data_4Y3 # _chem_comp.id 4Y3 _chem_comp.name "[[(2~{S},5~{R})-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3$l^{4}-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C8 H15 F N3 O12 P3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-06-19 _chem_comp.pdbx_modified_date 2024-02-24 _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 489.202 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 4Y3 _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 5C53 _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.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 4Y3 N1 N1 N 0 1 N N N N N N 24.269 51.164 -33.886 24.269 51.164 -33.886 N1 4Y3 1 4Y3 C2 C1 C 0 1 N N N N N N 24.449 49.935 -33.414 24.449 49.935 -33.414 C2 4Y3 2 4Y3 C4 C2 C 0 1 N N N N N N 22.179 49.497 -33.294 22.179 49.497 -33.294 C4 4Y3 3 4Y3 C5 C3 C 0 1 N N N N N N 21.917 50.799 -33.794 21.917 50.799 -33.794 C5 4Y3 4 4Y3 PA P1 P 0 1 N N N N N N 22.497 55.577 -36.693 22.497 55.577 -36.693 PA 4Y3 5 4Y3 PB P2 P 0 1 N N N N N N 23.237 55.554 -39.332 23.237 55.554 -39.332 PB 4Y3 6 4Y3 PG P3 P 0 1 N N N N N N 21.190 57.138 -40.427 21.190 57.138 -40.427 PG 4Y3 7 4Y3 "C5'" C4 C 0 1 N N N N N N 24.888 55.283 -35.614 24.888 55.283 -35.614 "C5'" 4Y3 8 4Y3 "O5'" O1 O 0 1 N N N N N N 23.764 54.680 -36.222 23.764 54.680 -36.222 "O5'" 4Y3 9 4Y3 "C4'" C5 C 0 1 N N S N N N 25.737 54.201 -34.913 25.737 54.201 -34.913 "C4'" 4Y3 10 4Y3 "O4'" O2 O 0 1 N N N N N N 25.024 53.554 -34.054 25.024 53.554 -34.054 "O4'" 4Y3 11 4Y3 S S S 0 1 N N N N N N 26.255 53.134 -35.950 26.255 53.134 -35.950 S 4Y3 12 4Y3 "C2'" C7 C 0 1 N N N N N N 25.821 51.785 -35.417 25.821 51.785 -35.417 "C2'" 4Y3 13 4Y3 "C1'" C8 C 0 1 N N R N N N 25.400 51.987 -34.174 25.400 51.987 -34.174 "C1'" 4Y3 14 4Y3 O1A O3 O 0 1 N N N N N N 21.278 55.179 -35.851 21.278 55.179 -35.851 O1A 4Y3 15 4Y3 O1B O4 O 0 1 N N N N N N 23.446 54.272 -40.080 23.446 54.272 -40.080 O1B 4Y3 16 4Y3 O1G O5 O 0 1 N N N N N N 20.750 57.717 -39.064 20.750 57.717 -39.064 O1G 4Y3 17 4Y3 O2 O6 O 0 1 N N N N N N 25.775 49.467 -33.209 25.775 49.467 -33.209 O2 4Y3 18 4Y3 O2A O7 O 0 1 N N N N N N 22.779 57.041 -36.515 22.779 57.041 -36.515 O2A 4Y3 19 4Y3 O2B O8 O 0 1 N N N N N N 24.535 56.014 -38.706 24.535 56.014 -38.706 O2B 4Y3 20 4Y3 O2G O9 O 0 1 N N N N N N 21.039 58.178 -41.468 21.039 58.178 -41.468 O2G 4Y3 21 4Y3 N3 N2 N 0 1 N N N N N N 23.440 49.118 -33.123 23.440 49.118 -33.123 N3 4Y3 22 4Y3 O3A O10 O 0 1 N N N N N N 22.196 55.304 -38.184 22.196 55.304 -38.184 O3A 4Y3 23 4Y3 O3B O11 O 0 1 N N N N N N 22.707 56.668 -40.334 22.707 56.668 -40.334 O3B 4Y3 24 4Y3 O3G O12 O 0 1 N N N N N N 20.314 55.950 -40.784 20.314 55.950 -40.784 O3G 4Y3 25 4Y3 N4 N3 N 0 1 N N N N N N 21.086 48.591 -32.972 21.086 48.591 -32.972 N4 4Y3 26 4Y3 C6 C9 C 0 1 N N N N N N 23.024 51.623 -34.086 23.024 51.623 -34.086 C6 4Y3 27 4Y3 F F1 F 0 1 N N N N N N 20.688 51.215 -33.978 20.688 51.215 -33.978 F 4Y3 28 4Y3 H1 H1 H 0 1 N N N N N N 25.495 55.785 -36.382 25.495 55.785 -36.382 H1 4Y3 29 4Y3 H2 H2 H 0 1 N N N N N N 24.551 56.022 -34.872 24.551 56.022 -34.872 H2 4Y3 30 4Y3 H3 H3 H 0 1 N N N N N N 26.611 54.685 -34.453 26.611 54.685 -34.453 H3 4Y3 31 4Y3 H4 H4 H 0 1 N N N N N N 27.551 53.187 -36.043 27.551 53.187 -36.043 H4 4Y3 32 4Y3 H5 H5 H 0 1 N N N N N N 25.728 53.348 -37.119 25.728 53.348 -37.119 H5 4Y3 33 4Y3 H6 H6 H 0 1 N N N N N N 25.005 51.378 -36.033 25.005 51.378 -36.033 H6 4Y3 34 4Y3 H7 H7 H 0 1 N N N N N N 26.669 51.084 -35.422 26.669 51.084 -35.422 H7 4Y3 35 4Y3 H8 H8 H 0 1 N N N N N N 26.199 51.786 -33.445 26.199 51.786 -33.445 H8 4Y3 36 4Y3 H9 H9 H 0 1 N N N N N N 20.950 55.941 -35.388 20.950 55.941 -35.388 H9 4Y3 37 4Y3 H10 H10 H 0 1 N N N N N N 20.474 58.619 -39.177 20.474 58.619 -39.177 H10 4Y3 38 4Y3 H11 H11 H 0 1 N N N N N N 25.225 55.395 -38.914 25.225 55.395 -38.914 H11 4Y3 39 4Y3 H12 H12 H 0 1 N N N N N N 19.856 56.127 -41.598 19.856 56.126 -41.598 H12 4Y3 40 4Y3 H13 H13 H 0 1 N N N N N N 21.282 47.676 -32.619 21.282 47.676 -32.619 H13 4Y3 41 4Y3 H14 H14 H 0 1 N N N N N N 20.139 48.884 -33.103 20.139 48.884 -33.103 H14 4Y3 42 4Y3 H15 H15 H 0 1 N N N N N N 22.870 52.621 -34.470 22.870 52.621 -34.470 H15 4Y3 43 # 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 4Y3 O2G PG DOUB N N 1 4Y3 O3G PG SING N N 2 4Y3 PG O3B SING N N 3 4Y3 PG O1G SING N N 4 4Y3 O3B PB SING N N 5 4Y3 O1B PB DOUB N N 6 4Y3 PB O2B SING N N 7 4Y3 PB O3A SING N N 8 4Y3 O3A PA SING N N 9 4Y3 PA O2A DOUB N N 10 4Y3 PA "O5'" SING N N 11 4Y3 PA O1A SING N N 12 4Y3 "O5'" "C5'" SING N N 13 4Y3 S "C2'" SING N N 14 4Y3 S "C4'" SING N N 15 4Y3 "C5'" "C4'" SING N N 16 4Y3 "C2'" "C1'" SING N N 17 4Y3 "C4'" "O4'" SING N N 18 4Y3 "C1'" "O4'" SING N N 19 4Y3 "C1'" N1 SING N N 20 4Y3 C6 N1 SING N N 21 4Y3 C6 C5 DOUB N N 22 4Y3 F C5 SING N N 23 4Y3 N1 C2 SING N N 24 4Y3 C5 C4 SING N N 25 4Y3 C2 O2 DOUB N N 26 4Y3 C2 N3 SING N N 27 4Y3 C4 N3 DOUB N N 28 4Y3 C4 N4 SING N N 29 4Y3 "C5'" H1 SING N N 30 4Y3 "C5'" H2 SING N N 31 4Y3 "C4'" H3 SING N N 32 4Y3 S H4 SING N N 33 4Y3 S H5 SING N N 34 4Y3 "C2'" H6 SING N N 35 4Y3 "C2'" H7 SING N N 36 4Y3 "C1'" H8 SING N N 37 4Y3 O1A H9 SING N N 38 4Y3 O1G H10 SING N N 39 4Y3 O2B H11 SING N N 40 4Y3 O3G H12 SING N N 41 4Y3 N4 H13 SING N N 42 4Y3 N4 H14 SING N N 43 4Y3 C6 H15 SING N N 44 # 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 4Y3 InChI InChI 1.06 "InChI=1S/C8H15FN3O12P3S/c9-4-1-12(8(13)11-7(4)10)5-3-28-6(22-5)2-21-26(17,18)24-27(19,20)23-25(14,15)16/h1,5-6H,2-3,28H2,(H,17,18)(H,19,20)(H2,10,11,13)(H2,14,15,16)/t5-,6+/m1/s1" 4Y3 InChIKey InChI 1.06 XWOCIBWGJKRZIQ-RITPCOANSA-N 4Y3 SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1F)[C@H]2C[SH2][C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2" 4Y3 SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1F)[CH]2C[SH2][CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2" 4Y3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1[C@@H](O[C@@H]([SH2]1)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N2C=C(C(=NC2=O)N)F" 4Y3 SMILES "OpenEye OEToolkits" 2.0.7 "C1C(OC([SH2]1)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N2C=C(C(=NC2=O)N)F" # _pdbx_chem_comp_identifier.comp_id 4Y3 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[[(2~{S},5~{R})-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3$l^{4}-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen 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 4Y3 "Create component" 2015-06-19 RCSB 4Y3 "Initial release" 2016-01-27 RCSB 4Y3 "Modify formula" 2024-02-24 RCSB 4Y3 "Modify name" 2024-02-24 RCSB #