data_Y3U
#

_chem_comp.id                                   Y3U
_chem_comp.name                                 "[(2~{R},3~{S},4~{R},5~{R})-5-[3-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-(4-hydroxyphenyl)propanoyl]sulfamate"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C19 H24 N4 O10 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2018-08-10
_chem_comp.pdbx_modified_date                   2019-04-12
_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                       500.480
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    Y3U
_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       6HB7
_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
Y3U  C3U    C1   C  0  1  N  N  N  -57.889   8.992  -51.317   5.254  -4.095   1.589  C3U    Y3U   1  
Y3U  N3     N1   N  0  1  N  N  N  -58.006   8.289  -50.026   4.331  -3.331   0.746  N3     Y3U   2  
Y3U  C4     C2   C  0  1  N  N  N  -59.078   8.618  -49.183   3.387  -3.974   0.029  C4     Y3U   3  
Y3U  O4     O1   O  0  1  N  N  N  -59.876   9.480  -49.532   3.299  -5.188   0.079  O4     Y3U   4  
Y3U  C5     C3   C  0  1  N  N  N  -59.149   7.880  -47.941   2.500  -3.226  -0.781  C5     Y3U   5  
Y3U  C6     C4   C  0  1  N  N  N  -58.223   6.946  -47.647   2.620  -1.881  -0.818  C6     Y3U   6  
Y3U  N1     N2   N  0  1  N  N  N  -57.180   6.684  -48.517   3.591  -1.266  -0.076  N1     Y3U   7  
Y3U  "C1'"  C5   C  0  1  N  N  R  -56.113   5.703  -48.186   3.720   0.192  -0.116  "C1'"  Y3U   8  
Y3U  "O4'"  O2   O  0  1  N  N  N  -56.657   4.402  -48.071   2.456   0.818   0.192  "O4'"  Y3U   9  
Y3U  "C4'"  C6   C  0  1  N  N  R  -55.680   3.588  -47.373   2.552   2.155  -0.345  "C4'"  Y3U  10  
Y3U  "C5'"  C7   C  0  1  N  N  N  -56.365   2.748  -46.321   1.157   2.748  -0.551  "C5'"  Y3U  11  
Y3U  "O5'"  O3   O  0  1  N  N  N  -56.921   3.677  -45.323   0.528   2.937   0.718  "O5'"  Y3U  12  
Y3U  SBI    S1   S  0  1  N  N  N  -56.741   3.350  -43.776  -0.873   3.526   0.633  SBI    Y3U  13  
Y3U  OAD    O4   O  0  1  N  N  N  -57.220   4.476  -43.053  -1.262   3.831   1.966  OAD    Y3U  14  
Y3U  OAE    O5   O  0  1  N  N  N  -57.316   2.065  -43.593  -0.840   4.493  -0.407  OAE    Y3U  15  
Y3U  NAT    N3   N  0  1  N  N  N  -55.170   3.150  -43.626  -1.882   2.318   0.117  NAT    Y3U  16  
Y3U  C      C8   C  0  1  N  N  N  -54.422   3.157  -42.483  -2.089   1.235   0.892  C      Y3U  17  
Y3U  O      O6   O  0  1  N  N  N  -54.928   3.370  -41.383  -1.536   1.145   1.968  O      Y3U  18  
Y3U  CA     C9   C  0  1  N  N  S  -52.977   2.798  -42.688  -3.006   0.136   0.422  CA     Y3U  19  
Y3U  N      N4   N  0  1  N  N  N  -52.181   3.139  -41.508  -2.711  -1.098   1.162  N      Y3U  20  
Y3U  CB     C10  C  0  1  N  N  N  -53.099   1.267  -42.839  -4.460   0.544   0.671  CB     Y3U  21  
Y3U  CG     C11  C  0  1  Y  N  N  -51.767   0.566  -42.871  -5.381  -0.498   0.091  CG     Y3U  22  
Y3U  CD1    C12  C  0  1  Y  N  N  -50.840   0.845  -43.875  -5.810  -0.387  -1.219  CD1    Y3U  23  
Y3U  CE1    C13  C  0  1  Y  N  N  -49.617   0.190  -43.919  -6.654  -1.342  -1.753  CE1    Y3U  24  
Y3U  CZ     C14  C  0  1  Y  N  N  -49.298  -0.744  -42.940  -7.070  -2.412  -0.974  CZ     Y3U  25  
Y3U  OH     O7   O  0  1  N  N  N  -48.087  -1.368  -42.974  -7.900  -3.352  -1.498  OH     Y3U  26  
Y3U  CE2    C15  C  0  1  Y  N  N  -50.214  -1.031  -41.932  -6.638  -2.520   0.339  CE2    Y3U  27  
Y3U  CD2    C16  C  0  1  Y  N  N  -51.430  -0.365  -41.895  -5.790  -1.566   0.867  CD2    Y3U  28  
Y3U  "C3'"  C17  C  0  1  N  N  S  -54.632   4.568  -46.816   3.269   1.985  -1.703  "C3'"  Y3U  29  
Y3U  "O3'"  O8   O  0  1  N  N  N  -53.468   4.593  -47.640   4.161   3.076  -1.939  "O3'"  Y3U  30  
Y3U  "C2'"  C18  C  0  1  N  N  R  -55.366   5.910  -46.884   4.056   0.663  -1.548  "C2'"  Y3U  31  
Y3U  "O2'"  O9   O  0  1  N  N  N  -54.473   7.003  -46.973   5.459   0.897  -1.683  "O2'"  Y3U  32  
Y3U  C2     C19  C  0  1  N  N  N  -57.038   7.333  -49.733   4.425  -1.989   0.694  C2     Y3U  33  
Y3U  O2     O10  O  0  1  N  N  N  -56.135   7.090  -50.521   5.278  -1.422   1.349  O2     Y3U  34  
Y3U  H1     H1   H  0  1  N  N  N  -58.713   9.714  -51.418   4.827  -4.208   2.585  H1     Y3U  35  
Y3U  H2     H2   H  0  1  N  N  N  -56.928   9.525  -51.358   5.418  -5.078   1.149  H2     Y3U  36  
Y3U  H3     H3   H  0  1  N  N  N  -57.939   8.262  -52.138   6.205  -3.565   1.658  H3     Y3U  37  
Y3U  H4     H4   H  0  1  N  N  N  -59.950   8.079  -47.244   1.738  -3.723  -1.362  H4     Y3U  38  
Y3U  H5     H5   H  0  1  N  N  N  -58.296   6.395  -46.721   1.952  -1.294  -1.431  H5     Y3U  39  
Y3U  H6     H6   H  0  1  N  N  N  -55.375   5.713  -49.001   4.488   0.524   0.584  H6     Y3U  40  
Y3U  H7     H7   H  0  1  N  N  N  -55.181   2.918  -48.089   3.141   2.789   0.318  H7     Y3U  41  
Y3U  H8     H8   H  0  1  N  N  N  -57.172   2.156  -46.777   1.241   3.708  -1.061  H8     Y3U  42  
Y3U  H9     H9   H  0  1  N  N  N  -55.639   2.073  -45.845   0.558   2.067  -1.155  H9     Y3U  43  
Y3U  H10    H10  H  0  1  N  N  N  -54.666   3.000  -44.477  -2.324   2.390  -0.743  H10    Y3U  44  
Y3U  H11    H11  H  0  1  N  N  N  -52.574   3.253  -43.605  -2.854  -0.033  -0.643  H11    Y3U  45  
Y3U  H12    H12  H  0  1  N  N  N  -52.113   4.133  -41.427  -1.777  -1.424   0.964  H12    Y3U  46  
Y3U  H13    H13  H  0  1  N  N  N  -52.621   2.767  -40.690  -2.845  -0.966   2.153  H13    Y3U  47  
Y3U  H15    H15  H  0  1  N  N  N  -53.631   1.050  -43.777  -4.635   0.628   1.743  H15    Y3U  48  
Y3U  H16    H16  H  0  1  N  N  N  -53.679   0.877  -41.990  -4.654   1.506   0.195  H16    Y3U  49  
Y3U  H17    H17  H  0  1  N  N  N  -51.077   1.581  -44.629  -5.486   0.446  -1.825  H17    Y3U  50  
Y3U  H18    H18  H  0  1  N  N  N  -48.915   0.405  -44.711  -6.990  -1.255  -2.776  H18    Y3U  51  
Y3U  H19    H19  H  0  1  N  N  N  -48.021  -1.972  -42.244  -7.441  -4.092  -1.918  H19    Y3U  52  
Y3U  H20    H20  H  0  1  N  N  N  -49.978  -1.770  -41.181  -6.961  -3.352   0.947  H20    Y3U  53  
Y3U  H21    H21  H  0  1  N  N  N  -52.126  -0.573  -41.096  -5.450  -1.653   1.888  H21    Y3U  54  
Y3U  H22    H22  H  0  1  N  N  N  -54.391   4.316  -45.773   2.543   1.904  -2.511  H22    Y3U  55  
Y3U  H23    H23  H  0  1  N  N  N  -52.836   5.203  -47.278   4.638   3.020  -2.778  H23    Y3U  56  
Y3U  H24    H24  H  0  1  N  N  N  -56.068   6.010  -46.043   3.718  -0.070  -2.281  H24    Y3U  57  
Y3U  H25    H25  H  0  1  N  N  N  -54.019   7.110  -46.145   5.725   1.196  -2.564  H25    Y3U  58  
#   #
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
Y3U  C3U    N3     SING  N  N   1  
Y3U  O2     C2     DOUB  N  N   2  
Y3U  N3     C2     SING  N  N   3  
Y3U  N3     C4     SING  N  N   4  
Y3U  C2     N1     SING  N  N   5  
Y3U  O4     C4     DOUB  N  N   6  
Y3U  C4     C5     SING  N  N   7  
Y3U  N1     "C1'"  SING  N  N   8  
Y3U  N1     C6     SING  N  N   9  
Y3U  "C1'"  "O4'"  SING  N  N  10  
Y3U  "C1'"  "C2'"  SING  N  N  11  
Y3U  "O4'"  "C4'"  SING  N  N  12  
Y3U  C5     C6     DOUB  N  N  13  
Y3U  "O3'"  "C3'"  SING  N  N  14  
Y3U  "C4'"  "C3'"  SING  N  N  15  
Y3U  "C4'"  "C5'"  SING  N  N  16  
Y3U  "O2'"  "C2'"  SING  N  N  17  
Y3U  "C2'"  "C3'"  SING  N  N  18  
Y3U  "C5'"  "O5'"  SING  N  N  19  
Y3U  "O5'"  SBI    SING  N  N  20  
Y3U  CE1    CD1    DOUB  Y  N  21  
Y3U  CE1    CZ     SING  Y  N  22  
Y3U  CD1    CG     SING  Y  N  23  
Y3U  SBI    NAT    SING  N  N  24  
Y3U  SBI    OAE    DOUB  N  N  25  
Y3U  SBI    OAD    DOUB  N  N  26  
Y3U  NAT    C      SING  N  N  27  
Y3U  OH     CZ     SING  N  N  28  
Y3U  CZ     CE2    DOUB  Y  N  29  
Y3U  CG     CB     SING  N  N  30  
Y3U  CG     CD2    DOUB  Y  N  31  
Y3U  CB     CA     SING  N  N  32  
Y3U  CA     C      SING  N  N  33  
Y3U  CA     N      SING  N  N  34  
Y3U  C      O      DOUB  N  N  35  
Y3U  CE2    CD2    SING  Y  N  36  
Y3U  C3U    H1     SING  N  N  37  
Y3U  C3U    H2     SING  N  N  38  
Y3U  C3U    H3     SING  N  N  39  
Y3U  C5     H4     SING  N  N  40  
Y3U  C6     H5     SING  N  N  41  
Y3U  "C1'"  H6     SING  N  N  42  
Y3U  "C4'"  H7     SING  N  N  43  
Y3U  "C5'"  H8     SING  N  N  44  
Y3U  "C5'"  H9     SING  N  N  45  
Y3U  NAT    H10    SING  N  N  46  
Y3U  CA     H11    SING  N  N  47  
Y3U  N      H12    SING  N  N  48  
Y3U  N      H13    SING  N  N  49  
Y3U  CB     H15    SING  N  N  50  
Y3U  CB     H16    SING  N  N  51  
Y3U  CD1    H17    SING  N  N  52  
Y3U  CE1    H18    SING  N  N  53  
Y3U  OH     H19    SING  N  N  54  
Y3U  CE2    H20    SING  N  N  55  
Y3U  CD2    H21    SING  N  N  56  
Y3U  "C3'"  H22    SING  N  N  57  
Y3U  "O3'"  H23    SING  N  N  58  
Y3U  "C2'"  H24    SING  N  N  59  
Y3U  "O2'"  H25    SING  N  N  60  
#   #
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
Y3U  InChI             InChI                 1.03   "InChI=1S/C19H24N4O10S/c1-22-14(25)6-7-23(19(22)29)18-16(27)15(26)13(33-18)9-32-34(30,31)21-17(28)12(20)8-10-2-4-11(24)5-3-10/h2-7,12-13,15-16,18,24,26-27H,8-9,20H2,1H3,(H,21,28)/t12-,13+,15+,16+,18+/m0/s1"  
Y3U  InChIKey          InChI                 1.03   JZICRHJSYJTEMP-IQNGCQKYSA-N  
Y3U  SMILES_CANONICAL  CACTVS                3.385  "CN1C(=O)C=CN([C@@H]2O[C@H](CO[S](=O)(=O)NC(=O)[C@@H](N)Cc3ccc(O)cc3)[C@@H](O)[C@H]2O)C1=O"  
Y3U  SMILES            CACTVS                3.385  "CN1C(=O)C=CN([CH]2O[CH](CO[S](=O)(=O)NC(=O)[CH](N)Cc3ccc(O)cc3)[CH](O)[CH]2O)C1=O"  
Y3U  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "CN1C(=O)C=CN(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COS(=O)(=O)NC(=O)[C@H](Cc3ccc(cc3)O)N)O)O"  
Y3U  SMILES            "OpenEye OEToolkits"  2.0.6  "CN1C(=O)C=CN(C1=O)C2C(C(C(O2)COS(=O)(=O)NC(=O)C(Cc3ccc(cc3)O)N)O)O"  
#
_pdbx_chem_comp_identifier.comp_id          Y3U
_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~{R},5~{R})-5-[3-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-(4-hydroxyphenyl)propanoyl]sulfamate"
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
Y3U  "Create component"  2018-08-10  EBI   
Y3U  "Initial release"   2019-04-17  RCSB  
##
