data_IU # _chem_comp.id IU _chem_comp.name "5-IODOURIDINE-5'-MONOPHOSPHATE" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H12 I N2 O9 P" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2005-05-31 _chem_comp.pdbx_modified_date 2024-09-27 _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 450.078 _chem_comp.one_letter_code U _chem_comp.three_letter_code IU _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1YVP _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm Y # 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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 IU P P P 0 1 N N N N N N 26.239 13.077 30.650 2.787 0.324 -4.407 P IU 1 IU OP1 O1P O 0 1 N N N N N N 25.263 13.309 31.752 3.659 1.172 -5.286 OP1 IU 2 IU OP2 O2P O 0 1 N N N N N N 26.533 14.185 29.699 1.198 0.588 -4.548 OP2 IU 3 IU OP3 O3P O 0 1 N Y N N N N ? ? ? 2.921 -1.270 -4.647 OP3 IU 4 IU "O5'" O5* O 0 1 N N N N N N 27.634 12.655 31.285 3.063 0.476 -2.819 "O5'" IU 5 IU "C5'" C5* C 0 1 N N N N N N 27.750 11.622 32.254 2.282 -0.292 -1.921 "C5'" IU 6 IU "C4'" C4* C 0 1 N N R N N N 29.179 11.566 32.717 2.725 0.023 -0.498 "C4'" IU 7 IU "O4'" O4* O 0 1 N N N N N N 29.959 11.358 31.541 2.470 1.422 -0.246 "O4'" IU 8 IU "C3'" C3* C 0 1 N N S N N N 29.652 12.870 33.350 1.940 -0.742 0.560 "C3'" IU 9 IU "O3'" O3* O 0 1 N N N N N N 29.830 12.574 34.743 2.742 -0.809 1.739 "O3'" IU 10 IU "C2'" C2* C 0 1 N N R N N N 30.960 13.231 32.633 0.748 0.163 0.786 "C2'" IU 11 IU "O2'" O2* O 0 1 N N N N N N 32.108 13.397 33.441 0.137 -0.058 2.041 "O2'" IU 12 IU "C1'" C1* C 0 1 N N R N N N 31.152 12.076 31.645 1.373 1.543 0.675 "C1'" IU 13 IU N1 N1 N 0 1 N N N N N N 31.592 12.414 30.294 0.452 2.524 0.177 N1 IU 14 IU C2 C2 C 0 1 N N N N N N 32.933 12.277 30.005 -0.299 3.336 1.055 C2 IU 15 IU O2 O2 O 0 1 N N N N N N 33.756 11.872 30.814 -0.225 3.267 2.283 O2 IU 16 IU N3 N3 N 0 1 N N N N N N 33.274 12.606 28.728 -1.157 4.249 0.432 N3 IU 17 IU C4 C4 C 0 1 N N N N N N 32.417 13.039 27.741 -1.340 4.432 -0.932 C4 IU 18 IU O4 O4 O 0 1 N N N N N N 32.858 13.272 26.622 -2.119 5.260 -1.396 O4 IU 19 IU C5 C5 C 0 1 N N N N N N 31.051 13.148 28.140 -0.515 3.539 -1.790 C5 IU 20 IU C6 C6 C 0 1 N N N N N N 30.702 12.835 29.365 0.309 2.664 -1.200 C6 IU 21 IU I5 I5 I 0 1 N N N N N N 29.640 13.991 26.855 -0.668 3.682 -3.827 I5 IU 22 IU HOP2 2HOP H 0 0 N N N N N N 27.155 14.037 28.996 0.799 0.616 -5.443 HOP2 IU 23 IU HOP3 3HOP H 0 0 N N N N N N 0.622 -0.147 -0.702 2.886 -1.617 -5.563 HOP3 IU 24 IU "H5'" 1H5* H 0 1 N N N N N N 27.030 11.741 33.097 1.229 -0.035 -2.051 "H5'" IU 25 IU "H5''" 2H5* H 0 0 N N N N N N 27.381 10.638 31.879 2.428 -1.352 -2.133 "H5''" IU 26 IU "H4'" H4* H 0 1 N N N N N N 29.279 10.765 33.486 3.804 -0.139 -0.410 "H4'" IU 27 IU "H3'" H3* H 0 1 N N N N N N 28.954 13.735 33.257 1.675 -1.764 0.277 "H3'" IU 28 IU "HO3'" H3T H 0 0 N Y N N N N 30.124 13.386 35.137 3.447 -0.153 1.628 "HO3'" IU 29 IU "H2'" H2* H 0 1 N N N N N N 30.861 14.243 32.175 -0.000 0.004 -0.000 "H2'" IU 30 IU "HO2'" 2HO* H 0 0 N N N N N N 32.917 13.620 32.997 -0.494 0.669 2.185 "HO2'" IU 31 IU "H1'" H1* H 0 1 N N N N N N 31.993 11.491 32.084 1.754 1.910 1.633 "H1'" IU 32 IU H3 H3 H 0 1 N N N N N N 34.261 12.520 28.488 -1.707 4.844 1.046 H3 IU 33 IU H6 H6 H 0 1 N N N N N N 29.633 12.928 29.620 0.931 1.991 -1.783 H6 IU 34 # 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 IU P OP1 DOUB N N 1 IU P OP2 SING N N 2 IU P OP3 SING N N 3 IU P "O5'" SING N N 4 IU OP2 HOP2 SING N N 5 IU OP3 HOP3 SING N N 6 IU "O5'" "C5'" SING N N 7 IU "C5'" "C4'" SING N N 8 IU "C5'" "H5'" SING N N 9 IU "C5'" "H5''" SING N N 10 IU "C4'" "O4'" SING N N 11 IU "C4'" "C3'" SING N N 12 IU "C4'" "H4'" SING N N 13 IU "O4'" "C1'" SING N N 14 IU "C3'" "O3'" SING N N 15 IU "C3'" "C2'" SING N N 16 IU "C3'" "H3'" SING N N 17 IU "O3'" "HO3'" SING N N 18 IU "C2'" "O2'" SING N N 19 IU "C2'" "C1'" SING N N 20 IU "C2'" "H2'" SING N N 21 IU "O2'" "HO2'" SING N N 22 IU "C1'" N1 SING N N 23 IU "C1'" "H1'" SING N N 24 IU N1 C2 SING N N 25 IU N1 C6 SING N N 26 IU C2 O2 DOUB N N 27 IU C2 N3 SING N N 28 IU N3 C4 SING N N 29 IU N3 H3 SING N N 30 IU C4 O4 DOUB N N 31 IU C4 C5 SING N N 32 IU C5 C6 DOUB N N 33 IU C5 I5 SING N N 34 IU C6 H6 SING N N 35 # 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 IU SMILES ACDLabs 10.04 "IC=1C(=O)NC(=O)N(C=1)C2OC(C(O)C2O)COP(=O)(O)O" IU SMILES_CANONICAL CACTVS 3.341 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(I)C(=O)NC2=O" IU SMILES CACTVS 3.341 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=C(I)C(=O)NC2=O" IU SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=C(C(=O)NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)I" IU SMILES "OpenEye OEToolkits" 1.5.0 "C1=C(C(=O)NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O)I" IU InChI InChI 1.03 "InChI=1S/C9H12IN2O9P/c10-3-1-12(9(16)11-7(3)15)8-6(14)5(13)4(21-8)2-20-22(17,18)19/h1,4-6,8,13-14H,2H2,(H,11,15,16)(H2,17,18,19)/t4-,5-,6-,8-/m1/s1" IU InChIKey InChI 1.03 HXJLWCWPONZYNP-UAKXSSHOSA-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 IU "SYSTEMATIC NAME" ACDLabs 10.04 ;5-iodouridine 5'-(dihydrogen phosphate) ; IU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-3,4-dihydroxy-5-(5-iodo-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site IU "Create component" 2005-05-31 RCSB IU "Modify descriptor" 2011-06-04 RCSB IU "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id IU _pdbx_chem_comp_pcm.modified_residue_id TYR _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom P _pdbx_chem_comp_pcm.modified_residue_id_linking_atom OH _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #