data_UPP # _chem_comp.id UPP _chem_comp.name "PHENYL-URIDINE-5'-DIPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H18 N2 O12 P2" _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 2011-06-04 _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 480.257 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UPP _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 2UDP _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 UPP N1 N1 N 0 1 N N N -7.925 27.152 -20.805 -0.544 0.472 5.031 N1 UPP 1 UPP C2 C2 C 0 1 N N N -9.102 26.861 -21.441 -1.275 -0.633 4.800 C2 UPP 2 UPP N3 N3 N 0 1 N N N -9.759 25.798 -20.885 -2.424 -0.854 5.465 N3 UPP 3 UPP C4 C4 C 0 1 N N N -9.345 25.025 -19.806 -2.868 0.040 6.371 C4 UPP 4 UPP C5 C5 C 0 1 N N N -8.084 25.381 -19.252 -2.111 1.210 6.620 C5 UPP 5 UPP C6 C6 C 0 1 N N N -7.477 26.453 -19.699 -0.959 1.404 5.942 C6 UPP 6 UPP O2 O2 O 0 1 N N N -9.522 27.456 -22.426 -0.887 -1.448 3.985 O2 UPP 7 UPP O4 O4 O 0 1 N N N -10.125 24.178 -19.410 -3.910 -0.156 6.969 O4 UPP 8 UPP C1B C1* C 0 1 N N R -7.101 28.151 -21.481 0.705 0.682 4.295 C1B UPP 9 UPP C2B C2* C 0 1 N N R -6.671 29.357 -20.679 1.696 -0.467 4.579 C2B UPP 10 UPP "O2'" O2* O 0 1 N N N -7.624 30.425 -20.809 2.640 -0.082 5.580 "O2'" UPP 11 UPP C3B C3* C 0 1 N N S -5.388 29.743 -21.436 2.405 -0.694 3.225 C3B UPP 12 UPP C4B C4* C 0 1 N N R -4.818 28.371 -21.799 1.758 0.343 2.280 C4B UPP 13 UPP "O4'" O4* O 0 1 N N N -5.957 27.507 -21.946 0.468 0.623 2.871 "O4'" UPP 14 UPP "O3'" O3* O 0 1 N N N -5.604 30.587 -22.585 3.808 -0.453 3.347 "O3'" UPP 15 UPP C5B C5* C 0 1 N N N -3.842 27.704 -20.838 1.585 -0.239 0.876 C5B UPP 16 UPP "O5'" O5* O 0 1 N N N -4.379 27.796 -19.509 0.920 0.713 0.044 "O5'" UPP 17 UPP PA PA P 0 1 N N R -3.873 26.843 -18.340 0.772 0.038 -1.409 PA UPP 18 UPP O1A O1A O 0 1 N N N -4.792 26.915 -17.167 2.115 -0.280 -1.944 O1A UPP 19 UPP O2A O2A O 0 1 N N N -3.643 25.457 -18.828 -0.090 -1.315 -1.287 O2A UPP 20 UPP O3A O3A O 0 1 N N N -2.405 27.466 -17.954 0.027 1.062 -2.403 O3A UPP 21 UPP PB PB P 0 1 N N S -1.923 28.920 -17.662 -0.085 0.325 -3.831 PB UPP 22 UPP O1B O1B O 0 1 N N N -1.731 29.520 -19.106 1.270 0.003 -4.328 O1B UPP 23 UPP O2B O2B O 0 1 N N N -2.823 29.799 -16.919 -0.934 -1.032 -3.668 O2B UPP 24 UPP O3B O3B O 0 1 N N N -0.668 28.826 -16.890 -0.824 1.298 -4.879 O3B UPP 25 UPP "C1'" "C1'" C 0 1 Y N N -0.469 28.261 -15.534 -0.891 0.627 -6.059 "C1'" UPP 26 UPP "C2'" "C2'" C 0 1 Y N N -0.129 26.899 -15.328 -1.986 -0.176 -6.340 "C2'" UPP 27 UPP "C3'" "C3'" C 0 1 Y N N 0.188 26.446 -14.022 -2.051 -0.858 -7.540 "C3'" UPP 28 UPP "C4'" "C4'" C 0 1 Y N N 0.192 27.356 -12.936 -1.026 -0.740 -8.460 "C4'" UPP 29 UPP "C5'" "C5'" C 0 1 Y N N -0.172 28.713 -13.139 0.067 0.059 -8.181 "C5'" UPP 30 UPP "C6'" "C6'" C 0 1 Y N N -0.477 29.170 -14.445 0.133 0.748 -6.986 "C6'" UPP 31 UPP HN3 HN3 H 0 1 N N N -10.649 25.556 -21.319 -2.937 -1.658 5.288 HN3 UPP 32 UPP H5 H5 H 0 1 N N N -7.566 24.814 -18.459 -2.450 1.938 7.342 H5 UPP 33 UPP H6 H6 H 0 1 N N N -6.580 26.769 -19.139 -0.368 2.291 6.119 H6 UPP 34 UPP "H1'" H1* H 0 1 N N N -7.756 28.571 -22.278 1.147 1.641 4.567 "H1'" UPP 35 UPP H2B H2* H 0 1 N N N -6.559 29.165 -19.586 1.161 -1.366 4.885 H2B UPP 36 UPP "HO2'" *HO2 H 0 0 N N N -7.353 31.183 -20.304 3.267 -0.813 5.669 "HO2'" UPP 37 UPP H3B H3* H 0 1 N N N -4.701 30.375 -20.826 2.222 -1.706 2.863 H3B UPP 38 UPP H4B H4* H 0 1 N N N -4.195 28.539 -22.708 2.364 1.248 2.243 H4B UPP 39 UPP "HO3'" *HO3 H 0 0 N N N -4.812 30.825 -23.052 4.151 -1.109 3.970 "HO3'" UPP 40 UPP "H5'1" 1H5* H 0 0 N N N -3.601 26.655 -21.131 2.564 -0.469 0.455 "H5'1" UPP 41 UPP "H5'2" 2H5* H 0 0 N N N -2.811 28.123 -20.913 0.990 -1.150 0.932 "H5'2" UPP 42 UPP HOA2 2HOA H 0 0 N N N -3.340 24.887 -18.129 -0.955 -1.063 -0.936 HOA2 UPP 43 UPP HOB2 2HOB H 0 0 N N N -2.529 30.684 -16.741 -1.809 -0.777 -3.342 HOB2 UPP 44 UPP "H2'" "H2'" H 0 1 N N N -0.111 26.196 -16.178 -2.787 -0.269 -5.622 "H2'" UPP 45 UPP "H3'" "H3'" H 0 1 N N N 0.431 25.384 -13.850 -2.903 -1.484 -7.759 "H3'" UPP 46 UPP "H4'" "H4'" H 0 1 N N N 0.479 27.007 -11.929 -1.078 -1.274 -9.397 "H4'" UPP 47 UPP "H5'" "H5'" H 0 1 N N N -0.217 29.409 -12.285 0.867 0.149 -8.901 "H5'" UPP 48 UPP "H6'" "H6'" H 0 1 N N N -0.720 30.232 -14.613 0.987 1.372 -6.769 "H6'" UPP 49 # 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 UPP N1 C2 SING N N 1 UPP N1 C6 SING N N 2 UPP N1 C1B SING N N 3 UPP C2 N3 SING N N 4 UPP C2 O2 DOUB N N 5 UPP N3 C4 SING N N 6 UPP N3 HN3 SING N N 7 UPP C4 C5 SING N N 8 UPP C4 O4 DOUB N N 9 UPP C5 C6 DOUB N N 10 UPP C5 H5 SING N N 11 UPP C6 H6 SING N N 12 UPP C1B C2B SING N N 13 UPP C1B "O4'" SING N N 14 UPP C1B "H1'" SING N N 15 UPP C2B "O2'" SING N N 16 UPP C2B C3B SING N N 17 UPP C2B H2B SING N N 18 UPP "O2'" "HO2'" SING N N 19 UPP C3B C4B SING N N 20 UPP C3B "O3'" SING N N 21 UPP C3B H3B SING N N 22 UPP C4B "O4'" SING N N 23 UPP C4B C5B SING N N 24 UPP C4B H4B SING N N 25 UPP "O3'" "HO3'" SING N N 26 UPP C5B "O5'" SING N N 27 UPP C5B "H5'1" SING N N 28 UPP C5B "H5'2" SING N N 29 UPP "O5'" PA SING N N 30 UPP PA O1A DOUB N N 31 UPP PA O2A SING N N 32 UPP PA O3A SING N N 33 UPP O2A HOA2 SING N N 34 UPP O3A PB SING N N 35 UPP PB O1B DOUB N N 36 UPP PB O2B SING N N 37 UPP PB O3B SING N N 38 UPP O2B HOB2 SING N N 39 UPP O3B "C1'" SING N N 40 UPP "C1'" "C2'" DOUB Y N 41 UPP "C1'" "C6'" SING Y N 42 UPP "C2'" "C3'" SING Y N 43 UPP "C2'" "H2'" SING N N 44 UPP "C3'" "C4'" DOUB Y N 45 UPP "C3'" "H3'" SING N N 46 UPP "C4'" "C5'" SING Y N 47 UPP "C4'" "H4'" SING N N 48 UPP "C5'" "C6'" DOUB Y N 49 UPP "C5'" "H5'" SING N N 50 UPP "C6'" "H6'" SING N N 51 # 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 UPP SMILES ACDLabs 10.04 "O=P(O)(Oc1ccccc1)OP(=O)(O)OCC3OC(N2C(=O)NC(=O)C=C2)C(O)C3O" UPP SMILES_CANONICAL CACTVS 3.341 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P@](O)(=O)O[P@](O)(=O)Oc2ccccc2)N3C=CC(=O)NC3=O" UPP SMILES CACTVS 3.341 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)Oc2ccccc2)N3C=CC(=O)NC3=O" UPP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1ccc(cc1)O[P@](=O)(O)O[P@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O" UPP SMILES "OpenEye OEToolkits" 1.5.0 "c1ccc(cc1)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O" UPP InChI InChI 1.03 "InChI=1S/C15H18N2O12P2/c18-11-6-7-17(15(21)16-11)14-13(20)12(19)10(27-14)8-26-30(22,23)29-31(24,25)28-9-4-2-1-3-5-9/h1-7,10,12-14,19-20H,8H2,(H,22,23)(H,24,25)(H,16,18,21)/t10-,12-,13-,14-/m1/s1" UPP InChIKey InChI 1.03 ZHUWBKDWWGKIEN-FMKGYKFTSA-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 UPP "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-[(R)-hydroxy{[(S)-hydroxy(phenoxy)phosphoryl]oxy}phosphoryl]uridine" UPP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl (hydroxy-phenoxy-phosphoryl) hydrogen 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 UPP "Create component" 1999-07-08 RCSB UPP "Modify descriptor" 2011-06-04 RCSB #