data_3DU # _chem_comp.id 3DU _chem_comp.name "4-hydroxy-1-(5-O-phosphono-beta-D-ribofuranosyl)pyridin-2(1H)-one" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H14 N O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "3-deazauridine 5'-monophosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-12-05 _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 323.193 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 3DU _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 4NT0 _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 3DU OP3 OP3 O 0 1 N N N 7.433 4.151 -10.300 -5.194 -0.023 -0.395 OP3 3DU 1 3DU P P P 0 1 N N N 6.324 3.359 -9.665 -4.189 -0.994 0.093 P 3DU 2 3DU OP1 OP1 O 0 1 N N N 6.939 2.163 -8.928 -4.770 -1.766 1.380 OP1 3DU 3 3DU OP2 OP2 O 0 1 N N N 5.429 4.314 -8.866 -3.863 -2.059 -1.070 OP2 3DU 4 3DU "O5'" "O5'" O 0 1 N N N 5.391 2.767 -10.814 -2.842 -0.212 0.499 "O5'" 3DU 5 3DU "C5'" "C5'" C 0 1 N N N 5.833 1.696 -11.641 -2.143 0.653 -0.399 "C5'" 3DU 6 3DU "C4'" "C4'" C 0 1 N N R 4.717 1.166 -12.506 -0.912 1.229 0.302 "C4'" 3DU 7 3DU "O4'" "O4'" O 0 1 N N N 5.235 0.074 -13.316 0.075 0.197 0.516 "O4'" 3DU 8 3DU "C3'" "C3'" C 0 1 N N S 3.520 0.595 -11.751 -0.210 2.264 -0.606 "C3'" 3DU 9 3DU "O3'" "O3'" O 0 1 N N N 2.350 0.737 -12.553 -0.592 3.591 -0.240 "O3'" 3DU 10 3DU "C2'" "C2'" C 0 1 N N R 3.874 -0.886 -11.646 1.295 2.040 -0.337 "C2'" 3DU 11 3DU "O2'" "O2'" O 0 1 N N N 2.757 -1.741 -11.457 1.888 3.222 0.203 "O2'" 3DU 12 3DU "C1'" "C1'" C 0 1 N N R 4.558 -1.129 -12.995 1.324 0.897 0.702 "C1'" 3DU 13 3DU N1 N1 N 0 1 N N N 5.558 -2.213 -13.004 2.454 0.001 0.442 N1 3DU 14 3DU C2 C2 C 0 1 N N N 5.428 -3.251 -13.856 2.517 -0.664 -0.726 C2 3DU 15 3DU O2 O2 O 0 1 N N N 4.376 -3.326 -14.682 1.636 -0.517 -1.559 O2 3DU 16 3DU C3 C3 C 0 1 N N N 6.382 -4.296 -13.896 3.591 -1.523 -0.989 C3 3DU 17 3DU C4 C4 C 0 1 N N N 7.482 -4.215 -13.035 4.579 -1.676 -0.034 C4 3DU 18 3DU O4 O4 O 0 1 N N N 8.438 -5.191 -13.041 5.631 -2.500 -0.260 O4 3DU 19 3DU C5 C5 C 0 1 N N N 7.616 -3.120 -12.161 4.476 -0.963 1.176 C5 3DU 20 3DU C6 C6 C 0 1 N N N 6.629 -2.122 -12.176 3.425 -0.141 1.383 C6 3DU 21 3DU H1 H1 H 0 1 N N N 7.883 2.179 -9.030 -5.583 -2.260 1.209 H1 3DU 22 3DU H2 H2 H 0 1 N N N 5.764 5.200 -8.941 -3.210 -2.727 -0.820 H2 3DU 23 3DU H3 H3 H 0 1 N N N 6.207 0.882 -11.002 -1.830 0.088 -1.278 H3 3DU 24 3DU H4 H4 H 0 1 N N N 6.646 2.057 -12.288 -2.801 1.466 -0.706 H4 3DU 25 3DU H5 H5 H 0 1 N N N 4.363 1.975 -13.163 -1.196 1.687 1.250 H5 3DU 26 3DU H6 H6 H 0 1 N N N 3.417 1.054 -10.757 -0.444 2.073 -1.653 H6 3DU 27 3DU H7 H7 H 0 1 N N N 1.601 0.383 -12.087 -0.181 4.281 -0.779 H7 3DU 28 3DU H8 H8 H 0 1 N N N 4.610 -1.025 -10.840 1.806 1.740 -1.252 H8 3DU 29 3DU H9 H9 H 0 1 N N N 2.360 -1.562 -10.613 1.843 3.989 -0.385 H9 3DU 30 3DU H10 H10 H 0 1 N N N 3.784 -1.341 -13.747 1.385 1.303 1.711 H10 3DU 31 3DU H11 H11 H 0 1 N N N 6.264 -5.131 -14.571 3.646 -2.059 -1.925 H11 3DU 32 3DU H12 H12 H 0 1 N N N 9.108 -4.982 -12.401 6.265 -2.537 0.470 H12 3DU 33 3DU H13 H13 H 0 1 N N N 8.461 -3.049 -11.492 5.237 -1.069 1.934 H13 3DU 34 3DU H14 H14 H 0 1 N N N 6.723 -1.270 -11.519 3.352 0.408 2.310 H14 3DU 35 # # 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 3DU O2 C2 DOUB N N 1 3DU C3 C2 SING N N 2 3DU C3 C4 DOUB N N 3 3DU C2 N1 SING N N 4 3DU "O4'" "C1'" SING N N 5 3DU "O4'" "C4'" SING N N 6 3DU O4 C4 SING N N 7 3DU C4 C5 SING N N 8 3DU N1 "C1'" SING N N 9 3DU N1 C6 SING N N 10 3DU "C1'" "C2'" SING N N 11 3DU "O3'" "C3'" SING N N 12 3DU "C4'" "C3'" SING N N 13 3DU "C4'" "C5'" SING N N 14 3DU C6 C5 DOUB N N 15 3DU "C3'" "C2'" SING N N 16 3DU "C2'" "O2'" SING N N 17 3DU "C5'" "O5'" SING N N 18 3DU "O5'" P SING N N 19 3DU OP3 P DOUB N N 20 3DU P OP1 SING N N 21 3DU P OP2 SING N N 22 3DU OP1 H1 SING N N 23 3DU OP2 H2 SING N N 24 3DU "C5'" H3 SING N N 25 3DU "C5'" H4 SING N N 26 3DU "C4'" H5 SING N N 27 3DU "C3'" H6 SING N N 28 3DU "O3'" H7 SING N N 29 3DU "C2'" H8 SING N N 30 3DU "O2'" H9 SING N N 31 3DU "C1'" H10 SING N N 32 3DU C3 H11 SING N N 33 3DU O4 H12 SING N N 34 3DU C5 H13 SING N N 35 3DU C6 H14 SING N N 36 # # 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 3DU SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OC(N1C(=O)C=C(O)C=C1)C(O)C2O" 3DU InChI InChI 1.03 "InChI=1S/C10H14NO9P/c12-5-1-2-11(7(13)3-5)10-9(15)8(14)6(20-10)4-19-21(16,17)18/h1-3,6,8-10,12,14-15H,4H2,(H2,16,17,18)/t6-,8-,9-,10-/m1/s1" 3DU InChIKey InChI 1.03 BMAAJONJGSMHCR-PEBGCTIMSA-N 3DU SMILES_CANONICAL CACTVS 3.385 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=CC2=O)O" 3DU SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=CC2=O)O" 3DU SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=O)C=C1O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O" 3DU SMILES "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=O)C=C1O)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 3DU "SYSTEMATIC NAME" ACDLabs 12.01 "4-hydroxy-1-(5-O-phosphono-beta-D-ribofuranosyl)pyridin-2(1H)-one" 3DU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,4R,5R)-3,4-bis(oxidanyl)-5-(4-oxidanyl-2-oxidanylidene-pyridin-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 3DU "Create component" 2013-12-05 RCSB 3DU "Initial release" 2013-12-18 RCSB 3DU "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 3DU _pdbx_chem_comp_synonyms.name "3-deazauridine 5'-monophosphate" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##