data_DU3 # _chem_comp.id DU3 _chem_comp.name "2',5'-dideoxy-5'-[(diphenylmethyl)amino]uridine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C22 H23 N3 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2011-08-18 _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 393.436 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DU3 _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 3T64 _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 DU3 N1 N1 N 0 1 N N N 17.694 21.937 -0.113 3.562 -0.382 -0.309 N1 DU3 1 DU3 C2 C2 C 0 1 N N N 18.513 22.893 -0.745 4.486 -0.350 -1.287 C2 DU3 2 DU3 O2 O2 O 0 1 N N N 19.742 22.821 -0.751 4.502 -1.230 -2.125 O2 DU3 3 DU3 N3 N3 N 0 1 N N N 17.915 23.963 -1.403 5.392 0.643 -1.350 N3 DU3 4 DU3 C4 C4 C 0 1 N N N 16.504 24.056 -1.447 5.387 1.627 -0.428 C4 DU3 5 DU3 O4 O4 O 0 1 N N N 16.005 25.020 -2.057 6.206 2.527 -0.484 O4 DU3 6 DU3 C5 C5 C 0 1 N N N 15.700 23.098 -0.817 4.420 1.605 0.606 C5 DU3 7 DU3 C6 C6 C 0 1 N N N 16.300 22.025 -0.156 3.520 0.600 0.642 C6 DU3 8 DU3 "C1'" "C1'" C 0 1 N N R 18.356 20.790 0.567 2.589 -1.477 -0.266 "C1'" DU3 9 DU3 C17 C17 C 0 1 N N N 18.179 18.371 -4.125 -2.917 -0.219 0.606 C17 DU3 10 DU3 C18 C18 C 0 1 Y N N 19.309 17.880 -5.049 -2.676 1.268 0.658 C18 DU3 11 DU3 C19 C19 C 0 1 Y N N 19.238 16.580 -5.538 -3.145 2.008 1.727 C19 DU3 12 DU3 "C2'" "C2'" C 0 1 N N N 17.452 20.039 1.548 2.808 -2.324 1.002 "C2'" DU3 13 DU3 C20 C20 C 0 1 Y N N 20.235 16.102 -6.377 -2.924 3.371 1.774 C20 DU3 14 DU3 C21 C21 C 0 1 Y N N 21.301 16.917 -6.732 -2.233 3.995 0.752 C21 DU3 15 DU3 C22 C22 C 0 1 Y N N 21.368 18.214 -6.250 -1.763 3.255 -0.317 C22 DU3 16 DU3 C23 C23 C 0 1 Y N N 20.374 18.700 -5.406 -1.979 1.890 -0.361 C23 DU3 17 DU3 C24 C24 C 0 1 Y N N 17.735 19.801 -4.479 -4.081 -0.507 -0.307 C24 DU3 18 DU3 C25 C25 C 0 1 Y N N 16.752 19.926 -5.469 -3.896 -0.530 -1.676 C25 DU3 19 DU3 C26 C26 C 0 1 Y N N 16.293 21.191 -5.825 -4.964 -0.794 -2.514 C26 DU3 20 DU3 C27 C27 C 0 1 Y N N 16.765 22.332 -5.185 -6.216 -1.036 -1.982 C27 DU3 21 DU3 C28 C28 C 0 1 Y N N 17.752 22.212 -4.202 -6.401 -1.014 -0.612 C28 DU3 22 DU3 C29 C29 C 0 1 Y N N 18.223 20.946 -3.838 -5.333 -0.754 0.226 C29 DU3 23 DU3 "C3'" "C3'" C 0 1 N N S 16.857 18.937 0.681 1.453 -2.248 1.747 "C3'" DU3 24 DU3 "O3'" "O3'" O 0 1 N N N 16.721 17.778 1.492 1.103 -3.519 2.299 "O3'" DU3 25 DU3 "C4'" "C4'" C 0 1 N N R 17.921 18.684 -0.381 0.478 -1.852 0.610 "C4'" DU3 26 DU3 "O4'" "O4'" O 0 1 N N N 18.675 19.915 -0.539 1.256 -0.942 -0.199 "O4'" DU3 27 DU3 "C5'" "C5'" C 0 1 N N N 17.366 18.288 -1.784 -0.757 -1.150 1.179 "C5'" DU3 28 DU3 "N5'" "N5'" N 0 1 N N N 18.524 18.201 -2.695 -1.716 -0.893 0.096 "N5'" DU3 29 DU3 H5 H5 H 0 1 N N N 14.624 23.189 -0.842 4.401 2.385 1.354 H5 DU3 30 DU3 H6 H6 H 0 1 N N N 15.692 21.269 0.318 2.774 0.567 1.424 H6 DU3 31 DU3 "H1'" "H1'" H 0 1 N N N 19.208 21.130 1.174 2.695 -2.102 -1.153 "H1'" DU3 32 DU3 H17 H17 H 0 1 N N N 17.302 17.730 -4.300 -3.142 -0.586 1.608 H17 DU3 33 DU3 H19 H19 H 0 1 N N N 18.409 15.944 -5.265 -3.686 1.520 2.525 H19 DU3 34 DU3 "H2'" "H2'" H 0 1 N N N 18.021 19.629 2.395 3.040 -3.355 0.737 "H2'" DU3 35 DU3 "H2'A" "H2'A" H 0 0 N N N 16.674 20.693 1.968 3.605 -1.898 1.612 "H2'A" DU3 36 DU3 H20 H20 H 0 1 N N N 20.181 15.092 -6.755 -3.291 3.950 2.609 H20 DU3 37 DU3 H21 H21 H 0 1 N N N 22.077 16.541 -7.383 -2.061 5.061 0.788 H21 DU3 38 DU3 H22 H22 H 0 1 N N N 22.195 18.850 -6.530 -1.223 3.742 -1.115 H22 DU3 39 DU3 H23 H23 H 0 1 N N N 20.429 19.711 -5.029 -1.612 1.312 -1.196 H23 DU3 40 DU3 H25 H25 H 0 1 N N N 16.353 19.047 -5.953 -2.917 -0.341 -2.092 H25 DU3 41 DU3 H26 H26 H 0 1 N N N 15.559 21.288 -6.611 -4.819 -0.811 -3.584 H26 DU3 42 DU3 H27 H27 H 0 1 N N N 16.372 23.304 -5.445 -7.051 -1.241 -2.636 H27 DU3 43 DU3 H28 H28 H 0 1 N N N 18.150 23.095 -3.725 -7.380 -1.202 -0.196 H28 DU3 44 DU3 H29 H29 H 0 1 N N N 18.966 20.852 -3.060 -5.477 -0.741 1.296 H29 DU3 45 DU3 "H3'" "H3'" H 0 1 N N N 15.880 19.191 0.245 1.478 -1.483 2.523 "H3'" DU3 46 DU3 "HO3'" "HO3'" H 0 0 N N N 16.351 17.071 0.976 1.734 -3.852 2.952 "HO3'" DU3 47 DU3 "H4'" "H4'" H 0 1 N N N 18.521 17.831 -0.031 0.188 -2.728 0.030 "H4'" DU3 48 DU3 "H5'" "H5'" H 0 1 N N N 16.848 17.319 -1.731 -1.221 -1.786 1.932 "H5'" DU3 49 DU3 "H5'A" "H5'A" H 0 0 N N N 16.654 19.047 -2.142 -0.461 -0.205 1.634 "H5'A" DU3 50 DU3 "HN5'" "HN5'" H 0 0 N N N 18.938 17.298 -2.582 -1.957 -1.747 -0.384 "HN5'" DU3 51 DU3 HN3 HN3 H 0 1 N N N 18.479 24.662 -1.842 6.051 0.651 -2.061 HN3 DU3 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 DU3 C2 N1 SING N N 1 DU3 C6 N1 SING N N 2 DU3 N1 "C1'" SING N N 3 DU3 N3 C2 SING N N 4 DU3 O2 C2 DOUB N N 5 DU3 C4 N3 SING N N 6 DU3 O4 C4 DOUB N N 7 DU3 C4 C5 SING N N 8 DU3 C5 C6 DOUB N N 9 DU3 C5 H5 SING N N 10 DU3 C6 H6 SING N N 11 DU3 "O4'" "C1'" SING N N 12 DU3 "C1'" "C2'" SING N N 13 DU3 "C1'" "H1'" SING N N 14 DU3 C18 C17 SING N N 15 DU3 C24 C17 SING N N 16 DU3 C17 "N5'" SING N N 17 DU3 C17 H17 SING N N 18 DU3 C19 C18 DOUB Y N 19 DU3 C23 C18 SING Y N 20 DU3 C20 C19 SING Y N 21 DU3 C19 H19 SING N N 22 DU3 "C3'" "C2'" SING N N 23 DU3 "C2'" "H2'" SING N N 24 DU3 "C2'" "H2'A" SING N N 25 DU3 C21 C20 DOUB Y N 26 DU3 C20 H20 SING N N 27 DU3 C21 C22 SING Y N 28 DU3 C21 H21 SING N N 29 DU3 C22 C23 DOUB Y N 30 DU3 C22 H22 SING N N 31 DU3 C23 H23 SING N N 32 DU3 C25 C24 DOUB Y N 33 DU3 C24 C29 SING Y N 34 DU3 C26 C25 SING Y N 35 DU3 C25 H25 SING N N 36 DU3 C26 C27 DOUB Y N 37 DU3 C26 H26 SING N N 38 DU3 C27 C28 SING Y N 39 DU3 C27 H27 SING N N 40 DU3 C28 C29 DOUB Y N 41 DU3 C28 H28 SING N N 42 DU3 C29 H29 SING N N 43 DU3 "C4'" "C3'" SING N N 44 DU3 "C3'" "O3'" SING N N 45 DU3 "C3'" "H3'" SING N N 46 DU3 "O3'" "HO3'" SING N N 47 DU3 "C5'" "C4'" SING N N 48 DU3 "O4'" "C4'" SING N N 49 DU3 "C4'" "H4'" SING N N 50 DU3 "N5'" "C5'" SING N N 51 DU3 "C5'" "H5'" SING N N 52 DU3 "C5'" "H5'A" SING N N 53 DU3 "N5'" "HN5'" SING N N 54 DU3 N3 HN3 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 DU3 SMILES ACDLabs 12.01 "O=C1NC(=O)N(C=C1)C2OC(C(O)C2)CNC(c3ccccc3)c4ccccc4" DU3 InChI InChI 1.03 "InChI=1S/C22H23N3O4/c26-17-13-20(25-12-11-19(27)24-22(25)28)29-18(17)14-23-21(15-7-3-1-4-8-15)16-9-5-2-6-10-16/h1-12,17-18,20-21,23,26H,13-14H2,(H,24,27,28)/t17-,18+,20+/m0/s1" DU3 InChIKey InChI 1.03 JJVBLAPDVHVENR-NLWGTHIKSA-N DU3 SMILES_CANONICAL CACTVS 3.370 "O[C@H]1C[C@@H](O[C@@H]1CNC(c2ccccc2)c3ccccc3)N4C=CC(=O)NC4=O" DU3 SMILES CACTVS 3.370 "O[CH]1C[CH](O[CH]1CNC(c2ccccc2)c3ccccc3)N4C=CC(=O)NC4=O" DU3 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "c1ccc(cc1)C(c2ccccc2)NC[C@@H]3[C@H](C[C@@H](O3)N4C=CC(=O)NC4=O)O" DU3 SMILES "OpenEye OEToolkits" 1.7.2 "c1ccc(cc1)C(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 DU3 "SYSTEMATIC NAME" ACDLabs 12.01 "2',5'-dideoxy-5'-[(diphenylmethyl)amino]uridine" DU3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "1-[(2R,4S,5R)-5-[[(diphenylmethyl)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 DU3 "Create component" 2011-08-18 RCSB DU3 "Initial release" 2012-08-24 RCSB #