data_A1A3L
# 
_chem_comp.id                                    A1A3L 
_chem_comp.name                                  "4-amino-1-{(3xi)-3-C-amino-2-deoxy-5-O-[(S)-hydroxy(phosphonooxy)phosphoryl]-beta-D-threo-pentofuranosyl}pyrimidin-2(1H)-one" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C9 H16 N4 O10 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-08-27 
_chem_comp.pdbx_modified_date                    2024-11-01 
_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                        402.192 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1A3L 
_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        9DB2 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              Y 
# 
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 
A1A3L C2    C1  C 0 1 N N N N N N 109.372 111.684 136.640 3.413  -1.024 -0.617 C2    A1A3L 1  
A1A3L N3    N1  N 0 1 N N N N N N 109.303 111.107 135.242 4.089  -2.112 -0.981 N3    A1A3L 2  
A1A3L C4    C2  C 0 1 N N N N N N 107.986 110.717 134.665 5.055  -2.598 -0.212 C4    A1A3L 3  
A1A3L C5    C3  C 0 1 N N N N N N 106.750 110.893 135.458 5.368  -1.956 1.003  C5    A1A3L 4  
A1A3L C6    C4  C 0 1 N N N N N N 106.856 111.488 136.890 4.671  -0.851 1.360  C6    A1A3L 5  
A1A3L "C1'" C5  C 0 1 N N R N N N 108.286 112.412 138.759 2.934  0.812  0.905  "C1'" A1A3L 6  
A1A3L "C2'" C6  C 0 1 N N N N N N 108.071 113.931 138.960 3.202  1.960  -0.100 "C2'" A1A3L 7  
A1A3L "C3'" C7  C 0 1 N N R N N N 107.309 114.130 140.277 1.926  2.825  0.047  "C3'" A1A3L 8  
A1A3L "C4'" C8  C 0 1 N N R N N N 106.566 112.754 140.338 0.886  1.862  0.652  "C4'" A1A3L 9  
A1A3L "C5'" C9  C 0 1 N N N N N N 105.230 112.868 139.642 -0.330 1.762  -0.271 "C5'" A1A3L 10 
A1A3L N01   N2  N 0 1 N N N N N N 107.987 114.283 141.566 2.171  3.954  0.954  N01   A1A3L 11 
A1A3L N1    N3  N 0 1 N N N N N N 108.173 111.860 137.446 3.691  -0.386 0.534  N1    A1A3L 12 
A1A3L N4    N4  N 0 1 N N N N N N 107.924 110.186 133.380 5.746  -3.723 -0.599 N4    A1A3L 13 
A1A3L O01   O1  O 0 1 N N N N N N 106.404 115.222 140.116 1.489  3.294  -1.230 O01   A1A3L 14 
A1A3L O1A   O2  O 0 1 N N N N N N 103.755 111.195 137.868 -2.533 0.044  -1.673 O1A   A1A3L 15 
A1A3L O1B   O3  O 0 1 N N N N N N 102.888 108.058 137.757 -5.522 -1.757 1.709  O1B   A1A3L 16 
A1A3L O2    O4  O 0 1 N N N N N N 110.400 111.989 137.088 2.530  -0.596 -1.342 O2    A1A3L 17 
A1A3L O2A   O5  O 0 1 N N N N N N 102.118 110.995 139.399 -3.593 2.010  -0.498 O2A   A1A3L 18 
A1A3L O2B   O6  O 0 1 N N N N N N 105.195 107.969 137.742 -5.795 -0.733 -0.581 O2B   A1A3L 19 
A1A3L O3A   O7  O 0 1 N N N N N N 104.105 109.370 139.652 -3.582 -0.387 0.581  O3A   A1A3L 20 
A1A3L O3B   O8  O 0 1 N N N N N N 104.004 106.797 139.329 -4.268 -2.734 -0.386 O3B   A1A3L 21 
A1A3L "O4'" O9  O 0 1 N N N N N N 107.353 111.766 139.690 1.515  0.576  0.777  "O4'" A1A3L 22 
A1A3L "O5'" O10 O 0 1 N N N N N N 104.282 111.983 140.255 -1.337 0.961  0.351  "O5'" A1A3L 23 
A1A3L PA    P1  P 0 1 N N N N N N 103.560 110.879 139.276 -2.756 0.644  -0.339 PA    A1A3L 24 
A1A3L PB    P2  P 0 1 N N N N N N 104.051 108.079 138.639 -4.813 -1.388 0.311  PB    A1A3L 25 
A1A3L H1    H1  H 0 1 N N N N N N 105.790 110.613 135.049 6.151  -2.340 1.640  H1    A1A3L 26 
A1A3L H2    H2  H 0 1 N N N N N N 105.963 111.630 137.481 4.892  -0.342 2.286  H2    A1A3L 27 
A1A3L H3    H3  H 0 1 N N N N N N 109.302 112.197 139.121 3.181  1.125  1.920  H3    A1A3L 28 
A1A3L H4    H4  H 0 1 N N N N N N 109.044 114.443 139.010 4.089  2.526  0.183  H4    A1A3L 29 
A1A3L H5    H5  H 0 1 N N N N N N 107.485 114.339 138.124 3.295  1.575  -1.116 H5    A1A3L 30 
A1A3L H6    H6  H 0 1 N N N N N N 106.405 112.489 141.393 0.576  2.220  1.634  H6    A1A3L 31 
A1A3L H7    H7  H 0 1 N N N N N N 105.347 112.599 138.582 -0.726 2.760  -0.461 H7    A1A3L 32 
A1A3L H8    H8  H 0 1 N N N N N N 104.866 113.903 139.720 -0.033 1.304  -1.215 H8    A1A3L 33 
A1A3L H9    H9  H 0 1 N N N N N N 107.306 114.400 142.289 2.896  4.556  0.594  H9    A1A3L 34 
A1A3L H10   H10 H 0 1 N N N N N N 108.535 113.468 141.753 1.322  4.471  1.125  H10   A1A3L 35 
A1A3L H12   H12 H 0 1 N N N N N N 108.762 110.067 132.847 5.529  -4.163 -1.435 H12   A1A3L 36 
A1A3L H13   H13 H 0 1 N N N N N N 107.042 109.923 132.990 6.452  -4.076 -0.034 H13   A1A3L 37 
A1A3L H14   H14 H 0 1 N N N N N N 105.924 115.358 140.924 2.132  3.857  -1.683 H14   A1A3L 38 
A1A3L H15   H15 H 0 1 N N N N N N 103.176 107.980 136.855 -6.274 -2.359 1.622  H15   A1A3L 39 
A1A3L H16   H16 H 0 1 N N N N N N 101.746 111.233 138.558 -3.777 2.459  0.338  H16   A1A3L 40 
A1A3L H17   H17 H 0 1 N N N N N N 104.712 106.244 139.020 -3.619 -3.216 0.145  H17   A1A3L 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 
A1A3L N4    C4    SING N N 1  
A1A3L C4    N3    DOUB N N 2  
A1A3L C4    C5    SING N N 3  
A1A3L N3    C2    SING N N 4  
A1A3L C5    C6    DOUB N N 5  
A1A3L C2    O2    DOUB N N 6  
A1A3L C2    N1    SING N N 7  
A1A3L C6    N1    SING N N 8  
A1A3L N1    "C1'" SING N N 9  
A1A3L O2B   PB    DOUB N N 10 
A1A3L O1B   PB    SING N N 11 
A1A3L O1A   PA    DOUB N N 12 
A1A3L PB    O3B   SING N N 13 
A1A3L PB    O3A   SING N N 14 
A1A3L "C1'" "C2'" SING N N 15 
A1A3L "C1'" "O4'" SING N N 16 
A1A3L "C2'" "C3'" SING N N 17 
A1A3L PA    O2A   SING N N 18 
A1A3L PA    O3A   SING N N 19 
A1A3L PA    "O5'" SING N N 20 
A1A3L "C5'" "O5'" SING N N 21 
A1A3L "C5'" "C4'" SING N N 22 
A1A3L "O4'" "C4'" SING N N 23 
A1A3L O01   "C3'" SING N N 24 
A1A3L "C3'" "C4'" SING N N 25 
A1A3L "C3'" N01   SING N N 26 
A1A3L C5    H1    SING N N 27 
A1A3L C6    H2    SING N N 28 
A1A3L "C1'" H3    SING N N 29 
A1A3L "C2'" H4    SING N N 30 
A1A3L "C2'" H5    SING N N 31 
A1A3L "C4'" H6    SING N N 32 
A1A3L "C5'" H7    SING N N 33 
A1A3L "C5'" H8    SING N N 34 
A1A3L N01   H9    SING N N 35 
A1A3L N01   H10   SING N N 36 
A1A3L N4    H12   SING N N 37 
A1A3L N4    H13   SING N N 38 
A1A3L O01   H14   SING N N 39 
A1A3L O1B   H15   SING N N 40 
A1A3L O2A   H16   SING N N 41 
A1A3L O3B   H17   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 
A1A3L SMILES           ACDLabs              14.52 "O=P(O)(O)OP(=O)(O)OCC1OC(CC1(N)O)N1C=CC(N)=NC1=O"                                                                                                                       
A1A3L InChI            InChI                1.06  "InChI=1S/C9H16N4O10P2/c10-6-1-2-13(8(14)12-6)7-3-9(11,15)5(22-7)4-21-25(19,20)23-24(16,17)18/h1-2,5,7,15H,3-4,11H2,(H,19,20)(H2,10,12,14)(H2,16,17,18)/t5-,7-,9-/m1/s1" 
A1A3L InChIKey         InChI                1.06  XAPJNFNJUSYHIU-SLBFFKMLSA-N                                                                                                                                              
A1A3L SMILES_CANONICAL CACTVS               3.385 "NC1=NC(=O)N(C=C1)[C@H]2C[C@@](N)(O)[C@@H](CO[P](O)(=O)O[P](O)(O)=O)O2"                                                                                                  
A1A3L SMILES           CACTVS               3.385 "NC1=NC(=O)N(C=C1)[CH]2C[C](N)(O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O2"                                                                                                       
A1A3L SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1[C@@H](O[C@@H]([C@]1(N)O)COP(=O)(O)OP(=O)(O)O)N2C=CC(=NC2=O)N"                                                                                                        
A1A3L SMILES           "OpenEye OEToolkits" 2.0.7 "C1C(OC(C1(N)O)COP(=O)(O)OP(=O)(O)O)N2C=CC(=NC2=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 
A1A3L "SYSTEMATIC NAME" ACDLabs              14.52 "4-amino-1-{(3xi)-3-C-amino-2-deoxy-5-O-[(S)-hydroxy(phosphonooxy)phosphoryl]-beta-D-threo-pentofuranosyl}pyrimidin-2(1H)-one"         
A1A3L "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{R},5~{R})-3-azanyl-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methyl 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 
A1A3L "Create component" 2024-08-27 RCSB 
A1A3L "Modify PCM"       2024-09-27 PDBE 
A1A3L "Initial release"  2024-11-06 RCSB 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            A1A3L 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               N01 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
