data_D3Y # _chem_comp.id D3Y _chem_comp.name "3'-deoxy-3'-(D-tyrosylamino)adenosine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C19 H23 N7 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-11-06 _chem_comp.pdbx_modified_date 2013-12-13 _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 429.430 _chem_comp.one_letter_code ? _chem_comp.three_letter_code D3Y _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 4NBI _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 D3Y CD1 CD1 C 0 1 Y N N -33.745 1.861 -25.292 -5.105 1.911 0.302 CD1 D3Y 1 D3Y CE1 CE1 C 0 1 Y N N -34.979 1.659 -25.909 -6.284 2.501 0.715 CE1 D3Y 2 D3Y CZ CZ C 0 1 Y N N -35.287 0.414 -26.454 -7.501 1.983 0.296 CZ D3Y 3 D3Y OH OH O 0 1 N N N -36.497 0.220 -27.053 -8.662 2.562 0.701 OH D3Y 4 D3Y CE2 CE2 C 0 1 Y N N -34.359 -0.627 -26.380 -7.531 0.874 -0.536 CE2 D3Y 5 D3Y CD2 CD2 C 0 1 Y N N -33.123 -0.422 -25.765 -6.349 0.288 -0.947 CD2 D3Y 6 D3Y CG CG C 0 1 Y N N -32.810 0.826 -25.226 -5.137 0.805 -0.528 CG D3Y 7 D3Y CB CB C 0 1 N N N -31.454 1.028 -24.536 -3.850 0.168 -0.983 CB D3Y 8 D3Y CA CA C 0 1 N N R -30.507 2.055 -25.171 -3.436 -0.914 0.017 CA D3Y 9 D3Y N N N 0 1 N N N -30.342 1.777 -26.614 -4.430 -1.995 0.008 N D3Y 10 D3Y C C C 0 1 N N N -31.044 3.479 -24.948 -2.088 -1.466 -0.370 C D3Y 11 D3Y O O O 0 1 N N N -31.307 3.916 -23.821 -2.013 -2.519 -0.967 O D3Y 12 D3Y N8 N8 N 0 1 N N N -31.218 4.161 -26.072 -0.966 -0.791 -0.052 N8 D3Y 13 D3Y "C3'" "C3'" C 0 1 N N S -31.753 5.522 -26.093 0.344 -1.328 -0.429 "C3'" D3Y 14 D3Y "C2'" "C2'" C 0 1 N N R -30.624 6.543 -26.094 1.393 -0.196 -0.502 "C2'" D3Y 15 D3Y "O2'" "O2'" O 0 1 N N N -29.542 6.133 -26.944 0.794 1.063 -0.186 "O2'" D3Y 16 D3Y "C4'" "C4'" C 0 1 N N S -32.418 5.757 -27.449 0.879 -2.269 0.673 "C4'" D3Y 17 D3Y "C5'" "C5'" C 0 1 N N N -33.890 5.308 -27.505 0.604 -3.729 0.306 "C5'" D3Y 18 D3Y "O5'" "O5'" O 0 1 N N N -34.680 6.130 -26.648 1.002 -4.575 1.388 "O5'" D3Y 19 D3Y "O4'" "O4'" O 0 1 N N N -32.304 7.199 -27.683 2.301 -2.018 0.714 "O4'" D3Y 20 D3Y "C1'" "C1'" C 0 1 N N R -31.319 7.739 -26.744 2.440 -0.584 0.565 "C1'" D3Y 21 D3Y N9 N9 N 0 1 Y N N -32.074 8.656 -25.830 3.789 -0.247 0.106 N9 D3Y 22 D3Y C8 C8 C 0 1 Y N N -33.313 9.102 -26.069 4.637 -1.067 -0.577 C8 D3Y 23 D3Y N7 N7 N 0 1 Y N N -33.692 9.914 -25.089 5.753 -0.445 -0.826 N7 D3Y 24 D3Y C5 C5 C 0 1 Y N N -32.681 9.992 -24.212 5.691 0.811 -0.321 C5 D3Y 25 D3Y C4 C4 C 0 1 Y N N -31.646 9.193 -24.684 4.429 0.955 0.278 C4 D3Y 26 D3Y N3 N3 N 0 1 Y N N -30.501 9.093 -23.967 4.113 2.113 0.849 N3 D3Y 27 D3Y C2 C2 C 0 1 Y N N -30.362 9.753 -22.818 4.967 3.114 0.853 C2 D3Y 28 D3Y N1 N1 N 0 1 Y N N -31.337 10.520 -22.339 6.164 3.027 0.301 N1 D3Y 29 D3Y C6 C6 C 0 1 Y N N -32.505 10.668 -23.010 6.571 1.906 -0.287 C6 D3Y 30 D3Y N6 N6 N 0 1 N N N -33.484 11.437 -22.530 7.826 1.826 -0.865 N6 D3Y 31 D3Y H1 H1 H 0 1 N N N -33.511 2.824 -24.863 -4.157 2.316 0.623 H1 D3Y 32 D3Y H2 H2 H 0 1 N N N -35.695 2.466 -25.964 -6.258 3.364 1.363 H2 D3Y 33 D3Y H3 H3 H 0 1 N N N -37.002 1.024 -27.016 -9.016 2.200 1.525 H3 D3Y 34 D3Y H4 H4 H 0 1 N N N -34.598 -1.593 -26.800 -8.477 0.469 -0.863 H4 D3Y 35 D3Y H5 H5 H 0 1 N N N -32.409 -1.230 -25.706 -6.372 -0.576 -1.595 H5 D3Y 36 D3Y H6 H6 H 0 1 N N N -31.650 1.349 -23.502 -3.994 -0.282 -1.965 H6 D3Y 37 D3Y H7 H7 H 0 1 N N N -30.936 0.057 -24.527 -3.069 0.926 -1.041 H7 D3Y 38 D3Y H8 H8 H 0 1 N N N -29.528 1.974 -24.676 -3.378 -0.482 1.016 H8 D3Y 39 D3Y H9 H9 H 0 1 N N N -29.993 0.848 -26.737 -5.328 -1.664 0.326 H9 D3Y 40 D3Y H10 H10 H 0 1 N N N -31.226 1.864 -27.073 -4.502 -2.412 -0.908 H10 D3Y 41 D3Y H12 H12 H 0 1 N N N -30.974 3.728 -26.939 -1.026 0.051 0.425 H12 D3Y 42 D3Y H13 H13 H 0 1 N N N -32.457 5.705 -25.268 0.281 -1.853 -1.382 H13 D3Y 43 D3Y H14 H14 H 0 1 N N N -30.296 6.779 -25.071 1.850 -0.162 -1.491 H14 D3Y 44 D3Y H15 H15 H 0 1 N N N -29.098 5.389 -26.555 1.408 1.809 -0.217 H15 D3Y 45 D3Y H16 H16 H 0 1 N N N -31.854 5.211 -28.220 0.424 -2.028 1.633 H16 D3Y 46 D3Y H17 H17 H 0 1 N N N -34.259 5.396 -28.537 -0.460 -3.861 0.114 H17 D3Y 47 D3Y H18 H18 H 0 1 N N N -33.965 4.261 -27.177 1.171 -3.992 -0.587 H18 D3Y 48 D3Y H19 H19 H 0 1 N N N -35.587 5.849 -26.686 0.856 -5.516 1.224 H19 D3Y 49 D3Y H20 H20 H 0 1 N N N -30.568 8.323 -27.296 2.223 -0.082 1.508 H20 D3Y 50 D3Y H21 H21 H 0 1 N N N -33.913 8.841 -26.928 4.416 -2.083 -0.868 H21 D3Y 51 D3Y H22 H22 H 0 1 N N N -29.439 9.663 -22.265 4.679 4.041 1.326 H22 D3Y 52 D3Y H23 H23 H 0 1 N N N -33.198 11.837 -21.660 8.107 1.005 -1.300 H23 D3Y 53 D3Y H24 H24 H 0 1 N N N -33.684 12.167 -23.183 8.424 2.589 -0.835 H24 D3Y 54 # 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 D3Y "O4'" "C4'" SING N N 1 D3Y "O4'" "C1'" SING N N 2 D3Y "C5'" "C4'" SING N N 3 D3Y "C5'" "O5'" SING N N 4 D3Y "C4'" "C3'" SING N N 5 D3Y OH CZ SING N N 6 D3Y "O2'" "C2'" SING N N 7 D3Y "C1'" "C2'" SING N N 8 D3Y "C1'" N9 SING N N 9 D3Y N CA SING N N 10 D3Y CZ CE2 DOUB Y N 11 D3Y CZ CE1 SING Y N 12 D3Y CE2 CD2 SING Y N 13 D3Y "C2'" "C3'" SING N N 14 D3Y "C3'" N8 SING N N 15 D3Y N8 C SING N N 16 D3Y C8 N9 SING Y N 17 D3Y C8 N7 DOUB Y N 18 D3Y CE1 CD1 DOUB Y N 19 D3Y N9 C4 SING Y N 20 D3Y CD2 CG DOUB Y N 21 D3Y CD1 CG SING Y N 22 D3Y CG CB SING N N 23 D3Y CA C SING N N 24 D3Y CA CB SING N N 25 D3Y N7 C5 SING Y N 26 D3Y C O DOUB N N 27 D3Y C4 C5 DOUB Y N 28 D3Y C4 N3 SING Y N 29 D3Y C5 C6 SING Y N 30 D3Y N3 C2 DOUB Y N 31 D3Y C6 N6 SING N N 32 D3Y C6 N1 DOUB Y N 33 D3Y C2 N1 SING Y N 34 D3Y CD1 H1 SING N N 35 D3Y CE1 H2 SING N N 36 D3Y OH H3 SING N N 37 D3Y CE2 H4 SING N N 38 D3Y CD2 H5 SING N N 39 D3Y CB H6 SING N N 40 D3Y CB H7 SING N N 41 D3Y CA H8 SING N N 42 D3Y N H9 SING N N 43 D3Y N H10 SING N N 44 D3Y N8 H12 SING N N 45 D3Y "C3'" H13 SING N N 46 D3Y "C2'" H14 SING N N 47 D3Y "O2'" H15 SING N N 48 D3Y "C4'" H16 SING N N 49 D3Y "C5'" H17 SING N N 50 D3Y "C5'" H18 SING N N 51 D3Y "O5'" H19 SING N N 52 D3Y "C1'" H20 SING N N 53 D3Y C8 H21 SING N N 54 D3Y C2 H22 SING N N 55 D3Y N6 H23 SING N N 56 D3Y N6 H24 SING N N 57 # 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 D3Y SMILES ACDLabs 12.01 "O=C(NC3C(OC(n2cnc1c(ncnc12)N)C3O)CO)C(N)Cc4ccc(O)cc4" D3Y InChI InChI 1.03 "InChI=1S/C19H23N7O5/c20-11(5-9-1-3-10(28)4-2-9)18(30)25-13-12(6-27)31-19(15(13)29)26-8-24-14-16(21)22-7-23-17(14)26/h1-4,7-8,11-13,15,19,27-29H,5-6,20H2,(H,25,30)(H2,21,22,23)/t11-,12-,13-,15-,19-/m1/s1" D3Y InChIKey InChI 1.03 GCCJIIJWAJOTAC-XDJZACDYSA-N D3Y SMILES_CANONICAL CACTVS 3.385 "N[C@H](Cc1ccc(O)cc1)C(=O)N[C@H]2[C@@H](O)[C@@H](O[C@@H]2CO)n3cnc4c(N)ncnc34" D3Y SMILES CACTVS 3.385 "N[CH](Cc1ccc(O)cc1)C(=O)N[CH]2[CH](O)[CH](O[CH]2CO)n3cnc4c(N)ncnc34" D3Y SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1cc(ccc1C[C@H](C(=O)N[C@@H]2[C@H](O[C@H]([C@@H]2O)n3cnc4c3ncnc4N)CO)N)O" D3Y SMILES "OpenEye OEToolkits" 1.7.6 "c1cc(ccc1CC(C(=O)NC2C(OC(C2O)n3cnc4c3ncnc4N)CO)N)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 D3Y "SYSTEMATIC NAME" ACDLabs 12.01 "3'-deoxy-3'-(D-tyrosylamino)adenosine" D3Y "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2R)-N-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-2-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl]-2-azanyl-3-(4-hydroxyphenyl)propanamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site D3Y "Create component" 2013-11-06 PDBJ D3Y "Initial release" 2013-12-18 RCSB #