data_A6U # _chem_comp.id A6U _chem_comp.name "1,5-anhydro-2-deoxy-2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-6-O-phosphono-D-altritol" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N2 O9 P" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms "((2R,3S,4S,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydro-2H-pyran-2-yl)methyl dihydrogen phosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-08-26 _chem_comp.pdbx_modified_date 2021-03-13 _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 338.208 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A6U _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 3OK2 _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 A6U P P P 0 1 N N N -4.571 3.528 35.499 4.281 0.668 -0.085 P A6U 1 A6U N1 N1 N 0 1 N N N -1.452 7.880 37.253 -2.551 -0.020 0.585 N1 A6U 2 A6U C2 C2 C 0 1 N N N -0.226 8.525 37.449 -3.658 -0.018 -0.180 C2 A6U 3 A6U O2 O2 O 0 1 N N N -0.062 9.700 37.772 -4.183 -1.073 -0.477 O2 A6U 4 A6U N3 N3 N 0 1 N N N 0.849 7.709 37.339 -4.192 1.136 -0.622 N3 A6U 5 A6U C4 C4 C 0 1 N N N 0.868 6.386 37.002 -3.621 2.315 -0.301 C4 A6U 6 A6U O4 O4 O 0 1 N N N 1.949 5.838 36.922 -4.104 3.360 -0.700 O4 A6U 7 A6U C5 C5 C 0 1 N N N -0.419 5.770 36.783 -2.456 2.328 0.503 C5 A6U 8 A6U C6 C6 C 0 1 N N N -1.508 6.515 36.970 -1.945 1.155 0.937 C6 A6U 9 A6U "C1'" "C1'" C 0 1 N N R -2.776 8.651 37.398 -1.993 -1.292 1.050 "C1'" A6U 10 A6U "C2'" "C2'" C 0 1 N N S -3.476 9.055 36.052 -1.527 -2.117 -0.153 "C2'" A6U 11 A6U "O2'" "O2'" O 0 1 N N N -4.614 9.920 36.321 -1.042 -3.385 0.295 "O2'" A6U 12 A6U "C3'" "C3'" C 0 1 N N S -4.116 7.932 35.312 -0.403 -1.363 -0.871 "C3'" A6U 13 A6U "O3'" "O3'" O 0 1 N N N -4.746 8.417 34.107 0.090 -2.157 -1.952 "O3'" A6U 14 A6U "C4'" "C4'" C 0 1 N N R -5.057 7.226 36.324 0.732 -1.090 0.121 "C4'" A6U 15 A6U "O4'" "O4'" O 0 1 N N N -4.398 6.900 37.569 0.224 -0.346 1.230 "O4'" A6U 16 A6U "C5'" "C5'" C 0 1 N N N -5.417 5.872 35.846 1.832 -0.285 -0.573 "C5'" A6U 17 A6U "O5'" "O5'" O 0 1 N N N -4.325 4.999 36.032 2.941 -0.129 0.316 "O5'" A6U 18 A6U "C6'" "C6'" C 0 1 N N N -3.817 8.003 38.274 -0.797 -1.021 1.967 "C6'" A6U 19 A6U OP1 OP1 O 0 1 N N N -5.682 3.739 34.547 4.840 0.097 -1.331 OP1 A6U 20 A6U OP2 OP2 O 0 1 N N N -3.340 2.842 35.013 3.932 2.223 -0.317 OP2 A6U 21 A6U OP3 OP3 O 0 1 N Y N -5.084 2.793 36.826 5.361 0.531 1.101 OP3 A6U 22 A6U H5 H5 H 0 1 N N N -0.497 4.737 36.477 -1.985 3.262 0.770 H5 A6U 23 A6U H6 H6 H 0 1 N N N -2.476 6.041 36.899 -1.057 1.145 1.551 H6 A6U 24 A6U "H1'" "H1'" H 0 1 N N N -2.404 9.558 37.897 -2.755 -1.845 1.599 "H1'" A6U 25 A6U "H2'" "H2'" H 0 1 N N N -2.657 9.501 35.469 -2.361 -2.267 -0.838 "H2'" A6U 26 A6U "HO2'" "HO2'" H 0 0 N N N -5.031 10.159 35.502 -0.730 -3.960 -0.416 "HO2'" A6U 27 A6U "H3'" "H3'" H 0 1 N N N -3.396 7.187 34.943 -0.786 -0.418 -1.256 "H3'" A6U 28 A6U "HO3'" "HO3'" H 0 0 N Y N -5.149 7.691 33.646 0.805 -1.740 -2.452 "HO3'" A6U 29 A6U "H4'" "H4'" H 0 1 N N N -5.896 7.928 36.441 1.141 -2.036 0.475 "H4'" A6U 30 A6U "H5'" "H5'" H 0 1 N N N -6.283 5.501 36.414 2.157 -0.811 -1.470 "H5'" A6U 31 A6U "H5'A" "H5'A" H 0 0 N N N -5.672 5.917 34.777 1.446 0.697 -0.847 "H5'A" A6U 32 A6U "H6'" "H6'" H 0 1 N N N -3.348 7.643 39.201 -1.115 -0.398 2.803 "H6'" A6U 33 A6U "H6'A" "H6'A" H 0 0 N N N -4.599 8.736 38.523 -0.408 -1.966 2.345 "H6'A" A6U 34 A6U HOP2 HOP2 H 0 0 N N N -3.443 2.618 34.096 3.560 2.662 0.460 HOP2 A6U 35 A6U HOP3 HOP3 H 0 0 N Y N -6.017 2.627 36.756 6.195 0.988 0.927 HOP3 A6U 36 A6U HN3 HN3 H 0 1 N N N 1.738 8.126 37.528 -4.990 1.120 -1.172 HN3 A6U 37 # # 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 A6U OP1 P DOUB N N 1 A6U OP2 P SING N N 2 A6U P "O5'" SING N N 3 A6U P OP3 SING N N 4 A6U C6 N1 SING N N 5 A6U N1 "C1'" SING N N 6 A6U N1 C2 SING N N 7 A6U N3 C2 SING N N 8 A6U C2 O2 DOUB N N 9 A6U C4 N3 SING N N 10 A6U C5 C4 SING N N 11 A6U O4 C4 DOUB N N 12 A6U C5 C6 DOUB N N 13 A6U C5 H5 SING N N 14 A6U C6 H6 SING N N 15 A6U "C2'" "C1'" SING N N 16 A6U "C1'" "C6'" SING N N 17 A6U "C1'" "H1'" SING N N 18 A6U "C3'" "C2'" SING N N 19 A6U "C2'" "O2'" SING N N 20 A6U "C2'" "H2'" SING N N 21 A6U "O2'" "HO2'" SING N N 22 A6U "O3'" "C3'" SING N N 23 A6U "C3'" "C4'" SING N N 24 A6U "C3'" "H3'" SING N N 25 A6U "O3'" "HO3'" SING N N 26 A6U "C5'" "C4'" SING N N 27 A6U "C4'" "O4'" SING N N 28 A6U "C4'" "H4'" SING N N 29 A6U "O4'" "C6'" SING N N 30 A6U "C5'" "O5'" SING N N 31 A6U "C5'" "H5'" SING N N 32 A6U "C5'" "H5'A" SING N N 33 A6U "C6'" "H6'" SING N N 34 A6U "C6'" "H6'A" SING N N 35 A6U OP2 HOP2 SING N N 36 A6U OP3 HOP3 SING N N 37 A6U N3 HN3 SING N N 38 # # 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 A6U SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OCC(N1C(=O)NC(=O)C=C1)C(O)C2O" A6U SMILES_CANONICAL CACTVS 3.370 "O[C@H]1[C@@H](O)[C@@H](CO[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O" A6U SMILES CACTVS 3.370 "O[CH]1[CH](O)[CH](CO[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O" A6U SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C1[C@H]([C@@H]([C@@H]([C@H](O1)COP(=O)(O)O)O)O)N2C=CC(=O)NC2=O" A6U SMILES "OpenEye OEToolkits" 1.7.0 "C1C(C(C(C(O1)COP(=O)(O)O)O)O)N2C=CC(=O)NC2=O" A6U InChI InChI 1.03 "InChI=1S/C10H15N2O9P/c13-7-1-2-12(10(16)11-7)5-3-20-6(9(15)8(5)14)4-21-22(17,18)19/h1-2,5-6,8-9,14-15H,3-4H2,(H,11,13,16)(H2,17,18,19)/t5-,6-,8+,9-/m1/s1" A6U InChIKey InChI 1.03 PXVDRBBXHNVTFS-MTSNSDSCSA-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 A6U "SYSTEMATIC NAME" ACDLabs 12.01 "1,5-anhydro-2-deoxy-2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-6-O-phosphono-D-altritol" A6U "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(2R,3S,4S,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxan-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 A6U "Create component" 2010-08-26 RCSB A6U "Modify descriptor" 2011-06-04 RCSB A6U "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id A6U _pdbx_chem_comp_synonyms.name "((2R,3S,4S,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydro-2H-pyran-2-yl)methyl dihydrogen phosphate" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##