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 
# 
