data_A1LXK
# 
_chem_comp.id                                    A1LXK 
_chem_comp.name                                  "[(2~{R},3~{S},5~{S})-5-[2-azanyl-6,8-bis(oxidanylidene)-1,7-dihydropurin-9-yl]-2,3,5-tris(oxidanyl)pentyl] dihydrogen phosphate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C10 H16 N5 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-02-01 
_chem_comp.pdbx_modified_date                    2025-07-18 
_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                        381.236 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1LXK 
_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        8XWU 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
_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 
A1LXK P     P1  P 0 1 N N N N N N 17.929 -20.101 -18.102 -6.291 0.193  -0.242 P     A1LXK 1  
A1LXK O2P   O1  O 0 1 N N N N N N 16.476 -19.856 -17.841 -6.656 -0.519 1.003  O2P   A1LXK 2  
A1LXK O3P   O2  O 0 1 N N N N N N 18.253 -21.254 -19.018 -6.505 1.776  -0.039 O3P   A1LXK 3  
A1LXK "O5'" O3  O 0 1 N N N N N N 18.570 -18.765 -18.796 -4.747 -0.099 -0.594 "O5'" A1LXK 4  
A1LXK "C2'" C1  C 0 1 N N N N N N 19.158 -14.550 -17.846 0.110  -0.475 0.047  "C2'" A1LXK 5  
A1LXK "C5'" C2  C 0 1 N N N N N N 18.583 -17.549 -18.095 -3.680 0.149  0.323  "C5'" A1LXK 6  
A1LXK "C4'" C3  C 0 1 N N R N N N 19.881 -16.853 -18.501 -2.349 -0.236 -0.326 "C4'" A1LXK 7  
A1LXK "O4'" O4  O 0 1 N N N N N N 19.695 -16.350 -19.794 -2.097 0.621  -1.441 "O4'" A1LXK 8  
A1LXK "C3'" C4  C 0 1 N N S N N N 20.150 -15.709 -17.532 -1.221 -0.089 0.697  "C3'" A1LXK 9  
A1LXK "C1'" C5  C 0 1 N N S N N N 19.599 -13.729 -19.086 1.252  -0.208 1.029  "C1'" A1LXK 10 
A1LXK "O3'" O5  O 0 1 N N N N N N 21.505 -15.324 -17.660 -1.473 -0.946 1.812  "O3'" A1LXK 11 
A1LXK C2    C6  C 0 1 N N N N N N 20.159 -13.485 -23.329 5.062  1.885  0.002  C2    A1LXK 12 
A1LXK C4    C7  C 0 1 N N N N N N 18.906 -13.610 -21.420 3.622  0.088  0.193  C4    A1LXK 13 
A1LXK C5    C8  C 0 1 N N N N N N 17.751 -13.271 -22.097 4.588  -0.755 -0.345 C5    A1LXK 14 
A1LXK C6    C9  C 0 1 N N N N N N 17.915 -13.055 -23.468 5.832  -0.220 -0.707 C6    A1LXK 15 
A1LXK C8    C10 C 0 1 N N N N N N 17.262 -13.581 -20.068 2.780  -1.960 0.104  C8    A1LXK 16 
A1LXK N1    N1  N 0 1 N N N N N N 19.096 -13.159 -24.049 6.042  1.103  -0.529 N1    A1LXK 17 
A1LXK N2    N2  N 0 1 N N N N N N 21.454 -13.643 -23.940 5.296  3.225  0.175  N2    A1LXK 18 
A1LXK N3    N3  N 0 1 N N N N N N 20.091 -13.682 -22.044 3.894  1.388  0.350  N3    A1LXK 19 
A1LXK N7    N4  N 0 1 N N N N N N 16.710 -13.280 -21.237 4.031  -2.036 -0.389 N7    A1LXK 20 
A1LXK N9    N5  N 0 1 N N N N N N 18.589 -13.754 -20.139 2.512  -0.688 0.454  N9    A1LXK 21 
A1LXK O6    O6  O 0 1 N N N N N N 16.841 -12.712 -24.257 6.703  -0.932 -1.182 O6    A1LXK 22 
A1LXK O8    O7  O 0 1 N N N N N N 16.564 -13.588 -18.888 2.009  -2.896 0.212  O8    A1LXK 23 
A1LXK "O9'" O8  O 0 1 N N N N N N 19.792 -12.400 -18.589 1.347  1.195  1.281  "O9'" A1LXK 24 
A1LXK H2    H2  H 0 1 N N N N N N 17.447 -21.669 -19.303 -6.285 2.306  -0.817 H2    A1LXK 25 
A1LXK H3    H3  H 0 1 N N N N N N 19.108 -13.880 -16.975 0.093  -1.533 -0.213 H3    A1LXK 26 
A1LXK H4    H4  H 0 1 N N N N N N 18.162 -14.977 -18.038 0.260  0.119  -0.854 H4    A1LXK 27 
A1LXK H5    H5  H 0 1 N N N N N N 18.568 -17.731 -17.010 -3.664 1.208  0.584  H5    A1LXK 28 
A1LXK H6    H6  H 0 1 N N N N N N 17.714 -16.935 -18.375 -3.830 -0.444 1.225  H6    A1LXK 29 
A1LXK H7    H7  H 0 1 N N N N N N 20.712 -17.572 -18.464 -2.398 -1.271 -0.667 H7    A1LXK 30 
A1LXK H8    H8  H 0 1 N N N N N N 19.528 -17.068 -20.393 -2.041 1.559  -1.211 H8    A1LXK 31 
A1LXK H9    H9  H 0 1 N N N N N N 19.953 -16.062 -16.509 -1.173 0.946  1.037  H9    A1LXK 32 
A1LXK H10   H10 H 0 1 N N N N N N 20.547 -14.139 -19.464 1.057  -0.733 1.965  H10   A1LXK 33 
A1LXK H11   H11 H 0 1 N N N N N N 22.065 -16.064 -17.458 -1.529 -1.884 1.582  H11   A1LXK 34 
A1LXK H12   H12 H 0 1 N N N N N N 22.244 -13.892 -23.380 6.152  3.605  -0.081 H12   A1LXK 35 
A1LXK H13   H13 H 0 1 N N N N N N 21.563 -13.503 -24.924 4.607  3.794  0.552  H13   A1LXK 36 
A1LXK H16   H16 H 0 1 N N N N N N 20.066 -11.832 -19.300 1.521  1.725  0.491  H16   A1LXK 37 
A1LXK O1P   O9  O 0 1 N N N N N N 18.716 -20.220 -16.767 -7.223 -0.324 -1.449 O1    A1LXK 38 
A1LXK H1    H1  H 0 1 N N N N N N 19.188 -12.992 -25.031 6.893  1.496  -0.780 H1    A1LXK 39 
A1LXK H14   H14 H 0 1 N N N N N N 15.746 -13.101 -21.435 4.469  -2.837 -0.717 H14   A1LXK 40 
A1LXK H15   H15 H 0 1 N N N N N N 18.119 -20.113 -16.036 -8.168 -0.180 -1.305 H15   A1LXK 41 
# 
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 
A1LXK "C1'" "C2'" SING N N 1  
A1LXK "C1'" N9    SING N N 2  
A1LXK "C1'" "O9'" SING N N 3  
A1LXK C2    N1    SING N N 4  
A1LXK C2    N2    SING N N 5  
A1LXK C2    N3    DOUB N N 6  
A1LXK "C2'" "C3'" SING N N 7  
A1LXK "C3'" "C4'" SING N N 8  
A1LXK "C3'" "O3'" SING N N 9  
A1LXK C4    C5    DOUB N N 10 
A1LXK C4    N3    SING N N 11 
A1LXK C4    N9    SING N N 12 
A1LXK "C4'" "C5'" SING N N 13 
A1LXK "C4'" "O4'" SING N N 14 
A1LXK C5    C6    SING N N 15 
A1LXK C5    N7    SING N N 16 
A1LXK "C5'" "O5'" SING N N 17 
A1LXK C6    N1    SING N N 18 
A1LXK C6    O6    DOUB N N 19 
A1LXK C8    N7    SING N N 20 
A1LXK C8    N9    SING N N 21 
A1LXK C8    O8    DOUB N N 22 
A1LXK O2P   P     DOUB N N 23 
A1LXK O3P   P     SING N N 24 
A1LXK "O5'" P     SING N N 25 
A1LXK O3P   H2    SING N N 26 
A1LXK "C2'" H3    SING N N 27 
A1LXK "C2'" H4    SING N N 28 
A1LXK "C5'" H5    SING N N 29 
A1LXK "C5'" H6    SING N N 30 
A1LXK "C4'" H7    SING N N 31 
A1LXK "O4'" H8    SING N N 32 
A1LXK "C3'" H9    SING N N 33 
A1LXK "C1'" H10   SING N N 34 
A1LXK "O3'" H11   SING N N 35 
A1LXK N2    H12   SING N N 36 
A1LXK N2    H13   SING N N 37 
A1LXK "O9'" H16   SING N N 38 
A1LXK P     O1P   SING N N 39 
A1LXK N1    H1    SING N N 40 
A1LXK N7    H14   SING N N 41 
A1LXK O1P   H15   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 
A1LXK InChI            InChI                1.06  "InChI=1S/C10H16N5O9P/c11-9-13-7-6(8(19)14-9)12-10(20)15(7)5(18)1-3(16)4(17)2-24-25(21,22)23/h3-5,16-18H,1-2H2,(H,12,20)(H2,21,22,23)(H3,11,13,14,19)/t3-,4+,5-/m0/s1" 
A1LXK InChIKey         InChI                1.06  RDUREGGLHYLIPW-LMVFSUKVSA-N                                                                                                                                            
A1LXK SMILES_CANONICAL CACTVS               3.385 "NC1=NC2=C(NC(=O)N2[C@@H](O)C[C@H](O)[C@H](O)CO[P](O)(O)=O)C(=O)N1"                                                                                                    
A1LXK SMILES           CACTVS               3.385 "NC1=NC2=C(NC(=O)N2[CH](O)C[CH](O)[CH](O)CO[P](O)(O)=O)C(=O)N1"                                                                                                        
A1LXK SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C([C@@H]([C@@H](COP(=O)(O)O)O)O)[C@@H](N1C2=C(C(=O)NC(=N2)N)NC1=O)O"                                                                                                  
A1LXK SMILES           "OpenEye OEToolkits" 2.0.7 "C(C(C(COP(=O)(O)O)O)O)C(N1C2=C(C(=O)NC(=N2)N)NC1=O)O"                                                                                                                 
# 
_pdbx_chem_comp_identifier.comp_id           A1LXK 
_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~{R},3~{S},5~{S})-5-[2-azanyl-6,8-bis(oxidanylidene)-1,7-dihydropurin-9-yl]-2,3,5-tris(oxidanyl)pentyl] 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 
A1LXK "Create component" 2024-02-01 PDBJ 
A1LXK "Initial release"  2025-07-23 RCSB 
# 
