data_UR3 # _chem_comp.id UR3 _chem_comp.name "3-METHYLURIDINE-5'-MONOPHOSHATE" _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 2004-03-17 _chem_comp.pdbx_modified_date 2011-12-06 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces 3MU _chem_comp.formula_weight 338.208 _chem_comp.one_letter_code U _chem_comp.three_letter_code UR3 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1S72 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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 UR3 P P P 0 1 N N N 83.450 123.847 103.670 -4.415 1.039 -0.133 P UR3 1 UR3 OP1 O1P O 0 1 N N N 84.632 122.966 103.596 -5.489 0.102 0.264 OP1 UR3 2 UR3 OP2 O2P O 0 1 N N N 83.358 125.029 102.775 -4.087 2.030 1.093 OP2 UR3 3 UR3 "O5'" "O5'" O 0 1 N N N 82.146 122.943 103.494 -3.092 0.207 -0.518 "O5'" UR3 4 UR3 "C5'" "C5'" C 0 1 N N N 82.010 121.689 104.212 -2.480 -0.735 0.365 "C5'" UR3 5 UR3 "C4'" "C4'" C 0 1 N N R 80.681 121.011 103.896 -1.249 -1.343 -0.311 "C4'" UR3 6 UR3 "O4'" "O4'" O 0 1 N N N 79.562 121.808 104.369 -0.242 -0.333 -0.493 "O4'" UR3 7 UR3 "C1'" "C1'" C 0 1 N N R 78.423 121.548 103.558 1.038 -0.982 -0.338 "C1'" UR3 8 UR3 N1 N1 N 0 1 N N N 77.927 122.815 103.002 2.075 -0.004 -0.002 N1 UR3 9 UR3 C6 C6 C 0 1 N N N 78.670 123.968 103.070 1.895 0.836 1.064 C6 UR3 10 UR3 C2 C2 C 0 1 N N N 76.675 122.810 102.411 3.198 0.058 -0.740 C2 UR3 11 UR3 O2 O2 O 0 1 N N N 75.997 121.793 102.303 3.339 -0.701 -1.680 O2 UR3 12 UR3 N3 N3 N 0 1 N N N 76.251 124.033 101.938 4.167 0.947 -0.454 N3 UR3 13 UR3 C3U C3U C 0 1 N N N 74.884 124.081 101.356 5.379 0.994 -1.274 C3U UR3 14 UR3 C4 C4 C 0 1 N N N 76.955 125.226 101.976 4.025 1.796 0.584 C4 UR3 15 UR3 O4 O4 O 0 1 N N N 76.478 126.242 101.461 4.900 2.602 0.843 O4 UR3 16 UR3 C5 C5 C 0 1 N N N 78.240 125.136 102.591 2.851 1.738 1.373 C5 UR3 17 UR3 "C2'" "C2'" C 0 1 N N R 78.844 120.548 102.483 0.807 -1.960 0.842 "C2'" UR3 18 UR3 "O2'" "O2'" O 0 1 N N N 78.525 119.241 102.913 1.722 -3.056 0.783 "O2'" UR3 19 UR3 "C3'" "C3'" C 0 1 N N S 80.344 120.786 102.434 -0.644 -2.437 0.590 "C3'" UR3 20 UR3 "O3'" "O3'" O 0 1 N N N 81.004 119.655 101.924 -0.646 -3.697 -0.084 "O3'" UR3 21 UR3 OP3 O3P O 0 1 N Y N ? ? ? -4.897 1.901 -1.405 OP3 UR3 22 UR3 HOP2 HOP2 H 0 0 N N N 84.132 125.072 102.225 -3.390 2.673 0.904 HOP2 UR3 23 UR3 "H5'" "H5'1" H 0 1 N N N 82.832 121.019 103.921 -2.178 -0.229 1.282 "H5'" UR3 24 UR3 "H5''" "H5'2" H 0 0 N N N 82.063 121.887 105.293 -3.191 -1.525 0.603 "H5''" UR3 25 UR3 "H4'" "H4'" H 0 1 N N N 80.666 120.036 104.405 -1.528 -1.766 -1.276 "H4'" UR3 26 UR3 "H1'" "H1'" H 0 1 N N N 77.631 121.088 104.167 1.305 -1.527 -1.244 "H1'" UR3 27 UR3 H6 H6 H 0 1 N N N 79.645 123.927 103.532 0.993 0.777 1.654 H6 UR3 28 UR3 H3U1 H3U1 H 0 0 N N N 74.665 125.104 101.017 5.234 1.692 -2.099 H3U1 UR3 29 UR3 H3U2 H3U2 H 0 0 N N N 74.825 123.391 100.501 6.219 1.325 -0.663 H3U2 UR3 30 UR3 H3U3 H3U3 H 0 0 N N N 74.150 123.783 102.119 5.588 0.001 -1.671 H3U3 UR3 31 UR3 H5 H5 H 0 1 N N N 78.864 126.014 102.668 2.721 2.407 2.212 H5 UR3 32 UR3 "H2'" "H2'" H 0 1 N N N 78.378 120.797 101.518 0.886 -1.442 1.798 "H2'" UR3 33 UR3 "HO2'" "HO'2" H 0 0 N N N 78.785 118.616 102.247 1.617 -3.696 1.501 "HO2'" UR3 34 UR3 "H3'" "H3'" H 0 1 N N N 80.566 121.690 101.849 -1.192 -2.504 1.529 "H3'" UR3 35 UR3 "HO3'" H3T H 0 0 N Y N 80.775 119.539 101.009 -0.275 -4.422 0.437 "HO3'" UR3 36 UR3 HOP3 HOP3 H 0 0 N N N -0.760 0.567 0.047 -5.691 2.429 -1.244 HOP3 UR3 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 UR3 P OP1 DOUB N N 1 UR3 P OP2 SING N N 2 UR3 P "O5'" SING N N 3 UR3 P OP3 SING N N 4 UR3 OP2 HOP2 SING N N 5 UR3 "O5'" "C5'" SING N N 6 UR3 "C5'" "C4'" SING N N 7 UR3 "C5'" "H5'" SING N N 8 UR3 "C5'" "H5''" SING N N 9 UR3 "C4'" "O4'" SING N N 10 UR3 "C4'" "C3'" SING N N 11 UR3 "C4'" "H4'" SING N N 12 UR3 "O4'" "C1'" SING N N 13 UR3 "C1'" N1 SING N N 14 UR3 "C1'" "C2'" SING N N 15 UR3 "C1'" "H1'" SING N N 16 UR3 N1 C6 SING N N 17 UR3 N1 C2 SING N N 18 UR3 C6 C5 DOUB N N 19 UR3 C6 H6 SING N N 20 UR3 C2 O2 DOUB N N 21 UR3 C2 N3 SING N N 22 UR3 N3 C3U SING N N 23 UR3 N3 C4 SING N N 24 UR3 C3U H3U1 SING N N 25 UR3 C3U H3U2 SING N N 26 UR3 C3U H3U3 SING N N 27 UR3 C4 O4 DOUB N N 28 UR3 C4 C5 SING N N 29 UR3 C5 H5 SING N N 30 UR3 "C2'" "O2'" SING N N 31 UR3 "C2'" "C3'" SING N N 32 UR3 "C2'" "H2'" SING N N 33 UR3 "O2'" "HO2'" SING N N 34 UR3 "C3'" "O3'" SING N N 35 UR3 "C3'" "H3'" SING N N 36 UR3 "O3'" "HO3'" SING N N 37 UR3 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 UR3 SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OC(N1C(=O)N(C(=O)C=C1)C)C(O)C2O" UR3 InChI InChI 1.03 "InChI=1S/C10H15N2O9P/c1-11-6(13)2-3-12(10(11)16)9-8(15)7(14)5(21-9)4-20-22(17,18)19/h2-3,5,7-9,14-15H,4H2,1H3,(H2,17,18,19)/t5-,7-,8-,9-/m1/s1" UR3 InChIKey InChI 1.03 KZSHODFDDQCIMT-ZOQUXTDFSA-N UR3 SMILES_CANONICAL CACTVS 3.370 "CN1C(=O)C=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C1=O" UR3 SMILES CACTVS 3.370 "CN1C(=O)C=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C1=O" UR3 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CN1C(=O)C=CN(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O" UR3 SMILES "OpenEye OEToolkits" 1.7.6 "CN1C(=O)C=CN(C1=O)C2C(C(C(O2)COP(=O)(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 UR3 "SYSTEMATIC NAME" ACDLabs 12.01 ;3-methyluridine 5'-(dihydrogen phosphate) ; UR3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,4R,5R)-5-[3-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(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 UR3 "Create component" 2004-03-17 PDBJ UR3 "Modify descriptor" 2011-06-04 RCSB UR3 "Other modification" 2011-12-06 RCSB #