data_A1CAK
# 
_chem_comp.id                                    A1CAK 
_chem_comp.name                                  "2-amino-9-(2-deoxy-2-fluoro-5-O-thiophosphono-alpha-D-arabinofuranosyl)-1,9-dihydro-6H-purin-6-one" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H13 F N5 O6 P S" 
_chem_comp.mon_nstd_parent_comp_id               G 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-04-23 
_chem_comp.pdbx_modified_date                    2026-04-24 
_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                        381.277 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1CAK 
_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        9OBD 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              ? 
# 
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 
A1CAK C2    C1  C 0 1 N N N N N N -28.996 36.121 34.840 5.199  0.424  0.952  C2    A1CAK 1  
A1CAK C4    C2  C 0 1 Y N N N N N -27.751 35.534 32.682 3.152  -0.260 0.130  C4    A1CAK 2  
A1CAK C5    C3  C 0 1 Y N N N N N -28.934 35.261 32.060 3.746  -1.388 -0.447 C5    A1CAK 3  
A1CAK C6    C4  C 0 1 N N N N N N -30.255 35.410 32.825 5.141  -1.569 -0.299 C6    A1CAK 4  
A1CAK C8    C5  C 0 1 Y N N N N N -27.334 34.925 30.632 1.630  -1.467 -0.911 C8    A1CAK 5  
A1CAK "C1'" C6  C 0 1 N N S N N N -25.435 35.576 32.307 0.787  0.630  0.213  "C1'" A1CAK 6  
A1CAK "C2'" C7  C 0 1 N N S N N N -24.973 34.380 33.197 0.678  1.759  -0.836 "C2'" A1CAK 7  
A1CAK "C3'" C8  C 0 1 N N R N N N -24.324 33.456 32.110 -0.835 2.066  -0.902 "C3'" A1CAK 8  
A1CAK "C4'" C9  C 0 1 N N R N N N -23.706 34.284 31.337 -1.461 1.086  0.115  "C4'" A1CAK 9  
A1CAK "C5'" C10 C 0 1 N N N N N N -23.574 33.683 29.968 -2.807 0.571  -0.400 "C5'" A1CAK 10 
A1CAK F     F1  F 0 1 N N N N N N -24.076 34.759 34.040 1.389  2.888  -0.416 F     A1CAK 11 
A1CAK N1    N1  N 0 1 N N N N N N -30.248 35.836 34.189 5.835  -0.652 0.409  N1    A1CAK 12 
A1CAK N2    N2  N 0 1 N N N N N N -28.986 36.553 36.226 5.932  1.344  1.661  N2    A1CAK 13 
A1CAK N3    N3  N 0 1 N N N N N N -27.739 35.979 34.107 3.906  0.610  0.813  N3    A1CAK 14 
A1CAK N7    N4  N 0 1 Y N N N N N -28.670 34.890 30.810 2.764  -2.086 -1.068 N7    A1CAK 15 
A1CAK N9    N5  N 0 1 Y N N N N N -26.783 35.324 31.794 1.820  -0.333 -0.176 N9    A1CAK 16 
A1CAK "O3'" O1  O 0 1 N N N N N N -23.375 32.497 32.740 -1.089 3.418  -0.516 "O3'" A1CAK 17 
A1CAK "O4'" O2  O 0 1 N N N N N N -24.513 35.558 31.250 -0.513 0.001  0.214  "O4'" A1CAK 18 
A1CAK "O5'" O3  O 0 1 N N N N N N -24.835 33.252 29.544 -3.422 -0.240 0.603  "O5'" A1CAK 19 
A1CAK O6    O4  O 0 1 N N N N N N -31.283 35.172 32.285 5.701  -2.535 -0.789 O6    A1CAK 20 
A1CAK OP1   O5  O 0 1 N N N N N N -26.548 32.689 27.702 -5.415 -1.440 1.828  OP1   A1CAK 21 
A1CAK P     P1  P 0 1 N N N N N N -25.227 33.378 27.949 -4.854 -0.948 0.401  P     A1CAK 22 
A1CAK SP2   S1  S 0 1 N N N N N N -25.359 35.162 27.474 -6.048 0.269  -0.350 SP2   A1CAK 23 
A1CAK H4    H1  H 0 1 N N N N N N -26.803 34.678 29.724 0.681  -1.801 -1.303 H4    A1CAK 24 
A1CAK H5    H2  H 0 1 N N N N N N -25.393 36.512 32.883 1.008  1.046  1.196  H5    A1CAK 25 
A1CAK H6    H3  H 0 1 N N N N N N -25.845 33.881 33.646 1.043  1.417  -1.804 H6    A1CAK 26 
A1CAK H8    H4  H 0 1 N N N N N N -25.123 32.903 31.594 -1.220 1.874  -1.903 H8    A1CAK 27 
A1CAK H10   H5  H 0 1 N N N N N N -22.702 34.529 31.714 -1.584 1.571  1.084  H10   A1CAK 28 
A1CAK H11   H6  H 0 1 N N N N N N -23.186 34.438 29.268 -3.454 1.417  -0.631 H11   A1CAK 29 
A1CAK H12   H7  H 0 1 N N N N N N -22.883 32.828 30.004 -2.648 -0.022 -1.300 H12   A1CAK 30 
A1CAK H1    H8  H 0 1 N N N N N N -31.108 35.936 34.689 6.792  -0.759 0.531  H1    A1CAK 31 
A1CAK H3    H9  H 0 1 N N N N N N -28.118 36.754 36.681 5.494  2.117  2.050  H3    A1CAK 32 
A1CAK H2    H10 H 0 1 N N N N N N -29.847 36.650 36.726 6.887  1.220  1.773  H2    A1CAK 33 
A1CAK H9    H11 H 0 1 N N N N N N -22.990 31.945 32.069 -0.668 4.075  -1.086 H9    A1CAK 34 
A1CAK H13   H12 H 0 1 N N N N N N -27.172 33.315 27.354 -6.276 -1.877 1.783  H13   A1CAK 35 
A1CAK OP3   OP3 O 0 1 N Y N N N N -24.294 32.311 27.301 -4.692 -2.216 -0.578 OP3   A1CAK 36 
A1CAK H7    H13 H 0 1 N N N N N N -24.436 32.294 26.362 -4.083 -2.891 -0.249 H7    A1CAK 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 
A1CAK P     "O5'" SING N N 1  
A1CAK N1    C2    SING N N 2  
A1CAK C2    N3    DOUB N N 3  
A1CAK C2    N2    SING N N 4  
A1CAK C4    N3    SING N N 5  
A1CAK C5    C4    DOUB Y N 6  
A1CAK C6    N1    SING N N 7  
A1CAK C6    C5    SING N N 8  
A1CAK O6    C6    DOUB N N 9  
A1CAK N7    C5    SING Y N 10 
A1CAK N7    C8    DOUB Y N 11 
A1CAK C8    N9    SING Y N 12 
A1CAK N9    C4    SING Y N 13 
A1CAK N9    "C1'" SING N N 14 
A1CAK "C1'" "O4'" SING N N 15 
A1CAK OP1   P     SING N N 16 
A1CAK "C2'" F     SING N N 17 
A1CAK "C2'" "C1'" SING N N 18 
A1CAK SP2   P     DOUB N N 19 
A1CAK "C3'" "C2'" SING N N 20 
A1CAK "C3'" "C4'" SING N N 21 
A1CAK "O3'" "C3'" SING N N 22 
A1CAK "C4'" "O4'" SING N N 23 
A1CAK "C5'" "C4'" SING N N 24 
A1CAK "O5'" "C5'" SING N N 25 
A1CAK C8    H4    SING N N 26 
A1CAK "C1'" H5    SING N N 27 
A1CAK "C2'" H6    SING N N 28 
A1CAK "C3'" H8    SING N N 29 
A1CAK "C4'" H10   SING N N 30 
A1CAK "C5'" H11   SING N N 31 
A1CAK "C5'" H12   SING N N 32 
A1CAK N1    H1    SING N N 33 
A1CAK N2    H3    SING N N 34 
A1CAK N2    H2    SING N N 35 
A1CAK "O3'" H9    SING N N 36 
A1CAK OP1   H13   SING N N 37 
A1CAK P     OP3   SING N N 38 
A1CAK OP3   H7    SING N N 39 
# 
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 
A1CAK SMILES           ACDLabs              14.52   "OP(O)(=S)OCC1OC(n2cnc3c2N=C(N)NC3=O)C(F)C1O"                                                                                                  
A1CAK InChI            InChI                1.06    "InChI=1S/C10H13FN5O6PS/c11-4-6(17)3(1-21-23(19,20)24)22-9(4)16-2-13-5-7(16)14-10(12)15-8(5)18/h2-4,6,9,17H,1H2,(H2,19,20,24)(H3,12,14,15,18)" 
A1CAK InChIKey         InChI                1.06    PRFLIPGKVYQLKB-UHFFFAOYSA-N                                                                                                                    
A1CAK SMILES_CANONICAL CACTVS               3.385   "NC1=Nc2n(cnc2C(=O)N1)[C@H]3O[C@H](CO[P](O)(O)=S)[C@@H](O)[C@@H]3F"                                                                            
A1CAK SMILES           CACTVS               3.385   "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(O)=S)[CH](O)[CH]3F"                                                                                  
A1CAK SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=S)(O)O)O)F)N=C(NC2=O)N"                                                                            
A1CAK SMILES           "OpenEye OEToolkits" 3.1.0.0 "c1nc2c(n1C3C(C(C(O3)COP(=S)(O)O)O)F)N=C(NC2=O)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 
A1CAK "SYSTEMATIC NAME" ACDLabs              14.52   "2-amino-9-(2-deoxy-2-fluoro-5-O-thiophosphono-alpha-D-arabinofuranosyl)-1,9-dihydro-6H-purin-6-one"                                    
A1CAK "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "2-azanyl-9-[(2~{R},3~{R},4~{R},5~{R})-5-[bis(oxidanyl)phosphinothioyloxymethyl]-3-fluoranyl-4-oxidanyl-oxolan-2-yl]-1~{H}-purin-6-one" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1CAK "Create component" 2025-04-23 RCSB 
A1CAK "Initial release"  2026-04-29 RCSB 
# 
