data_A1BGF
# 
_chem_comp.id                                    A1BGF 
_chem_comp.name                                  "5'-deoxy-5'-(4-{5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentyl}-1H-1,2,3-triazol-1-yl)adenosine" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C22 H30 N10 O4 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-11-10 
_chem_comp.pdbx_modified_date                    2025-04-04 
_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                        530.603 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1BGF 
_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        9DRN 
_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 
A1BGF C18 C1  C 0 1 N N N N N N -5.077 -6.666  8.283  2.080  1.463  -0.993 C18 A1BGF 1  
A1BGF C17 C2  C 0 1 Y N N N N N -4.177 -5.520  7.882  0.680  1.269  -0.470 C17 A1BGF 2  
A1BGF C16 C3  C 0 1 Y N N N N N -4.204 -4.160  8.219  -0.068 2.178  0.199  C16 A1BGF 3  
A1BGF C14 C4  C 0 1 N N N N N N -2.701 -2.128  7.601  -2.378 2.169  1.181  C14 A1BGF 4  
A1BGF C13 C5  C 0 1 N N R N N N -3.767 -1.037  7.823  -3.636 2.069  0.317  C13 A1BGF 5  
A1BGF C10 C6  C 0 1 Y N N N N N -5.645 -0.640  13.041 -7.565 -2.193 0.239  C10 A1BGF 6  
A1BGF C11 C7  C 0 1 N N R N N N -4.906 0.010   9.437  -5.461 0.760  -0.161 C11 A1BGF 7  
A1BGF C20 C8  C 0 1 N N N N N N -3.826 -7.555  10.432 4.409  0.559  -0.973 C20 A1BGF 8  
A1BGF C21 C9  C 0 1 N N N N N N -3.733 -8.705  11.433 5.317  -0.541 -0.421 C21 A1BGF 9  
A1BGF C22 C10 C 0 1 N N N N N N -3.509 -8.332  12.938 6.738  -0.344 -0.952 C22 A1BGF 10 
A1BGF C23 C11 C 0 1 N N S N N N -3.390 -9.547  13.886 7.646  -1.445 -0.401 C23 A1BGF 11 
A1BGF C25 C12 C 0 1 N N N N N N -2.929 -10.530 16.108 9.491  -2.089 1.474  C25 A1BGF 12 
A1BGF C26 C13 C 0 1 N N R N N N -1.860 -11.061 15.209 10.134 -1.636 0.149  C26 A1BGF 13 
A1BGF C28 C14 C 0 1 N N N N N N 0.058  -9.829  14.496 10.356 0.572  -0.419 C28 A1BGF 14 
A1BGF N30 N1  N 0 1 N N N N N N -0.894 -9.695  13.459 9.338  0.153  -1.184 N30 A1BGF 15 
A1BGF C31 C15 C 0 1 N N S N N N -2.137 -10.417 13.776 9.089  -1.271 -0.913 C31 A1BGF 16 
A1BGF C02 C16 C 0 1 Y N N N N N -6.593 -0.951  14.054 -8.711 -2.905 -0.154 C02 A1BGF 17 
A1BGF C04 C17 C 0 1 Y N N N N N -8.191 -0.947  12.363 -9.203 -1.220 -1.652 C04 A1BGF 18 
A1BGF C06 C18 C 0 1 Y N N N N N -6.114 -0.502  11.674 -7.300 -0.964 -0.389 C06 A1BGF 19 
A1BGF C08 C19 C 0 1 Y N N N N N -3.920 -0.190  11.805 -5.734 -1.410 1.097  C08 A1BGF 20 
A1BGF C19 C20 C 0 1 N N N N N N -4.481 -7.874  9.038  2.988  0.362  -0.442 C19 A1BGF 21 
A1BGF C34 C21 C 0 1 N N S N N N -2.996 0.332   7.919  -4.814 2.804  0.994  C34 A1BGF 22 
A1BGF C36 C22 C 0 1 N N R N N N -3.781 1.036   9.006  -6.042 1.924  0.672  C36 A1BGF 23 
A1BGF N01 N2  N 0 1 N N N N N N -6.281 -1.110  15.412 -9.020 -4.124 0.425  N01 A1BGF 24 
A1BGF N03 N3  N 0 1 Y N N N N N -7.885 -1.095  13.684 -9.490 -2.382 -1.094 N03 A1BGF 25 
A1BGF N05 N4  N 0 1 Y N N N N N -7.394 -0.656  11.324 -8.137 -0.522 -1.322 N05 A1BGF 26 
A1BGF N07 N5  N 0 1 Y N N N N N -5.033 -0.223  10.896 -6.140 -0.495 0.172  N07 A1BGF 27 
A1BGF N09 N6  N 0 1 Y N N N N N -4.246 -0.427  13.080 -6.572 -2.405 1.135  N09 A1BGF 28 
A1BGF N15 N7  N 0 1 Y N N N N N -3.147 -3.534  7.561  -1.247 1.570  0.468  N15 A1BGF 29 
A1BGF N27 N8  N 0 1 N N N N N N -0.488 -10.611 15.510 10.869 -0.381 0.371  N27 A1BGF 30 
A1BGF N32 N9  N 0 1 Y N N N N N -3.079 -5.612  7.027  -0.070 0.167  -0.581 N32 A1BGF 31 
A1BGF N33 N10 N 0 1 Y N N N N N -2.514 -4.505  6.862  -1.204 0.376  -0.009 N33 A1BGF 32 
A1BGF O12 O1  O 0 1 N N N N N N -4.440 -1.180  8.901  -4.069 0.694  0.217  O12 A1BGF 33 
A1BGF O29 O2  O 0 1 N N N N N N 1.190  -9.316  14.468 10.775 1.714  -0.439 O29 A1BGF 34 
A1BGF O35 O3  O 0 1 N N N N N N -3.071 0.943   6.701  -4.975 4.110  0.437  O35 A1BGF 35 
A1BGF O37 O4  O 0 1 N N N N N N -4.343 2.135   8.393  -6.998 2.659  -0.094 O37 A1BGF 36 
A1BGF S24 S1  S 0 1 N N N N N N -3.422 -8.890  15.548 7.840  -1.279 1.421  S24 A1BGF 37 
A1BGF H1  H1  H 0 1 N N N N N N -5.865 -6.245  8.925  2.071  1.415  -2.082 H1  A1BGF 38 
A1BGF H2  H2  H 0 1 N N N N N N -5.528 -7.057  7.359  2.455  2.436  -0.676 H2  A1BGF 39 
A1BGF H3  H3  H 0 1 N N N N N N -4.918 -3.682  8.873  0.219  3.185  0.464  H3  A1BGF 40 
A1BGF H4  H4  H 0 1 N N N N N N -1.968 -2.040  8.417  -2.162 3.218  1.388  H4  A1BGF 41 
A1BGF H5  H5  H 0 1 N N N N N N -2.208 -1.914  6.641  -2.538 1.639  2.120  H5  A1BGF 42 
A1BGF H6  H6  H 0 1 N N N N N N -4.412 -0.999  6.933  -3.450 2.482  -0.674 H6  A1BGF 43 
A1BGF H7  H7  H 0 1 N N N N N N -5.869 0.317   9.003  -5.557 0.971  -1.226 H7  A1BGF 44 
A1BGF H8  H8  H 0 1 N N N N N N -2.804 -7.195  10.244 4.784  1.533  -0.655 H8  A1BGF 45 
A1BGF H9  H9  H 0 1 N N N N N N -4.672 -9.274  11.370 5.326  -0.493 0.668  H9  A1BGF 46 
A1BGF H10 H10 H 0 1 N N N N N N -2.582 -7.745  13.013 6.729  -0.393 -2.041 H10 A1BGF 47 
A1BGF H11 H11 H 0 1 N N N N N N -4.359 -7.718  13.271 7.113  0.629  -0.635 H11 A1BGF 48 
A1BGF H12 H12 H 0 1 N N N N N N -4.285 -10.178 13.781 7.257  -2.430 -0.660 H12 A1BGF 49 
A1BGF H13 H13 H 0 1 N N N N N N -3.798 -11.203 16.082 9.388  -3.173 1.503  H13 A1BGF 50 
A1BGF H14 H14 H 0 1 N N N N N N -2.545 -10.466 17.137 10.071 -1.734 2.326  H14 A1BGF 51 
A1BGF H15 H15 H 0 1 N N N N N N -1.914 -12.157 15.138 10.808 -2.406 -0.226 H15 A1BGF 52 
A1BGF H16 H16 H 0 1 N N N N N N -0.742 -9.176  12.618 8.846  0.701  -1.815 H16 A1BGF 53 
A1BGF H17 H17 H 0 1 N N N N N N -2.309 -11.225 13.050 9.242  -1.860 -1.818 H17 A1BGF 54 
A1BGF H18 H18 H 0 1 N N N N N N -9.233 -1.085  12.116 -9.864 -0.832 -2.413 H18 A1BGF 55 
A1BGF H19 H19 H 0 1 N N N N N N -2.908 0.009   11.486 -4.848 -1.323 1.709  H19 A1BGF 56 
A1BGF H20 H20 H 0 1 N N N N N N -5.290 -8.601  9.204  2.997  0.410  0.647  H20 A1BGF 57 
A1BGF H21 H21 H 0 1 N N N N N N -3.709 -8.325  8.397  2.613  -0.611 -0.759 H21 A1BGF 58 
A1BGF H22 H22 H 0 1 N N N N N N -1.961 0.153   8.245  -4.658 2.864  2.071  H22 A1BGF 59 
A1BGF H23 H23 H 0 1 N N N N N N -3.141 1.288   9.865  -6.494 1.548  1.590  H23 A1BGF 60 
A1BGF H24 H24 H 0 1 N N N N N N -7.115 -1.318  15.924 -8.443 -4.495 1.111  H24 A1BGF 61 
A1BGF H25 H25 H 0 1 N N N N N N -5.629 -1.861  15.518 -9.814 -4.606 0.146  H25 A1BGF 62 
A1BGF H26 H26 H 0 1 N N N N N N -0.002 -10.843 16.353 11.606 -0.262 0.990  H26 A1BGF 63 
A1BGF H27 H27 H 0 1 N N N N N N -2.611 1.774   6.734  -5.701 4.617  0.826  H27 A1BGF 64 
A1BGF H28 H28 H 0 1 N N N N N N -4.854 2.625   9.027  -7.351 3.437  0.360  H28 A1BGF 65 
A1BGF H29 H29 H 0 1 N N N N N N -4.416 -6.754  10.901 4.400  0.511  -2.062 H29 A1BGF 66 
A1BGF H30 H30 H 0 1 N N N N N N -2.894 -9.346  11.123 4.942  -1.515 -0.739 H30 A1BGF 67 
# 
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 
A1BGF O35 C34 SING N N 1  
A1BGF N33 N32 DOUB Y N 2  
A1BGF N33 N15 SING Y N 3  
A1BGF N32 C17 SING Y N 4  
A1BGF N15 C14 SING N N 5  
A1BGF N15 C16 SING Y N 6  
A1BGF C14 C13 SING N N 7  
A1BGF C13 C34 SING N N 8  
A1BGF C13 O12 SING N N 9  
A1BGF C17 C16 DOUB Y N 10 
A1BGF C17 C18 SING N N 11 
A1BGF C34 C36 SING N N 12 
A1BGF C18 C19 SING N N 13 
A1BGF O37 C36 SING N N 14 
A1BGF O12 C11 SING N N 15 
A1BGF C36 C11 SING N N 16 
A1BGF C19 C20 SING N N 17 
A1BGF C11 N07 SING N N 18 
A1BGF C20 C21 SING N N 19 
A1BGF N07 C06 SING Y N 20 
A1BGF N07 C08 SING Y N 21 
A1BGF N05 C06 DOUB Y N 22 
A1BGF N05 C04 SING Y N 23 
A1BGF C21 C22 SING N N 24 
A1BGF C06 C10 SING Y N 25 
A1BGF C08 N09 DOUB Y N 26 
A1BGF C04 N03 DOUB Y N 27 
A1BGF C22 C23 SING N N 28 
A1BGF C10 N09 SING Y N 29 
A1BGF C10 C02 DOUB Y N 30 
A1BGF N30 C31 SING N N 31 
A1BGF N30 C28 SING N N 32 
A1BGF N03 C02 SING Y N 33 
A1BGF C31 C23 SING N N 34 
A1BGF C31 C26 SING N N 35 
A1BGF C23 S24 SING N N 36 
A1BGF C02 N01 SING N N 37 
A1BGF O29 C28 DOUB N N 38 
A1BGF C28 N27 SING N N 39 
A1BGF C26 N27 SING N N 40 
A1BGF C26 C25 SING N N 41 
A1BGF S24 C25 SING N N 42 
A1BGF C18 H1  SING N N 43 
A1BGF C18 H2  SING N N 44 
A1BGF C16 H3  SING N N 45 
A1BGF C14 H4  SING N N 46 
A1BGF C14 H5  SING N N 47 
A1BGF C13 H6  SING N N 48 
A1BGF C11 H7  SING N N 49 
A1BGF C20 H8  SING N N 50 
A1BGF C21 H9  SING N N 51 
A1BGF C22 H10 SING N N 52 
A1BGF C22 H11 SING N N 53 
A1BGF C23 H12 SING N N 54 
A1BGF C25 H13 SING N N 55 
A1BGF C25 H14 SING N N 56 
A1BGF C26 H15 SING N N 57 
A1BGF N30 H16 SING N N 58 
A1BGF C31 H17 SING N N 59 
A1BGF C04 H18 SING N N 60 
A1BGF C08 H19 SING N N 61 
A1BGF C19 H20 SING N N 62 
A1BGF C19 H21 SING N N 63 
A1BGF C34 H22 SING N N 64 
A1BGF C36 H23 SING N N 65 
A1BGF N01 H24 SING N N 66 
A1BGF N01 H25 SING N N 67 
A1BGF N27 H26 SING N N 68 
A1BGF O35 H27 SING N N 69 
A1BGF O37 H28 SING N N 70 
A1BGF C20 H29 SING N N 71 
A1BGF C21 H30 SING N N 72 
# 
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 
A1BGF SMILES           ACDLabs              14.52   "O=C1NC2C(CCCCCc3cn(CC4OC(n5cnc6c(N)ncnc65)C(O)C4O)nn3)SCC2N1"                                                                                                                                                                                         
A1BGF InChI            InChI                1.06    "InChI=1S/C22H30N10O4S/c23-19-16-20(25-9-24-19)32(10-26-16)21-18(34)17(33)13(36-21)7-31-6-11(29-30-31)4-2-1-3-5-14-15-12(8-37-14)27-22(35)28-15/h6,9-10,12-15,17-18,21,33-34H,1-5,7-8H2,(H2,23,24,25)(H2,27,28,35)/t12-,13+,14-,15-,17+,18+,21+/m0/s1" 
A1BGF InChIKey         InChI                1.06    PNZFOGQAKKAJAB-ZOFBHSOPSA-N                                                                                                                                                                                                                            
A1BGF SMILES_CANONICAL CACTVS               3.385   "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](Cn4cc(CCCCC[C@@H]5SC[C@@H]6NC(=O)N[C@H]56)nn4)[C@@H](O)[C@H]3O"                                                                                                                                                         
A1BGF SMILES           CACTVS               3.385   "Nc1ncnc2n(cnc12)[CH]3O[CH](Cn4cc(CCCCC[CH]5SC[CH]6NC(=O)N[CH]56)nn4)[CH](O)[CH]3O"                                                                                                                                                                    
A1BGF SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "c1c(nnn1C[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)CCCCC[C@H]5[C@@H]6[C@H](CS5)NC(=O)N6"                                                                                                                                                        
A1BGF SMILES           "OpenEye OEToolkits" 3.1.0.0 "c1c(nnn1CC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)CCCCCC5C6C(CS5)NC(=O)N6"                                                                                                                                                                                       
# 
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 
A1BGF "SYSTEMATIC NAME" ACDLabs              14.52   "5'-deoxy-5'-(4-{5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentyl}-1H-1,2,3-triazol-1-yl)adenosine"                                                                                           
A1BGF "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "(3~{a}~{S},4~{S},6~{a}~{R})-4-[5-[1-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl]-1,2,3-triazol-4-yl]pentyl]-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-2-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 
A1BGF "Create component" 2024-11-10 RCSB 
A1BGF "Initial release"  2025-04-09 RCSB 
# 
