data_UY1 # _chem_comp.id UY1 _chem_comp.name "2'-O-methylpseudouridine-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 ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-06-04 _chem_comp.pdbx_modified_date 2021-05-27 _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 ? _chem_comp.three_letter_code UY1 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 6XA1 _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 UY1 "C1'" C1 C 0 1 N N S 262.981 252.145 234.489 1.279 -0.682 -0.879 "C1'" UY1 1 UY1 C2 C2 C 0 1 N N N 260.199 255.111 233.582 4.336 2.067 0.114 C2 UY1 2 UY1 "C2'" C3 C 0 1 N N R 262.335 250.771 234.671 1.340 -1.894 0.070 "C2'" UY1 3 UY1 "C3'" C4 C 0 1 N N R 262.713 250.055 233.381 -0.052 -1.917 0.746 "C3'" UY1 4 UY1 C4 C5 C 0 1 N N N 261.455 254.067 235.191 2.365 0.966 0.715 C4 UY1 5 UY1 "C4'" C6 C 0 1 N N R 264.039 250.690 233.027 -0.911 -1.097 -0.250 "C4'" UY1 6 UY1 C5 C7 C 0 1 N N N 262.002 253.184 234.164 2.372 0.297 -0.532 C5 UY1 7 UY1 "C5'" C8 C 0 1 N N N 264.418 250.657 231.580 -2.119 -0.482 0.459 "C5'" UY1 8 UY1 C6 C9 C 0 1 N N N 261.575 253.379 232.879 3.370 0.546 -1.406 C6 UY1 9 UY1 CM2 C10 C 0 1 N N N 261.974 249.782 236.732 2.275 -4.101 0.052 CM2 UY1 10 UY1 N1 N1 N 0 1 N N N 260.690 254.326 232.629 4.354 1.437 -1.075 N1 UY1 11 UY1 N3 N2 N 0 1 N N N 260.577 254.988 234.844 3.353 1.837 1.004 N3 UY1 12 UY1 O2 O1 O 0 1 N N N 259.370 255.993 233.296 5.223 2.852 0.390 O2 UY1 13 UY1 "O2'" O2 O 0 1 N N N 262.954 250.147 235.776 1.558 -3.098 -0.669 "O2'" UY1 14 UY1 "O3'" O3 O 0 1 N N N 262.802 248.647 233.523 -0.542 -3.255 0.860 "O3'" UY1 15 UY1 O4 O4 O 0 1 N N N 261.814 253.947 236.369 1.474 0.758 1.520 O4 UY1 16 UY1 "O4'" O5 O 0 1 N N N 263.886 252.059 233.427 -0.007 -0.065 -0.703 "O4'" UY1 17 UY1 "O5'" O6 O 0 1 N N N 265.150 249.492 231.289 -2.953 0.170 -0.501 "O5'" UY1 18 UY1 OP1 O7 O 0 1 N N N 267.017 251.015 230.810 -5.202 -0.002 0.633 OP1 UY1 19 UY1 OP2 O8 O 0 1 N N N 267.378 248.778 231.987 -3.977 2.196 0.826 OP2 UY1 20 UY1 P P1 P 0 1 N N N 266.686 249.571 230.941 -4.318 0.928 -0.105 P UY1 21 UY1 "H1'" "H1'" H 0 1 N N N 263.504 252.413 235.419 1.393 -1.013 -1.911 "H1'" UY1 22 UY1 "H2'" "H2'" H 0 1 N N N 261.243 250.854 234.778 2.125 -1.757 0.814 "H2'" UY1 23 UY1 "H3'" "H3'" H 0 1 N N N 261.977 250.312 232.605 -0.019 -1.433 1.722 "H3'" UY1 24 UY1 "H4'" "H4'" H 0 1 N N N 264.833 250.212 233.619 -1.230 -1.720 -1.085 "H4'" UY1 25 UY1 "H5'" "H5'" H 0 1 N N N 265.033 251.539 231.347 -2.685 -1.267 0.959 "H5'" UY1 26 UY1 "H5''" "H5''" H 0 0 N N N 263.505 250.674 230.966 -1.777 0.245 1.196 "H5''" UY1 27 UY1 H6 H6 H 0 1 N N N 261.958 252.765 232.078 3.392 0.044 -2.362 H6 UY1 28 UY1 H21 H21 H 0 1 N N N 262.461 249.297 237.590 1.718 -4.371 0.950 H21 UY1 29 UY1 H23 H23 H 0 1 N N N 261.442 250.682 237.073 2.398 -4.983 -0.577 H23 UY1 30 UY1 H22 H22 H 0 1 N N N 261.258 249.084 236.274 3.254 -3.716 0.335 H22 UY1 31 UY1 HN3 HN3 H 0 1 N N N 260.195 255.597 235.539 3.355 2.300 1.856 HN3 UY1 32 UY1 HO3 HO3 H 0 1 N N N 261.947 248.296 233.744 -1.412 -3.321 1.277 HO3 UY1 33 UY1 HOP2 HOP2 H 0 0 N N N 267.979 249.338 232.464 -3.399 2.849 0.405 HOP2 UY1 34 UY1 OP3 OP3 O 0 1 N Y N 266.763 248.813 229.534 -5.061 1.428 -1.443 OP3 UY1 35 UY1 HOP3 HOP3 H 0 0 N N N 267.010 249.429 228.855 -5.892 1.894 -1.280 HOP3 UY1 36 UY1 HN1 HN1 H 0 1 N N N 260.378 254.457 231.688 5.072 1.616 -1.703 HN1 UY1 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 UY1 OP1 P DOUB N N 1 UY1 P "O5'" SING N N 2 UY1 P OP2 SING N N 3 UY1 "O5'" "C5'" SING N N 4 UY1 "C5'" "C4'" SING N N 5 UY1 N1 C6 SING N N 6 UY1 N1 C2 SING N N 7 UY1 C6 C5 DOUB N N 8 UY1 "C4'" "C3'" SING N N 9 UY1 "C4'" "O4'" SING N N 10 UY1 O2 C2 DOUB N N 11 UY1 "C3'" "O3'" SING N N 12 UY1 "C3'" "C2'" SING N N 13 UY1 "O4'" "C1'" SING N N 14 UY1 C2 N3 SING N N 15 UY1 C5 "C1'" SING N N 16 UY1 C5 C4 SING N N 17 UY1 "C1'" "C2'" SING N N 18 UY1 "C2'" "O2'" SING N N 19 UY1 N3 C4 SING N N 20 UY1 C4 O4 DOUB N N 21 UY1 "O2'" CM2 SING N N 22 UY1 "C1'" "H1'" SING N N 23 UY1 "C2'" "H2'" SING N N 24 UY1 "C3'" "H3'" SING N N 25 UY1 "C4'" "H4'" SING N N 26 UY1 "C5'" "H5'" SING N N 27 UY1 "C5'" "H5''" SING N N 28 UY1 C6 H6 SING N N 29 UY1 CM2 H21 SING N N 30 UY1 CM2 H23 SING N N 31 UY1 CM2 H22 SING N N 32 UY1 N3 HN3 SING N N 33 UY1 "O3'" HO3 SING N N 34 UY1 OP2 HOP2 SING N N 35 UY1 P OP3 SING N N 36 UY1 OP3 HOP3 SING N N 37 UY1 N1 HN1 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 UY1 SMILES ACDLabs 12.01 "C1(C(OC)C(O)C(O1)COP(=O)(O)O)C2C(=O)NC(N=C2)=O" UY1 InChI InChI 1.03 "InChI=1S/C10H15N2O9P/c1-19-8-6(13)5(3-20-22(16,17)18)21-7(8)4-2-11-10(15)12-9(4)14/h2,5-8,13H,3H2,1H3,(H2,16,17,18)(H2,11,12,14,15)/t5-,6-,7+,8-/m1/s1" UY1 InChIKey InChI 1.03 VLDJGRCZRDFORR-OOJXKGFFSA-N UY1 SMILES_CANONICAL CACTVS 3.385 "CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1C2=CNC(=O)NC2=O" UY1 SMILES CACTVS 3.385 "CO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1C2=CNC(=O)NC2=O" UY1 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CO[C@@H]1[C@@H]([C@H](O[C@H]1C2=CNC(=O)NC2=O)COP(=O)(O)O)O" UY1 SMILES "OpenEye OEToolkits" 2.0.7 "COC1C(C(OC1C2=CNC(=O)NC2=O)COP(=O)(O)O)O" # # 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 UY1 "SYSTEMATIC NAME" ACDLabs 12.01 "(1S)-1,4-anhydro-1-[(5S)-2,6-dioxo-1,2,5,6-tetrahydropyrimidin-5-yl]-2-O-methyl-5-O-phosphono-D-ribitol" UY1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{R},4~{R},5~{S})-5-[2,4-bis(oxidanylidene)-1~{H}-pyrimidin-5-yl]-4-methoxy-3-oxidanyl-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 UY1 "Create component" 2020-06-04 RCSB UY1 "Initial release" 2020-10-07 RCSB UY1 "Modify model coordinates code" 2021-05-12 PDBE UY1 "Modify name" 2021-05-27 PDBE ##