data_A1ID5
# 
_chem_comp.id                                    A1ID5 
_chem_comp.name                                  
;N3-propargyl adenosine-5'-monophosphate
;
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C13 H17 N5 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               A 
_chem_comp.pdbx_synonyms                         "[(2R,3S,4R,5R)-5-(6-azanyl-3-prop-2-ynyl-purin-3-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2024-06-13 
_chem_comp.pdbx_modified_date                    2025-01-31 
_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                        386.277 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1ID5 
_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        9FN3 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_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 
A1ID5 C2     C1  C 0 1 Y N N N N N 24.699 42.098 36.548 4.932  0.282  0.455  C2     A1ID5 1  
A1ID5 "C1'"  C2  C 0 1 N N R N N N 21.707 44.482 34.076 0.492  0.640  -0.097 "C1'"  A1ID5 2  
A1ID5 "C2'"  C3  C 0 1 N N R N N N 20.424 45.225 33.726 0.269  1.361  -1.451 "C2'"  A1ID5 3  
A1ID5 "C3'"  C4  C 0 1 N N S N N N 20.874 46.042 32.517 -1.132 1.991  -1.256 "C3'"  A1ID5 4  
A1ID5 "C4'"  C5  C 0 1 N N R N N N 22.357 46.319 32.808 -1.764 1.162  -0.121 "C4'"  A1ID5 5  
A1ID5 "C5'"  C6  C 0 1 N N N N N N 22.690 47.747 33.177 -3.066 0.521  -0.608 "C5'"  A1ID5 6  
A1ID5 C1P    C7  C 0 1 N N N N N N 24.469 43.033 34.323 3.151  1.892  0.617  C1P    A1ID5 7  
A1ID5 C2P    C8  C 0 1 N N N N N N 25.812 42.360 34.041 2.720  1.972  2.022  C2P    A1ID5 8  
A1ID5 C3P    C9  C 0 1 N N N N N N 26.879 41.863 33.886 2.376  2.035  3.143  C3P    A1ID5 9  
A1ID5 C4     C10 C 0 1 Y N N N N N 22.751 43.248 36.032 2.796  -0.406 -0.042 C4     A1ID5 10 
A1ID5 C5     C11 C 0 1 Y N N N N N 22.313 42.990 37.317 3.286  -1.696 -0.310 C5     A1ID5 11 
A1ID5 C6     C12 C 0 1 Y N N N N N 23.124 42.265 38.196 4.666  -1.923 -0.171 C6     A1ID5 12 
A1ID5 C8     C13 C 0 1 Y N N N N N 20.781 44.107 36.331 1.143  -1.738 -0.637 C8     A1ID5 13 
A1ID5 N1     N1  N 0 1 Y N N N N N 24.301 41.838 37.784 5.438  -0.913 0.214  N1     A1ID5 14 
A1ID5 N3     N2  N 1 1 Y N N N N N 23.966 42.782 35.671 3.647  0.543  0.334  N3     A1ID5 15 
A1ID5 N6     N3  N 0 1 N N N N N N 22.671 41.987 39.546 5.206  -3.173 -0.421 N6     A1ID5 16 
A1ID5 N7     N4  N 0 1 Y N N N N N 21.100 43.530 37.473 2.225  -2.459 -0.668 N7     A1ID5 17 
A1ID5 N9     N5  N 0 1 Y N N N N N 21.758 43.962 35.449 1.441  -0.465 -0.251 N9     A1ID5 18 
A1ID5 "O2'"  O1  O 0 1 N N N N N N 19.359 44.337 33.460 1.258  2.370  -1.660 "O2'"  A1ID5 19 
A1ID5 "O3'"  O2  O 0 1 N N N N N N 20.753 45.238 31.347 -1.017 3.362  -0.869 "O3'"  A1ID5 20 
A1ID5 "O4'"  O3  O 0 1 N N N N N N 22.726 45.436 33.904 -0.820 0.139  0.242  "O4'"  A1ID5 21 
A1ID5 "O5'"  O4  O 0 1 N N N N N N 21.674 48.333 33.983 -3.704 -0.148 0.482  "O5'"  A1ID5 22 
A1ID5 OP1    O5  O 0 1 N N N N N N 20.679 49.627 32.082 -4.985 -1.941 -0.749 OP1    A1ID5 23 
A1ID5 OP2    O6  O 0 1 N N N N N N 19.865 49.991 34.539 -5.453 -1.673 1.717  OP2    A1ID5 24 
A1ID5 P      P1  P 0 1 N N N N N N 20.978 49.702 33.558 -5.100 -0.935 0.331  P      A1ID5 25 
A1ID5 H2     H1  H 0 1 N N N N N N 25.668 41.737 36.235 5.596  1.075  0.766  H2     A1ID5 26 
A1ID5 "H1'"  H2  H 0 1 N N N N N N 21.838 43.652 33.366 0.842  1.342  0.659  "H1'"  A1ID5 27 
A1ID5 "H2'"  H3  H 0 1 N N N N N N 20.166 45.909 34.548 0.263  0.648  -2.275 "H2'"  A1ID5 28 
A1ID5 "H3'"  H4  H 0 1 N N N N N N 20.307 46.982 32.444 -1.720 1.899  -2.169 "H3'"  A1ID5 29 
A1ID5 "H4'"  H5  H 0 1 N N N N N N 22.937 46.047 31.914 -1.965 1.802  0.738  "H4'"  A1ID5 30 
A1ID5 "H5''" H6  H 0 0 N N N N N N 23.638 47.759 33.734 -3.728 1.295  -0.997 "H5''" A1ID5 31 
A1ID5 "H5'"  H7  H 0 1 N N N N N N 22.799 48.337 32.255 -2.844 -0.198 -1.396 "H5'"  A1ID5 32 
A1ID5 H1     H8  H 0 1 N N N N N N 24.589 44.119 34.192 2.306  2.112  -0.035 H1     A1ID5 33 
A1ID5 H3     H9  H 0 1 N N N N N N 23.731 42.656 33.600 3.946  2.616  0.439  H3     A1ID5 34 
A1ID5 H4     H10 H 0 1 N N N N N N 27.832 41.419 33.748 2.069  2.092  4.146  H4     A1ID5 35 
A1ID5 H8     H11 H 0 1 N N N N N N 19.853 44.625 36.142 0.153  -2.096 -0.878 H8     A1ID5 36 
A1ID5 H62    H12 H 0 1 N N N N N N 23.370 41.462 40.031 4.630  -3.904 -0.695 H62    A1ID5 37 
A1ID5 H61    H13 H 0 1 N N N N N N 22.507 42.849 40.027 6.160  -3.317 -0.322 H61    A1ID5 38 
A1ID5 "HO2'" H14 H 0 0 N N N N N N 19.134 43.865 34.253 1.161  2.850  -2.494 "HO2'" A1ID5 39 
A1ID5 "HO3'" H15 H 0 0 N Y N N N N 19.835 45.070 31.171 -0.625 3.930  -1.547 "HO3'" A1ID5 40 
A1ID5 HOP2   H17 H 0 0 N N N N N N 19.047 50.099 34.068 -6.284 -2.168 1.699  HOP2   A1ID5 41 
A1ID5 OP3    O7  O 0 1 N Y N N N N 22.121 50.808 33.771 -6.269 0.111  -0.033 OP3    A1ID5 42 
A1ID5 HOP3   H18 H 0 0 N Y N N N N 22.365 51.178 32.931 -6.400 0.801  0.632  HOP3   A1ID5 43 
# 
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 
A1ID5 "O3'" "C3'"  SING N N 1  
A1ID5 OP1   P      DOUB N N 2  
A1ID5 "C3'" "C4'"  SING N N 3  
A1ID5 "C3'" "C2'"  SING N N 4  
A1ID5 "C4'" "C5'"  SING N N 5  
A1ID5 "C4'" "O4'"  SING N N 6  
A1ID5 "C5'" "O5'"  SING N N 7  
A1ID5 "O2'" "C2'"  SING N N 8  
A1ID5 P     "O5'"  SING N N 9  
A1ID5 P     OP2    SING N N 10 
A1ID5 "C2'" "C1'"  SING N N 11 
A1ID5 C3P   C2P    TRIP N N 12 
A1ID5 "O4'" "C1'"  SING N N 13 
A1ID5 C2P   C1P    SING N N 14 
A1ID5 "C1'" N9     SING N N 15 
A1ID5 C1P   N3     SING N N 16 
A1ID5 N9    C4     SING Y N 17 
A1ID5 N9    C8     SING Y N 18 
A1ID5 N3    C4     SING Y N 19 
A1ID5 N3    C2     DOUB Y N 20 
A1ID5 C4    C5     DOUB Y N 21 
A1ID5 C8    N7     DOUB Y N 22 
A1ID5 C2    N1     SING Y N 23 
A1ID5 C5    N7     SING Y N 24 
A1ID5 C5    C6     SING Y N 25 
A1ID5 N1    C6     DOUB Y N 26 
A1ID5 C6    N6     SING N N 27 
A1ID5 C2    H2     SING N N 28 
A1ID5 "C1'" "H1'"  SING N N 29 
A1ID5 "C2'" "H2'"  SING N N 30 
A1ID5 "C3'" "H3'"  SING N N 31 
A1ID5 "C4'" "H4'"  SING N N 32 
A1ID5 "C5'" "H5''" SING N N 33 
A1ID5 "C5'" "H5'"  SING N N 34 
A1ID5 C1P   H1     SING N N 35 
A1ID5 C1P   H3     SING N N 36 
A1ID5 C3P   H4     SING N N 37 
A1ID5 C8    H8     SING N N 38 
A1ID5 N6    H62    SING N N 39 
A1ID5 N6    H61    SING N N 40 
A1ID5 "O2'" "HO2'" SING N N 41 
A1ID5 "O3'" "HO3'" SING N N 42 
A1ID5 OP2   HOP2   SING N N 43 
A1ID5 P     OP3    SING N N 44 
A1ID5 OP3   HOP3   SING N N 45 
# 
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 
A1ID5 InChI            InChI                1.06  "InChI=1S/C13H16N5O7P/c1-2-3-17-5-16-11(14)8-12(17)18(6-15-8)13-10(20)9(19)7(25-13)4-24-26(21,22)23/h1,5-7,9-10,13-14,19-20H,3-4H2,(H2,21,22,23)/p+1/t7-,9-,10-,13-/m1/s1" 
A1ID5 InChIKey         InChI                1.06  STQVXBAAZLTCOR-QYVSTXNMSA-O                                                                                                                                                
A1ID5 SMILES_CANONICAL CACTVS               3.385 "Nc1nc[n+](CC#C)c2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O"                                                                                                    
A1ID5 SMILES           CACTVS               3.385 "Nc1nc[n+](CC#C)c2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O"                                                                                                          
A1ID5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C#CC[n+]1cnc(c2c1n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N"                                                                                                    
A1ID5 SMILES           "OpenEye OEToolkits" 2.0.7 "C#CC[n+]1cnc(c2c1n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N"                                                                                                                      
# 
_pdbx_chem_comp_identifier.comp_id           A1ID5 
_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},4~{R},5~{R})-5-(6-azanyl-3-prop-2-ynyl-purin-3-ium-9-yl)-3,4-bis(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 
A1ID5 "Create component" 2024-06-13 PDBE 
A1ID5 "Modify name"      2024-08-30 PDBE 
A1ID5 "Initial release"  2025-02-05 RCSB 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      A1ID5 
_pdbx_chem_comp_synonyms.name         "[(2R,3S,4R,5R)-5-(6-azanyl-3-prop-2-ynyl-purin-3-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" 
_pdbx_chem_comp_synonyms.provenance   PDB 
_pdbx_chem_comp_synonyms.type         ? 
# 
