data_A1A6R
# 
_chem_comp.id                                    A1A6R 
_chem_comp.name                                  "2-chloro-7-{(4xi)-2-deoxy-4-ethynyl-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C13 H16 Cl N4 O12 P3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-09-16 
_chem_comp.pdbx_modified_date                    2025-09-12 
_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                        548.660 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1A6R 
_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        9DM9 
_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 
A1A6R N1  N1  N  0 1 Y N N N N N -37.919 -3.118 -27.934 6.015  0.308  -0.668 N1  A1A6R 1  
A1A6R N3  N2  N  0 1 N N N N N N -39.636 -3.748 -31.639 6.834  3.720  1.456  N3  A1A6R 2  
A1A6R C4  C1  C  0 1 N N S N N N -40.878 -1.061 -24.840 2.282  -3.009 0.367  C4  A1A6R 3  
A1A6R C5  C2  C  0 1 N N N N N N -39.517 -1.600 -25.280 3.482  -2.078 0.663  C5  A1A6R 4  
A1A6R C6  C3  C  0 1 N N R N N N -39.849 -3.037 -25.629 3.118  -0.810 -0.151 C6  A1A6R 5  
A1A6R C7  C4  C  0 1 Y N N N N N -39.240 -3.279 -28.059 5.049  0.776  0.121  C7  A1A6R 6  
A1A6R C8  C5  C  0 1 Y N N N N N -37.306 -3.203 -29.102 7.174  0.926  -0.749 C8  A1A6R 7  
A1A6R C10 C6  C  0 1 Y N N N N N -39.930 -3.510 -29.253 5.294  1.944  0.865  C10 A1A6R 8  
A1A6R N   N3  N  0 1 Y N N N N N -40.150 -3.262 -27.035 3.775  0.372  0.413  N   A1A6R 9  
A1A6R C   C7  C  0 1 N N N N N N -40.472 -2.644 -21.662 0.480  -2.595 -2.588 C   A1A6R 10 
A1A6R O   O1  O  0 1 N N N N N N -43.595 -2.371 -25.231 -1.123 -1.393 0.326  O   A1A6R 11 
A1A6R C1  C8  C  0 1 N N N N N N -40.886 -2.469 -22.750 0.784  -2.354 -1.480 C1  A1A6R 12 
A1A6R C11 C9  C  0 1 Y N N N N N -41.315 -3.652 -28.914 4.073  2.209  1.624  C11 A1A6R 13 
A1A6R C12 C10 C  0 1 Y N N N N N -41.412 -3.494 -27.577 3.203  1.236  1.311  C12 A1A6R 14 
A1A6R C2  C11 C  0 1 N N R N N N -41.478 -2.279 -24.079 1.164  -2.052 -0.091 C2  A1A6R 15 
A1A6R C3  C12 C  0 1 N N N N N N -43.003 -2.356 -23.926 -0.052 -2.197 0.825  C3  A1A6R 16 
A1A6R C9  C13 C  0 1 Y N N N N N -39.130 -3.547 -30.417 6.545  2.569  0.745  C9  A1A6R 17 
A1A6R N2  N4  N  0 1 Y N N N N N -37.798 -3.382 -30.318 7.446  2.026  -0.068 N2  A1A6R 18 
A1A6R O1  O2  O  0 1 N N N N N N -45.716 -1.254 -24.581 -2.397 -0.621 2.493  O1  A1A6R 19 
A1A6R O10 O3  O  0 1 N N N N N N -40.764 0.133  -24.053 2.609  -3.930 -0.676 O10 A1A6R 20 
A1A6R O11 O4  O  0 1 N N N N N N -41.012 -3.377 -24.883 1.685  -0.715 -0.004 O11 A1A6R 21 
A1A6R O2  O5  O  0 1 N N N N N N -43.940 0.150  -25.707 -3.557 -0.416 0.142  O2  A1A6R 22 
A1A6R O3  O6  O  0 1 N N N N N N -44.166 0.722  -23.257 -5.861 -1.489 -0.529 O3  A1A6R 23 
A1A6R O4  O7  O  0 1 N N N N N N -44.902 2.334  -25.053 -5.504 1.106  -0.756 O4  A1A6R 24 
A1A6R O5  O8  O  0 1 N N N N N N -47.070 1.239  -24.277 -6.374 3.428  -1.628 O5  A1A6R 25 
A1A6R O6  O9  O  0 1 N N N N N N -46.907 3.615  -24.299 -7.969 1.339  -1.640 O6  A1A6R 26 
A1A6R O7  O10 O  0 1 N N N N N N -46.995 2.452  -26.552 -7.239 2.423  0.520  O7  A1A6R 27 
A1A6R O8  O11 O  0 1 N N N N N N -42.423 1.932  -24.680 -5.643 -0.010 1.504  O8  A1A6R 28 
A1A6R O9  O12 O  0 1 N N N N N N -45.071 -1.598 -27.100 -3.120 -2.665 1.200  O9  A1A6R 29 
A1A6R P   P1  P  0 1 N N N N N N -44.658 -1.273 -25.711 -2.561 -1.304 1.044  P   A1A6R 30 
A1A6R P1  P2  P  0 1 N N N N N N -43.766 1.303  -24.623 -5.152 -0.198 0.121  P1  A1A6R 31 
A1A6R P2  P3  P  0 1 N N N N N N -46.496 2.400  -25.109 -6.782 2.081  -0.846 P2  A1A6R 32 
A1A6R CL  CL1 CL 0 0 N N N N N N -35.571 -3.153 -29.014 8.396  0.270  -1.793 CL  A1A6R 33 
A1A6R H1  H1  H  0 1 N N N N N N -38.896 -3.741 -32.312 7.703  4.141  1.365  H1  A1A6R 34 
A1A6R H2  H2  H  0 1 N N N N N N -40.102 -4.632 -31.665 6.168  4.105  2.046  H2  A1A6R 35 
A1A6R H3  H3  H  0 1 N N N N N N -41.491 -0.870 -25.733 1.980  -3.545 1.267  H3  A1A6R 36 
A1A6R H4  H4  H  0 1 N N N N N N -38.782 -1.546 -24.463 3.545  -1.851 1.727  H4  A1A6R 37 
A1A6R H5  H5  H  0 1 N N N N N N -39.134 -1.054 -26.155 4.413  -2.517 0.305  H5  A1A6R 38 
A1A6R H6  H6  H  0 1 N N N N N N -39.007 -3.677 -25.326 3.389  -0.937 -1.199 H6  A1A6R 39 
A1A6R H7  H7  H  0 1 N N N N N N -40.099 -2.802 -20.682 0.209  -2.811 -3.579 H7  A1A6R 40 
A1A6R H8  H8  H  0 1 N N N N N N -42.127 -3.848 -29.598 3.903  3.031  2.304  H8  A1A6R 41 
A1A6R H9  H9  H  0 1 N N N N N N -42.331 -3.541 -27.012 2.202  1.146  1.708  H9  A1A6R 42 
A1A6R H10 H10 H  0 1 N N N N N N -43.364 -1.481 -23.366 0.209  -1.869 1.831  H10 A1A6R 43 
A1A6R H11 H11 H  0 1 N N N N N N -43.275 -3.275 -23.385 -0.364 -3.241 0.852  H11 A1A6R 44 
A1A6R H12 H12 H  0 1 N N N N N N -46.568 -1.469 -24.941 -2.035 0.275  2.467  H12 A1A6R 45 
A1A6R H13 H13 H  0 1 N N N N N N -41.413 0.765  -24.339 3.307  -4.557 -0.442 H13 A1A6R 46 
A1A6R H14 H14 H  0 1 N N N N N N -43.462 0.861  -22.635 -5.586 -1.673 -1.438 H14 A1A6R 47 
A1A6R H15 H15 H  0 1 N N N N N N -47.662 0.726  -24.815 -7.097 4.064  -1.719 H15 A1A6R 48 
A1A6R H16 H16 H  0 1 N N N N N N -47.413 4.205  -24.846 -7.739 1.085  -2.544 H16 A1A6R 49 
# 
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 
A1A6R N3  C9  SING N N 1  
A1A6R C9  N2  DOUB Y N 2  
A1A6R C9  C10 SING Y N 3  
A1A6R N2  C8  SING Y N 4  
A1A6R C10 C11 SING Y N 5  
A1A6R C10 C7  DOUB Y N 6  
A1A6R C8  CL  SING N N 7  
A1A6R C8  N1  DOUB Y N 8  
A1A6R C11 C12 DOUB Y N 9  
A1A6R C7  N1  SING Y N 10 
A1A6R C7  N   SING Y N 11 
A1A6R C12 N   SING Y N 12 
A1A6R O9  P   DOUB N N 13 
A1A6R N   C6  SING N N 14 
A1A6R O7  P2  DOUB N N 15 
A1A6R P   O2  SING N N 16 
A1A6R P   O   SING N N 17 
A1A6R P   O1  SING N N 18 
A1A6R O2  P1  SING N N 19 
A1A6R C6  C5  SING N N 20 
A1A6R C6  O11 SING N N 21 
A1A6R C5  C4  SING N N 22 
A1A6R O   C3  SING N N 23 
A1A6R P2  O4  SING N N 24 
A1A6R P2  O6  SING N N 25 
A1A6R P2  O5  SING N N 26 
A1A6R O4  P1  SING N N 27 
A1A6R O11 C2  SING N N 28 
A1A6R C4  C2  SING N N 29 
A1A6R C4  O10 SING N N 30 
A1A6R O8  P1  DOUB N N 31 
A1A6R P1  O3  SING N N 32 
A1A6R C2  C3  SING N N 33 
A1A6R C2  C1  SING N N 34 
A1A6R C1  C   TRIP N N 35 
A1A6R N3  H1  SING N N 36 
A1A6R N3  H2  SING N N 37 
A1A6R C4  H3  SING N N 38 
A1A6R C5  H4  SING N N 39 
A1A6R C5  H5  SING N N 40 
A1A6R C6  H6  SING N N 41 
A1A6R C   H7  SING N N 42 
A1A6R C11 H8  SING N N 43 
A1A6R C12 H9  SING N N 44 
A1A6R C3  H10 SING N N 45 
A1A6R C3  H11 SING N N 46 
A1A6R O1  H12 SING N N 47 
A1A6R O10 H13 SING N N 48 
A1A6R O3  H14 SING N N 49 
A1A6R O5  H15 SING N N 50 
A1A6R O6  H16 SING N N 51 
# 
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 
A1A6R SMILES           ACDLabs              14.52 "O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC1(C#C)OC(CC1O)n1ccc2c(N)nc(Cl)nc21"                                                                                                                                               
A1A6R InChI            InChI                1.06  "InChI=1S/C13H16ClN4O12P3/c1-2-13(6-27-32(23,24)30-33(25,26)29-31(20,21)22)8(19)5-9(28-13)18-4-3-7-10(15)16-12(14)17-11(7)18/h1,3-4,8-9,19H,5-6H2,(H,23,24)(H,25,26)(H2,15,16,17)(H2,20,21,22)/t8-,9+,13+/m0/s1" 
A1A6R InChIKey         InChI                1.06  NQMWULQTTWGPJA-IGJMFERPSA-N                                                                                                                                                                                      
A1A6R SMILES_CANONICAL CACTVS               3.385 "Nc1nc(Cl)nc2n(ccc12)[C@H]3C[C@H](O)[C@@](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)(O3)C#C"                                                                                                                           
A1A6R SMILES           CACTVS               3.385 "Nc1nc(Cl)nc2n(ccc12)[CH]3C[CH](O)[C](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)(O3)C#C"                                                                                                                               
A1A6R SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C#C[C@]1([C@H](C[C@@H](O1)n2ccc3c2nc(nc3N)Cl)O)COP(=O)(O)OP(=O)(O)OP(=O)(O)O"                                                                                                                                   
A1A6R SMILES           "OpenEye OEToolkits" 2.0.7 "C#CC1(C(CC(O1)n2ccc3c2nc(nc3N)Cl)O)COP(=O)(O)OP(=O)(O)OP(=O)(O)O"                                                                                                                                               
# 
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 
A1A6R "SYSTEMATIC NAME" ACDLabs              14.52 "2-chloro-7-{(4xi)-2-deoxy-4-ethynyl-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine" 
A1A6R "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[[(2~{R},3~{S},5~{R})-5-(4-azanyl-2-chloranyl-pyrrolo[2,3-d]pyrimidin-7-yl)-2-ethynyl-3-oxidanyl-oxolan-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 
A1A6R "Create component" 2024-09-16 RCSB 
A1A6R "Initial release"  2025-09-17 RCSB 
# 
