data_A1CEB
# 
_chem_comp.id                                    A1CEB 
_chem_comp.name                                  "[(2~{R},3~{R},4~{S},5~{R})-5-(6-azanyl-3-methyl-purin-9-yl)-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C11 H16 F N5 O6 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2025-05-27 
_chem_comp.pdbx_modified_date                    2025-11-14 
_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                        364.247 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1CEB 
_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        9OSO 
_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 
A1CEB C2     C1  C 0 1 Y N N N N N 18.586 5.125  4.539 5.062  0.581  1.041  C2     A1CEB 1  
A1CEB C4     C2  C 0 1 Y N N N N N 20.206 6.496  3.884 3.009  -0.152 0.312  C4     A1CEB 2  
A1CEB C5     C3  C 0 1 Y N N N N N 20.216 5.876  2.619 3.621  -1.297 -0.225 C5     A1CEB 3  
A1CEB C6     C4  C 0 1 Y N N N N N 19.306 4.812  2.405 5.014  -1.430 -0.092 C6     A1CEB 4  
A1CEB P      P1  P 0 1 N N N N N N 23.722 11.954 1.993 -5.025 -0.881 0.242  P      A1CEB 5  
A1CEB OP1    O1  O 0 1 N N N N N N 24.098 13.136 2.810 -6.010 0.152  -0.149 OP1    A1CEB 6  
A1CEB OP2    O2  O 0 1 N N N N N N 24.782 11.039 1.496 -4.860 -1.946 -0.954 OP2    A1CEB 7  
A1CEB "O5'"  O3  O 0 1 N N N N N N 22.667 11.094 2.820 -3.605 -0.184 0.539  "O5'"  A1CEB 8  
A1CEB N9     N1  N 0 1 Y N N N N N 21.204 7.493  3.790 1.671  -0.272 0.035  N9     A1CEB 9  
A1CEB N3     N2  N 1 1 Y N N N N N 19.363 6.135  4.929 3.762  0.752  0.931  N3     A1CEB 10 
A1CEB C28    C5  C 0 1 N N N N N N 19.303 6.635  6.329 3.138  1.951  1.496  C28    A1CEB 11 
A1CEB N1     N3  N 0 1 Y N N N N N 18.511 4.473  3.401 5.682  -0.476 0.548  N1     A1CEB 12 
A1CEB N6     N4  N 0 1 N N N N N N 19.176 4.108  1.278 5.671  -2.536 -0.600 N6     A1CEB 13 
A1CEB N7     N5  N 0 1 Y N N N N N 21.161 6.453  1.789 2.643  -2.043 -0.792 N7     A1CEB 14 
A1CEB C8     C6  C 0 1 Y N N N N N 21.708 7.390  2.515 1.498  -1.444 -0.641 C8     A1CEB 15 
A1CEB "F2'"  F1  F 0 1 N N N N N N 23.459 9.053  3.355 1.101  1.433  -1.853 "F2'"  A1CEB 16 
A1CEB "C2'"  C7  C 0 1 N N S N N N 23.124 8.879  4.647 0.570  1.840  -0.624 "C2'"  A1CEB 17 
A1CEB "C5'"  C8  C 0 1 N N N N N N 21.825 11.682 3.807 -2.935 0.653  -0.407 "C5'"  A1CEB 18 
A1CEB "C4'"  C9  C 0 1 N N R N N N 21.764 10.780 5.014 -1.618 1.148  0.193  "C4'"  A1CEB 19 
A1CEB "O4'"  O4  O 0 1 N N N N N N 20.910 9.636  4.726 -0.678 0.058  0.312  "O4'"  A1CEB 20 
A1CEB "C1'"  C10 C 0 1 N N R N N N 21.681 8.441  4.811 0.621  0.683  0.398  "C1'"  A1CEB 21 
A1CEB "C3'"  C11 C 0 1 N N R N N N 23.108 10.180 5.414 -0.936 2.153  -0.762 "C3'"  A1CEB 22 
A1CEB "O3'"  O5  O 0 1 N N N N N N 23.133 9.933  6.821 -1.208 3.495  -0.353 "O3'"  A1CEB 23 
A1CEB H2     H1  H 0 1 N N N N N N 17.894 4.781  5.294 5.645  1.334  1.551  H2     A1CEB 24 
A1CEB HOP2   H3  H 0 0 N N N N N N 25.631 11.350 1.786 -4.228 -2.654 -0.766 HOP2   A1CEB 25 
A1CEB H28B   H4  H 0 0 N N N N N N 18.501 6.113  6.871 3.019  2.702  0.715  H28B   A1CEB 26 
A1CEB H28A   H5  H 0 0 N N N N N N 20.266 6.447  6.827 2.160  1.694  1.904  H28A   A1CEB 27 
A1CEB H4     H6  H 0 1 N N N N N N 19.098 7.716  6.324 3.770  2.350  2.290  H4     A1CEB 28 
A1CEB H62    H7  H 0 1 N N N N N N 18.464 3.416  1.397 5.171  -3.231 -1.055 H62    A1CEB 29 
A1CEB H61    H8  H 0 1 N N N N N N 18.923 4.721  0.530 6.633  -2.616 -0.502 H61    A1CEB 30 
A1CEB H8     H9  H 0 1 N N N N N N 22.493 8.032  2.144 0.550  -1.819 -0.997 H8     A1CEB 31 
A1CEB "H2''" H10 H 0 0 N N N N N N 23.786 8.161  5.153 1.110  2.708  -0.245 "H2''" A1CEB 32 
A1CEB "H5'"  H11 H 0 1 N N N N N N 22.232 12.661 4.100 -2.730 0.083  -1.314 "H5'"  A1CEB 33 
A1CEB "H5''" H12 H 0 0 N N N N N N 20.813 11.814 3.395 -3.568 1.506  -0.649 "H5''" A1CEB 34 
A1CEB "H4'"  H13 H 0 1 N N N N N N 21.358 11.345 5.866 -1.793 1.608  1.165  "H4'"  A1CEB 35 
A1CEB "H1'"  H14 H 0 1 N N N N N N 21.562 7.990  5.807 0.792  1.070  1.402  "H1'"  A1CEB 36 
A1CEB "H3'"  H15 H 0 1 N N N N N N 23.934 10.833 5.094 -1.268 1.991  -1.788 "H3'"  A1CEB 37 
A1CEB "HO3'" H16 H 0 0 N Y N N N N 23.123 10.760 7.288 -0.756 4.167  -0.882 "HO3'" A1CEB 38 
A1CEB OP3    O6  O 0 1 N Y N N N N 22.880 12.486 0.730 -5.539 -1.637 1.567  OP3    A1CEB 39 
A1CEB HOP3   H16 H 0 0 N Y N N N N 22.804 13.432 0.775 -6.391 -2.081 1.461  HOP3   A1CEB 40 
# 
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 
A1CEB N6    C6     SING N N 1  
A1CEB OP2   P      SING N N 2  
A1CEB N7    C8     DOUB Y N 3  
A1CEB N7    C5     SING Y N 4  
A1CEB P     OP1    DOUB N N 5  
A1CEB P     "O5'"  SING N N 6  
A1CEB C6    C5     DOUB Y N 7  
A1CEB C6    N1     SING Y N 8  
A1CEB C8    N9     SING Y N 9  
A1CEB C5    C4     SING Y N 10 
A1CEB "O5'" "C5'"  SING N N 11 
A1CEB "F2'" "C2'"  SING N N 12 
A1CEB N1    C2     DOUB Y N 13 
A1CEB N9    C4     SING Y N 14 
A1CEB N9    "C1'"  SING N N 15 
A1CEB "C5'" "C4'"  SING N N 16 
A1CEB C4    N3     DOUB Y N 17 
A1CEB C2    N3     SING Y N 18 
A1CEB "C2'" "C1'"  SING N N 19 
A1CEB "C2'" "C3'"  SING N N 20 
A1CEB "O4'" "C1'"  SING N N 21 
A1CEB "O4'" "C4'"  SING N N 22 
A1CEB N3    C28    SING N N 23 
A1CEB "C4'" "C3'"  SING N N 24 
A1CEB "C3'" "O3'"  SING N N 25 
A1CEB C2    H2     SING N N 26 
A1CEB OP2   HOP2   SING N N 27 
A1CEB C28   H28B   SING N N 28 
A1CEB C28   H28A   SING N N 29 
A1CEB C28   H4     SING N N 30 
A1CEB N6    H62    SING N N 31 
A1CEB N6    H61    SING N N 32 
A1CEB C8    H8     SING N N 33 
A1CEB "C2'" "H2''" SING N N 34 
A1CEB "C5'" "H5'"  SING N N 35 
A1CEB "C5'" "H5''" SING N N 36 
A1CEB "C4'" "H4'"  SING N N 37 
A1CEB "C1'" "H1'"  SING N N 38 
A1CEB "C3'" "H3'"  SING N N 39 
A1CEB "O3'" "HO3'" SING N N 40 
A1CEB P     OP3    SING N N 41 
A1CEB OP3   HOP3   SING N N 42 
# 
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 
A1CEB SMILES           ACDLabs              14.52   "O=P(O)(O)OCC1OC(n2cnc3c2[n+](C)cnc3N)C(F)C1O"                                                                                                                 
A1CEB InChI            InChI                1.06    "InChI=1S/C11H15FN5O6P/c1-16-3-15-9(13)7-10(16)17(4-14-7)11-6(12)8(18)5(23-11)2-22-24(19,20)21/h3-6,8,11,13,18H,2H2,1H3,(H2,19,20,21)/p+1/t5-,6+,8-,11-/m1/s1" 
A1CEB InChIKey         InChI                1.06    ZQSBYIWBVXJKCN-WCGPTHBMSA-O                                                                                                                                    
A1CEB SMILES_CANONICAL CACTVS               3.385   "C[n+]1cnc(N)c2ncn([C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@@H]3F)c12"                                                                                          
A1CEB SMILES           CACTVS               3.385   "C[n+]1cnc(N)c2ncn([CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3F)c12"                                                                                                 
A1CEB SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "C[n+]1cnc(c2c1n(cn2)[C@H]3[C@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)F)N"                                                                                            
A1CEB SMILES           "OpenEye OEToolkits" 3.1.0.0 "C[n+]1cnc(c2c1n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)F)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 
A1CEB "SYSTEMATIC NAME" ACDLabs              14.52   "6-amino-9-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)-3-methyl-9H-purin-3-ium"                                       
A1CEB "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "[(2~{R},3~{R},4~{S},5~{R})-5-(6-azanyl-3-methyl-purin-3-ium-9-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 
A1CEB "Create component" 2025-05-27 RCSB 
A1CEB "Initial release"  2025-11-19 RCSB 
# 
