data_5IU # _chem_comp.id 5IU _chem_comp.name "5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H12 I N2 O8 P" _chem_comp.mon_nstd_parent_comp_id DU _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _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 5IT _chem_comp.formula_weight 434.078 _chem_comp.one_letter_code U _chem_comp.three_letter_code 5IU _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 3VTK _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 5IU N1 N1 N 0 1 N N N N N N 39.382 15.046 31.269 0.612 -0.291 0.632 N1 5IU 1 5IU C2 C2 C 0 1 N N N N N N 38.777 13.858 30.872 0.169 -1.553 0.490 C2 5IU 2 5IU N3 N3 N 0 1 N N N N N N 38.687 12.833 31.766 -0.417 -2.200 1.514 N3 5IU 3 5IU C4 C4 C 0 1 N N N N N N 39.147 12.911 33.064 -0.582 -1.585 2.702 C4 5IU 4 5IU C5 C5 C 0 1 N N N N N N 39.764 14.130 33.480 -0.126 -0.254 2.864 C5 5IU 5 5IU C6 C6 C 0 1 N N N N N N 39.886 15.192 32.534 0.464 0.369 1.822 C6 5IU 6 5IU O2 O2 O 0 1 N N N N N N 38.311 13.699 29.754 0.311 -2.122 -0.575 O2 5IU 7 5IU O4 O4 O 0 1 N N N N N N 39.008 11.923 33.825 -1.118 -2.167 3.627 O4 5IU 8 5IU I5 I5 I 0 1 N N N N N N 40.485 14.312 35.463 -0.365 0.734 4.696 I5 5IU 9 5IU "C1'" C1* C 0 1 N N R N N N 39.547 16.172 30.270 1.253 0.384 -0.498 "C1'" 5IU 10 5IU "C2'" C2* C 0 1 N N N N N N 38.556 17.322 30.416 2.515 -0.389 -0.942 "C2'" 5IU 11 5IU "C3'" C3* C 0 1 N N S N N N 39.413 18.498 30.000 2.516 -0.252 -2.481 "C3'" 5IU 12 5IU "C4'" C4* C 0 1 N N R N N N 40.712 18.204 30.667 1.256 0.585 -2.788 "C4'" 5IU 13 5IU "O3'" O3* O 0 1 N N N N N N 39.652 18.573 28.605 3.691 0.431 -2.921 "O3'" 5IU 14 5IU "O4'" O4* O 0 1 N N N N N N 40.832 16.761 30.600 0.386 0.370 -1.652 "O4'" 5IU 15 5IU "C5'" C5* C 0 1 N N N N N N 40.830 18.656 32.126 0.584 0.099 -4.073 "C5'" 5IU 16 5IU "O5'" O5* O 0 1 N N N N N N 41.039 20.088 32.202 -0.616 0.842 -4.294 "O5'" 5IU 17 5IU P P P 0 1 N N N N N N 40.226 21.046 33.254 -1.267 0.280 -5.655 P 5IU 18 5IU OP1 O1P O 0 1 N N N N N N 39.816 20.218 34.413 -1.562 -1.161 -5.503 OP1 5IU 19 5IU OP2 O2P O 0 1 N N N N N N 39.019 21.618 32.589 -2.631 1.077 -5.966 OP2 5IU 20 5IU OP3 O3P O 0 1 N Y N N N N 41.094 22.131 33.710 -0.233 0.491 -6.871 OP3 5IU 21 5IU HN3 HN3 H 0 1 N N N N N N 38.254 11.965 31.448 -0.727 -3.112 1.395 HN3 5IU 22 5IU H6 H6 H 0 1 N N N N N N 40.380 16.145 32.785 0.819 1.383 1.927 H6 5IU 23 5IU "H1'" H1* H 0 1 N N N N N N 39.415 15.740 29.250 1.511 1.409 -0.229 "H1'" 5IU 24 5IU "H2'" 1H2* H 0 1 N N N N N N 37.599 17.204 29.854 2.442 -1.437 -0.651 "H2'" 5IU 25 5IU "H2''" 2H2* H 0 0 N N N N N N 38.071 17.412 31.416 3.410 0.064 -0.517 "H2''" 5IU 26 5IU "H3'" H3* H 0 1 N N N N N N 38.918 19.459 30.272 2.447 -1.233 -2.951 "H3'" 5IU 27 5IU "H4'" H4* H 0 1 N N N N N N 41.518 18.773 30.148 1.515 1.641 -2.872 "H4'" 5IU 28 5IU "HO3'" *HO3 H 0 0 N Y N N N N 40.189 19.311 28.343 4.445 -0.123 -2.677 "HO3'" 5IU 29 5IU "H5'" 1H5* H 0 1 N N N N N N 39.950 18.333 32.731 1.261 0.245 -4.915 "H5'" 5IU 30 5IU "H5''" 2H5* H 0 0 N N N N N N 41.623 18.092 32.670 0.344 -0.959 -3.979 "H5''" 5IU 31 5IU HOP2 2HOP H 0 0 N N N N N N 38.547 22.173 33.198 -2.987 0.711 -6.787 HOP2 5IU 32 5IU HOP3 3HOP H 0 0 N N N N N N 40.622 22.686 34.319 -0.068 1.442 -6.936 HOP3 5IU 33 # 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 5IU N1 C2 SING N N 1 5IU N1 C6 SING N N 2 5IU N1 "C1'" SING N N 3 5IU C2 N3 SING N N 4 5IU C2 O2 DOUB N N 5 5IU N3 C4 SING N N 6 5IU N3 HN3 SING N N 7 5IU C4 C5 SING N N 8 5IU C4 O4 DOUB N N 9 5IU C5 C6 DOUB N N 10 5IU C5 I5 SING N N 11 5IU C6 H6 SING N N 12 5IU "C1'" "C2'" SING N N 13 5IU "C1'" "O4'" SING N N 14 5IU "C1'" "H1'" SING N N 15 5IU "C2'" "C3'" SING N N 16 5IU "C2'" "H2'" SING N N 17 5IU "C2'" "H2''" SING N N 18 5IU "C3'" "C4'" SING N N 19 5IU "C3'" "O3'" SING N N 20 5IU "C3'" "H3'" SING N N 21 5IU "C4'" "O4'" SING N N 22 5IU "C4'" "C5'" SING N N 23 5IU "C4'" "H4'" SING N N 24 5IU "O3'" "HO3'" SING N N 25 5IU "C5'" "O5'" SING N N 26 5IU "C5'" "H5'" SING N N 27 5IU "C5'" "H5''" SING N N 28 5IU "O5'" P SING N N 29 5IU P OP1 DOUB N N 30 5IU P OP2 SING N N 31 5IU P OP3 SING N N 32 5IU OP2 HOP2 SING N N 33 5IU OP3 HOP3 SING N N 34 # 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 5IU SMILES ACDLabs 10.04 "IC=1C(=O)NC(=O)N(C=1)C2OC(C(O)C2)COP(=O)(O)O" 5IU SMILES_CANONICAL CACTVS 3.341 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(I)C(=O)NC2=O" 5IU SMILES CACTVS 3.341 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C(I)C(=O)NC2=O" 5IU SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)I)COP(=O)(O)O)O" 5IU SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=C(C(=O)NC2=O)I)COP(=O)(O)O)O" 5IU InChI InChI 1.03 "InChI=1S/C9H12IN2O8P/c10-4-2-12(9(15)11-8(4)14)7-1-5(13)6(20-7)3-19-21(16,17)18/h2,5-7,13H,1,3H2,(H,11,14,15)(H2,16,17,18)/t5-,6+,7+/m0/s1" 5IU InChIKey InChI 1.03 WXFYBFRZROJDLL-RRKCRQDMSA-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 5IU "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-deoxy-5-iodouridine 5'-(dihydrogen phosphate) ; 5IU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-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 5IU "Create component" 1999-07-08 RCSB 5IU "Modify descriptor" 2011-06-04 RCSB 5IU "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id 5IU _pdbx_chem_comp_pcm.modified_residue_id PTR _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 "C3'" _pdbx_chem_comp_pcm.modified_residue_id_linking_atom O3P _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #