data_UF2 # _chem_comp.id UF2 _chem_comp.name "1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H12 F N2 O8 P" _chem_comp.mon_nstd_parent_comp_id DU _chem_comp.pdbx_synonyms "2'-fluoro-2'-deoxyuridine" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2011-11-04 _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 326.172 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UF2 _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 3UFJ _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 UF2 P P P 0 1 N N N -30.781 57.510 -9.715 -4.273 1.002 -0.011 P UF2 1 UF2 O1P O1P O 0 1 N N N -32.117 57.873 -10.259 -4.070 1.663 1.298 O1P UF2 2 UF2 "O5'" "O5'" O 0 1 N N N -29.671 58.277 -10.567 -2.913 0.266 -0.458 "O5'" UF2 3 UF2 "C5'" "C5'" C 0 1 N N N -29.796 58.503 -11.988 -2.241 -0.692 0.361 "C5'" UF2 4 UF2 "C4'" "C4'" C 0 1 N N R -29.023 59.743 -12.368 -0.989 -1.192 -0.361 "C4'" UF2 5 UF2 "C3'" "C3'" C 0 1 N N R -27.539 59.688 -12.004 -0.314 -2.321 0.450 "C3'" UF2 6 UF2 "O3'" "O3'" O 0 1 N N N -26.758 59.516 -13.198 -0.683 -3.600 -0.069 "O3'" UF2 7 UF2 "C2'" "C2'" C 0 1 N N S -27.245 61.009 -11.303 1.198 -2.072 0.254 "C2'" UF2 8 UF2 "F2'" "F2'" F 0 1 N N N -26.803 60.785 -10.033 1.817 -1.817 1.482 "F2'" UF2 9 UF2 "C1'" "C1'" C 0 1 N N R -28.567 61.752 -11.218 1.258 -0.823 -0.653 "C1'" UF2 10 UF2 "O4'" "O4'" O 0 1 N N N -29.578 60.854 -11.643 0.003 -0.145 -0.431 "O4'" UF2 11 UF2 N1 N1 N 0 1 N N N -28.948 62.252 -9.887 2.379 0.036 -0.263 N1 UF2 12 UF2 C6 C6 C 0 1 N N N -29.825 61.542 -9.099 2.378 0.633 0.968 C6 UF2 13 UF2 C5 C5 C 0 1 N N N -30.239 61.976 -7.905 3.411 1.426 1.327 C5 UF2 14 UF2 C4 C4 C 0 1 N N N -29.771 63.234 -7.407 4.478 1.622 0.417 C4 UF2 15 UF2 N3 N3 N 0 1 N N N -28.891 63.893 -8.241 4.440 1.016 -0.787 N3 UF2 16 UF2 C2 C2 C 0 1 N N N -28.454 63.477 -9.475 3.401 0.227 -1.117 C2 UF2 17 UF2 O2 O2 O 0 1 N N N -27.690 64.144 -10.150 3.384 -0.318 -2.204 O2 UF2 18 UF2 O4 O4 O 0 1 N N N -30.079 63.743 -6.328 5.420 2.332 0.718 O4 UF2 19 UF2 O2P O2P O 0 1 N N N -30.525 57.659 -8.260 -5.455 -0.084 0.115 O2P UF2 20 UF2 O1 O1 O 0 1 N Y N -30.414 55.982 -10.011 -4.674 2.106 -1.113 O1 UF2 21 UF2 H1 H1 H 0 1 N N N -30.857 58.638 -12.246 -1.956 -0.228 1.305 H1 UF2 22 UF2 H2 H2 H 0 1 N N N -29.393 57.637 -12.534 -2.907 -1.533 0.557 H2 UF2 23 UF2 H3 H3 H 0 1 N N N -29.103 59.836 -13.461 -1.243 -1.544 -1.361 H3 UF2 24 UF2 H4 H4 H 0 1 N N N -27.286 58.843 -11.347 -0.580 -2.244 1.505 H4 UF2 25 UF2 H5 H5 H 0 1 N N N -25.836 59.482 -12.972 -0.288 -4.345 0.404 H5 UF2 26 UF2 H6 H6 H 0 1 N N N -26.476 61.573 -11.852 1.664 -2.925 -0.240 H6 UF2 27 UF2 H7 H7 H 0 1 N N N -28.451 62.648 -11.846 1.352 -1.117 -1.699 H7 UF2 28 UF2 H8 H8 H 0 1 N N N -30.194 60.594 -9.461 1.556 0.472 1.649 H8 UF2 29 UF2 H9 H9 H 0 1 N N N -30.923 61.381 -7.319 3.423 1.903 2.296 H9 UF2 30 UF2 H10 H10 H 0 1 N N N -28.533 64.767 -7.912 5.167 1.145 -1.416 H10 UF2 31 UF2 H11 H11 H 0 1 N N N -31.306 57.992 -7.833 -5.643 -0.557 -0.707 H11 UF2 32 UF2 H12 H12 H 0 1 N N N -31.125 55.572 -10.489 -5.486 2.590 -0.908 H12 UF2 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 UF2 "O3'" "C3'" SING N N 1 UF2 "C4'" "C3'" SING N N 2 UF2 "C4'" "C5'" SING N N 3 UF2 "C4'" "O4'" SING N N 4 UF2 "C3'" "C2'" SING N N 5 UF2 "C5'" "O5'" SING N N 6 UF2 "O4'" "C1'" SING N N 7 UF2 "C2'" "C1'" SING N N 8 UF2 "C2'" "F2'" SING N N 9 UF2 "C1'" N1 SING N N 10 UF2 "O5'" P SING N N 11 UF2 O1P P DOUB N N 12 UF2 O2 C2 DOUB N N 13 UF2 N1 C2 SING N N 14 UF2 N1 C6 SING N N 15 UF2 P O2P SING N N 16 UF2 C2 N3 SING N N 17 UF2 C6 C5 DOUB N N 18 UF2 N3 C4 SING N N 19 UF2 C5 C4 SING N N 20 UF2 C4 O4 DOUB N N 21 UF2 P O1 SING N N 22 UF2 "C5'" H1 SING N N 23 UF2 "C5'" H2 SING N N 24 UF2 "C4'" H3 SING N N 25 UF2 "C3'" H4 SING N N 26 UF2 "O3'" H5 SING N N 27 UF2 "C2'" H6 SING N N 28 UF2 "C1'" H7 SING N N 29 UF2 C6 H8 SING N N 30 UF2 C5 H9 SING N N 31 UF2 N3 H10 SING N N 32 UF2 O2P H11 SING N N 33 UF2 O1 H12 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 UF2 SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(F)C2O" UF2 InChI InChI 1.03 "InChI=1S/C9H12FN2O8P/c10-6-7(14)4(3-19-21(16,17)18)20-8(6)12-2-1-5(13)11-9(12)15/h1-2,4,6-8,14H,3H2,(H,11,13,15)(H2,16,17,18)/t4-,6+,7-,8-/m1/s1" UF2 InChIKey InChI 1.03 RTGGYPQTXNSBPD-PXBUCIJWSA-N UF2 SMILES_CANONICAL CACTVS 3.370 "O[C@H]1[C@H](F)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O" UF2 SMILES CACTVS 3.370 "O[CH]1[CH](F)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O" UF2 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "C1=CN(C(=O)NC1=O)[C@H]2[C@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)F" UF2 SMILES "OpenEye OEToolkits" 1.7.2 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)F" # # 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 UF2 "SYSTEMATIC NAME" ACDLabs 12.01 "1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione" UF2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "[(2R,3R,4S,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-fluoranyl-3-oxidanyl-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 UF2 "Create component" 2011-11-04 RCSB UF2 "Modify parent residue" 2011-11-04 RCSB UF2 "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id UF2 _pdbx_chem_comp_synonyms.name "2'-fluoro-2'-deoxyuridine" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##