data_A1B8A
# 
_chem_comp.id                                    A1B8A 
_chem_comp.name                                  
;3'-deoxy-3'-(L-lysylamino)adenosine 5'-(dihydrogen phosphate)
;
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C16 H27 N8 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-04-09 
_chem_comp.pdbx_modified_date                    2025-06-20 
_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                        474.409 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1B8A 
_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        9O3H 
_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 
A1B8A C5    C1  C 0 1 Y N N N N N 85.766 -45.052 2.004  5.475  0.733  -0.154 C5    A1B8A 1  
A1B8A C6    C2  C 0 1 Y N N N N N 85.350 -44.035 2.731  6.619  1.511  0.090  C6    A1B8A 2  
A1B8A C8    C3  C 0 1 Y N N N N N 86.685 -46.429 0.639  3.954  -0.680 -0.782 C8    A1B8A 3  
A1B8A C2    C4  C 0 1 Y N N N N N 83.831 -45.374 3.824  5.372  2.838  1.509  C2    A1B8A 4  
A1B8A C4    C5  C 0 1 Y N N N N N 85.191 -46.259 2.164  4.280  1.088  0.495  C4    A1B8A 5  
A1B8A N1    N1  N 0 1 Y N N N N N 84.382 -44.172 3.644  6.518  2.543  0.921  N1    A1B8A 6  
A1B8A N3    N2  N 0 1 Y N N N N N 84.214 -46.412 3.080  4.275  2.138  1.310  N3    A1B8A 7  
A1B8A N     N3  N 0 1 N N N N N N 87.770 -50.523 -5.295 -3.345 3.917  -1.176 N     A1B8A 8  
A1B8A CA    C6  C 0 1 N N S N N N 86.603 -50.334 -4.428 -3.148 2.730  -0.333 CA    A1B8A 9  
A1B8A C     C7  C 0 1 N N N N N N 87.057 -49.850 -3.093 -1.994 1.921  -0.867 C     A1B8A 10 
A1B8A O     O1  O 0 1 N N N N N N 88.179 -49.366 -2.966 -1.629 2.069  -2.014 O     A1B8A 11 
A1B8A CB    C8  C 0 1 N N N N N N 85.816 -51.619 -4.235 -4.418 1.877  -0.348 CB    A1B8A 12 
A1B8A CG    C9  C 0 1 N N N N N N 86.611 -52.675 -3.509 -5.562 2.654  0.308  CG    A1B8A 13 
A1B8A CD    C10 C 0 1 N N N N N N 86.673 -53.915 -4.362 -6.832 1.801  0.293  CD    A1B8A 14 
A1B8A CE    C11 C 0 1 N N N N N N 85.546 -54.897 -4.046 -7.975 2.578  0.950  CE    A1B8A 15 
A1B8A NZ    N4  N 0 1 N N N N N N 85.302 -55.695 -5.274 -9.195 1.759  0.936  NZ    A1B8A 16 
A1B8A "C1'" C12 C 0 1 N N R N N N 85.438 -48.592 1.182  1.935  0.137  0.492  "C1'" A1B8A 17 
A1B8A "C2'" C13 C 0 1 N N R N N N 85.008 -48.927 -0.245 1.079  1.028  -0.435 "C2'" A1B8A 18 
A1B8A "C3'" C14 C 0 1 N N S N N N 86.334 -49.376 -0.818 -0.245 0.248  -0.589 "C3'" A1B8A 19 
A1B8A "C4'" C15 C 0 1 N N S N N N 86.862 -50.240 0.285  -0.034 -1.023 0.264  "C4'" A1B8A 20 
A1B8A "C5'" C16 C 0 1 N N N N N N 88.366 -50.413 0.108  -0.688 -2.231 -0.409 "C5'" A1B8A 21 
A1B8A "N3'" N5  N 0 1 N N N N N N 86.170 -50.044 -2.113 -1.367 1.034  -0.070 "N3'" A1B8A 22 
A1B8A N6    N6  N 0 1 N N N N N N 85.917 -42.826 2.553  7.824  1.210  -0.520 N6    A1B8A 23 
A1B8A N7    N7  N 0 1 Y N N N N N 86.675 -45.182 1.067  5.206  -0.353 -0.918 N7    A1B8A 24 
A1B8A N9    N8  N 0 1 Y N N N N N 85.770 -47.139 1.338  3.341  0.177  0.084  N9    A1B8A 25 
A1B8A "O2'" O2  O 0 1 N N N N N N 84.084 -50.026 -0.198 0.844  2.300  0.170  "O2'" A1B8A 26 
A1B8A "O4'" O3  O 0 1 N N N N N N 86.610 -49.425 1.467  1.399  -1.194 0.322  "O4'" A1B8A 27 
A1B8A "O5'" O4  O 0 1 N N N N N N 88.906 -49.185 -0.359 -0.582 -3.369 0.449  "O5'" A1B8A 28 
A1B8A OP1   O5  O 0 1 N N N N N N 91.433 -49.466 -0.292 -0.602 -5.242 -1.243 OP1   A1B8A 29 
A1B8A OP2   O6  O 0 1 N N N N N N 90.342 -47.155 0.074  -0.755 -5.885 1.194  OP2   A1B8A 30 
A1B8A P     P1  P 0 1 N N N N N N 90.307 -48.642 0.199  -1.164 -4.819 0.059  P     A1B8A 31 
A1B8A H1    H1  H 0 1 N N N N N N 87.320 -46.820 -0.142 3.472  -1.508 -1.279 H1    A1B8A 32 
A1B8A H2    H2  H 0 1 N N N N N N 83.069 -45.507 4.578  5.334  3.686  2.177  H2    A1B8A 33 
A1B8A H3    H3  H 0 1 N N N N N N 88.256 -49.655 -5.394 -3.548 3.655  -2.129 H3    A1B8A 34 
A1B8A H4    H4  H 0 1 N N N N N N 88.381 -51.203 -4.888 -4.072 4.509  -0.802 H4    A1B8A 35 
A1B8A H6    H6  H 0 1 N N N N N N 85.938 -49.580 -4.874 -2.932 3.041  0.689  H6    A1B8A 36 
A1B8A H7    H7  H 0 1 N N N N N N 84.911 -51.395 -3.652 -4.685 1.640  -1.378 H7    A1B8A 37 
A1B8A H8    H8  H 0 1 N N N N N N 85.529 -52.009 -5.222 -4.243 0.954  0.204  H8    A1B8A 38 
A1B8A H9    H9  H 0 1 N N N N N N 86.124 -52.910 -2.551 -5.295 2.891  1.338  H9    A1B8A 39 
A1B8A H10   H10 H 0 1 N N N N N N 87.630 -52.305 -3.321 -5.738 3.577  -0.243 H10   A1B8A 40 
A1B8A H11   H11 H 0 1 N N N N N N 87.637 -54.416 -4.188 -7.098 1.564  -0.737 H11   A1B8A 41 
A1B8A H12   H12 H 0 1 N N N N N N 86.599 -53.620 -5.419 -6.656 0.878  0.845  H12   A1B8A 42 
A1B8A H13   H13 H 0 1 N N N N N N 84.635 -54.348 -3.766 -7.709 2.815  1.980  H13   A1B8A 43 
A1B8A H14   H14 H 0 1 N N N N N N 85.844 -55.559 -3.219 -8.151 3.501  0.398  H14   A1B8A 44 
A1B8A H15   H15 H 0 1 N N N N N N 84.567 -56.352 -5.105 -9.038 0.869  1.385  H15   A1B8A 45 
A1B8A H16   H16 H 0 1 N N N N N N 85.038 -55.085 -6.021 -9.965 2.250  1.364  H16   A1B8A 46 
A1B8A H18   H18 H 0 1 N N N N N N 84.621 -48.853 1.871  1.832  0.457  1.529  H18   A1B8A 47 
A1B8A H19   H19 H 0 1 N N N N N N 84.609 -48.046 -0.769 1.567  1.151  -1.403 H19   A1B8A 48 
A1B8A H20   H20 H 0 1 N N N N N N 86.988 -48.499 -0.935 -0.414 -0.017 -1.633 H20   A1B8A 49 
A1B8A H21   H21 H 0 1 N N N N N N 86.347 -51.211 0.326  -0.440 -0.879 1.265  H21   A1B8A 50 
A1B8A H22   H22 H 0 1 N N N N N N 88.565 -51.209 -0.625 -1.739 -2.016 -0.600 H22   A1B8A 51 
A1B8A H23   H23 H 0 1 N N N N N N 88.825 -50.678 1.072  -0.182 -2.439 -1.352 H23   A1B8A 52 
A1B8A H24   H24 H 0 1 N N N N N N 85.388 -50.649 -2.264 -1.659 0.915  0.848  H24   A1B8A 53 
A1B8A H25   H25 H 0 1 N N N N N N 85.498 -42.166 3.176  7.885  0.454  -1.125 H25   A1B8A 54 
A1B8A H26   H26 H 0 1 N N N N N N 86.897 -42.887 2.742  8.607  1.755  -0.344 H26   A1B8A 55 
A1B8A H27   H27 H 0 1 N N N N N N 83.257 -49.730 0.163  1.648  2.808  0.345  H27   A1B8A 56 
A1B8A H29   H29 H 0 1 N N N N N N 91.154 -46.891 -0.342 -1.073 -6.782 1.024  H29   A1B8A 57 
A1B8A OP3   OP3 O 0 1 N Y N N N N 89.942 -48.637 1.710  -2.769 -4.741 -0.050 OP3   A1B8A 58 
A1B8A HO3   H5  H 0 1 N Y N N N N 90.534 -49.212 2.181  -3.206 -4.468 0.769  HO3   A1B8A 59 
# 
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 
A1B8A N     CA    SING N N 1  
A1B8A NZ    CE    SING N N 2  
A1B8A CA    CB    SING N N 3  
A1B8A CA    C     SING N N 4  
A1B8A CD    CE    SING N N 5  
A1B8A CD    CG    SING N N 6  
A1B8A CB    CG    SING N N 7  
A1B8A C     O     DOUB N N 8  
A1B8A C     "N3'" SING N N 9  
A1B8A "N3'" "C3'" SING N N 10 
A1B8A "C3'" "C2'" SING N N 11 
A1B8A "C3'" "C4'" SING N N 12 
A1B8A "O5'" "C5'" SING N N 13 
A1B8A "O5'" P     SING N N 14 
A1B8A OP1   P     DOUB N N 15 
A1B8A "C2'" "O2'" SING N N 16 
A1B8A "C2'" "C1'" SING N N 17 
A1B8A OP2   P     SING N N 18 
A1B8A "C5'" "C4'" SING N N 19 
A1B8A "C4'" "O4'" SING N N 20 
A1B8A C8    N7    DOUB Y N 21 
A1B8A C8    N9    SING Y N 22 
A1B8A N7    C5    SING Y N 23 
A1B8A "C1'" N9    SING N N 24 
A1B8A "C1'" "O4'" SING N N 25 
A1B8A N9    C4    SING Y N 26 
A1B8A C5    C4    DOUB Y N 27 
A1B8A C5    C6    SING Y N 28 
A1B8A C4    N3    SING Y N 29 
A1B8A N6    C6    SING N N 30 
A1B8A C6    N1    DOUB Y N 31 
A1B8A N3    C2    DOUB Y N 32 
A1B8A N1    C2    SING Y N 33 
A1B8A C8    H1    SING N N 34 
A1B8A C2    H2    SING N N 35 
A1B8A N     H3    SING N N 36 
A1B8A N     H4    SING N N 37 
A1B8A CA    H6    SING N N 38 
A1B8A CB    H7    SING N N 39 
A1B8A CB    H8    SING N N 40 
A1B8A CG    H9    SING N N 41 
A1B8A CG    H10   SING N N 42 
A1B8A CD    H11   SING N N 43 
A1B8A CD    H12   SING N N 44 
A1B8A CE    H13   SING N N 45 
A1B8A CE    H14   SING N N 46 
A1B8A NZ    H15   SING N N 47 
A1B8A NZ    H16   SING N N 48 
A1B8A "C1'" H18   SING N N 49 
A1B8A "C2'" H19   SING N N 50 
A1B8A "C3'" H20   SING N N 51 
A1B8A "C4'" H21   SING N N 52 
A1B8A "C5'" H22   SING N N 53 
A1B8A "C5'" H23   SING N N 54 
A1B8A "N3'" H24   SING N N 55 
A1B8A N6    H25   SING N N 56 
A1B8A N6    H26   SING N N 57 
A1B8A "O2'" H27   SING N N 58 
A1B8A OP2   H29   SING N N 59 
A1B8A P     OP3   SING N N 60 
A1B8A OP3   HO3   SING N N 61 
# 
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 
A1B8A SMILES           ACDLabs              14.52   "NCCCCC(N)C(=O)NC1C(COP(=O)(O)O)OC(n2cnc3c(N)ncnc32)C1O"                                                                                                                                                         
A1B8A InChI            InChI                1.06    "InChI=1S/C16H27N8O7P/c17-4-2-1-3-8(18)15(26)23-10-9(5-30-32(27,28)29)31-16(12(10)25)24-7-22-11-13(19)20-6-21-14(11)24/h6-10,12,16,25H,1-5,17-18H2,(H,23,26)(H2,19,20,21)(H2,27,28,29)/t8-,9+,10+,12+,16+/m0/s1" 
A1B8A InChIKey         InChI                1.06    ARAKIZUQYBAJIL-GBPQWNHNSA-N                                                                                                                                                                                      
A1B8A SMILES_CANONICAL CACTVS               3.385   "NCCCC[C@H](N)C(=O)N[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3c(N)ncnc23"                                                                                                                                
A1B8A SMILES           CACTVS               3.385   "NCCCC[CH](N)C(=O)N[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)n2cnc3c(N)ncnc23"                                                                                                                                        
A1B8A SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)NC(=O)[C@H](CCCCN)N)O)N"                                                                                                                             
A1B8A SMILES           "OpenEye OEToolkits" 3.1.0.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)NC(=O)C(CCCCN)N)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 
A1B8A "SYSTEMATIC NAME" ACDLabs              14.52   
;3'-deoxy-3'-(L-lysylamino)adenosine 5'-(dihydrogen phosphate)
;
A1B8A "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-[[(2~{S})-2,6-bis(azanyl)hexanoyl]amino]-4-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 
A1B8A "Create component" 2025-04-09 RCSB 
A1B8A "Initial release"  2025-06-25 RCSB 
# 
