data_87E
#

_chem_comp.id                                   87E
_chem_comp.name                                 "(2S)-2-[[(2R)-2-[(2R,3R,4R,5S,6R)-3-acetamido-2-[[[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-6-(hydroxymethyl)-5-oxidanyl-oxan-4-yl]oxypropanoyl]amino]-3-oxidanyl-propanoic acid"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C23 H36 N4 O21 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "Uridine-5'-diphosphate-n-acetylmuramoyl-L-Serine"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-11-26
_chem_comp.pdbx_modified_date                   2021-12-24
_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                       766.494
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    87E
_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       7W1G
_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
87E  N1   N1   N  0  1  N  N  N  15.587  11.637  15.442   8.136   1.583   2.983  N1   87E   1  
87E  C2   C1   C  0  1  N  N  N  15.759  10.379  15.857   7.325   2.062   2.022  C2   87E   2  
87E  O2   O1   O  0  1  N  N  N  17.084  10.014  16.253   6.920   3.206   2.094  O2   87E   3  
87E  N3   N2   N  0  1  N  N  N   9.687   6.200   8.719  -3.907  -0.695  -0.956  N3   87E   4  
87E  C4   C2   C  0  1  N  N  N  13.279  11.215  15.033   8.222  -0.500   1.822  C4   87E   5  
87E  O4   O2   O  0  1  N  N  N  14.211   8.078  18.720   7.538   3.149  -1.521  O4   87E   6  
87E  C5   C3   C  0  1  N  N  R  14.878   8.122  16.256   6.072   1.842  -0.050  C5   87E   7  
87E  C6   C4   C  0  1  N  N  R  13.762   7.619  17.388   6.807   1.926  -1.411  C6   87E   8  
87E  P1   P1   P  0  1  N  N  N  10.356   7.074  14.643   2.062  -1.847  -2.095  P1   87E   9  
87E  P2   P2   P  0  1  N  N  N  10.721   7.918  11.881  -0.561  -2.969  -1.292  P2   87E  10  
87E  C1   C5   C  0  1  N  N  N  14.376  12.069  15.039   8.598   0.318   2.914  C1   87E  11  
87E  O1   O3   O  0  1  N  N  N  14.238  13.190  14.684   9.333  -0.116   3.783  O1   87E  12  
87E  N2   N3   N  0  1  N  N  N  14.716   9.505  15.867   6.956   1.293   0.981  N2   87E  13  
87E  C3   C6   C  0  1  N  N  N  13.462   9.896  15.450   7.399   0.003   0.877  C3   87E  14  
87E  O3   O4   O  0  1  N  N  N  14.709   7.320  15.203   4.974   0.942  -0.315  O3   87E  15  
87E  N4   N4   N  0  1  N  N  N   5.072   5.978   5.991  -5.187   3.314   1.049  N4   87E  16  
87E  O5   O5   O  0  1  N  N  N  14.875   5.700  17.950   5.296   3.217  -2.839  O5   87E  17  
87E  O6   O6   O  0  1  N  N  N  12.016   7.052  14.928   2.840  -0.515  -1.631  O6   87E  18  
87E  C7   C7   C  0  1  N  N  S  13.714   6.371  17.262   5.632   1.893  -2.418  C7   87E  19  
87E  O7   O7   O  0  1  N  N  N  10.099   8.175  13.400   0.760  -2.056  -1.172  O7   87E  20  
87E  C8   C8   C  0  1  N  N  R  13.962   6.100  15.687   4.470   1.269  -1.621  C8   87E  21  
87E  O8   O8   O  0  1  N  N  N   9.755   5.785  14.309   1.648  -1.710  -3.509  O8   87E  22  
87E  C9   C9   C  0  1  N  N  N  12.773   5.842  14.965   3.980   0.001  -2.322  C9   87E  23  
87E  O9   O9   O  0  1  N  N  N   9.661   7.503  15.859   3.038  -3.118  -1.942  O9   87E  24  
87E  C10  C10  C  0  1  N  N  R   8.885   6.248  11.012  -3.046  -2.893  -0.312  C10  87E  25  
87E  O10  O10  O  0  1  N  N  N  11.791   6.916  11.895  -0.218  -4.472  -0.828  O10  87E  26  
87E  C11  C11  C  0  1  N  N  R   6.564   7.013  11.571  -2.790  -3.476   2.000  C11  87E  27  
87E  O11  O11  O  0  1  N  N  N  11.373   9.177  11.406  -1.027  -2.980  -2.697  O11  87E  28  
87E  C12  C12  C  0  1  N  N  S   6.169   6.529  10.180  -3.765  -2.378   2.435  C12  87E  29  
87E  O12  O12  O  0  1  N  N  N   9.454   7.474  10.920  -1.717  -2.367  -0.347  O12  87E  30  
87E  C13  C13  C  0  1  N  N  R   7.291   6.763   9.194  -3.708  -1.228   1.425  C13  87E  31  
87E  O13  O13  O  0  1  N  N  N   7.732   6.252  12.008  -3.127  -3.916   0.683  O13  87E  32  
87E  C14  C14  C  0  1  N  N  R   8.444   5.919   9.587  -4.030  -1.772   0.029  C14  87E  33  
87E  O14  O14  O  0  1  N  N  N   6.729   6.377   7.883  -4.668  -0.231   1.782  O14  87E  34  
87E  C15  C15  C  0  1  N  N  N   5.410   6.797  12.548  -2.885  -4.655   2.971  C15  87E  35  
87E  O15  O15  O  0  1  N  N  N   4.965   7.132   9.722  -3.396  -1.897   3.729  O15  87E  36  
87E  C16  C16  C  0  1  N  N  R   7.070   7.161   6.816  -4.208   1.110   1.599  C16  87E  37  
87E  O16  O16  O  0  1  N  N  N   4.972   5.453  12.402  -1.895  -5.630   2.634  O16  87E  38  
87E  C17  C17  C  0  1  N  N  N   6.406   6.509   5.643  -5.387   2.016   1.350  C17  87E  39  
87E  O17  O17  O  0  1  N  N  N   6.960   6.555   4.612  -6.515   1.576   1.421  O17  87E  40  
87E  C18  C18  C  0  1  N  N  N   6.209   8.443   6.880  -3.467   1.571   2.856  C18  87E  41  
87E  O18  O18  O  0  1  N  N  N  10.239   3.975   8.680  -5.365  -1.676  -2.311  O18  87E  42  
87E  C19  C19  C  0  1  N  N  N  10.546   5.088   8.316  -4.620  -0.742  -2.099  C19  87E  43  
87E  O19  O19  O  0  1  N  N  N   2.380   6.920   5.424  -7.801   4.796  -1.084  O19  87E  44  
87E  C20  C20  C  0  1  N  N  N  11.803   5.397   7.436  -4.493   0.366  -3.113  C20  87E  45  
87E  O20  O20  O  0  1  N  N  N   3.149   6.500   3.337  -6.172   3.332  -1.380  O20  87E  46  
87E  C21  C21  C  0  1  N  N  S   4.056   5.331   5.181  -6.333   4.194   0.808  C21  87E  47  
87E  O21  O21  O  0  1  N  N  N   2.718   3.419   5.525  -4.934   6.061   0.174  O21  87E  48  
87E  C22  C22  C  0  1  N  N  N   3.120   6.348   4.581  -6.762   4.076  -0.632  C22  87E  49  
87E  C23  C23  C  0  1  N  N  N   3.122   4.615   6.150  -5.936   5.642   1.104  C23  87E  50  
87E  H1   H1   H  0  1  N  N  N  16.365  12.265  15.430   8.393   2.152   3.726  H1   87E  51  
87E  H2   H2   H  0  1  N  N  N   9.903   7.134   8.434  -3.312   0.052  -0.787  H2   87E  52  
87E  H3   H3   H  0  1  N  N  N  12.308  11.564  14.713   8.582  -1.516   1.750  H3   87E  53  
87E  H4   H4   H  0  1  N  N  N  13.586   7.800  19.379   8.016   3.249  -2.356  H4   87E  54  
87E  H5   H5   H  0  1  N  N  N  15.872   7.982  16.706   5.701   2.823   0.247  H5   87E  55  
87E  H6   H6   H  0  1  N  N  N  12.809   8.109  17.139   7.465   1.069  -1.552  H6   87E  56  
87E  H7   H7   H  0  1  N  N  N  12.639   9.197  15.446   7.101  -0.607   0.037  H7   87E  57  
87E  H8   H8   H  0  1  N  N  N   4.826   6.083   6.954  -4.285   3.666   0.993  H8   87E  58  
87E  H9   H9   H  0  1  N  N  N  14.798   5.818  18.890   6.013   3.678  -3.295  H9   87E  59  
87E  H10  H10  H  0  1  N  N  N  12.763   5.908  17.564   5.883   1.272  -3.278  H10  87E  60  
87E  H11  H11  H  0  1  N  N  N  14.634   5.232  15.612   3.653   1.986  -1.534  H11  87E  61  
87E  H12  H12  H  0  1  N  N  N  12.194   5.053  15.467   4.774  -0.746  -2.319  H12  87E  62  
87E  H13  H13  H  0  1  N  N  N  13.018   5.522  13.942   3.706   0.236  -3.350  H13  87E  63  
87E  H14  H14  H  0  1  N  N  N   9.019   6.848  16.105   3.349  -3.269  -1.039  H14  87E  64  
87E  H15  H15  H  0  1  N  N  N   9.621   5.496  11.332  -3.297  -3.313  -1.286  H15  87E  65  
87E  H16  H16  H  0  1  N  N  N  12.603   7.315  11.606   0.095  -4.541   0.084  H16  87E  66  
87E  H17  H17  H  0  1  N  N  N   6.805   8.085  11.527  -1.774  -3.083   2.004  H17  87E  67  
87E  H18  H18  H  0  1  N  N  N   6.012   5.442  10.246  -4.777  -2.782   2.471  H18  87E  68  
87E  H19  H19  H  0  1  N  N  N   7.576   7.826   9.193  -2.710  -0.791   1.425  H19  87E  69  
87E  H20  H20  H  0  1  N  N  N   8.180   4.854   9.517  -5.047  -2.163   0.016  H20  87E  70  
87E  H21  H21  H  0  1  N  N  N   5.753   6.970  13.579  -2.715  -4.302   3.988  H21  87E  71  
87E  H22  H22  H  0  1  N  N  N   4.586   7.488  12.315  -3.875  -5.104   2.903  H22  87E  72  
87E  H23  H23  H  0  1  N  N  N   4.272   6.975  10.353  -3.406  -2.576   4.418  H23  87E  73  
87E  H24  H24  H  0  1  N  N  N   8.142   7.362   6.673  -3.533   1.149   0.745  H24  87E  74  
87E  H25  H25  H  0  1  N  N  N   4.252   5.288  12.999  -1.897  -6.407   3.209  H25  87E  75  
87E  H26  H26  H  0  1  N  N  N   6.555   9.077   7.710  -2.667   0.868   3.084  H26  87E  76  
87E  H27  H27  H  0  1  N  N  N   6.303   8.995   5.933  -3.044   2.561   2.686  H27  87E  77  
87E  H28  H28  H  0  1  N  N  N   5.156   8.170   7.042  -4.164   1.613   3.694  H28  87E  78  
87E  H29  H29  H  0  1  N  N  N   1.801   7.527   4.978  -8.039   4.687  -2.015  H29  87E  79  
87E  H30  H30  H  0  1  N  N  N  12.336   4.460   7.216  -5.141   0.155  -3.964  H30  87E  80  
87E  H31  H31  H  0  1  N  N  N  11.484   5.867   6.494  -4.788   1.311  -2.657  H31  87E  81  
87E  H32  H32  H  0  1  N  N  N  12.472   6.081   7.979  -3.459   0.432  -3.451  H32  87E  82  
87E  H33  H33  H  0  1  N  N  N   4.472   4.648   4.426  -7.158   3.904   1.458  H33  87E  83  
87E  H34  H34  H  0  1  N  N  N   2.132   2.942   6.101  -4.634   6.971   0.303  H34  87E  84  
87E  H35  H35  H  0  1  N  N  N   3.651   4.391   7.088  -6.811   6.285   1.010  H35  87E  85  
87E  H36  H36  H  0  1  N  N  N   2.245   5.244   6.364  -5.542   5.710   2.118  H36  87E  86  
#   #
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
87E  O20  C22  DOUB  N  N   1  
87E  C22  C21  SING  N  N   2  
87E  C22  O19  SING  N  N   3  
87E  O17  C17  DOUB  N  N   4  
87E  C21  N4   SING  N  N   5  
87E  C21  C23  SING  N  N   6  
87E  O21  C23  SING  N  N   7  
87E  C17  N4   SING  N  N   8  
87E  C17  C16  SING  N  N   9  
87E  C16  C18  SING  N  N  10  
87E  C16  O14  SING  N  N  11  
87E  C20  C19  SING  N  N  12  
87E  O14  C13  SING  N  N  13  
87E  C19  O18  DOUB  N  N  14  
87E  C19  N3   SING  N  N  15  
87E  N3   C14  SING  N  N  16  
87E  C13  C14  SING  N  N  17  
87E  C13  C12  SING  N  N  18  
87E  C14  C10  SING  N  N  19  
87E  O15  C12  SING  N  N  20  
87E  C12  C11  SING  N  N  21  
87E  O12  C10  SING  N  N  22  
87E  O12  P2   SING  N  N  23  
87E  C10  O13  SING  N  N  24  
87E  O11  P2   DOUB  N  N  25  
87E  C11  O13  SING  N  N  26  
87E  C11  C15  SING  N  N  27  
87E  P2   O10  SING  N  N  28  
87E  P2   O7   SING  N  N  29  
87E  O16  C15  SING  N  N  30  
87E  O7   P1   SING  N  N  31  
87E  O8   P1   DOUB  N  N  32  
87E  P1   O6   SING  N  N  33  
87E  P1   O9   SING  N  N  34  
87E  O1   C1   DOUB  N  N  35  
87E  O6   C9   SING  N  N  36  
87E  C9   C8   SING  N  N  37  
87E  C4   C1   SING  N  N  38  
87E  C4   C3   DOUB  N  N  39  
87E  C1   N1   SING  N  N  40  
87E  O3   C8   SING  N  N  41  
87E  O3   C5   SING  N  N  42  
87E  N1   C2   SING  N  N  43  
87E  C3   N2   SING  N  N  44  
87E  C8   C7   SING  N  N  45  
87E  C2   N2   SING  N  N  46  
87E  C2   O2   DOUB  N  N  47  
87E  N2   C5   SING  N  N  48  
87E  C5   C6   SING  N  N  49  
87E  C7   C6   SING  N  N  50  
87E  C7   O5   SING  N  N  51  
87E  C6   O4   SING  N  N  52  
87E  N1   H1   SING  N  N  53  
87E  N3   H2   SING  N  N  54  
87E  C4   H3   SING  N  N  55  
87E  O4   H4   SING  N  N  56  
87E  C5   H5   SING  N  N  57  
87E  C6   H6   SING  N  N  58  
87E  C3   H7   SING  N  N  59  
87E  N4   H8   SING  N  N  60  
87E  O5   H9   SING  N  N  61  
87E  C7   H10  SING  N  N  62  
87E  C8   H11  SING  N  N  63  
87E  C9   H12  SING  N  N  64  
87E  C9   H13  SING  N  N  65  
87E  O9   H14  SING  N  N  66  
87E  C10  H15  SING  N  N  67  
87E  O10  H16  SING  N  N  68  
87E  C11  H17  SING  N  N  69  
87E  C12  H18  SING  N  N  70  
87E  C13  H19  SING  N  N  71  
87E  C14  H20  SING  N  N  72  
87E  C15  H21  SING  N  N  73  
87E  C15  H22  SING  N  N  74  
87E  O15  H23  SING  N  N  75  
87E  C16  H24  SING  N  N  76  
87E  O16  H25  SING  N  N  77  
87E  C18  H26  SING  N  N  78  
87E  C18  H27  SING  N  N  79  
87E  C18  H28  SING  N  N  80  
87E  O19  H29  SING  N  N  81  
87E  C20  H30  SING  N  N  82  
87E  C20  H31  SING  N  N  83  
87E  C20  H32  SING  N  N  84  
87E  C21  H33  SING  N  N  85  
87E  O21  H34  SING  N  N  86  
87E  C23  H35  SING  N  N  87  
87E  C23  H36  SING  N  N  88  
#   #
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
87E  InChI             InChI                 1.03   "InChI=1S/C23H36N4O21P2/c1-8(19(35)25-10(5-28)21(36)37)44-18-14(24-9(2)30)22(46-11(6-29)16(18)33)47-50(41,42)48-49(39,40)43-7-12-15(32)17(34)20(45-12)27-4-3-13(31)26-23(27)38/h3-4,8,10-12,14-18,20,22,28-29,32-34H,5-7H2,1-2H3,(H,24,30)(H,25,35)(H,36,37)(H,39,40)(H,41,42)(H,26,31,38)/t8-,10+,11-,12-,14-,15-,16-,17-,18-,20-,22-/m1/s1"  
87E  InChIKey          InChI                 1.03   IACRIBHKJKCIBJ-KWWGHZHGSA-N  
87E  SMILES_CANONICAL  CACTVS                3.385  "C[C@@H](O[C@H]1[C@H](O)[C@@H](CO)O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@@H]1NC(C)=O)C(=O)N[C@@H](CO)C(O)=O"  
87E  SMILES            CACTVS                3.385  "C[CH](O[CH]1[CH](O)[CH](CO)O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH]1NC(C)=O)C(=O)N[CH](CO)C(O)=O"  
87E  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "C[C@H](C(=O)N[C@@H](CO)C(=O)O)O[C@@H]1[C@H]([C@H](O[C@@H]([C@H]1O)CO)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C"  
87E  SMILES            "OpenEye OEToolkits"  2.0.7  "CC(C(=O)NC(CO)C(=O)O)OC1C(C(OC(C1O)CO)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C"  
#
_pdbx_chem_comp_identifier.comp_id          87E
_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~{S})-2-[[(2~{R})-2-[(2~{R},3~{R},4~{R},5~{S},6~{R})-3-acetamido-2-[[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-6-(hydroxymethyl)-5-oxidanyl-oxan-4-yl]oxypropanoyl]amino]-3-oxidanyl-propanoic acid"
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     87E
_pdbx_chem_comp_synonyms.name        "Uridine-5'-diphosphate-n-acetylmuramoyl-L-Serine"
_pdbx_chem_comp_synonyms.provenance  AUTHOR
_pdbx_chem_comp_synonyms.type        ?
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
87E  "Create component"  2021-11-26  PDBJ  
87E  "Initial release"   2021-12-29  RCSB  
##
