data_5DD
#

_chem_comp.id                                   5DD
_chem_comp.name                                 "[(2~{R},3~{S},4~{S})-5-[(4~{a}~{R})-7,8-dimethyl-2,4-bis(oxidanylidene)-4~{a},5-dihydropyrimido[4,5-b]quinolin-10-yl]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C18 H24 N3 O9 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2018-10-31
_chem_comp.pdbx_modified_date                   2019-05-24
_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                       457.372
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    5DD
_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       6I25
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 EBI
#   #
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
5DD  O3P    O1   O  0  1  N  N  N  -37.754  46.138   5.330   7.490   0.352  -1.669  O3P    5DD   1  
5DD  P      P1   P  0  1  N  N  N  -37.105  45.034   4.530   6.675   0.090  -0.306  P      5DD   2  
5DD  O1P    O2   O  0  1  N  N  N  -35.646  44.869   4.930   7.129  -1.318   0.329  O1P    5DD   3  
5DD  O2P    O3   O  0  1  N  N  N  -37.196  45.363   3.051   6.959   1.179   0.655  O2P    5DD   4  
5DD  "O5'"  O4   O  0  1  N  N  N  -37.915  43.666   4.825   5.097   0.052  -0.622  "O5'"  5DD   5  
5DD  "C5'"  C1   C  0  1  N  N  N  -37.504  42.399   4.328   4.101  -0.059   0.397  "C5'"  5DD   6  
5DD  "C4'"  C2   C  0  1  N  N  R  -36.389  41.825   5.197   2.712  -0.066  -0.245  "C4'"  5DD   7  
5DD  "O4'"  O5   O  0  1  N  N  N  -35.224  42.662   5.122   2.565  -1.240  -1.047  "O4'"  5DD   8  
5DD  "C3'"  C3   C  0  1  N  N  S  -36.867  41.692   6.643   1.644  -0.059   0.850  "C3'"  5DD   9  
5DD  "O3'"  O6   O  0  1  N  N  N  -38.124  41.002   6.625   1.791   1.114   1.652  "O3'"  5DD  10  
5DD  "C2'"  C4   C  0  1  N  N  S  -35.859  40.942   7.528   0.255  -0.067   0.207  "C2'"  5DD  11  
5DD  "O2'"  O7   O  0  1  N  N  N  -36.354  40.772   8.855   0.108  -1.240  -0.595  "O2'"  5DD  12  
5DD  "C1'"  C5   C  0  1  N  N  N  -35.566  39.582   6.918  -0.813  -0.060   1.302  "C1'"  5DD  13  
5DD  N10    N1   N  0  1  N  N  N  -35.118  38.620   7.912  -2.143  -0.036   0.687  N10    5DD  14  
5DD  C9A    C6   C  0  1  Y  N  N  -36.048  37.928   8.677  -2.707   1.181   0.294  C9A    5DD  15  
5DD  C9     C7   C  0  1  Y  N  N  -37.314  38.451   8.912  -2.172   2.374   0.762  C9     5DD  16  
5DD  C8     C8   C  0  1  Y  N  N  -38.220  37.713   9.663  -2.721   3.578   0.367  C8     5DD  17  
5DD  C8M    C9   C  0  1  N  N  N  -39.586  38.250   9.959  -2.141   4.872   0.876  C8M    5DD  18  
5DD  C7     C10  C  0  1  Y  N  N  -37.847  36.376  10.184  -3.803   3.598  -0.495  C7     5DD  19  
5DD  C7M    C11  C  0  1  N  N  N  -38.834  35.584  10.993  -4.396   4.915  -0.927  C7M    5DD  20  
5DD  C6     C12  C  0  1  Y  N  N  -36.592  35.857   9.924  -4.341   2.412  -0.961  C6     5DD  21  
5DD  C5A    C13  C  0  1  Y  N  N  -35.677  36.577   9.175  -3.800   1.206  -0.565  C5A    5DD  22  
5DD  C10    C14  C  0  1  N  N  N  -33.802  38.179   7.888  -2.820  -1.194   0.496  C10    5DD  23  
5DD  N1     N2   N  0  1  N  N  N  -33.037  38.732   6.928  -2.220  -2.337   0.700  N1     5DD  24  
5DD  C4A    C15  C  0  1  N  N  R  -33.289  37.119   8.846  -4.252  -1.139   0.043  C4A    5DD  25  
5DD  C4     C16  C  0  1  N  N  N  -31.919  36.714   8.439  -4.723  -2.483  -0.421  C4     5DD  26  
5DD  O4     O8   O  0  1  N  N  N  -31.379  35.828   9.132  -5.777  -2.576  -1.013  O4     5DD  27  
5DD  N3     N3   N  0  1  N  N  N  -31.229  37.371   7.490  -3.992  -3.587  -0.190  N3     5DD  28  
5DD  C2     C17  C  0  1  N  N  N  -31.773  38.340   6.743  -2.799  -3.511   0.423  C2     5DD  29  
5DD  O2     O9   O  0  1  N  N  N  -31.106  38.905   5.855  -2.228  -4.539   0.735  O2     5DD  30  
5DD  C1     C18  C  0  1  N  N  N  -34.305  35.985   8.907  -4.403  -0.089  -1.053  C1     5DD  31  
5DD  H1     H1   H  0  1  N  N  N  -38.083  46.806   4.740   8.449   0.387  -1.554  H1     5DD  32  
5DD  H2     H2   H  0  1  N  N  N  -35.092  45.006   4.171   6.972  -2.078  -0.247  H2     5DD  33  
5DD  H3     H3   H  0  1  N  N  N  -38.362  41.710   4.337   4.250  -0.985   0.951  H3     5DD  34  
5DD  H4     H4   H  0  1  N  N  N  -37.137  42.515   3.297   4.182   0.789   1.078  H4     5DD  35  
5DD  H5     H5   H  0  1  N  N  N  -36.143  40.820   4.822   2.597   0.819  -0.871  H5     5DD  36  
5DD  H6     H6   H  0  1  N  N  N  -34.536  42.297   5.666   2.656  -2.067  -0.555  H6     5DD  37  
5DD  H7     H7   H  0  1  N  N  N  -37.005  42.702   7.057   1.759  -0.944   1.476  H7     5DD  38  
5DD  H8     H8   H  0  1  N  N  N  -38.445  40.905   7.514   1.700   1.941   1.159  H8     5DD  39  
5DD  H9     H9   H  0  1  N  N  N  -34.924  41.521   7.552   0.140   0.818  -0.419  H9     5DD  40  
5DD  H10    H10  H  0  1  N  N  N  -35.710  40.307   9.376   0.204  -2.067  -0.103  H10    5DD  41  
5DD  H11    H11  H  0  1  N  N  N  -36.483  39.201   6.444  -0.712  -0.956   1.914  H11    5DD  42  
5DD  H12    H12  H  0  1  N  N  N  -34.780  39.697   6.157  -0.687   0.824   1.928  H12    5DD  43  
5DD  H13    H13  H  0  1  N  N  N  -37.589  39.417   8.516  -1.327   2.361   1.434  H13    5DD  44  
5DD  H14    H14  H  0  1  N  N  N  -40.282  37.943   9.164  -1.361   5.213   0.195  H14    5DD  45  
5DD  H15    H15  H  0  1  N  N  N  -39.934  37.854  10.924  -2.927   5.625   0.933  H15    5DD  46  
5DD  H16    H16  H  0  1  N  N  N  -39.546  39.348  10.006  -1.715   4.715   1.867  H16    5DD  47  
5DD  H17    H17  H  0  1  N  N  N  -39.435  34.952  10.323  -3.898   5.257  -1.834  H17    5DD  48  
5DD  H18    H18  H  0  1  N  N  N  -38.294  34.948  11.709  -5.461   4.786  -1.122  H18    5DD  49  
5DD  H19    H19  H  0  1  N  N  N  -39.496  36.272  11.540  -4.258   5.652  -0.137  H19    5DD  50  
5DD  H20    H20  H  0  1  N  N  N  -36.324  34.884  10.308  -5.185   2.430  -1.634  H20    5DD  51  
5DD  H21    H21  H  0  1  N  N  N  -33.231  37.571   9.847  -4.869  -0.842   0.891  H21    5DD  52  
5DD  H22    H22  H  0  1  N  N  N  -30.272  37.126   7.336  -4.331  -4.452  -0.468  H22    5DD  53  
5DD  H23    H23  H  0  1  N  N  N  -34.315  35.445   7.949  -5.459   0.059  -1.276  H23    5DD  54  
5DD  H24    H24  H  0  1  N  N  N  -34.037  35.290   9.717  -3.879  -0.419  -1.950  H24    5DD  55  
#   #
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
5DD  O2P    P      DOUB  N  N   1  
5DD  "C5'"  "O5'"  SING  N  N   2  
5DD  "C5'"  "C4'"  SING  N  N   3  
5DD  P      "O5'"  SING  N  N   4  
5DD  P      O1P    SING  N  N   5  
5DD  P      O3P    SING  N  N   6  
5DD  "O4'"  "C4'"  SING  N  N   7  
5DD  "C4'"  "C3'"  SING  N  N   8  
5DD  O2     C2     DOUB  N  N   9  
5DD  "O3'"  "C3'"  SING  N  N  10  
5DD  "C3'"  "C2'"  SING  N  N  11  
5DD  C2     N1     SING  N  N  12  
5DD  C2     N3     SING  N  N  13  
5DD  "C1'"  "C2'"  SING  N  N  14  
5DD  "C1'"  N10    SING  N  N  15  
5DD  N1     C10    DOUB  N  N  16  
5DD  N3     C4     SING  N  N  17  
5DD  "C2'"  "O2'"  SING  N  N  18  
5DD  C10    N10    SING  N  N  19  
5DD  C10    C4A    SING  N  N  20  
5DD  N10    C9A    SING  N  N  21  
5DD  C4     C4A    SING  N  N  22  
5DD  C4     O4     DOUB  N  N  23  
5DD  C9A    C9     DOUB  Y  N  24  
5DD  C9A    C5A    SING  Y  N  25  
5DD  C4A    C1     SING  N  N  26  
5DD  C1     C5A    SING  N  N  27  
5DD  C9     C8     SING  Y  N  28  
5DD  C5A    C6     DOUB  Y  N  29  
5DD  C8     C8M    SING  N  N  30  
5DD  C8     C7     DOUB  Y  N  31  
5DD  C6     C7     SING  Y  N  32  
5DD  C7     C7M    SING  N  N  33  
5DD  O3P    H1     SING  N  N  34  
5DD  O1P    H2     SING  N  N  35  
5DD  "C5'"  H3     SING  N  N  36  
5DD  "C5'"  H4     SING  N  N  37  
5DD  "C4'"  H5     SING  N  N  38  
5DD  "O4'"  H6     SING  N  N  39  
5DD  "C3'"  H7     SING  N  N  40  
5DD  "O3'"  H8     SING  N  N  41  
5DD  "C2'"  H9     SING  N  N  42  
5DD  "O2'"  H10    SING  N  N  43  
5DD  "C1'"  H11    SING  N  N  44  
5DD  "C1'"  H12    SING  N  N  45  
5DD  C9     H13    SING  N  N  46  
5DD  C8M    H14    SING  N  N  47  
5DD  C8M    H15    SING  N  N  48  
5DD  C8M    H16    SING  N  N  49  
5DD  C7M    H17    SING  N  N  50  
5DD  C7M    H18    SING  N  N  51  
5DD  C7M    H19    SING  N  N  52  
5DD  C6     H20    SING  N  N  53  
5DD  C4A    H21    SING  N  N  54  
5DD  N3     H22    SING  N  N  55  
5DD  C1     H23    SING  N  N  56  
5DD  C1     H24    SING  N  N  57  
#   #
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
5DD  InChI             InChI                 1.03   "InChI=1S/C18H24N3O9P/c1-8-3-10-5-11-16(19-18(26)20-17(11)25)21(12(10)4-9(8)2)6-13(22)15(24)14(23)7-30-31(27,28)29/h3-4,11,13-15,22-24H,5-7H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,13+,14-,15+/m1/s1"  
5DD  InChIKey          InChI                 1.03   MPTDYDRCOLGCLP-BEAPCOKYSA-N  
5DD  SMILES_CANONICAL  CACTVS                3.385  "Cc1cc2C[C@H]3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c2cc1C"  
5DD  SMILES            CACTVS                3.385  "Cc1cc2C[CH]3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c2cc1C"  
5DD  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)[C@@H]3C2)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O"  
5DD  SMILES            "OpenEye OEToolkits"  2.0.6  "Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3C2)CC(C(C(COP(=O)(O)O)O)O)O"  
#
_pdbx_chem_comp_identifier.comp_id          5DD
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.6
_pdbx_chem_comp_identifier.identifier       "[(2~{R},3~{S},4~{S})-5-[(4~{a}~{R})-7,8-dimethyl-2,4-bis(oxidanylidene)-4~{a},5-dihydropyrimido[4,5-b]quinolin-10-yl]-2,3,4-tris(oxidanyl)pentyl] 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
5DD  "Create component"  2018-10-31  EBI   
5DD  "Initial release"   2019-05-29  RCSB  
##
