data_UDM
#

_chem_comp.id                                   UDM
_chem_comp.name                                 URIDINE-DIPHOSPHATE-METHYLENE-N-ACETYL-GLUCOSAMINE
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C18 H29 N3 O16 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        
;((2S,3R,4R,5S,6R)-3-ACETAMIDO-4,5-DIHYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2-YL)METHYLPHOSPHONIC
(((2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHYL PHOSPHORIC)
ANHYDRIDE
;

_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2005-09-21
_chem_comp.pdbx_modified_date                   2020-06-17
_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                       605.381
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    UDM
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       ?
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       2APC
_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
UDM  "C1'"   "C1'"   C  0  1  N  N  S   2.860  20.118  15.010   4.962   0.463   0.495  "C1'"   UDM   1  
UDM  "C2'"   "C2'"   C  0  1  N  N  R   2.519  18.753  15.657   6.201   0.286  -0.384  "C2'"   UDM   2  
UDM  "C3'"   "C3'"   C  0  1  N  N  R   1.347  18.200  14.847   6.163  -1.104  -1.031  "C3'"   UDM   3  
UDM  "C4'"   "C4'"   C  0  1  N  N  S   0.132  19.158  14.952   5.991  -2.153   0.073  "C4'"   UDM   4  
UDM  "C5'"   "C5'"   C  0  1  N  N  R   0.509  20.595  14.559   4.766  -1.793   0.916  "C5'"   UDM   5  
UDM  "C6'"   "C6'"   C  0  1  N  N  N  -0.572  21.555  15.101   4.566  -2.853   2.001  "C6'"   UDM   6  
UDM  "C7'"   "C7'"   C  0  1  N  N  N   4.279  17.382  16.665   7.377   1.690  -1.992  "C7'"   UDM   7  
UDM  "C8'"   "C8'"   C  0  1  N  N  N   5.444  16.452  16.501   7.387   2.746  -3.067  "C8'"   UDM   8  
UDM  "N2'"   "N2'"   N  0  1  N  N  N   3.669  17.829  15.550   6.212   1.313  -1.429  "N2'"   UDM   9  
UDM  CB      CB      C  0  1  N  N  N   3.150  20.190  13.511   3.706   0.301  -0.364  CB      UDM  10  
UDM  "O3'"   "O3'"   O  0  1  N  N  N   0.944  16.911  15.344   7.385  -1.339  -1.734  "O3'"   UDM  11  
UDM  "O4'"   "O4'"   O  0  1  N  N  N  -0.996  18.780  14.145   5.805  -3.442  -0.518  "O4'"   UDM  12  
UDM  "O5'"   "O5'"   O  0  1  N  N  N   1.712  20.982  15.271   4.958  -0.520   1.529  "O5'"   UDM  13  
UDM  "O6'"   "O6'"   O  0  1  N  N  N  -0.239  22.934  14.811   3.358  -2.583   2.715  "O6'"   UDM  14  
UDM  "O7'"   "O7'"   O  0  1  N  N  N   3.920  17.698  17.803   8.417   1.179  -1.634  "O7'"   UDM  15  
UDM  N1      N1      N  0  1  N  N  N  -0.678  19.650   6.941  -6.504  -0.440  -0.972  N1      UDM  16  
UDM  C2      C2      C  0  1  N  N  N  -1.928  20.010   6.396  -6.172  -1.455  -0.154  C2      UDM  17  
UDM  N3      N3      N  0  1  N  N  N  -1.895  21.164   5.659  -6.729  -2.672  -0.300  N3      UDM  18  
UDM  C4      C4      C  0  1  N  N  N  -0.750  21.969   5.431  -7.626  -2.896  -1.281  C4      UDM  19  
UDM  C5      C5      C  0  1  N  N  N   0.475  21.509   6.044  -7.980  -1.838  -2.153  C5      UDM  20  
UDM  C6      C6      C  0  1  N  N  N   0.479  20.406   6.752  -7.410  -0.626  -1.981  C6      UDM  21  
UDM  O2      O2      O  0  1  N  N  N  -2.954  19.364   6.556  -5.365  -1.269   0.736  O2      UDM  22  
UDM  O4      O4      O  0  1  N  N  N  -0.878  22.973   4.748  -8.127  -3.997  -1.417  O4      UDM  23  
UDM  C1D     C1*     C  0  1  N  N  R  -0.615  18.409   7.742  -5.885   0.874  -0.785  C1D     UDM  24  
UDM  C2D     C2*     C  0  1  N  N  R   0.496  17.434   7.442  -6.218   1.444   0.617  C2D     UDM  25  
UDM  "O2'"   O2*     O  0  1  N  N  N   0.155  16.617   6.318  -7.465   2.142   0.600  "O2'"   UDM  26  
UDM  C3D     C3*     C  0  1  N  N  S   0.600  16.638   8.758  -5.040   2.424   0.858  C3D     UDM  27  
UDM  C4D     C4*     C  0  1  N  N  R   0.190  17.649   9.829  -3.940   1.928  -0.101  C4D     UDM  28  
UDM  O4D     O4*     O  0  1  N  N  N  -0.504  18.727   9.124  -4.446   0.761  -0.769  O4D     UDM  29  
UDM  O3D     O3*     O  0  1  N  N  N  -0.299  15.503   8.778  -5.427   3.761   0.538  O3D     UDM  30  
UDM  C5D     C5*     C  0  1  N  N  N   1.286  18.265  10.697  -2.681   1.570   0.691  C5D     UDM  31  
UDM  O5D     O5*     O  0  1  N  N  N   2.221  18.933   9.852  -1.633   1.217  -0.214  O5D     UDM  32  
UDM  PA      PA      P  0  1  N  N  R   3.781  18.666   9.920  -0.346   0.854   0.683  PA      UDM  33  
UDM  O1A     O1A     O  0  1  N  N  N   4.053  17.228  10.186  -0.037   1.987   1.584  O1A     UDM  34  
UDM  O2A     O2A     O  0  1  N  N  N   4.326  19.222   8.669  -0.657  -0.459   1.561  O2A     UDM  35  
UDM  O3A     O3A     O  0  1  N  N  N   4.460  19.530  11.141   0.915   0.572  -0.277  O3A     UDM  36  
UDM  PB      PB      P  0  1  N  N  S   4.544  19.425  12.713   2.227   0.613   0.655  PB      UDM  37  
UDM  O1B     O1B     O  0  1  N  N  N   4.668  17.953  12.953   2.339   1.945   1.292  O1B     UDM  38  
UDM  O2B     O2B     O  0  1  N  N  N   5.805  20.155  13.084   2.112  -0.519   1.794  O2B     UDM  39  
UDM  "H1'"   "H1'"   H  0  1  N  N  N   3.821  20.404  15.462   4.970   1.457   0.941  "H1'"   UDM  40  
UDM  "H2'"   "H2'"   H  0  1  N  N  N   2.277  18.863  16.725   7.099   0.379   0.227  "H2'"   UDM  41  
UDM  "H3'"   "H3'"   H  0  1  N  N  N   1.676  18.107  13.801   5.325  -1.161  -1.725  "H3'"   UDM  42  
UDM  "H4'"   "H4'"   H  0  1  N  N  N  -0.160  19.093  16.011   6.878  -2.167   0.705  "H4'"   UDM  43  
UDM  "H5'"   "H5'"   H  0  1  N  N  N   0.625  20.641  13.466   3.883  -1.758   0.277  "H5'"   UDM  44  
UDM  "H6'1"  "1H6'"  H  0  0  N  N  N  -0.633  21.432  16.192   4.502  -3.839   1.539  "H6'1"  UDM  45  
UDM  "H6'2"  "2H6'"  H  0  0  N  N  N  -1.534  21.313  14.626   5.409  -2.830   2.692  "H6'2"  UDM  46  
UDM  "H8'1"  "1H8'"  H  0  0  N  N  N   5.249  15.520  17.052   8.412   2.916  -3.399  "H8'1"  UDM  47  
UDM  "H8'2"  "2H8'"  H  0  0  N  N  N   6.353  16.929  16.897   6.783   2.412  -3.911  "H8'2"  UDM  48  
UDM  "H8'3"  "3H8'"  H  0  0  N  N  N   5.585  16.224  15.434   6.975   3.673  -2.669  "H8'3"  UDM  49  
UDM  H3      H3      H  0  1  N  N  N   3.994  17.536  14.651   5.380   1.721  -1.716  H3      UDM  50  
UDM  HB1     1HB     H  0  1  N  N  N   3.396  21.256  13.393   3.736   1.013  -1.189  HB1     UDM  51  
UDM  HB2     2HB     H  0  1  N  N  N   2.270  19.733  13.034   3.666  -0.713  -0.762  HB2     UDM  52  
UDM  H4      H4      H  0  1  N  N  N   0.855  16.305  14.618   7.318  -2.221  -2.124  H4      UDM  53  
UDM  H7      H7      H  0  1  N  N  N  -1.766  18.697  14.695   5.701  -4.070   0.210  H7      UDM  54  
UDM  "H6'"   "H6'"   H  0  1  N  N  N  -0.166  23.420  15.624   3.270  -3.272   3.388  "H6'"   UDM  55  
UDM  HN3     HN3     H  0  1  N  N  N  -2.754  21.465   5.245  -6.482  -3.392   0.302  HN3     UDM  56  
UDM  H5      H5      H  0  1  N  N  N   1.387  22.074   5.919  -8.697  -1.997  -2.945  H5      UDM  57  
UDM  H6      H6      H  0  1  N  N  N   1.403  20.073   7.201  -7.668   0.193  -2.636  H6      UDM  58  
UDM  H1D     H1*     H  0  1  N  N  N  -1.551  17.904   7.462  -6.207   1.563  -1.566  H1D     UDM  59  
UDM  H2D     H2*     H  0  1  N  N  N   1.452  17.899   7.161  -6.228   0.653   1.366  H2D     UDM  60  
UDM  H1      H1      H  0  1  N  N  N   0.079  17.160   5.542  -7.613   2.470   1.498  H1      UDM  61  
UDM  H3D     H3*     H  0  1  N  N  N   1.608  16.223   8.905  -4.699   2.363   1.892  H3D     UDM  62  
UDM  H4D     H4*     H  0  1  N  N  N  -0.414  17.084  10.554  -3.710   2.703  -0.832  H4D     UDM  63  
UDM  H2      H2      H  0  1  N  N  N  -0.496  15.239   7.887  -6.156   3.991   1.131  H2      UDM  64  
UDM  "H5'1"  1H5*    H  0  0  N  N  N   1.797  17.476  11.269  -2.893   0.727   1.349  "H5'1"  UDM  65  
UDM  "H5'2"  2H5*    H  0  0  N  N  N   0.841  18.985  11.400  -2.372   2.428   1.289  "H5'2"  UDM  66  
UDM  H2A     H2A     H  0  1  N  N  N   4.443  20.160   8.763  -0.853  -1.172   0.937  H2A     UDM  67  
UDM  H2B     H2B     H  0  1  N  N  N   6.324  20.309  12.303   2.042  -1.368   1.338  H2B     UDM  68  
#   #
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
UDM  "C1'"  "C2'"   SING  N  N   1  
UDM  "C1'"  CB      SING  N  N   2  
UDM  "C1'"  "O5'"   SING  N  N   3  
UDM  "C1'"  "H1'"   SING  N  N   4  
UDM  "C2'"  "C3'"   SING  N  N   5  
UDM  "C2'"  "N2'"   SING  N  N   6  
UDM  "C2'"  "H2'"   SING  N  N   7  
UDM  "C3'"  "C4'"   SING  N  N   8  
UDM  "C3'"  "O3'"   SING  N  N   9  
UDM  "C3'"  "H3'"   SING  N  N  10  
UDM  "C4'"  "C5'"   SING  N  N  11  
UDM  "C4'"  "O4'"   SING  N  N  12  
UDM  "C4'"  "H4'"   SING  N  N  13  
UDM  "C5'"  "C6'"   SING  N  N  14  
UDM  "C5'"  "O5'"   SING  N  N  15  
UDM  "C5'"  "H5'"   SING  N  N  16  
UDM  "C6'"  "O6'"   SING  N  N  17  
UDM  "C6'"  "H6'1"  SING  N  N  18  
UDM  "C6'"  "H6'2"  SING  N  N  19  
UDM  "C7'"  "C8'"   SING  N  N  20  
UDM  "C7'"  "N2'"   SING  N  N  21  
UDM  "C7'"  "O7'"   DOUB  N  N  22  
UDM  "C8'"  "H8'1"  SING  N  N  23  
UDM  "C8'"  "H8'2"  SING  N  N  24  
UDM  "C8'"  "H8'3"  SING  N  N  25  
UDM  "N2'"  H3      SING  N  N  26  
UDM  CB     PB      SING  N  N  27  
UDM  CB     HB1     SING  N  N  28  
UDM  CB     HB2     SING  N  N  29  
UDM  "O3'"  H4      SING  N  N  30  
UDM  "O4'"  H7      SING  N  N  31  
UDM  "O6'"  "H6'"   SING  N  N  32  
UDM  N1     C2      SING  N  N  33  
UDM  N1     C6      SING  N  N  34  
UDM  N1     C1D     SING  N  N  35  
UDM  C2     N3      SING  N  N  36  
UDM  C2     O2      DOUB  N  N  37  
UDM  N3     C4      SING  N  N  38  
UDM  N3     HN3     SING  N  N  39  
UDM  C4     C5      SING  N  N  40  
UDM  C4     O4      DOUB  N  N  41  
UDM  C5     C6      DOUB  N  N  42  
UDM  C5     H5      SING  N  N  43  
UDM  C6     H6      SING  N  N  44  
UDM  C1D    C2D     SING  N  N  45  
UDM  C1D    O4D     SING  N  N  46  
UDM  C1D    H1D     SING  N  N  47  
UDM  C2D    "O2'"   SING  N  N  48  
UDM  C2D    C3D     SING  N  N  49  
UDM  C2D    H2D     SING  N  N  50  
UDM  "O2'"  H1      SING  N  N  51  
UDM  C3D    C4D     SING  N  N  52  
UDM  C3D    O3D     SING  N  N  53  
UDM  C3D    H3D     SING  N  N  54  
UDM  C4D    O4D     SING  N  N  55  
UDM  C4D    C5D     SING  N  N  56  
UDM  C4D    H4D     SING  N  N  57  
UDM  O3D    H2      SING  N  N  58  
UDM  C5D    O5D     SING  N  N  59  
UDM  C5D    "H5'1"  SING  N  N  60  
UDM  C5D    "H5'2"  SING  N  N  61  
UDM  O5D    PA      SING  N  N  62  
UDM  PA     O1A     DOUB  N  N  63  
UDM  PA     O2A     SING  N  N  64  
UDM  PA     O3A     SING  N  N  65  
UDM  O2A    H2A     SING  N  N  66  
UDM  O3A    PB      SING  N  N  67  
UDM  PB     O1B     DOUB  N  N  68  
UDM  PB     O2B     SING  N  N  69  
UDM  O2B    H2B     SING  N  N  70  
#   #
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
UDM  SMILES_CANONICAL  CACTVS                3.341  "CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]1C[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O"  
UDM  SMILES            CACTVS                3.341  "CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1C[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O"  
UDM  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "CC(=O)N[C@H]1[C@H](O[C@@H]([C@H]([C@@H]1O)O)CO)C[P@](=O)(O)O[P@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O"  
UDM  SMILES            "OpenEye OEToolkits"  1.5.0  "CC(=O)NC1C(OC(C(C1O)O)CO)CP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O"  
UDM  InChI             InChI                 1.03   "InChI=1S/C18H29N3O16P2/c1-7(23)19-12-10(35-8(4-22)13(25)15(12)27)6-38(30,31)37-39(32,33)34-5-9-14(26)16(28)17(36-9)21-3-2-11(24)20-18(21)29/h2-3,8-10,12-17,22,25-28H,4-6H2,1H3,(H,19,23)(H,30,31)(H,32,33)(H,20,24,29)/t8-,9-,10-,12+,13-,14-,15-,16-,17-/m1/s1"  
UDM  InChIKey          InChI                 1.03   KUFKOJZYUNOEES-DLLWPQOWSA-N  
#
_pdbx_chem_comp_identifier.comp_id          UDM
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  1.5.0
_pdbx_chem_comp_identifier.identifier       "[(2S,3R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]methyl-[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-phosphinic acid"
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
UDM  "Create component"   2005-09-21  RCSB  
UDM  "Modify descriptor"  2011-06-04  RCSB  
UDM  "Modify synonyms"    2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     UDM
_pdbx_chem_comp_synonyms.name        "((2S,3R,4R,5S,6R)-3-ACETAMIDO-4,5-DIHYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2-YL)METHYLPHOSPHONIC (((2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHYL PHOSPHORIC) ANHYDRIDE"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
