data_3AU # _chem_comp.id 3AU _chem_comp.name "3-[(3S)-3-amino-3-carboxypropyl]uridine 5'-(dihydrogen phosphate)" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H20 N3 O11 P" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2011-01-18 _chem_comp.pdbx_modified_date 2021-05-11 _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 425.285 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 3AU _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 3IZV _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 3AU P P P 0 1 N N N -0.125 -0.116 -0.035 5.480 -1.929 0.134 P 3AU 1 3AU N1 N1 N 0 1 N N N 5.652 -1.219 -2.784 -0.405 1.003 0.477 N1 3AU 2 3AU C2 C2 C 0 1 N N N 6.991 -1.466 -3.013 -1.682 1.024 0.053 C2 3AU 3 3AU O2 O2 O 0 1 N N N 7.846 -0.695 -2.508 -1.924 1.306 -1.105 O2 3AU 4 3AU N3 N3 N 0 1 N N N 7.418 -2.533 -3.780 -2.695 0.739 0.892 N3 3AU 5 3AU C4 C4 C 0 1 N N N 6.481 -3.379 -4.323 -2.444 0.425 2.179 C4 3AU 6 3AU O4 O4 O 0 1 N N N 6.792 -4.386 -5.006 -3.360 0.166 2.938 O4 3AU 7 3AU C5 C5 C 0 1 N N N 5.112 -3.151 -4.126 -1.105 0.398 2.639 C5 3AU 8 3AU C6 C6 C 0 1 N N N 4.725 -2.052 -3.352 -0.108 0.689 1.776 C6 3AU 9 3AU "C1'" "C1'" C 0 1 N N R 5.204 -0.074 -1.994 0.677 1.312 -0.461 "C1'" 3AU 10 3AU C10 C10 C 0 1 N N N 8.839 -2.789 -3.989 -4.076 0.770 0.405 C10 3AU 11 3AU C11 C11 C 0 1 N N N 9.411 -3.682 -2.853 -4.462 -0.613 -0.124 C11 3AU 12 3AU C12 C12 C 0 1 N N S 10.929 -4.000 -2.979 -5.905 -0.580 -0.633 C12 3AU 13 3AU C13 C13 C 0 1 N N N 11.382 -4.806 -1.852 -6.244 -1.906 -1.265 C13 3AU 14 3AU "C2'" "C2'" C 0 1 N N R 5.015 1.182 -2.868 1.406 2.614 -0.042 "C2'" 3AU 15 3AU "O2'" "O2'" O 0 1 N N N 6.253 1.817 -3.177 0.746 3.763 -0.578 "O2'" 3AU 16 3AU "C3'" "C3'" C 0 1 N N S 4.063 2.062 -2.038 2.800 2.427 -0.688 "C3'" 3AU 17 3AU "O3'" "O3'" O 0 1 N N N 4.753 3.105 -1.349 2.873 3.122 -1.934 "O3'" 3AU 18 3AU O30 O30 O 0 1 N N N 11.336 -6.027 -1.882 -6.877 -2.727 -0.644 O30 3AU 19 3AU O31 O31 O 0 1 N N N 11.785 -4.286 -0.817 -5.844 -2.174 -2.518 O31 3AU 20 3AU "C4'" "C4'" C 0 1 N N R 3.413 1.063 -1.042 2.911 0.906 -0.912 "C4'" 3AU 21 3AU "O4'" "O4'" O 0 1 N N N 3.924 -0.243 -1.359 1.712 0.309 -0.391 "O4'" 3AU 22 3AU N40 N40 N 0 1 N N N 11.223 -4.675 -4.255 -6.815 -0.327 0.492 N40 3AU 23 3AU "C5'" "C5'" C 0 1 N N N 1.866 1.058 -1.108 4.131 0.358 -0.169 "C5'" 3AU 24 3AU "O5'" "O5'" O 0 1 N N N 1.353 0.196 -0.220 4.293 -1.028 -0.476 "O5'" 3AU 25 3AU OP1 OP1 O 0 1 N N N -0.851 1.098 0.391 5.455 -1.844 1.611 OP1 3AU 26 3AU OP2 OP2 O 0 1 N N N -0.695 -0.618 -1.342 5.279 -3.460 -0.320 OP2 3AU 27 3AU H5 H5 H 0 1 N N N 4.374 -3.808 -4.561 -0.884 0.149 3.666 H5 3AU 28 3AU H6 H6 H 0 1 N N N 3.674 -1.856 -3.199 0.919 0.674 2.108 H6 3AU 29 3AU "H1'" "H1'" H 0 1 N N N 6.001 0.023 -1.242 0.290 1.398 -1.476 "H1'" 3AU 30 3AU H10 H10 H 0 1 N N N 8.973 -3.304 -4.952 -4.743 1.046 1.222 H10 3AU 31 3AU H10A H10A H 0 0 N N N 9.379 -1.831 -3.998 -4.162 1.503 -0.398 H10A 3AU 32 3AU H11 H11 H 0 1 N N N 9.256 -3.154 -1.901 -3.795 -0.889 -0.941 H11 3AU 33 3AU H11A H11A H 0 0 N N N 8.865 -4.637 -2.870 -4.376 -1.346 0.678 H11A 3AU 34 3AU H12 H12 H 0 1 N N N 11.478 -3.047 -2.965 -6.011 0.213 -1.372 H12 3AU 35 3AU "H2'" "H2'" H 0 1 N N N 4.599 0.956 -3.861 1.485 2.684 1.043 "H2'" 3AU 36 3AU "HO2'" "HO2'" H 0 0 N N N 6.091 2.583 -3.715 1.166 4.602 -0.344 "HO2'" 3AU 37 3AU "H3'" "H3'" H 0 1 N N N 3.327 2.584 -2.668 3.583 2.773 -0.013 "H3'" 3AU 38 3AU "HO3'" "HO3'" H 0 0 N N N 4.131 3.622 -0.851 2.750 4.079 -1.858 "HO3'" 3AU 39 3AU "H4'" "H4'" H 0 1 N N N 3.668 1.367 -0.016 2.998 0.694 -1.978 "H4'" 3AU 40 3AU HN40 HN40 H 0 0 N N N 12.202 -4.868 -4.312 -7.768 -0.236 0.173 HN40 3AU 41 3AU HN4A HN4A H 0 0 N N N 10.711 -5.532 -4.304 -6.735 -1.049 1.192 HN4A 3AU 42 3AU "H5'" "H5'" H 0 1 N N N 1.495 2.068 -0.882 5.022 0.905 -0.479 "H5'" 3AU 43 3AU "H5'A" "H5'A" H 0 0 N N N 1.552 0.760 -2.119 3.987 0.478 0.905 "H5'A" 3AU 44 3AU O11 O11 O 0 1 N N N -0.272 -1.193 1.015 6.897 -1.389 -0.410 O11 3AU 45 3AU H18 H18 H 0 1 N N N 12.002 -4.962 -0.186 -6.086 -3.037 -2.880 H18 3AU 46 3AU H19 H19 H 0 1 N N N -1.403 -0.048 -1.619 5.960 -4.061 0.013 H19 3AU 47 3AU H20 H20 H 0 1 N N N -0.802 -0.866 1.733 6.984 -1.416 -1.373 H20 3AU 48 # # 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 3AU P "O5'" SING N N 1 3AU P OP1 DOUB N N 2 3AU P OP2 SING N N 3 3AU N1 C2 SING N N 4 3AU N1 C6 SING N N 5 3AU N1 "C1'" SING N N 6 3AU C2 O2 DOUB N N 7 3AU C2 N3 SING N N 8 3AU N3 C4 SING N N 9 3AU N3 C10 SING N N 10 3AU C4 O4 DOUB N N 11 3AU C4 C5 SING N N 12 3AU C5 C6 DOUB N N 13 3AU C5 H5 SING N N 14 3AU C6 H6 SING N N 15 3AU "C1'" "C2'" SING N N 16 3AU "C1'" "O4'" SING N N 17 3AU "C1'" "H1'" SING N N 18 3AU C10 C11 SING N N 19 3AU C10 H10 SING N N 20 3AU C10 H10A SING N N 21 3AU C11 C12 SING N N 22 3AU C11 H11 SING N N 23 3AU C11 H11A SING N N 24 3AU C12 C13 SING N N 25 3AU C12 N40 SING N N 26 3AU C12 H12 SING N N 27 3AU C13 O30 DOUB N N 28 3AU C13 O31 SING N N 29 3AU "C2'" "O2'" SING N N 30 3AU "C2'" "C3'" SING N N 31 3AU "C2'" "H2'" SING N N 32 3AU "O2'" "HO2'" SING N N 33 3AU "C3'" "O3'" SING N N 34 3AU "C3'" "C4'" SING N N 35 3AU "C3'" "H3'" SING N N 36 3AU "O3'" "HO3'" SING N N 37 3AU "C4'" "O4'" SING N N 38 3AU "C4'" "C5'" SING N N 39 3AU "C4'" "H4'" SING N N 40 3AU N40 HN40 SING N N 41 3AU N40 HN4A SING N N 42 3AU "C5'" "O5'" SING N N 43 3AU "C5'" "H5'" SING N N 44 3AU "C5'" "H5'A" SING N N 45 3AU P O11 SING N N 46 3AU O31 H18 SING N N 47 3AU OP2 H19 SING N N 48 3AU O11 H20 SING N N 49 # # 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 3AU SMILES ACDLabs 12.01 "O=C(O)C(N)CCN1C(=O)C=CN(C1=O)C2OC(C(O)C2O)COP(=O)(O)O" 3AU SMILES_CANONICAL CACTVS 3.370 "N[C@@H](CCN1C(=O)C=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C1=O)C(O)=O" 3AU SMILES CACTVS 3.370 "N[CH](CCN1C(=O)C=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C1=O)C(O)=O" 3AU SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C1=CN(C(=O)N(C1=O)CC[C@@H](C(=O)O)N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O" 3AU SMILES "OpenEye OEToolkits" 1.7.0 "C1=CN(C(=O)N(C1=O)CCC(C(=O)O)N)C2C(C(C(O2)COP(=O)(O)O)O)O" 3AU InChI InChI 1.03 "InChI=1S/C13H20N3O11P/c14-6(12(20)21)1-3-15-8(17)2-4-16(13(15)22)11-10(19)9(18)7(27-11)5-26-28(23,24)25/h2,4,6-7,9-11,18-19H,1,3,5,14H2,(H,20,21)(H2,23,24,25)/t6-,7+,9+,10+,11+/m0/s1" 3AU InChIKey InChI 1.03 CJKRCYMKRHIIKR-CNYIRLTGSA-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 3AU "SYSTEMATIC NAME" ACDLabs 12.01 "3-[(3S)-3-amino-3-carboxypropyl]uridine 5'-(dihydrogen phosphate)" 3AU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "(2S)-2-azanyl-4-[3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(phosphonooxymethyl)oxolan-2-yl]-2,6-dioxo-pyrimidin-1-yl]butanoic acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 3AU "Create component" 2011-01-18 RCSB 3AU "Modify descriptor" 2011-06-04 RCSB 3AU "Modify synonyms" 2020-06-05 PDBE 3AU "Modify synonyms" 2021-05-11 RCSB ##