data_U5P # _chem_comp.id U5P _chem_comp.name "URIDINE-5'-MONOPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H13 N2 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _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 U25 _chem_comp.formula_weight 324.181 _chem_comp.one_letter_code ? _chem_comp.three_letter_code U5P _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 ? _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 U5P N1 N1 N 0 1 N N N N N N 8.177 -5.970 34.616 2.462 0.039 0.457 N1 U5P 1 U5P C2 C2 C 0 1 N N N N N N 9.479 -5.506 34.855 2.453 -0.768 -0.619 C2 U5P 2 U5P N3 N3 N 0 1 N N N N N N 9.576 -4.182 35.185 3.483 -1.596 -0.871 N3 U5P 3 U5P C4 C4 C 0 1 N N N N N N 8.523 -3.268 35.305 4.543 -1.636 -0.038 C4 U5P 4 U5P C5 C5 C 0 1 N N N N N N 7.222 -3.821 35.050 4.563 -0.795 1.101 C5 U5P 5 U5P C6 C6 C 0 1 N N N N N N 7.087 -5.101 34.725 3.518 0.029 1.327 C6 U5P 6 U5P O2 O2 O 0 1 N N N N N N 10.440 -6.260 34.763 1.504 -0.743 -1.379 O2 U5P 7 U5P O4 O4 O 0 1 N N N N N N 8.793 -2.131 35.597 5.474 -2.388 -0.263 O4 U5P 8 U5P "C1'" C1* C 0 1 N N R N N N 8.039 -7.389 34.252 1.328 0.933 0.703 "C1'" U5P 9 U5P "C2'" C2* C 0 1 N N R N N N 7.203 -8.277 35.153 1.226 1.993 -0.416 "C2'" U5P 10 U5P "O2'" O2* O 0 1 N N N N N N 7.905 -8.710 36.329 1.823 3.223 -0.001 "O2'" U5P 11 U5P "C3'" C3* C 0 1 N N S N N N 6.732 -9.409 34.230 -0.294 2.173 -0.626 "C3'" U5P 12 U5P "C4'" C4* C 0 1 N N R N N N 6.558 -8.659 32.922 -0.934 1.201 0.390 "C4'" U5P 13 U5P "O3'" O3* O 0 1 N N N N N N 7.686 -10.506 34.190 -0.683 3.519 -0.343 "O3'" U5P 14 U5P "O4'" O4* O 0 1 N N N N N N 7.568 -7.601 32.936 0.084 0.203 0.633 "O4'" U5P 15 U5P "C5'" C5* C 0 1 N N N N N N 5.231 -7.971 32.636 -2.187 0.551 -0.201 "C5'" U5P 16 U5P "O5'" O5* O 0 1 N N N N N N 5.157 -7.416 31.315 -2.782 -0.309 0.773 "O5'" U5P 17 U5P P P P 0 1 N N N N N N 4.537 -8.239 30.080 -4.087 -0.956 0.087 P U5P 18 U5P O1P O1P O 0 1 N N N N N N 3.103 -8.686 30.202 -4.968 0.123 -0.413 O1P U5P 19 U5P O2P O2P O 0 1 N N N N N N 5.315 -9.488 29.842 -3.639 -1.895 -1.141 O2P U5P 20 U5P O3P O3P O 0 1 N N N N N N 4.857 -7.204 28.843 -4.883 -1.838 1.174 O3P U5P 21 U5P HN3 HN3 H 0 1 N N N N N N 10.496 -3.830 35.359 3.462 -2.169 -1.654 HN3 U5P 22 U5P H5 H5 H 0 1 N N N N N N 6.348 -3.191 35.123 5.403 -0.813 1.779 H5 U5P 23 U5P H6 H6 H 0 1 N N N N N N 6.096 -5.487 34.537 3.516 0.678 2.191 H6 U5P 24 U5P "H1'" H1* H 0 1 N N N N N N 9.089 -7.693 34.371 1.430 1.417 1.675 "H1'" U5P 25 U5P "H2'" H2* H 0 1 N N N N N N 6.346 -7.747 35.594 1.697 1.630 -1.330 "H2'" U5P 26 U5P "HO2'" *HO2 H 0 0 N N N N N N 8.829 -8.806 36.130 1.675 3.860 -0.713 "HO2'" U5P 27 U5P "H3'" H3* H 0 1 N N N N N N 5.813 -9.926 34.542 -0.574 1.902 -1.643 "H3'" U5P 28 U5P "H4'" H4* H 0 1 N N N N N N 6.634 -9.434 32.145 -1.180 1.726 1.313 "H4'" U5P 29 U5P "HO3'" *HO3 H 0 0 N N N N N N 7.894 -10.713 33.286 -0.231 4.082 -0.987 "HO3'" U5P 30 U5P "H5'1" 1H5* H 0 0 N N N N N N 4.427 -8.714 32.743 -2.899 1.326 -0.485 "H5'1" U5P 31 U5P "H5'2" 2H5* H 0 0 N N N N N N 5.130 -7.139 33.349 -1.913 -0.031 -1.081 "H5'2" U5P 32 U5P HOP2 2HOP H 0 0 N N N N N N 5.481 -9.586 28.912 -3.068 -2.583 -0.773 HOP2 U5P 33 U5P HOP3 3HOP H 0 0 N N N N N N 4.919 -6.318 29.179 -5.655 -2.206 0.723 HOP3 U5P 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 U5P N1 C2 SING N N 1 U5P N1 C6 SING N N 2 U5P N1 "C1'" SING N N 3 U5P C2 N3 SING N N 4 U5P C2 O2 DOUB N N 5 U5P N3 C4 SING N N 6 U5P N3 HN3 SING N N 7 U5P C4 C5 SING N N 8 U5P C4 O4 DOUB N N 9 U5P C5 C6 DOUB N N 10 U5P C5 H5 SING N N 11 U5P C6 H6 SING N N 12 U5P "C1'" "C2'" SING N N 13 U5P "C1'" "O4'" SING N N 14 U5P "C1'" "H1'" SING N N 15 U5P "C2'" "O2'" SING N N 16 U5P "C2'" "C3'" SING N N 17 U5P "C2'" "H2'" SING N N 18 U5P "O2'" "HO2'" SING N N 19 U5P "C3'" "C4'" SING N N 20 U5P "C3'" "O3'" SING N N 21 U5P "C3'" "H3'" SING N N 22 U5P "C4'" "O4'" SING N N 23 U5P "C4'" "C5'" SING N N 24 U5P "C4'" "H4'" SING N N 25 U5P "O3'" "HO3'" SING N N 26 U5P "C5'" "O5'" SING N N 27 U5P "C5'" "H5'1" SING N N 28 U5P "C5'" "H5'2" SING N N 29 U5P "O5'" P SING N N 30 U5P P O1P DOUB N N 31 U5P P O2P SING N N 32 U5P P O3P SING N N 33 U5P O2P HOP2 SING N N 34 U5P O3P HOP3 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 U5P SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)COP(=O)(O)O" U5P SMILES_CANONICAL CACTVS 3.341 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O" U5P SMILES CACTVS 3.341 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O" U5P SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O" U5P SMILES "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O" U5P InChI InChI 1.03 "InChI=1S/C9H13N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1" U5P InChIKey InChI 1.03 DJJCXFVJDGTHFX-XVFCMESISA-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 U5P "SYSTEMATIC NAME" ACDLabs 10.04 ;5'-uridylic acid ; U5P "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-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 U5P "Create component" 1999-07-08 RCSB U5P "Modify descriptor" 2011-06-04 RCSB U5P "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 U5P TYR UMPylation "Nucleotide monophosphate" "Amino-acid side chain" "Any position" P OH PTM-0333 ? 2 U5P HIS UMPylation "Nucleotide monophosphate" "Amino-acid side chain" "Any position" P NE2 PTM-0500 ? 3 U5P SER UMPylation "Nucleotide monophosphate" "Amino-acid side chain" "Any position" P OG PTM-0501 ? 4 U5P THR UMPylation "Nucleotide monophosphate" "Amino-acid side chain" "Any position" P OG1 PTM-0502 ? 5 U5P ASN UMPylation "Nucleotide monophosphate" "Amino-acid backbone" N-terminal P N ? ? 6 U5P LYS UMPylation "Nucleotide monophosphate" "Amino-acid side chain" "Any position" C6 NZ ? ? #