data_D4F
#

_chem_comp.id                                   D4F
_chem_comp.name                                 "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (4S)-2-(6-oxidanyl-1,3-benzothiazol-2-yl)-4,5-dihydro-1,3-thiazole-4-carboxylate"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C21 H20 N7 O9 P S2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "Luciferyl adenylate"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2019-06-25
_chem_comp.pdbx_modified_date                   2021-03-01
_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                       609.529
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    D4F
_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       6K4D
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBJ
#   #
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
D4F  C13  C1   C  0  1  Y  N  N  -22.827  -30.269  28.625    9.501  -2.864   1.652  C13  D4F   1  
D4F  C24  C2   C  0  1  N  N  R  -22.911  -33.315  16.442   -4.208   1.902   0.449  C24  D4F   2  
D4F  C26  C3   C  0  1  N  N  R  -24.107  -35.248  16.851   -6.531   1.436   1.014  C26  D4F   3  
D4F  C1   C4   C  0  1  N  N  N  -22.261  -28.130  20.149    3.186   1.628  -2.353  C01  D4F   4  
D4F  C2   C5   C  0  1  N  N  S  -21.308  -29.343  20.312    2.829   0.435  -1.452  C02  D4F   5  
D4F  C4   C6   C  0  1  N  N  N  -22.448  -29.550  22.284    5.173   0.312  -1.168  C04  D4F   6  
D4F  C6   C7   C  0  1  Y  N  N  -22.576  -29.726  23.865    6.456  -0.214  -0.657  C06  D4F   7  
D4F  C8   C8   C  0  1  Y  N  N  -22.739  -29.834  26.196    7.804  -1.584   0.518  C08  D4F   8  
D4F  C9   C9   C  0  1  Y  N  N  -22.506  -31.215  26.034    8.807  -0.774  -0.033  C09  D4F   9  
D4F  C11  C10  C  0  1  Y  N  N  -22.398  -32.152  27.129   10.148  -1.018   0.257  C11  D4F  10  
D4F  C12  C11  C  0  1  Y  N  N  -22.609  -31.675  28.432   10.494  -2.059   1.096  C12  D4F  11  
D4F  C14  C12  C  0  1  Y  N  N  -22.890  -29.373  27.553    8.190  -2.642   1.374  C14  D4F  12  
D4F  C16  C13  C  0  1  N  N  N  -21.128  -30.027  18.917    1.936   0.910  -0.335  C16  D4F  13  
D4F  C23  C14  C  0  1  N  N  N  -22.749  -31.758  16.534   -2.864   1.954   1.178  C23  D4F  14  
D4F  C25  C15  C  0  1  N  N  S  -24.377  -33.712  16.581   -5.348   2.355   1.389  C25  D4F  15  
D4F  C27  C16  C  0  1  N  N  R  -22.777  -35.234  17.714   -5.967   0.536  -0.108  C27  D4F  16  
D4F  C30  C17  C  0  1  Y  N  N  -22.968  -34.171  20.143   -5.893  -1.871   0.648  C30  D4F  17  
D4F  C32  C18  C  0  1  Y  N  N  -23.613  -35.950  21.279   -7.772  -2.634  -0.119  C32  D4F  18  
D4F  C33  C19  C  0  1  Y  N  N  -23.480  -36.357  19.926   -7.690  -1.280  -0.485  C33  D4F  19  
D4F  C35  C20  C  0  1  Y  N  N  -24.111  -38.491  20.458   -9.740  -1.451  -1.509  C35  D4F  20  
D4F  C37  C21  C  0  1  Y  N  N  -24.011  -36.936  22.263   -8.912  -3.358  -0.507  C37  D4F  21  
D4F  N3   N1   N  0  1  N  N  N  -22.025  -30.298  21.304    4.015  -0.168  -0.887  N03  D4F  22  
D4F  N7   N2   N  0  1  Y  N  N  -22.724  -28.985  24.965    6.575  -1.222   0.138  N07  D4F  23  
D4F  N29  N3   N  0  1  Y  N  N  -23.090  -35.224  19.194   -6.496  -0.825   0.015  N29  D4F  24  
D4F  N31  N4   N  0  1  Y  N  N  -23.251  -34.591  21.381   -6.641  -2.932   0.565  N31  D4F  25  
D4F  N34  N5   N  0  1  Y  N  N  -23.748  -37.634  19.489   -8.688  -0.735  -1.173  N34  D4F  26  
D4F  N36  N6   N  0  1  Y  N  N  -24.275  -38.213  21.802   -9.860  -2.727  -1.193  N36  D4F  27  
D4F  N38  N7   N  0  1  N  N  N  -24.166  -36.597  23.604   -9.044  -4.697  -0.184  N38  D4F  28  
D4F  O15  O1   O  0  1  N  N  N  -22.580  -32.470  29.548   11.802  -2.298   1.380  O15  D4F  29  
D4F  O17  O2   O  0  1  N  N  N  -20.832  -31.209  19.003    2.400   1.123   0.761  O17  D4F  30  
D4F  O18  O3   O  0  1  N  N  N  -21.244  -29.421  18.059    0.626   1.098  -0.556  O18  D4F  31  
D4F  O20  O4   O  0  1  N  N  N  -19.415  -29.916  16.135    0.214   3.084   1.117  O20  D4F  32  
D4F  O21  O5   O  0  1  N  N  N  -21.756  -29.041  15.666   -0.085   0.682   1.830  O21  D4F  33  
D4F  O22  O6   O  0  1  N  N  N  -21.408  -31.554  16.361   -1.812   1.645   0.262  O22  D4F  34  
D4F  O28  O7   O  0  1  N  N  N  -22.172  -34.015  17.466   -4.538   0.540   0.100  O28  D4F  35  
D4F  O39  O8   O  0  1  N  N  N  -23.823  -35.903  15.683   -7.634   2.206   0.531  O39  D4F  36  
D4F  O40  O9   O  0  1  N  N  N  -25.014  -33.343  15.419   -5.681   3.724   1.148  O40  D4F  37  
D4F  P19  P1   P  0  1  N  N  N  -20.843  -29.902  16.387   -0.260   1.607   0.688  P19  D4F  38  
D4F  S5   S1   S  0  1  N  N  N  -22.665  -27.906  21.916    5.005   1.693  -2.259  S05  D4F  39  
D4F  S10  S2   S  0  1  Y  N  N  -22.381  -31.458  24.244    8.039   0.446  -1.045  S10  D4F  40  
D4F  H1   H1   H  0  1  N  N  N  -22.946  -29.891  29.630    9.778  -3.677   2.307  H1   D4F  41  
D4F  H2   H2   H  0  1  N  N  N  -22.557  -33.634  15.451   -4.180   2.528  -0.442  H2   D4F  42  
D4F  H3   H3   H  0  1  N  N  N  -24.935  -35.692  17.424   -6.834   0.834   1.871  H3   D4F  43  
D4F  H4   H4   H  0  1  N  N  N  -21.753  -27.253  19.721    2.860   1.447  -3.377  H4   D4F  44  
D4F  H5   H5   H  0  1  N  N  N  -23.147  -28.372  19.544    2.748   2.547  -1.966  H5   D4F  45  
D4F  H6   H6   H  0  1  N  N  N  -20.335  -29.023  20.714    2.295  -0.310  -2.041  H6   D4F  46  
D4F  H8   H8   H  0  1  N  N  N  -22.162  -33.190  26.950   10.916  -0.391  -0.170  H8   D4F  47  
D4F  H9   H9   H  0  1  N  N  N  -23.054  -28.323  27.744    7.435  -3.279   1.811  H9   D4F  48  
D4F  H10  H10  H  0  1  N  N  N  -23.077  -31.388  17.517   -2.710   2.954   1.584  H10  D4F  49  
D4F  H11  H11  H  0  1  N  N  N  -23.326  -31.257  15.742   -2.863   1.228   1.991  H11  D4F  50  
D4F  H12  H12  H  0  1  N  N  N  -24.819  -33.249  17.476   -5.065   2.208   2.431  H12  D4F  51  
D4F  H13  H13  H  0  1  N  N  N  -22.145  -36.094  17.448   -6.211   0.950  -1.086  H13  D4F  52  
D4F  H14  H14  H  0  1  N  N  N  -22.683  -33.159  19.895   -4.933  -1.826   1.141  H14  D4F  53  
D4F  H15  H15  H  0  1  N  N  N  -24.295  -39.510  20.153  -10.535  -0.977  -2.067  H15  D4F  54  
D4F  H18  H18  H  0  1  N  N  N  -24.479  -37.397  24.116   -8.345  -5.147   0.316  H18  D4F  55  
D4F  H19  H19  H  0  1  N  N  N  -23.290  -36.287  23.973   -9.836  -5.186  -0.458  H19  D4F  56  
D4F  H20  H20  H  0  1  N  N  N  -22.748  -31.941  30.319   12.128  -1.824   2.157  H20  D4F  57  
D4F  H21  H21  H  0  1  N  N  N  -19.208  -29.291  15.450    0.127   3.744   0.415  H21  D4F  58  
D4F  H22  H22  H  0  1  N  N  N  -23.664  -36.822  15.865   -8.027   2.789   1.194  H22  D4F  59  
D4F  H23  H23  H  0  1  N  N  N  -25.933  -33.577  15.473   -6.391   4.061   1.711  H23  D4F  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
D4F  O40  C25  SING  N  N   1  
D4F  O21  P19  DOUB  N  N   2  
D4F  O39  C26  SING  N  N   3  
D4F  O20  P19  SING  N  N   4  
D4F  O22  P19  SING  N  N   5  
D4F  O22  C23  SING  N  N   6  
D4F  P19  O18  SING  N  N   7  
D4F  C24  C23  SING  N  N   8  
D4F  C24  C25  SING  N  N   9  
D4F  C24  O28  SING  N  N  10  
D4F  C25  C26  SING  N  N  11  
D4F  C26  C27  SING  N  N  12  
D4F  O28  C27  SING  N  N  13  
D4F  C27  N29  SING  N  N  14  
D4F  O18  C16  SING  N  N  15  
D4F  C16  O17  DOUB  N  N  16  
D4F  C16  C2   SING  N  N  17  
D4F  N29  C33  SING  Y  N  18  
D4F  N29  C30  SING  Y  N  19  
D4F  N34  C33  DOUB  Y  N  20  
D4F  N34  C35  SING  Y  N  21  
D4F  C33  C32  SING  Y  N  22  
D4F  C30  N31  DOUB  Y  N  23  
D4F  C1   C2   SING  N  N  24  
D4F  C1   S5   SING  N  N  25  
D4F  C2   N3   SING  N  N  26  
D4F  C35  N36  DOUB  Y  N  27  
D4F  C32  N31  SING  Y  N  28  
D4F  C32  C37  DOUB  Y  N  29  
D4F  N3   C4   DOUB  N  N  30  
D4F  N36  C37  SING  Y  N  31  
D4F  S5   C4   SING  N  N  32  
D4F  C37  N38  SING  N  N  33  
D4F  C4   C6   SING  N  N  34  
D4F  C6   S10  SING  Y  N  35  
D4F  C6   N7   DOUB  Y  N  36  
D4F  S10  C9   SING  Y  N  37  
D4F  N7   C8   SING  Y  N  38  
D4F  C9   C8   DOUB  Y  N  39  
D4F  C9   C11  SING  Y  N  40  
D4F  C8   C14  SING  Y  N  41  
D4F  C11  C12  DOUB  Y  N  42  
D4F  C14  C13  DOUB  Y  N  43  
D4F  C12  C13  SING  Y  N  44  
D4F  C12  O15  SING  N  N  45  
D4F  C13  H1   SING  N  N  46  
D4F  C24  H2   SING  N  N  47  
D4F  C26  H3   SING  N  N  48  
D4F  C1   H4   SING  N  N  49  
D4F  C1   H5   SING  N  N  50  
D4F  C2   H6   SING  N  N  51  
D4F  C11  H8   SING  N  N  52  
D4F  C14  H9   SING  N  N  53  
D4F  C23  H10  SING  N  N  54  
D4F  C23  H11  SING  N  N  55  
D4F  C25  H12  SING  N  N  56  
D4F  C27  H13  SING  N  N  57  
D4F  C30  H14  SING  N  N  58  
D4F  C35  H15  SING  N  N  59  
D4F  N38  H18  SING  N  N  60  
D4F  N38  H19  SING  N  N  61  
D4F  O15  H20  SING  N  N  62  
D4F  O20  H21  SING  N  N  63  
D4F  O39  H22  SING  N  N  64  
D4F  O40  H23  SING  N  N  65  
#   #
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
D4F  InChI             InChI                 1.03   "InChI=1S/C21H20N7O9PS2/c22-16-13-17(24-6-23-16)28(7-25-13)20-15(31)14(30)11(36-20)4-35-38(33,34)37-21(32)10-5-39-18(27-10)19-26-9-2-1-8(29)3-12(9)40-19/h1-3,6-7,10-11,14-15,20,29-31H,4-5H2,(H,33,34)(H2,22,23,24)/t10-,11-,14-,15-,20-/m1/s1"  
D4F  InChIKey          InChI                 1.03   DVLIEEOCYVGZDS-RIWZETFMSA-N  
D4F  SMILES_CANONICAL  CACTVS                3.385  "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)OC(=O)[C@H]4CSC(=N4)c5sc6cc(O)ccc6n5)[C@@H](O)[C@H]3O"  
D4F  SMILES            CACTVS                3.385  "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)OC(=O)[CH]4CSC(=N4)c5sc6cc(O)ccc6n5)[CH](O)[CH]3O"  
D4F  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1cc2c(cc1O)sc(n2)C3=N[C@H](CS3)C(=O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O"  
D4F  SMILES            "OpenEye OEToolkits"  2.0.7  "c1cc2c(cc1O)sc(n2)C3=NC(CS3)C(=O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O"  
#
_pdbx_chem_comp_identifier.comp_id          D4F
_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-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (4~{S})-2-(6-oxidanyl-1,3-benzothiazol-2-yl)-4,5-dihydro-1,3-thiazole-4-carboxylate"
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
D4F  "Create component"  2019-06-25  PDBJ  
D4F  "Initial release"   2020-05-27  RCSB  
D4F  "Modify synonyms"   2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     D4F
_pdbx_chem_comp_synonyms.name        "Luciferyl adenylate"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
