data_OMU # _chem_comp.id OMU _chem_comp.name ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 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 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 ? _chem_comp.formula_weight 338.208 _chem_comp.one_letter_code U _chem_comp.three_letter_code OMU _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 1NAO _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 OMU N1 N1 N 0 1 N N N N N N 7.470 3.202 -7.830 -0.226 -0.550 -2.303 N1 OMU 1 OMU C2 C2 C 0 1 N N N N N N 6.607 4.269 -8.020 -0.961 0.573 -2.218 C2 OMU 2 OMU N3 N3 N 0 1 N N N N N N 5.285 3.947 -8.243 -1.871 0.878 -3.162 N3 OMU 3 OMU C4 C4 C 0 1 N N N N N N 4.756 2.676 -8.289 -2.068 0.050 -4.208 C4 OMU 4 OMU C5 C5 C 0 1 N N N N N N 5.705 1.627 -8.079 -1.306 -1.137 -4.307 C5 OMU 5 OMU C6 C6 C 0 1 N N N N N N 7.022 1.909 -7.861 -0.396 -1.416 -3.349 C6 OMU 6 OMU O2 O2 O 0 1 N N N N N N 6.986 5.434 -7.976 -0.794 1.329 -1.280 O2 OMU 7 OMU O4 O4 O 0 1 N N N N N N 3.574 2.502 -8.502 -2.895 0.323 -5.060 O4 OMU 8 OMU "C1'" C1* C 0 1 N N R N N N 8.899 3.514 -7.586 0.760 -0.852 -1.264 "C1'" OMU 9 OMU "C2'" C2* C 0 1 N N R N N N 9.131 3.855 -6.150 1.768 0.313 -1.106 "C2'" OMU 10 OMU "O2'" O2* O 0 1 N N N N N N 10.128 4.886 -6.019 2.849 0.181 -2.031 "O2'" OMU 11 OMU CM2 CM2 C 0 1 N N N N N N 9.544 6.110 -6.309 3.340 1.499 -2.284 CM2 OMU 12 OMU "C3'" C3* C 0 1 N N R N N N 9.606 2.570 -5.553 2.260 0.123 0.348 "C3'" OMU 13 OMU "C4'" C4* C 0 1 N N R N N N 10.384 1.938 -6.681 1.155 -0.718 1.014 "C4'" OMU 14 OMU "O3'" O3* O 0 1 N N N N N N 10.405 2.773 -4.384 3.506 -0.576 0.368 "O3'" OMU 15 OMU "O4'" O4* O 0 1 N N N N N N 9.751 2.385 -7.899 0.127 -0.927 0.031 "O4'" OMU 16 OMU "C5'" C5* C 0 1 N N N N N N 10.407 0.413 -6.568 0.583 0.032 2.218 "C5'" OMU 17 OMU "O5'" O5* O 0 1 N N N N N N 9.096 -0.149 -6.455 -0.440 -0.756 2.829 "O5'" OMU 18 OMU P P P 0 1 N N N N N N 8.918 -1.684 -5.990 -0.994 0.089 4.081 P OMU 19 OMU OP1 O1P O 0 1 N N N N N N 9.880 -1.952 -4.897 -1.539 1.379 3.603 OP1 OMU 20 OMU OP2 O2P O 0 1 N N N N N N 7.473 -1.937 -5.779 -2.157 -0.743 4.819 OP2 OMU 21 OMU OP3 O3P O 0 1 N Y N N N N 9.397 -2.518 -7.291 0.207 0.365 5.116 OP3 OMU 22 OMU HN3 HN3 H 0 1 N N N N N N 4.637 4.721 -8.387 -2.390 1.694 -3.087 HN3 OMU 23 OMU H5 H5 H 0 1 N N N N N N 5.411 0.563 -8.085 -1.449 -1.812 -5.138 H5 OMU 24 OMU H6 H6 H 0 1 N N N N N N 7.734 1.080 -7.707 0.194 -2.318 -3.408 H6 OMU 25 OMU "H1'" H1* H 0 1 N N N N N N 9.148 4.378 -8.244 1.281 -1.782 -1.490 "H1'" OMU 26 OMU "H2'" H2* H 0 1 N N N N N N 8.218 4.252 -5.647 1.272 1.276 -1.226 "H2'" OMU 27 OMU HM21 1HM2 H 0 0 N N N N N N 10.315 6.908 -6.207 4.170 1.449 -2.989 HM21 OMU 28 OMU HM22 2HM2 H 0 0 N N N N N N 9.048 6.120 -7.308 2.542 2.109 -2.707 HM22 OMU 29 OMU HM23 3HM2 H 0 0 N N N N N N 8.640 6.309 -5.686 3.682 1.945 -1.351 HM23 OMU 30 OMU "H3'" H3* H 0 1 N N N N N N 8.771 1.926 -5.189 2.358 1.088 0.847 "H3'" OMU 31 OMU "H4'" H4* H 0 1 N N N N N N 11.455 2.244 -6.655 1.561 -1.677 1.334 "H4'" OMU 32 OMU "HO3'" *HO3 H 0 0 N Y N N N N 10.707 1.956 -4.004 3.762 -0.664 1.296 "HO3'" OMU 33 OMU "H5'" 1H5* H 0 1 N N N N N N 10.967 -0.043 -7.417 1.377 0.218 2.941 "H5'" OMU 34 OMU "H5''" 2H5* H 0 0 N N N N N N 11.058 0.083 -5.725 0.162 0.981 1.888 "H5''" OMU 35 OMU HOP2 2HOP H 0 0 N N N N N N 7.368 -2.840 -5.505 -2.461 -0.203 5.562 HOP2 OMU 36 OMU HOP3 3HOP H 0 0 N N N N N N 9.292 -3.421 -7.017 0.533 -0.498 5.403 HOP3 OMU 37 # 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 OMU N1 C2 SING N N 1 OMU N1 C6 SING N N 2 OMU N1 "C1'" SING N N 3 OMU C2 N3 SING N N 4 OMU C2 O2 DOUB N N 5 OMU N3 C4 SING N N 6 OMU N3 HN3 SING N N 7 OMU C4 C5 SING N N 8 OMU C4 O4 DOUB N N 9 OMU C5 C6 DOUB N N 10 OMU C5 H5 SING N N 11 OMU C6 H6 SING N N 12 OMU "C1'" "C2'" SING N N 13 OMU "C1'" "O4'" SING N N 14 OMU "C1'" "H1'" SING N N 15 OMU "C2'" "O2'" SING N N 16 OMU "C2'" "C3'" SING N N 17 OMU "C2'" "H2'" SING N N 18 OMU "O2'" CM2 SING N N 19 OMU CM2 HM21 SING N N 20 OMU CM2 HM22 SING N N 21 OMU CM2 HM23 SING N N 22 OMU "C3'" "C4'" SING N N 23 OMU "C3'" "O3'" SING N N 24 OMU "C3'" "H3'" SING N N 25 OMU "C4'" "O4'" SING N N 26 OMU "C4'" "C5'" SING N N 27 OMU "C4'" "H4'" SING N N 28 OMU "O3'" "HO3'" SING N N 29 OMU "C5'" "O5'" SING N N 30 OMU "C5'" "H5'" SING N N 31 OMU "C5'" "H5''" SING N N 32 OMU "O5'" P SING N N 33 OMU P OP1 DOUB N N 34 OMU P OP2 SING N N 35 OMU P OP3 SING N N 36 OMU OP2 HOP2 SING N N 37 OMU OP3 HOP3 SING N N 38 # 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 OMU SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1)C2OC(C(O)C2OC)COP(=O)(O)O" OMU SMILES_CANONICAL CACTVS 3.341 "CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=O)NC2=O" OMU SMILES CACTVS 3.341 "CO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=O)NC2=O" OMU SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O" OMU SMILES "OpenEye OEToolkits" 1.5.0 "COC1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O" OMU InChI InChI 1.03 "InChI=1S/C10H15N2O9P/c1-19-8-7(14)5(4-20-22(16,17)18)21-9(8)12-3-2-6(13)11-10(12)15/h2-3,5,7-9,14H,4H2,1H3,(H,11,13,15)(H2,16,17,18)/t5-,7-,8-,9-/m1/s1" OMU InChIKey InChI 1.03 FHMMECZNEPGJSJ-ZOQUXTDFSA-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 OMU "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-O-methyluridine 5'-(dihydrogen phosphate) ; OMU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3-hydroxy-4-methoxy-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 OMU "Create component" 1999-07-08 RCSB OMU "Modify descriptor" 2011-06-04 RCSB OMU "Modify PCM" 2024-09-27 PDBE # loop_ _pdbx_chem_comp_pcm.pcm_id _pdbx_chem_comp_pcm.comp_id _pdbx_chem_comp_pcm.modified_residue_id _pdbx_chem_comp_pcm.type _pdbx_chem_comp_pcm.category _pdbx_chem_comp_pcm.position _pdbx_chem_comp_pcm.polypeptide_position _pdbx_chem_comp_pcm.comp_id_linking_atom _pdbx_chem_comp_pcm.modified_residue_id_linking_atom _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession 1 OMU ARG None "Covalent chemical modification" "Amino-acid side chain" "Any position" OP2 NH2 ? ? 2 OMU LYS None "Covalent chemical modification" "Amino-acid side chain" "Any position" OP2 NZ ? ? #