data_PYO # _chem_comp.id PYO _chem_comp.name "1-(BETA-D-RIBOFURANOSYL)-PYRIMIDIN-2-ONE-5'-PHOSPHATE" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H13 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2000-09-13 _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 308.182 _chem_comp.one_letter_code U _chem_comp.three_letter_code PYO _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 ? _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 PYO OP3 O3P O 0 1 N Y N -16.115 106.143 5.841 -1.825 1.007 -4.603 OP3 PYO 1 PYO P P P 0 1 N N N -15.321 107.173 6.777 -0.773 0.044 -3.855 P PYO 2 PYO OP1 O1P O 0 1 N N N -15.917 107.091 8.137 0.502 -0.196 -4.805 OP1 PYO 3 PYO OP2 O2P O 0 1 N N N -15.244 108.489 6.093 -1.419 -1.253 -3.557 OP2 PYO 4 PYO "O5'" O5* O 0 1 N N N -13.845 106.592 6.871 -0.297 0.735 -2.481 "O5'" PYO 5 PYO "C5'" C5* C 0 1 N N N -12.839 107.388 7.463 0.629 -0.163 -1.867 "C5'" PYO 6 PYO "C4'" C4* C 0 1 N N R -11.479 106.765 7.312 1.123 0.436 -0.549 "C4'" PYO 7 PYO "O4'" O4* O 0 1 N N N -11.264 106.277 5.958 0.018 0.625 0.364 "O4'" PYO 8 PYO "C3'" C3* C 0 1 N N S -10.391 107.794 7.565 2.068 -0.547 0.176 "C3'" PYO 9 PYO "C1'" C1* C 0 1 N N R -10.199 106.995 5.356 0.615 0.707 1.676 "C1'" PYO 10 PYO "O3'" O3* O 0 1 N N N -9.271 107.152 8.144 3.433 -0.205 -0.070 "O3'" PYO 11 PYO "C2'" C2* C 0 1 N N R -10.087 108.295 6.157 1.726 -0.366 1.672 "C2'" PYO 12 PYO "O2'" O2* O 0 1 N N N -8.814 108.902 6.048 2.870 0.089 2.395 "O2'" PYO 13 PYO N1 N1 N 0 1 N N N -10.486 107.151 3.915 -0.377 0.409 2.711 N1 PYO 14 PYO C6 C6 C 0 1 N N N -11.658 106.769 3.415 -0.606 1.302 3.708 C6 PYO 15 PYO C2 C2 C 0 1 N N N -9.482 107.700 3.104 -1.066 -0.746 2.668 C2 PYO 16 PYO C5 C5 C 0 1 N N N -11.885 106.900 2.097 -1.531 1.010 4.661 C5 PYO 17 PYO O2 O2 O 0 1 N N N -8.371 108.077 3.581 -0.852 -1.540 1.767 O2 PYO 18 PYO N3 N3 N 0 1 N N N -9.730 107.823 1.767 -1.972 -1.041 3.603 N3 PYO 19 PYO C4 C4 C 0 1 N N N -10.900 107.427 1.299 -2.223 -0.201 4.588 C4 PYO 20 PYO HOP3 3HOP H 0 0 N N N -15.734 106.195 4.972 -2.084 0.558 -5.419 HOP3 PYO 21 PYO HOP1 1HOP H 0 0 N N N -15.446 107.701 8.691 0.893 0.671 -4.975 HOP1 PYO 22 PYO "H5''" 2H5* H 0 0 N N N -12.856 108.429 7.064 0.136 -1.115 -1.671 "H5''" PYO 23 PYO "H5'" 1H5* H 0 1 N N N -13.069 107.607 8.531 1.476 -0.322 -2.534 "H5'" PYO 24 PYO "H4'" H4* H 0 1 N N N -11.434 105.927 8.046 1.631 1.383 -0.731 "H4'" PYO 25 PYO "H3'" H3* H 0 1 N N N -10.672 108.617 8.262 1.869 -1.571 -0.140 "H3'" PYO 26 PYO "H1'" H1* H 0 1 N N N -9.207 106.485 5.387 1.044 1.696 1.836 "H1'" PYO 27 PYO HO3 3HO H 0 1 N Y N -8.590 107.795 8.302 3.973 -0.831 0.430 HO3 PYO 28 PYO "H2'" H2* H 0 1 N N N -10.767 109.106 5.806 1.356 -1.300 2.094 "H2'" PYO 29 PYO HO2 2HO H 0 1 N N N -8.624 109.214 5.170 3.548 -0.593 2.306 HO2 PYO 30 PYO HC6 HC6 H 0 1 N N N -12.429 106.350 4.082 -0.059 2.233 3.745 HC6 PYO 31 PYO HC5 HC5 H 0 1 N N N -12.855 106.582 1.680 -1.729 1.706 5.464 HC5 PYO 32 PYO HC4 HC4 H 0 1 N N N -11.058 107.539 0.213 -2.962 -0.450 5.336 HC4 PYO 33 # 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 PYO OP3 P SING N N 1 PYO OP3 HOP3 SING N N 2 PYO P OP1 SING N N 3 PYO P OP2 DOUB N N 4 PYO P "O5'" SING N N 5 PYO OP1 HOP1 SING N N 6 PYO "O5'" "C5'" SING N N 7 PYO "C5'" "C4'" SING N N 8 PYO "C5'" "H5''" SING N N 9 PYO "C5'" "H5'" SING N N 10 PYO "C4'" "O4'" SING N N 11 PYO "C4'" "C3'" SING N N 12 PYO "C4'" "H4'" SING N N 13 PYO "O4'" "C1'" SING N N 14 PYO "C3'" "O3'" SING N N 15 PYO "C3'" "C2'" SING N N 16 PYO "C3'" "H3'" SING N N 17 PYO "C1'" "C2'" SING N N 18 PYO "C1'" N1 SING N N 19 PYO "C1'" "H1'" SING N N 20 PYO "O3'" HO3 SING N N 21 PYO "C2'" "O2'" SING N N 22 PYO "C2'" "H2'" SING N N 23 PYO "O2'" HO2 SING N N 24 PYO N1 C6 SING N N 25 PYO N1 C2 SING N N 26 PYO C6 C5 DOUB N N 27 PYO C6 HC6 SING N N 28 PYO C2 O2 DOUB N N 29 PYO C2 N3 SING N N 30 PYO C5 C4 SING N N 31 PYO C5 HC5 SING N N 32 PYO N3 C4 DOUB N N 33 PYO C4 HC4 SING N N 34 # 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 PYO SMILES ACDLabs 10.04 "O=C1N=CC=CN1C2OC(C(O)C2O)COP(=O)(O)O" PYO SMILES_CANONICAL CACTVS 3.341 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC=NC2=O" PYO SMILES CACTVS 3.341 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC=NC2=O" PYO SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O" PYO SMILES "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1)C2C(C(C(O2)COP(=O)(O)O)O)O" PYO InChI InChI 1.03 "InChI=1S/C9H13N2O8P/c12-6-5(4-18-20(15,16)17)19-8(7(6)13)11-3-1-2-10-9(11)14/h1-3,5-8,12-13H,4H2,(H2,15,16,17)/t5-,6-,7-,8-/m1/s1" PYO InChIKey InChI 1.03 LBWXMAFPEFFHIJ-WCTZXXKLSA-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 PYO "SYSTEMATIC NAME" ACDLabs 10.04 "1-(5-O-phosphono-beta-D-ribofuranosyl)pyrimidin-2(1H)-one" PYO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-oxopyrimidin-1-yl)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 PYO "Create component" 2000-09-13 EBI PYO "Modify descriptor" 2011-06-04 RCSB #