data_C5Y
#

_chem_comp.id                                   C5Y
_chem_comp.name                                 "5'-O-[(S)-hydroxy(octanoyloxy)phosphoryl]adenosine"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C18 H28 N5 O8 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-11-19
_chem_comp.pdbx_modified_date                   2021-12-31
_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                       473.417
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    C5Y
_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       7KYD
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 RCSB
#   #
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.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
C5Y  C15   C1   C  0  1  N  N  N  -16.061   -6.251  12.667   -5.090   0.250  -0.670  C15   C5Y   1  
C5Y  C17   C2   C  0  1  N  N  N  -14.508   -8.071  12.046   -7.427   1.134  -0.666  C17   C5Y   2  
C5Y  C20   C3   C  0  1  N  N  N  -11.958   -9.931   9.969  -11.094   2.027   0.094  C20   C5Y   3  
C5Y  C21   C4   C  0  1  N  N  N  -11.446  -11.367  10.079  -12.101   2.900  -0.658  C21   C5Y   4  
C5Y  C24   C5   C  0  1  N  N  S  -17.052   -1.573   8.692    3.177  -2.854   0.025  C24   C5Y   5  
C5Y  C26   C6   C  0  1  N  N  R  -15.839   -0.863   8.099    4.248  -1.772   0.306  C26   C5Y   6  
C5Y  C28   C7   C  0  1  Y  N  N  -13.909   -3.452   9.274    3.588   1.529   0.743  C28   C5Y   7  
C5Y  C02   C8   C  0  1  Y  N  N  -11.099   -3.645   6.876    6.667   3.252   0.277  C02   C5Y   8  
C5Y  C03   C9   C  0  1  Y  N  N  -12.282   -3.388   7.825    5.511   2.457   0.365  C03   C5Y   9  
C5Y  C04   C10  C  0  1  Y  N  N  -12.854   -2.149   7.896    5.490   1.239  -0.335  C04   C5Y  10  
C5Y  C06   C11  C  0  1  N  N  R  -14.731   -1.048   9.169    3.773  -0.603  -0.594  C06   C5Y  11  
C5Y  C08   C12  C  0  1  N  N  R  -16.974   -1.290   9.953    1.975  -2.062  -0.525  C08   C5Y  12  
C5Y  C09   C13  C  0  1  N  N  N  -17.586   -2.328  10.888    0.748  -2.299   0.356  C09   C5Y  13  
C5Y  C14   C14  C  0  1  N  N  N  -16.163   -4.781  13.058   -4.098  -0.609   0.071  C14   C5Y  14  
C5Y  C16   C15  C  0  1  N  N  N  -14.599   -6.682  12.668   -6.420   0.261   0.086  C16   C5Y  15  
C5Y  C18   C16  C  0  1  N  N  N  -13.287   -8.162  11.136   -8.757   1.144   0.090  C18   C5Y  16  
C5Y  C19   C17  C  0  1  N  N  N  -12.709   -9.569  11.248   -9.764   2.017  -0.662  C19   C5Y  17  
C5Y  C31   C18  C  0  1  Y  N  N  -11.198   -1.277   6.138    7.615   1.662  -1.101  C31   C5Y  18  
C5Y  N01   N1   N  0  1  N  N  N  -10.483   -4.958   6.790    6.746   4.462   0.945  N01   C5Y  19  
C5Y  N05   N2   N  0  1  Y  N  N  -13.851   -2.196   8.787    4.264   0.678  -0.079  N05   C5Y  20  
C5Y  N29   N3   N  0  1  Y  N  N  -12.938   -4.174   8.675    4.320   2.574   1.000  N29   C5Y  21  
C5Y  N30   N4   N  0  1  Y  N  N  -12.324   -1.039   7.044    6.554   0.885  -1.048  N30   C5Y  22  
C5Y  N32   N5   N  0  1  Y  N  N  -10.596   -2.584   6.065    7.682   2.815  -0.461  N32   C5Y  23  
C5Y  O07   O1   O  0  1  N  N  N  -15.376   -1.220  10.269    2.333  -0.670  -0.500  O07   C5Y  24  
C5Y  O10   O2   O  0  1  N  N  N  -16.963   -2.192  12.141   -0.388  -1.656  -0.225  O10   C5Y  25  
C5Y  O12   O3   O  0  1  N  N  N  -19.201   -2.620  13.369   -1.781  -1.204   1.831  O12   C5Y  26  
C5Y  O13   O4   O  0  1  N  N  N  -17.311   -4.324  13.711   -2.855  -0.766  -0.411  O13   C5Y  27  
C5Y  O22   O5   O  0  1  N  N  N  -15.277   -4.031  12.812   -4.422  -1.157   1.098  O22   C5Y  28  
C5Y  O23   O6   O  0  1  N  N  N  -17.236   -1.959  14.714   -2.401  -3.214   0.435  O23   C5Y  29  
C5Y  O25   O7   O  0  1  N  N  N  -18.311   -0.971   8.122    3.649  -3.787  -0.949  O25   C5Y  30  
C5Y  O27   O8   O  0  1  N  N  N  -16.130    0.454   7.915    5.545  -2.224  -0.089  O27   C5Y  31  
C5Y  P11   P1   P  0  1  N  N  N  -17.703   -2.743  13.509   -1.855  -1.699   0.438  P11   C5Y  32  
C5Y  H151  H1   H  0  0  N  N  N  -16.483   -6.392  11.661   -4.705   1.268  -0.743  H151  C5Y  33  
C5Y  H152  H2   H  0  0  N  N  N  -16.623   -6.861  13.389   -5.244  -0.153  -1.671  H152  C5Y  34  
C5Y  H172  H3   H  0  0  N  N  N  -15.416   -8.265  11.456   -7.043   2.151  -0.739  H172  C5Y  35  
C5Y  H171  H4   H  0  0  N  N  N  -14.422   -8.822  12.845   -7.581   0.730  -1.667  H171  C5Y  36  
C5Y  H201  H5   H  0  0  N  N  N  -11.108   -9.246   9.835  -10.940   2.431   1.095  H201  C5Y  37  
C5Y  H202  H6   H  0  0  N  N  N  -12.636   -9.847   9.107  -11.479   1.010   0.168  H202  C5Y  38  
C5Y  H212  H7   H  0  0  N  N  N  -10.904  -11.635   9.160  -11.717   3.917  -0.731  H212  C5Y  39  
C5Y  H213  H8   H  0  0  N  N  N  -10.769  -11.450  10.942  -12.255   2.497  -1.658  H213  C5Y  40  
C5Y  H211  H9   H  0  0  N  N  N  -12.297  -12.050  10.214  -13.049   2.908  -0.119  H211  C5Y  41  
C5Y  H241  H10  H  0  0  N  N  N  -17.007   -2.650   8.472    2.905  -3.369   0.946  H241  C5Y  42  
C5Y  H261  H11  H  0  0  N  N  N  -15.535   -1.359   7.166    4.242  -1.482   1.356  H261  C5Y  43  
C5Y  H281  H12  H  0  0  N  N  N  -14.608   -3.816  10.012    2.590   1.364   1.122  H281  C5Y  44  
C5Y  H061  H13  H  0  0  N  N  N  -14.124   -0.131   9.190    4.097  -0.754  -1.623  H061  C5Y  45  
C5Y  H081  H14  H  0  0  N  N  N  -17.402   -0.304  10.188    1.765  -2.372  -1.549  H081  C5Y  46  
C5Y  H091  H15  H  0  0  N  N  N  -18.668   -2.153  10.986    0.559  -3.370   0.435  H091  C5Y  47  
C5Y  H092  H16  H  0  0  N  N  N  -17.413   -3.339  10.491    0.929  -1.889   1.350  H092  C5Y  48  
C5Y  H162  H17  H  0  0  N  N  N  -14.221   -6.712  13.701   -6.804  -0.756   0.159  H162  C5Y  49  
C5Y  H161  H18  H  0  0  N  N  N  -14.001   -5.971  12.079   -6.266   0.664   1.087  H161  C5Y  50  
C5Y  H182  H19  H  0  0  N  N  N  -12.534   -7.424  11.450   -9.141   0.127   0.164  H182  C5Y  51  
C5Y  H181  H20  H  0  0  N  N  N  -13.583   -7.963  10.095   -8.603   1.548   1.091  H181  C5Y  52  
C5Y  H192  H21  H  0  0  N  N  N  -13.527  -10.287  11.405   -9.918   1.614  -1.663  H192  C5Y  53  
C5Y  H191  H22  H  0  0  N  N  N  -12.016   -9.611  12.101   -9.380   3.034  -0.735  H191  C5Y  54  
C5Y  H311  H23  H  0  0  N  N  N  -10.819   -0.473   5.525    8.463   1.344  -1.689  H311  C5Y  55  
C5Y  H012  H24  H  0  0  N  N  N   -9.737   -4.934   6.125    5.999   4.770   1.481  H012  C5Y  56  
C5Y  H011  H25  H  0  0  N  N  N  -10.122   -5.216   7.686    7.549   5.002   0.877  H011  C5Y  57  
C5Y  H1    H26  H  0  1  N  N  N  -17.983   -1.550  15.135   -2.475  -3.603  -0.447  H1    C5Y  58  
C5Y  H251  H27  H  0  0  N  N  N  -19.068   -1.412   8.490    4.405  -4.314  -0.655  H251  C5Y  59  
C5Y  H271  H28  H  0  0  N  N  N  -15.375    0.897   7.546    5.849  -3.010   0.384  H271  C5Y  60  
#   #
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
C5Y  N32  C31   DOUB  Y  N   1  
C5Y  N32  C02   SING  Y  N   2  
C5Y  C31  N30   SING  Y  N   3  
C5Y  N01  C02   SING  N  N   4  
C5Y  C02  C03   DOUB  Y  N   5  
C5Y  N30  C04   DOUB  Y  N   6  
C5Y  C03  C04   SING  Y  N   7  
C5Y  C03  N29   SING  Y  N   8  
C5Y  C04  N05   SING  Y  N   9  
C5Y  O27  C26   SING  N  N  10  
C5Y  C26  C24   SING  N  N  11  
C5Y  C26  C06   SING  N  N  12  
C5Y  O25  C24   SING  N  N  13  
C5Y  N29  C28   DOUB  Y  N  14  
C5Y  C24  C08   SING  N  N  15  
C5Y  N05  C06   SING  N  N  16  
C5Y  N05  C28   SING  Y  N  17  
C5Y  C06  O07   SING  N  N  18  
C5Y  C08  O07   SING  N  N  19  
C5Y  C08  C09   SING  N  N  20  
C5Y  C20  C21   SING  N  N  21  
C5Y  C20  C19   SING  N  N  22  
C5Y  C09  O10   SING  N  N  23  
C5Y  C18  C19   SING  N  N  24  
C5Y  C18  C17   SING  N  N  25  
C5Y  C17  C16   SING  N  N  26  
C5Y  O10  P11   SING  N  N  27  
C5Y  C15  C16   SING  N  N  28  
C5Y  C15  C14   SING  N  N  29  
C5Y  O22  C14   DOUB  N  N  30  
C5Y  C14  O13   SING  N  N  31  
C5Y  O12  P11   DOUB  N  N  32  
C5Y  P11  O13   SING  N  N  33  
C5Y  P11  O23   SING  N  N  34  
C5Y  C15  H151  SING  N  N  35  
C5Y  C15  H152  SING  N  N  36  
C5Y  C17  H172  SING  N  N  37  
C5Y  C17  H171  SING  N  N  38  
C5Y  C20  H201  SING  N  N  39  
C5Y  C20  H202  SING  N  N  40  
C5Y  C21  H212  SING  N  N  41  
C5Y  C21  H213  SING  N  N  42  
C5Y  C21  H211  SING  N  N  43  
C5Y  C24  H241  SING  N  N  44  
C5Y  C26  H261  SING  N  N  45  
C5Y  C28  H281  SING  N  N  46  
C5Y  C06  H061  SING  N  N  47  
C5Y  C08  H081  SING  N  N  48  
C5Y  C09  H091  SING  N  N  49  
C5Y  C09  H092  SING  N  N  50  
C5Y  C16  H162  SING  N  N  51  
C5Y  C16  H161  SING  N  N  52  
C5Y  C18  H182  SING  N  N  53  
C5Y  C18  H181  SING  N  N  54  
C5Y  C19  H192  SING  N  N  55  
C5Y  C19  H191  SING  N  N  56  
C5Y  C31  H311  SING  N  N  57  
C5Y  N01  H012  SING  N  N  58  
C5Y  N01  H011  SING  N  N  59  
C5Y  O23  H1    SING  N  N  60  
C5Y  O25  H251  SING  N  N  61  
C5Y  O27  H271  SING  N  N  62  
#   #
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
C5Y  SMILES            ACDLabs               12.01  "CCCCCCCC(=O)OP(=O)(O)OCC1OC(n2cnc3c(N)ncnc32)C(O)C1O"  
C5Y  InChI             InChI                 1.03   "InChI=1S/C18H28N5O8P/c1-2-3-4-5-6-7-12(24)31-32(27,28)29-8-11-14(25)15(26)18(30-11)23-10-22-13-16(19)20-9-21-17(13)23/h9-11,14-15,18,25-26H,2-8H2,1H3,(H,27,28)(H2,19,20,21)/t11-,14-,15-,18-/m1/s1"  
C5Y  InChIKey          InChI                 1.03   AJYSFZDSJUTHRW-XKLVTHTNSA-N  
C5Y  SMILES_CANONICAL  CACTVS                3.385  "CCCCCCCC(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23"  
C5Y  SMILES            CACTVS                3.385  "CCCCCCCC(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23"  
C5Y  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CCCCCCCC(=O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O"  
C5Y  SMILES            "OpenEye OEToolkits"  2.0.7  "CCCCCCCC(=O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O"  
#   #
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
C5Y  "SYSTEMATIC NAME"  ACDLabs               12.01  "5'-O-[(S)-hydroxy(octanoyloxy)phosphoryl]adenosine"  
C5Y  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] octanoate"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
C5Y  "Create component"  2021-11-19  RCSB  
C5Y  "Initial release"   2022-01-05  RCSB  
##
