data_UP6 # _chem_comp.id UP6 _chem_comp.name "6-AZA URIDINE 5'-MONOPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C8 H12 N3 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms 6-AZA-UMP _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2000-02-02 _chem_comp.pdbx_modified_date 2020-06-17 _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 325.169 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UP6 _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 1DVJ _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 UP6 N1 N1 N 0 1 Y N N 53.335 75.495 2.023 0.010 0.147 2.391 N1 UP6 1 UP6 C2 C2 C 0 1 Y N N 52.823 74.700 0.993 -0.663 1.081 3.085 C2 UP6 2 UP6 N3 N3 N 0 1 Y N N 53.110 75.112 -0.293 -1.454 0.740 4.120 N3 UP6 3 UP6 C4 C4 C 0 1 Y N N 53.870 76.265 -0.607 -1.572 -0.553 4.481 C4 UP6 4 UP6 C5 C5 C 0 1 Y N N 54.345 77.015 0.517 -0.835 -1.575 3.731 C5 UP6 5 UP6 N6 N6 N 0 1 Y N N 54.098 76.655 1.752 -0.083 -1.207 2.732 N6 UP6 6 UP6 O2 O2 O 0 1 N N N 52.193 73.699 1.263 -0.563 2.251 2.768 O2 UP6 7 UP6 O4 O4 O 0 1 N N N 54.077 76.532 -1.777 -2.281 -0.869 5.418 O4 UP6 8 UP6 "C1'" C1* C 0 1 N N R 53.144 75.133 3.423 0.858 0.553 1.268 "C1'" UP6 9 UP6 "C2'" C2* C 0 1 N N R 51.742 74.939 3.962 2.046 -0.421 1.111 "C2'" UP6 10 UP6 "C3'" C3* C 0 1 N N S 51.964 73.892 5.046 2.238 -0.536 -0.417 "C3'" UP6 11 UP6 "C4'" C4* C 0 1 N N R 53.093 73.058 4.495 1.143 0.379 -1.006 "C4'" UP6 12 UP6 "O2'" O2* O 0 1 N N N 51.197 76.165 4.446 3.221 0.114 1.724 "O2'" UP6 13 UP6 "O3'" O3* O 0 1 N N N 52.317 74.541 6.256 3.536 -0.073 -0.795 "O3'" UP6 14 UP6 "O4'" O4* O 0 1 N N N 53.867 73.949 3.707 0.131 0.451 0.024 "O4'" UP6 15 UP6 "C5'" C5* C 0 1 N N N 52.761 71.824 3.671 0.561 -0.228 -2.283 "C5'" UP6 16 UP6 "O5'" O5* O 0 1 N N N 51.935 71.040 4.531 -0.497 0.601 -2.766 "O5'" UP6 17 UP6 P P P 0 1 N N N 51.261 69.641 4.007 -1.061 -0.094 -4.104 P UP6 18 UP6 O1P O1P O 0 1 N N N 50.546 69.873 2.689 -1.561 -1.449 -3.782 O1P UP6 19 UP6 O2P O2P O 0 1 N N N 50.309 69.308 5.084 -2.262 0.793 -4.705 O2P UP6 20 UP6 O3P O3P O 0 1 N N N 52.363 68.521 3.884 0.121 -0.203 -5.191 O3P UP6 21 UP6 HN3 HN3 H 0 1 N N N 52.741 74.535 -1.049 -1.936 1.426 4.608 HN3 UP6 22 UP6 H5 H5 H 0 1 N N N 54.944 77.936 0.424 -0.915 -2.617 4.002 H5 UP6 23 UP6 "H1'" H1* H 0 1 N N N 53.508 76.051 3.940 1.219 1.571 1.414 "H1'" UP6 24 UP6 "H2'" H2* H 0 1 N N N 50.991 74.612 3.205 1.802 -1.393 1.540 "H2'" UP6 25 UP6 "H3'" H3* H 0 1 N N N 51.068 73.270 5.280 2.092 -1.566 -0.743 "H3'" UP6 26 UP6 "H4'" H4* H 0 1 N N N 53.603 72.611 5.380 1.549 1.370 -1.209 "H4'" UP6 27 UP6 "HO2'" *HO2 H 0 0 N N N 50.317 76.043 4.784 3.939 -0.506 1.542 "HO2'" UP6 28 UP6 "HO3'" *HO3 H 0 0 N N N 52.455 73.888 6.932 4.177 -0.663 -0.375 "HO3'" UP6 29 UP6 "H5'1" 1H5* H 0 0 N N N 52.305 72.046 2.678 1.341 -0.299 -3.041 "H5'1" UP6 30 UP6 "H5'2" 2H5* H 0 0 N N N 53.653 71.283 3.277 0.172 -1.223 -2.067 "H5'2" UP6 31 UP6 HOP2 2HOP H 0 0 N N N 49.918 68.497 4.780 -2.570 0.342 -5.503 HOP2 UP6 32 UP6 HOP3 3HOP H 0 0 N N N 51.972 67.710 3.580 0.418 0.698 -5.373 HOP3 UP6 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 UP6 N1 C2 SING Y N 1 UP6 N1 N6 SING Y N 2 UP6 N1 "C1'" SING N N 3 UP6 C2 N3 SING Y N 4 UP6 C2 O2 DOUB N N 5 UP6 N3 C4 SING Y N 6 UP6 N3 HN3 SING N N 7 UP6 C4 C5 SING Y N 8 UP6 C4 O4 DOUB N N 9 UP6 C5 N6 DOUB Y N 10 UP6 C5 H5 SING N N 11 UP6 "C1'" "C2'" SING N N 12 UP6 "C1'" "O4'" SING N N 13 UP6 "C1'" "H1'" SING N N 14 UP6 "C2'" "C3'" SING N N 15 UP6 "C2'" "O2'" SING N N 16 UP6 "C2'" "H2'" SING N N 17 UP6 "C3'" "C4'" SING N N 18 UP6 "C3'" "O3'" SING N N 19 UP6 "C3'" "H3'" SING N N 20 UP6 "C4'" "O4'" SING N N 21 UP6 "C4'" "C5'" SING N N 22 UP6 "C4'" "H4'" SING N N 23 UP6 "O2'" "HO2'" SING N N 24 UP6 "O3'" "HO3'" SING N N 25 UP6 "C5'" "O5'" SING N N 26 UP6 "C5'" "H5'1" SING N N 27 UP6 "C5'" "H5'2" SING N N 28 UP6 "O5'" P SING N N 29 UP6 P O1P DOUB N N 30 UP6 P O2P SING N N 31 UP6 P O3P SING N N 32 UP6 O2P HOP2 SING N N 33 UP6 O3P HOP3 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 UP6 SMILES ACDLabs 10.04 "O=C1N(N=CC(=O)N1)C2OC(C(O)C2O)COP(=O)(O)O" UP6 SMILES_CANONICAL CACTVS 3.341 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2N=CC(=O)NC2=O" UP6 SMILES CACTVS 3.341 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2N=CC(=O)NC2=O" UP6 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=NN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O" UP6 SMILES "OpenEye OEToolkits" 1.5.0 "C1=NN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O" UP6 InChI InChI 1.03 "InChI=1S/C8H12N3O9P/c12-4-1-9-11(8(15)10-4)7-6(14)5(13)3(20-7)2-19-21(16,17)18/h1,3,5-7,13-14H,2H2,(H,10,12,15)(H2,16,17,18)/t3-,5-,6-,7-/m1/s1" UP6 InChIKey InChI 1.03 LRVZOSYMNMNQFR-SHUUEZRQSA-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 UP6 "SYSTEMATIC NAME" ACDLabs 10.04 "2-(5-O-phosphono-beta-D-ribofuranosyl)-1,2,4-triazine-3,5(2H,4H)-dione" UP6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(3,5-dioxo-1,2,4-triazin-2-yl)-3,4-dihydroxy-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 UP6 "Create component" 2000-02-02 RCSB UP6 "Modify descriptor" 2011-06-04 RCSB UP6 "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id UP6 _pdbx_chem_comp_synonyms.name 6-AZA-UMP _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##