data_A1CYZ
# 
_chem_comp.id                                    A1CYZ 
_chem_comp.name                                  "5'-O-[(R)-{[(2R)-2-amino-3-sulfanylpropanoyl]oxy}(hydroxy)phosphoryl]adenosine" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C13 H19 N6 O8 P S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         Cysteinyl-AMP 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-10-20 
_chem_comp.pdbx_modified_date                    2025-11-03 
_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                        450.364 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1CYZ 
_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        9YS2 
_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 
A1CYZ N1    N1  N 0 1 Y N N N N N 16.872 -31.452 3.609  -7.092 -2.155 -0.683 N1    A1CYZ 1  
A1CYZ N3    N2  N 0 1 Y N N N N N 19.061 -31.110 2.662  -5.541 -0.597 -1.396 N3    A1CYZ 2  
A1CYZ C4    C1  C 0 1 Y N N N N N 18.752 -29.802 2.675  -4.771 -0.815 -0.335 C4    A1CYZ 3  
A1CYZ C5    C2  C 0 1 Y N N N N N 17.573 -29.243 3.131  -5.178 -1.762 0.621  C5    A1CYZ 4  
A1CYZ C6    C3  C 0 1 Y N N N N N 16.585 -30.127 3.620  -6.389 -2.441 0.408  C6    A1CYZ 5  
A1CYZ C8    C4  C 0 1 Y N N N N N 18.767 -27.613 2.467  -3.286 -0.940 1.290  C8    A1CYZ 6  
A1CYZ N     N3  N 0 1 N N N N N N 25.159 -22.221 -0.446 7.508  -0.424 -0.452 N     A1CYZ 7  
A1CYZ CA    C5  C 0 1 N N R N N N 24.301 -22.876 -1.473 6.118  -0.845 -0.671 CA    A1CYZ 8  
A1CYZ C     C6  C 0 1 N N N N N N 23.099 -23.466 -0.754 5.191  0.072  0.084  C     A1CYZ 9  
A1CYZ O     O1  O 0 1 N N N N N N 22.252 -24.100 -1.328 5.612  0.735  1.002  O     A1CYZ 10 
A1CYZ CB    C7  C 0 1 N N N N N N 25.067 -23.939 -2.259 5.934  -2.279 -0.172 CB    A1CYZ 11 
A1CYZ SG    S1  S 0 1 N N N N N N 26.570 -23.375 -3.115 7.050  -3.384 -1.081 SG    A1CYZ 12 
A1CYZ "C1'" C8  C 0 1 N N R N N N 20.855 -28.749 1.683  -2.760 0.707  -0.548 "C1'" A1CYZ 13 
A1CYZ C2    C9  C 0 1 Y N N N N N 18.067 -31.848 3.153  -6.669 -1.256 -1.553 C2    A1CYZ 14 
A1CYZ "C2'" C10 C 0 1 N N R N N N 20.954 -27.979 0.356  -3.197 2.119  -0.101 "C2'" A1CYZ 15 
A1CYZ "C3'" C11 C 0 1 N N S N N N 22.475 -27.776 0.263  -1.874 2.912  -0.014 "C3'" A1CYZ 16 
A1CYZ "C4'" C12 C 0 1 N N R N N N 22.847 -27.537 1.738  -0.794 1.885  -0.419 "C4'" A1CYZ 17 
A1CYZ "C5'" C13 C 0 1 N N N N N N 23.082 -26.081 2.080  0.474  2.090  0.412  "C5'" A1CYZ 18 
A1CYZ N6    N4  N 0 1 N N N N N N 15.403 -29.725 4.085  -6.841 -3.384 1.314  N6    A1CYZ 19 
A1CYZ N7    N5  N 0 1 Y N N N N N 17.595 -27.863 2.998  -4.227 -1.789 1.585  N7    A1CYZ 20 
A1CYZ N9    N6  N 0 1 Y N N N N N 19.516 -28.734 2.251  -3.576 -0.314 0.114  N9    A1CYZ 21 
A1CYZ O1P   O2  O 0 1 N N N N N N 20.650 -23.200 1.269  3.567  2.510  0.577  O1P   A1CYZ 22 
A1CYZ "O2'" O3  O 0 1 N N N N N N 20.408 -28.668 -0.738 -4.071 2.703  -1.069 "O2'" A1CYZ 23 
A1CYZ O2P   O4  O 0 1 N N N N N N 22.433 -23.221 3.048  2.871  0.630  2.110  O2P   A1CYZ 24 
A1CYZ "O3'" O5  O 0 1 N N N N N N 23.128 -28.940 -0.240 -1.888 4.011  -0.927 "O3'" A1CYZ 25 
A1CYZ O3P   O6  O 0 1 N N N N N N 23.098 -23.262 0.581  3.897  0.153  -0.264 O3P   A1CYZ 26 
A1CYZ "O4'" O7  O 0 1 N N N N N N 21.743 -28.033 2.535  -1.381 0.598  -0.131 "O4'" A1CYZ 27 
A1CYZ "O5'" O8  O 0 1 N N N N N N 21.893 -25.310 1.764  1.498  1.210  -0.056 "O5'" A1CYZ 28 
A1CYZ P     P1  P 0 1 N N N N N N 21.981 -23.654 1.710  2.971  1.156  0.591  P     A1CYZ 29 
A1CYZ H1    H1  H 0 1 N N N N N N 19.107 -26.617 2.224  -2.405 -0.758 1.888  H1    A1CYZ 30 
A1CYZ H2    H2  H 0 1 N N N N N N 24.625 -21.534 0.046  7.746  -0.459 0.528  H2    A1CYZ 31 
A1CYZ H3    H3  H 0 1 N N N N N N 25.491 -22.909 0.199  8.146  -0.984 -0.999 H3    A1CYZ 32 
A1CYZ H5    H5  H 0 1 N N N N N N 23.945 -22.112 -2.179 5.888  -0.798 -1.736 H5    A1CYZ 33 
A1CYZ H6    H6  H 0 1 N N N N N N 24.385 -24.354 -3.016 6.164  -2.326 0.892  H6    A1CYZ 34 
A1CYZ H7    H7  H 0 1 N N N N N N 25.359 -24.732 -1.555 4.903  -2.591 -0.335 H7    A1CYZ 35 
A1CYZ H8    H8  H 0 1 N N N N N N 26.988 -24.470 -3.677 6.784  -4.589 -0.547 H8    A1CYZ 36 
A1CYZ H9    H9  H 0 1 N N N N N N 21.200 -29.783 1.533  -2.837 0.609  -1.631 H9    A1CYZ 37 
A1CYZ H10   H10 H 0 1 N N N N N N 18.250 -32.912 3.188  -7.271 -1.055 -2.427 H10   A1CYZ 38 
A1CYZ H11   H11 H 0 1 N N N N N N 20.472 -26.998 0.478  -3.682 2.077  0.874  H11   A1CYZ 39 
A1CYZ H12   H12 H 0 1 N N N N N N 22.705 -26.883 -0.337 -1.705 3.263  1.005  H12   A1CYZ 40 
A1CYZ H13   H13 H 0 1 N N N N N N 23.758 -28.109 1.967  -0.568 1.971  -1.482 H13   A1CYZ 41 
A1CYZ H14   H14 H 0 1 N N N N N N 23.304 -25.988 3.153  0.810  3.122  0.315  H14   A1CYZ 42 
A1CYZ H15   H15 H 0 1 N N N N N N 23.932 -25.700 1.495  0.261  1.874  1.459  H15   A1CYZ 43 
A1CYZ H16   H16 H 0 1 N N N N N N 14.871 -30.520 4.375  -7.679 -3.846 1.156  H16   A1CYZ 44 
A1CYZ H17   H17 H 0 1 N N N N N N 15.542 -29.114 4.864  -6.319 -3.584 2.107  H17   A1CYZ 45 
A1CYZ H18   H18 H 0 1 N N N N N N 19.470 -28.760 -0.619 -4.377 3.591  -0.838 H18   A1CYZ 46 
A1CYZ H19   H19 H 0 1 N N N N N N 21.762 -22.683 3.451  2.489  -0.254 2.196  H19   A1CYZ 47 
A1CYZ H20   H20 H 0 1 N N N N N N 24.064 -28.784 -0.286 -2.587 4.657  -0.755 H20   A1CYZ 48 
# 
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 
A1CYZ SG    CB    SING N N 1  
A1CYZ CB    CA    SING N N 2  
A1CYZ CA    C     SING N N 3  
A1CYZ CA    N     SING N N 4  
A1CYZ O     C     DOUB N N 5  
A1CYZ C     O3P   SING N N 6  
A1CYZ "O2'" "C2'" SING N N 7  
A1CYZ "O3'" "C3'" SING N N 8  
A1CYZ "C3'" "C2'" SING N N 9  
A1CYZ "C3'" "C4'" SING N N 10 
A1CYZ "C2'" "C1'" SING N N 11 
A1CYZ O3P   P     SING N N 12 
A1CYZ O1P   P     DOUB N N 13 
A1CYZ "C1'" N9    SING N N 14 
A1CYZ "C1'" "O4'" SING N N 15 
A1CYZ P     "O5'" SING N N 16 
A1CYZ P     O2P   SING N N 17 
A1CYZ "C4'" "C5'" SING N N 18 
A1CYZ "C4'" "O4'" SING N N 19 
A1CYZ "O5'" "C5'" SING N N 20 
A1CYZ N9    C8    SING Y N 21 
A1CYZ N9    C4    SING Y N 22 
A1CYZ C8    N7    DOUB Y N 23 
A1CYZ N3    C4    DOUB Y N 24 
A1CYZ N3    C2    SING Y N 25 
A1CYZ C4    C5    SING Y N 26 
A1CYZ N7    C5    SING Y N 27 
A1CYZ C5    C6    DOUB Y N 28 
A1CYZ C2    N1    DOUB Y N 29 
A1CYZ N1    C6    SING Y N 30 
A1CYZ C6    N6    SING N N 31 
A1CYZ C8    H1    SING N N 32 
A1CYZ N     H2    SING N N 33 
A1CYZ N     H3    SING N N 34 
A1CYZ CA    H5    SING N N 35 
A1CYZ CB    H6    SING N N 36 
A1CYZ CB    H7    SING N N 37 
A1CYZ SG    H8    SING N N 38 
A1CYZ "C1'" H9    SING N N 39 
A1CYZ C2    H10   SING N N 40 
A1CYZ "C2'" H11   SING N N 41 
A1CYZ "C3'" H12   SING N N 42 
A1CYZ "C4'" H13   SING N N 43 
A1CYZ "C5'" H14   SING N N 44 
A1CYZ "C5'" H15   SING N N 45 
A1CYZ N6    H16   SING N N 46 
A1CYZ N6    H17   SING N N 47 
A1CYZ "O2'" H18   SING N N 48 
A1CYZ O2P   H19   SING N N 49 
A1CYZ "O3'" H20   SING N N 50 
# 
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 
A1CYZ SMILES           ACDLabs              14.52   "SCC(N)C(=O)OP(=O)(O)OCC1OC(n2cnc3c(N)ncnc32)C(O)C1O"                                                                                                                                      
A1CYZ InChI            InChI                1.06    "InChI=1S/C13H19N6O8PS/c14-5(2-29)13(22)27-28(23,24)25-1-6-8(20)9(21)12(26-6)19-4-18-7-10(15)16-3-17-11(7)19/h3-6,8-9,12,20-21,29H,1-2,14H2,(H,23,24)(H2,15,16,17)/t5-,6+,8+,9+,12+/m0/s1" 
A1CYZ InChIKey         InChI                1.06    CHQCHJWWSCSGOJ-MACXSXHHSA-N                                                                                                                                                                
A1CYZ SMILES_CANONICAL CACTVS               3.385   "N[C@@H](CS)C(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23"                                                                                                              
A1CYZ SMILES           CACTVS               3.385   "N[CH](CS)C(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23"                                                                                                                     
A1CYZ 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)OC(=O)[C@H](CS)N)O)O)N"                                                                                                          
A1CYZ SMILES           "OpenEye OEToolkits" 3.1.0.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OC(=O)C(CS)N)O)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 
A1CYZ "SYSTEMATIC NAME" ACDLabs              14.52   "5'-O-[(R)-{[(2R)-2-amino-3-sulfanylpropanoyl]oxy}(hydroxy)phosphoryl]adenosine"                                                                     
A1CYZ "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2~{R})-2-azanyl-3-sulfanyl-propanoate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1CYZ "Create component" 2025-10-20 RCSB 
A1CYZ "Initial release"  2025-10-29 RCSB 
A1CYZ "Modify synonyms"  2025-11-03 RCSB 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      A1CYZ 
_pdbx_chem_comp_synonyms.name         Cysteinyl-AMP 
_pdbx_chem_comp_synonyms.provenance   AUTHOR 
_pdbx_chem_comp_synonyms.type         ? 
# 
