y N N 21.242 17.352 -7.211 -1.523 3.514 1.787 C21 DU4 15 DU4 C22 C22 C 0 1 Y N N 21.422 18.344 -6.250 -1.056 2.936 0.621 C22 DU4 16 DU4 C23 C23 C 0 1 Y N N 20.398 18.640 -5.343 -1.512 1.689 0.237 C23 DU4 17 DU4 C24 C24 C 0 1 Y N N 17.572 19.691 -4.663 -3.925 -0.177 -0.540 C24 DU4 18 DU4 C25 C25 C 0 1 Y N N 16.583 19.903 -5.627 -5.278 -0.353 -0.312 C25 DU4 19 DU4 C26 C26 C 0 1 Y N N 16.139 21.195 -5.910 -6.178 -0.209 -1.352 C26 DU4 20 DU4 C27 C27 C 0 1 Y N N 16.684 22.280 -5.224 -5.726 0.110 -2.618 C27 DU4 21 DU4 C28 C28 C 0 1 Y N N 17.681 22.073 -4.269 -4.374 0.286 -2.846 C28 DU4 22 DU4 C29 C29 C 0 1 Y N N 18.128 20.783 -3.987 -3.474 0.147 -1.806 C29 DU4 23 DU4 "C3'" "C3'" C 0 1 N N S 16.721 18.646 0.437 1.475 -2.224 1.783 "C3'" DU4 24 DU4 "O3'" "O3'" O 0 1 N N N 16.544 17.437 1.180 1.225 -3.489 2.398 "O3'" DU4 25 DU4 "C4'" "C4'" C 0 1 N N R 17.815 18.456 -0.619 0.452 -1.946 0.652 "C4'" DU4 26 DU4 "O4'" "O4'" O 0 1 N N N 18.488 19.728 -0.734 1.148 -1.024 -0.213 "O4'" DU4 27 DU4 C41 C41 C 0 1 N N N 18.912 16.573 -2.851 -2.270 -2.471 -0.321 C41 DU4 28 DU4 "C5'" "C5'" C 0 1 N N N 17.274 18.089 -2.036 -0.814 -1.300 1.219 "C5'" DU4 29 DU4 "N5'" "N5'" N 0 1 N N N 18.400 17.956 -2.990 -1.812 -1.158 0.150 "N5'" DU4 30 DU4 HN3 HN3 H 0 1 N N N 18.305 24.526 -1.866 5.779 0.806 -2.262 HN3 DU4 31 DU4 H5 H5 H 0 1 N N N 14.435 23.068 -0.973 4.080 2.582 1.107 H5 DU4 32 DU4 H6 H6 H 0 1 N N N 15.473 21.132 0.175 2.594 0.657 1.304 H6 DU4 33 DU4 "H1'" "H1'" H 0 1 N N N 18.947 20.942 1.057 2.643 -2.125 -1.150 "H1'" DU4 34 DU4 H17 H17 H 0 1 N N N 17.180 17.569 -4.583 -3.437 -0.816 1.437 H17 DU4 35 DU4 H19 H19 H 0 1 N N N 18.077 16.410 -6.417 -3.633 1.081 2.789 H19 DU4 36 DU4 "H2'" "H2'" H 0 1 N N N 17.886 19.290 2.167 3.113 -3.265 0.783 "H2'" DU4 37 DU4 "H2'A" "H2'A" H 0 0 N N N 16.485 20.316 1.822 3.593 -1.735 1.581 "H2'A" DU4 38 DU4 H20 H20 H 0 1 N N N 19.893 15.881 -8.015 -2.814 3.299 3.477 H20 DU4 39 DU4 H21 H21 H 0 1 N N N 22.034 17.125 -7.909 -1.164 4.487 2.088 H21 DU4 40 DU4 H22 H22 H 0 1 N N N 22.355 18.887 -6.205 -0.332 3.457 0.012 H22 DU4 41 DU4 H23 H23 H 0 1 N N N 20.542 19.411 -4.600 -1.145 1.235 -0.671 H23 DU4 42 DU4 H25 H25 H 0 1 N N N 16.160 19.062 -6.156 -5.631 -0.602 0.677 H25 DU4 43 DU4 H26 H26 H 0 1 N N N 15.376 21.354 -6.658 -7.234 -0.347 -1.174 H26 DU4 44 DU4 H27 H27 H 0 1 N N N 16.335 23.281 -5.432 -6.429 0.221 -3.431 H27 DU4 45 DU4 H28 H28 H 0 1 N N N 18.108 22.916 -3.746 -4.021 0.535 -3.836 H28 DU4 46 DU4 H29 H29 H 0 1 N N N 18.901 20.627 -3.249 -2.418 0.289 -1.982 H29 DU4 47 DU4 "H3'" "H3'" H 0 1 N N N 15.748 18.912 -0.002 1.464 -1.424 2.523 "H3'" DU4 48 DU4 "HO3'" "HO3'" H 0 0 N N N 16.193 16.763 0.610 1.891 -3.748 3.049 "HO3'" DU4 49 DU4 "H4'" "H4'" H 0 1 N N N 18.458 17.624 -0.296 0.210 -2.865 0.119 "H4'" DU4 50 DU4 H41 H41 H 0 1 N N N 19.177 16.384 -1.800 -3.032 -2.336 -1.089 H41 DU4 51 DU4 H41A H41A H 0 0 N N N 18.135 15.861 -3.167 -1.427 -3.022 -0.739 H41A DU4 52 DU4 H41B H41B H 0 0 N N N 19.804 16.447 -3.483 -2.690 -3.031 0.514 H41B DU4 53 DU4 "H5'" "H5'" H 0 1 N N N 16.730 17.135 -1.981 -1.219 -1.929 2.012 "H5'" DU4 54 DU4 "H5'A" "H5'A" H 0 0 N N N 16.596 18.883 -2.383 -0.572 -0.317 1.623 "H5'A" DU4 55 # 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 DU4 N1 C2 SING N N 1 DU4 N1 C6 SING N N 2 DU4 N1 "C1'" SING N N 3 DU4 C2 O2 DOUB N N 4 DU4 C2 N3 SING N N 5 DU4 N3 C4 SING N N 6 DU4 C4 O4 DOUB N N 7 DU4 C4 C5 SING N N 8 DU4 C5 C6 DOUB N N 9 DU4 "C1'" "C2'" SING N N 10 DU4 "C1'" "O4'" SING N N 11 DU4 C17 C18 SING N N 12 DU4 C17 C24 SING N N 13 DU4 C17 "N5'" SING N N 14 DU4 C18 C19 DOUB Y N 15 DU4 C18 C23 SING Y N 16 DU4 C19 C20 SING Y N 17 DU4 "C2'" "C3'" SING N N 18 DU4 C20 C21 DOUB Y N 19 DU4 C21 C22 SING Y N 20 DU4 C22 C23 DOUB Y N 21 DU4 C24 C25 DOUB Y N 22 DU4 C24 C29 SING Y N 23 DU4 C25 C26 SING Y N 24 DU4 C26 C27 DOUB Y N 25 DU4 C27 C28 SING Y N 26 DU4 C28 C29 DOUB Y N 27 DU4 "C3'" "O3'" SING N N 28 DU4 "C3'" "C4'" SING N N 29 DU4 "C4'" "O4'" SING N N 30 DU4 "C4'" "C5'" SING N N 31 DU4 C41 "N5'" SING N N 32 DU4 "C5'" "N5'" SING N N 33 DU4 N3 HN3 SING N N 34 DU4 C5 H5 SING N N 35 DU4 C6 H6 SING N N 36 DU4 "C1'" "H1'" SING N N 37 DU4 C17 H17 SING N N 38 DU4 C19 H19 SING N N 39 DU4 "C2'" "H2'" SING N N 40 DU4 "C2'" "H2'A" SING N N 41 DU4 C20 H20 SING N N 42 DU4 C21 H21 SING N N 43 DU4 C22 H22 SING N N 44 DU4 C23 H23 SING N N 45 DU4 C25 H25 SING N N 46 DU4 C26 H26 SING N N 47 DU4 C27 H27 SING N N 48 DU4 C28 H28 SING N N 49 DU4 C29 H29 SING N N 50 DU4 "C3'" "H3'" SING N N 51 DU4 "O3'" "HO3'" SING N N 52 DU4 "C4'" "H4'" SING N N 53 DU4 C41 H41 SING N N 54 DU4 C41 H41A SING N N 55 DU4 C41 H41B SING N N 56 DU4 "C5'" "H5'" SING N N 57 DU4 "C5'" "H5'A" SING N N 58 # 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 DU4 SMILES ACDLabs 12.01 "O=C1NC(=O)N(C=C1)C2OC(C(O)C2)CN(C(c3ccccc3)c4ccccc4)C" DU4 InChI InChI 1.03 "InChI=1S/C23H25N3O4/c1-25(22(16-8-4-2-5-9-16)17-10-6-3-7-11-17)15-19-18(27)14-21(30-19)26-13-12-20(28)24-23(26)29/h2-13,18-19,21-22,27H,14-15H2,1H3,(H,24,28,29)/t18-,19+,21+/m0/s1" DU4 InChIKey InChI 1.03 GMULPQZINUAVEX-QKNQBKEWSA-N DU4 SMILES_CANONICAL CACTVS 3.370 "CN(C[C@H]1O[C@H](C[C@@H]1O)N2C=CC(=O)NC2=O)C(c3ccccc3)c4ccccc4" DU4 SMILES CACTVS 3.370 "CN(C[CH]1O[CH](C[CH]1O)N2C=CC(=O)NC2=O)C(c3ccccc3)c4ccccc4" DU4 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "C[N@](C[C@@H]1[C@H](C[C@@H](O1)N2C=CC(=O)NC2=O)O)C(c3ccccc3)c4ccccc4" DU4 SMILES "OpenEye OEToolkits" 1.7.2 "CN(CC1C(CC(O1)N2C=CC(=O)NC2=O)O)C(c3ccccc3)c4ccccc4" # 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 DU4 "SYSTEMATIC NAME" ACDLabs 12.01 "2',5'-dideoxy-5'-[(diphenylmethyl)(methyl)amino]uridine" DU4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "1-[(2R,4S,5R)-5-[[(diphenylmethyl)-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 DU4 "Create component" 2011-11-10 PDBJ DU4 "Initial release" 2012-08-24 RCSB #