data_U2P # _chem_comp.id U2P _chem_comp.name ;PHOSPHORIC ACID MONO-[2-(2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-4-HYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-YL] ESTER ; _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H13 N2 O9 P" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms "URIDINE-2'-PHOSPHATE; 2'-URIDINEMONOPHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2003-02-26 _chem_comp.pdbx_modified_date 2020-06-17 _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 324.181 _chem_comp.one_letter_code U _chem_comp.three_letter_code U2P _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 1O0M _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 U2P "O5'" "O5'" O 0 1 N N N 39.783 2.730 22.605 3.616 3.305 -0.430 "O5'" U2P 1 U2P "C5'" "C5'" C 0 1 N N N 40.314 1.479 23.084 3.398 1.934 -0.767 "C5'" U2P 2 U2P "C4'" "C4'" C 0 1 N N R 39.194 0.569 23.538 2.670 1.236 0.383 "C4'" U2P 3 U2P "O4'" "O4'" O 0 1 N N N 38.419 1.229 24.571 1.342 1.769 0.517 "O4'" U2P 4 U2P "C1'" "C1'" C 0 1 N N R 37.047 0.886 24.436 0.491 0.682 0.940 "C1'" U2P 5 U2P N1 N1 N 0 1 N N N 36.288 2.130 24.215 -0.910 0.971 0.625 N1 U2P 6 U2P C6 C6 C 0 1 N N N 36.754 3.113 23.370 -1.855 0.899 1.612 C6 U2P 7 U2P C5 C5 C 0 1 N N N 36.112 4.270 23.180 -3.147 1.166 1.322 C5 U2P 8 U2P C4 C4 C 0 1 N N N 34.887 4.523 23.870 -3.497 1.515 -0.005 C4 U2P 9 U2P O4 O4 O 0 1 N N N 34.224 5.558 23.805 -4.655 1.760 -0.291 O4 U2P 10 U2P N3 N3 N 0 1 N N N 34.463 3.495 24.688 -2.536 1.574 -0.949 N3 U2P 11 U2P C2 C2 C 0 1 N N N 35.091 2.293 24.900 -1.255 1.309 -0.631 C2 U2P 12 U2P O2 O2 O 0 1 N N N 34.620 1.440 25.636 -0.399 1.366 -1.493 O2 U2P 13 U2P "C2'" "C2'" C 0 1 N N R 36.951 -0.168 23.326 1.004 -0.522 0.109 "C2'" U2P 14 U2P "O2'" "O2'" O 0 1 N N N 37.061 -1.436 23.955 0.704 -1.757 0.764 "O2'" U2P 15 U2P P P P 0 1 N N N 36.475 -2.759 23.247 -0.228 -2.602 -0.241 P U2P 16 U2P O1P O1P O 0 1 N N N 37.230 -2.947 21.940 -1.409 -1.792 -0.616 O1P U2P 17 U2P O2P O2P O 0 1 N N N 36.757 -3.876 24.238 0.609 -2.975 -1.565 O2P U2P 18 U2P O3P O3P O 0 1 N Y N 34.983 -2.535 23.043 -0.713 -3.954 0.486 O3P U2P 19 U2P "C3'" "C3'" C 0 1 N N R 38.170 0.194 22.479 2.534 -0.269 0.080 "C3'" U2P 20 U2P "O3'" "O3'" O 0 1 N N N 38.649 -0.897 21.699 3.189 -1.049 1.083 "O3'" U2P 21 U2P "H5'" "H5'" H 0 1 N N N 40.486 3.302 22.320 4.076 3.708 -1.180 "H5'" U2P 22 U2P "H5'1" "1H5'" H 0 0 N N N 41.076 1.631 23.884 2.791 1.874 -1.671 "H5'1" U2P 23 U2P "H5'2" "2H5'" H 0 0 N N N 40.966 0.987 22.325 4.357 1.445 -0.940 "H5'2" U2P 24 U2P "H4'" "H4'" H 0 1 N N N 39.727 -0.355 23.863 3.222 1.378 1.312 "H4'" U2P 25 U2P "H1'" "H1'" H 0 1 N N N 36.595 0.422 25.343 0.612 0.492 2.006 "H1'" U2P 26 U2P H6 H6 H 0 1 N N N 37.695 2.965 22.814 -1.569 0.631 2.618 H6 U2P 27 U2P H5 H5 H 0 1 N N N 36.575 4.988 22.482 -3.903 1.113 2.091 H5 U2P 28 U2P HN3 HN3 H 0 1 N N N 33.588 3.640 25.192 -2.768 1.813 -1.860 HN3 U2P 29 U2P "H2'" "H2'" H 0 1 N N N 36.018 -0.199 22.717 0.586 -0.507 -0.897 "H2'" U2P 30 U2P H2P H2P H 0 1 N N N 36.411 -4.656 23.821 1.368 -3.501 -1.277 H2P U2P 31 U2P H3P H3P H 0 1 N N N 34.637 -3.315 22.626 -1.268 -4.429 -0.148 H3P U2P 32 U2P "H3'" "H3'" H 0 1 N N N 37.946 0.994 21.735 2.940 -0.498 -0.905 "H3'" U2P 33 U2P H1 H1 H 0 1 N N N 38.009 -1.131 21.037 4.133 -0.852 1.018 H1 U2P 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 U2P "O5'" "C5'" SING N N 1 U2P "O5'" "H5'" SING N N 2 U2P "C5'" "C4'" SING N N 3 U2P "C5'" "H5'1" SING N N 4 U2P "C5'" "H5'2" SING N N 5 U2P "C4'" "O4'" SING N N 6 U2P "C4'" "C3'" SING N N 7 U2P "C4'" "H4'" SING N N 8 U2P "O4'" "C1'" SING N N 9 U2P "C1'" N1 SING N N 10 U2P "C1'" "C2'" SING N N 11 U2P "C1'" "H1'" SING N N 12 U2P N1 C6 SING N N 13 U2P N1 C2 SING N N 14 U2P C6 C5 DOUB N N 15 U2P C6 H6 SING N N 16 U2P C5 C4 SING N N 17 U2P C5 H5 SING N N 18 U2P C4 O4 DOUB N N 19 U2P C4 N3 SING N N 20 U2P N3 C2 SING N N 21 U2P N3 HN3 SING N N 22 U2P C2 O2 DOUB N N 23 U2P "C2'" "O2'" SING N N 24 U2P "C2'" "C3'" SING N N 25 U2P "C2'" "H2'" SING N N 26 U2P "O2'" P SING N N 27 U2P P O1P DOUB N N 28 U2P P O2P SING N N 29 U2P P O3P SING N N 30 U2P O2P H2P SING N N 31 U2P O3P H3P SING N N 32 U2P "C3'" "O3'" SING N N 33 U2P "C3'" "H3'" SING N N 34 U2P "O3'" H1 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 U2P SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1)C2OC(C(O)C2OP(=O)(O)O)CO" U2P SMILES_CANONICAL CACTVS 3.341 "OC[C@H]1O[C@H]([C@H](O[P](O)(O)=O)[C@@H]1O)N2C=CC(=O)NC2=O" U2P SMILES CACTVS 3.341 "OC[CH]1O[CH]([CH](O[P](O)(O)=O)[CH]1O)N2C=CC(=O)NC2=O" U2P SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)OP(=O)(O)O" U2P SMILES "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)CO)O)OP(=O)(O)O" U2P InChI InChI 1.03 "InChI=1S/C9H13N2O9P/c12-3-4-6(14)7(20-21(16,17)18)8(19-4)11-2-1-5(13)10-9(11)15/h1-2,4,6-8,12,14H,3H2,(H,10,13,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1" U2P InChIKey InChI 1.03 HQIDPEYTETUCNF-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 U2P "SYSTEMATIC NAME" ACDLabs 10.04 "2'-uridylic acid" U2P "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-2-(2,4-dioxopyrimidin-1-yl)-4-hydroxy-5-(hydroxymethyl)oxolan-3-yl] 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 U2P "Create component" 2003-02-26 RCSB U2P "Modify descriptor" 2011-06-04 RCSB U2P "Modify synonyms" 2020-06-05 PDBE # # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 U2P "URIDINE-2'-PHOSPHATE" ? ? 2 U2P "2'-URIDINEMONOPHOSPHATE" ? ? ##