data_UBD # _chem_comp.id UBD _chem_comp.name ;URIDINE 3',5'-BIS(DIHYDROGEN PHOSPHATE) ; _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H14 N2 O12 P2" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2007-06-07 _chem_comp.pdbx_modified_date 2013-03-22 _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 404.161 _chem_comp.one_letter_code U _chem_comp.three_letter_code UBD _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details "Corina V3.40" _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 # 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 UBD C2 C2 C 0 1 N N N -2.797 -2.735 35.357 3.856 0.081 0.934 C2 UBD 1 UBD C4 C4 C 0 1 N N N -5.039 -3.615 35.597 5.218 -1.194 -0.472 C4 UBD 2 UBD C5 C5 C 0 1 N N N -4.498 -4.893 36.033 4.096 -1.469 -1.292 C5 UBD 3 UBD C6 C6 C 0 1 N N N -3.153 -5.055 36.117 2.894 -0.955 -0.953 C6 UBD 4 UBD N1 N1 N 0 1 N N N -2.271 -4.016 35.793 2.781 -0.177 0.167 N1 UBD 5 UBD O2 O2 O 0 1 N N N -2.038 -1.797 35.061 3.732 0.775 1.924 O2 UBD 6 UBD P1 P1 P 0 1 N N N -2.005 -7.397 39.337 -3.000 -3.307 0.054 P1 UBD 7 UBD O1P O1P O 0 1 N N N -1.124 -6.983 40.506 -3.177 -4.363 1.257 O1P UBD 8 UBD O2P O2P O 0 1 N N N -3.432 -6.951 39.536 -2.356 -4.049 -1.221 O2P UBD 9 UBD O3P O3P O 0 1 N Y N -2.022 -9.011 39.134 -4.321 -2.752 -0.313 O3P UBD 10 UBD "O5'" O5* O 0 1 N N N -1.454 -6.805 37.943 -2.029 -2.113 0.527 "O5'" UBD 11 UBD "C5'" C5* C 0 1 N N N -0.170 -7.206 37.437 -1.757 -0.965 -0.279 "C5'" UBD 12 UBD "C4'" C4* C 0 1 N N R 0.502 -6.092 36.634 -0.801 -0.032 0.467 "C4'" UBD 13 UBD "O4'" O4* O 0 1 N N N -0.364 -5.545 35.560 0.482 -0.663 0.613 "O4'" UBD 14 UBD "C3'" C3* C 0 1 N N S 0.890 -4.885 37.481 -0.586 1.258 -0.348 "C3'" UBD 15 UBD "O3'" O3* O 0 1 N N N 2.159 -4.399 36.971 -1.009 2.399 0.403 "O3'" UBD 16 UBD "C2'" C2* C 0 1 N N R -0.213 -3.863 37.265 0.942 1.305 -0.590 "C2'" UBD 17 UBD "O2'" O2* O 0 1 N N N 0.273 -2.533 37.359 1.442 2.635 -0.437 "O2'" UBD 18 UBD "C1'" C1* C 0 1 N N R -0.774 -4.200 35.880 1.477 0.380 0.534 "C1'" UBD 19 UBD N3 N3 N 0 1 N N N -4.177 -2.565 35.269 5.064 -0.423 0.623 N3 UBD 20 UBD O4 O4 O 0 1 N N N -6.275 -3.453 35.515 6.311 -1.651 -0.754 O4 UBD 21 UBD P2 P2 P 0 1 N N N 3.440 -4.139 37.937 -2.168 3.398 -0.098 P2 UBD 22 UBD O4P O4P O 0 1 N N N 3.860 -2.691 37.835 -1.688 4.149 -1.439 O4P UBD 23 UBD O5P O5P O 0 1 N N N 4.568 -5.025 37.490 -3.398 2.624 -0.381 O5P UBD 24 UBD O6P O6P O 0 1 N N N 3.060 -4.482 39.451 -2.471 4.486 1.048 O6P UBD 25 UBD H5 H5 H 0 1 N N N -5.161 -5.706 36.288 4.200 -2.084 -2.173 H5 UBD 26 UBD H6 H6 H 0 1 N N N -2.754 -6.005 36.441 2.027 -1.153 -1.566 H6 UBD 27 UBD HO1P HO1P H 0 0 N N N -0.225 -6.897 40.211 -3.750 -5.111 1.042 HO1P UBD 28 UBD HO2P HO2P H 0 0 N N N -3.608 -6.857 40.465 -1.487 -4.438 -1.052 HO2P UBD 29 UBD "H5'1" 1H5* H 0 0 N N N 0.477 -7.466 38.287 -1.300 -1.280 -1.217 "H5'1" UBD 30 UBD "H5'2" 2H5* H 0 0 N N N -0.320 -8.066 36.768 -2.689 -0.439 -0.488 "H5'2" UBD 31 UBD "H4'" H4* H 0 1 N N N 1.391 -6.591 36.221 -1.209 0.210 1.448 "H4'" UBD 32 UBD "H3'" H3* H 0 1 N N N 0.999 -5.106 38.553 -1.123 1.206 -1.295 "H3'" UBD 33 UBD "H2'" H2* H 0 1 N N N -0.994 -3.912 38.038 1.192 0.907 -1.573 "H2'" UBD 34 UBD "HO2'" HO2* H 0 0 N N N 0.382 -2.299 38.273 2.396 2.715 -0.579 "HO2'" UBD 35 UBD "H1'" H1* H 0 1 N N N -0.369 -3.497 35.137 1.543 0.920 1.479 "H1'" UBD 36 UBD HN3 HN3 H 0 1 N N N -4.552 -1.688 34.970 5.828 -0.230 1.189 HN3 UBD 37 UBD HO4P HO4P H 0 0 N N N 3.948 -2.324 38.707 -0.885 4.677 -1.327 HO4P UBD 38 UBD HO6P HO6P H 0 0 N N N 3.853 -4.550 39.969 -3.161 5.122 0.814 HO6P UBD 39 # 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 UBD C2 O2 DOUB N N 1 UBD C2 N3 SING N N 2 UBD C2 N1 SING N N 3 UBD C4 N3 SING N N 4 UBD C4 O4 DOUB N N 5 UBD C4 C5 SING N N 6 UBD C5 C6 DOUB N N 7 UBD C5 H5 SING N N 8 UBD C6 N1 SING N N 9 UBD C6 H6 SING N N 10 UBD N1 "C1'" SING N N 11 UBD P1 "O5'" SING N N 12 UBD P1 O3P DOUB N N 13 UBD P1 O2P SING N N 14 UBD P1 O1P SING N N 15 UBD O1P HO1P SING N N 16 UBD O2P HO2P SING N N 17 UBD "O5'" "C5'" SING N N 18 UBD "C5'" "C4'" SING N N 19 UBD "C5'" "H5'1" SING N N 20 UBD "C5'" "H5'2" SING N N 21 UBD "C4'" "O4'" SING N N 22 UBD "C4'" "C3'" SING N N 23 UBD "C4'" "H4'" SING N N 24 UBD "O4'" "C1'" SING N N 25 UBD "C3'" "O3'" SING N N 26 UBD "C3'" "C2'" SING N N 27 UBD "C3'" "H3'" SING N N 28 UBD "O3'" P2 SING N N 29 UBD "C2'" "C1'" SING N N 30 UBD "C2'" "O2'" SING N N 31 UBD "C2'" "H2'" SING N N 32 UBD "O2'" "HO2'" SING N N 33 UBD "C1'" "H1'" SING N N 34 UBD N3 HN3 SING N N 35 UBD P2 O5P DOUB N N 36 UBD P2 O4P SING N N 37 UBD P2 O6P SING N N 38 UBD O4P HO4P SING N N 39 UBD O6P HO6P SING N N 40 # 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 UBD SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1)C2OC(C(OP(=O)(O)O)C2O)COP(=O)(O)O" UBD SMILES_CANONICAL CACTVS 3.341 "O[C@@H]1[C@H](O[P](O)(O)=O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=O)NC2=O" UBD SMILES CACTVS 3.341 "O[CH]1[CH](O[P](O)(O)=O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=O)NC2=O" UBD 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)OP(=O)(O)O)O" UBD SMILES "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)OP(=O)(O)O)O" UBD InChI InChI 1.03 "InChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(14)10-5)8-6(13)7(23-25(18,19)20)4(22-8)3-21-24(15,16)17/h1-2,4,6-8,13H,3H2,(H,10,12,14)(H2,15,16,17)(H2,18,19,20)/t4-,6-,7-,8-/m1/s1" UBD InChIKey InChI 1.03 ZPVPRWPOZBXDKD-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 UBD "SYSTEMATIC NAME" ACDLabs 10.04 ;uridine 3',5'-bis(dihydrogen phosphate) ; UBD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-4-hydroxy-3-phosphonooxy-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 UBD "Create component" 2007-06-07 RCSB UBD "Modify descriptor" 2011-06-04 RCSB UBD "Initial release" 2013-03-27 RCSB #