data_UDN
# 
_chem_comp.id                                    UDN 
_chem_comp.name                                  Uridine-Diphosphate-Methylene-N-acetyl-galactosamine 
_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                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2017-10-15 
_chem_comp.pdbx_modified_date                    2018-02-02 
_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                     UDN 
_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        6EJK 
_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 
UDN "C1'" C1  C 0 1 N N S 68.806 -6.609  22.499 4.859  0.057  -0.554 "C1'" UDN 1  
UDN "C2'" C2  C 0 1 N N R 68.197 -5.724  23.575 5.578  -1.263 -0.264 "C2'" UDN 2  
UDN "C3'" C3  C 0 1 N N R 68.118 -4.294  23.067 5.218  -1.732 1.149  "C3'" UDN 3  
UDN "C4'" C4  C 0 1 N N R 69.430 -3.724  22.583 5.591  -0.635 2.150  "C4'" UDN 4  
UDN "C5'" C5  C 0 1 N N R 70.119 -4.675  21.617 4.871  0.661  1.767  "C5'" UDN 5  
UDN "C6'" C6  C 0 1 N N N 71.485 -4.207  21.267 5.285  1.778  2.728  "C6'" UDN 6  
UDN "C7'" C7  C 0 1 N N N 66.388 -6.501  25.277 5.968  -3.312 -1.523 "C7'" UDN 7  
UDN "C8'" C8  C 0 1 N N N 64.993 -7.098  25.457 5.536  -4.352 -2.525 "C8'" UDN 8  
UDN "N2'" N1  N 0 1 N N N 66.851 -6.303  23.917 5.158  -2.273 -1.238 "N2'" UDN 9  
UDN CB    C9  C 0 1 N N N 67.905 -6.635  21.441 3.346  -0.166 -0.511 CB    UDN 10 
UDN "O3'" O1  O 0 1 N N N 67.502 -3.420  24.035 5.942  -2.925 1.456  "O3'" UDN 11 
UDN "O4'" O2  O 0 1 N N N 70.319 -3.453  23.669 7.003  -0.422 2.122  "O4'" UDN 12 
UDN "O5'" O3  O 0 1 N N N 70.149 -6.096  22.129 5.226  1.025  0.432  "O5'" UDN 13 
UDN "O6'" O4  O 0 1 N N N 72.396 -4.707  22.228 4.528  2.956  2.443  "O6'" UDN 14 
UDN "O7'" O5  O 0 1 N N N 67.041 -6.209  26.236 7.045  -3.410 -0.973 "O7'" UDN 15 
UDN N1    N2  N 0 1 N N N 66.813 -10.134 12.696 -6.092 -1.213 -0.069 N1    UDN 16 
UDN C2    C10 C 0 1 N N N 67.395 -10.899 11.716 -5.879 -1.853 1.096  C2    UDN 17 
UDN N3    N3  N 0 1 N N N 66.651 -11.820 11.084 -6.336 -3.103 1.291  N3    UDN 18 
UDN C4    C11 C 0 1 N N N 65.367 -12.001 11.389 -7.017 -3.739 0.317  C4    UDN 19 
UDN C5    C12 C 0 1 N N N 64.760 -11.239 12.384 -7.248 -3.077 -0.914 C5    UDN 20 
UDN C6    C13 C 0 1 N N N 65.534 -10.296 13.038 -6.779 -1.822 -1.083 C6    UDN 21 
UDN O2    O6  O 0 1 N N N 68.556 -10.745 11.414 -5.265 -1.293 1.984  O2    UDN 22 
UDN O4    O7  O 0 1 N N N 64.710 -12.822 10.804 -7.430 -4.871 0.493  O4    UDN 23 
UDN C1D   C14 C 0 1 N N R 67.598 -9.110  13.420 -5.588 0.150  -0.250 C1D   UDN 24 
UDN C2D   C15 C 0 1 N N R 67.655 -7.720  13.097 -6.245 1.108  0.775  C2D   UDN 25 
UDN "O2'" O8  O 0 1 N N N 68.044 -7.116  11.887 -7.487 1.616  0.282  "O2'" UDN 26 
UDN C3D   C16 C 0 1 N N S 68.012 -7.102  14.303 -5.175 2.230  0.859  C3D   UDN 27 
UDN C4D   C17 C 0 1 N N S 67.816 -8.116  15.258 -3.859 1.442  0.680  C4D   UDN 28 
UDN O4D   O9  O 0 1 N N N 67.850 -9.268  14.680 -4.181 0.204  0.035  O4D   UDN 29 
UDN O3D   O10 O 0 1 N N N 68.953 -6.063  14.305 -5.347 3.178  -0.196 O3D   UDN 30 
UDN C5D   C18 C 0 1 N N N 67.767 -7.925  16.751 -2.888 2.243  -0.189 C5D   UDN 31 
UDN O5D   O11 O 0 1 N N N 67.596 -6.538  16.890 -1.634 1.562  -0.254 O5D   UDN 32 
UDN PA    P1  P 0 1 N N N 67.039 -6.185  18.393 -0.374 2.122  -1.086 PA    UDN 33 
UDN O1A   O12 O 0 1 N N N 67.740 -5.016  18.953 -0.730 2.133  -2.656 O1A   UDN 34 
UDN O2A   O13 O 0 1 N N N 65.596 -5.870  18.365 -0.062 3.499  -0.641 O2A   UDN 35 
UDN O3A   O14 O 0 1 N N N 67.298 -7.697  19.086 0.902  1.174  -0.830 O3A   UDN 36 
UDN PB    P2  P 0 1 N N N 67.259 -8.001  20.713 2.491  1.367  -1.001 PB    UDN 37 
UDN O1B   O15 O 0 1 N N N 68.000 -9.219  20.939 2.947  2.483  -0.142 O1B   UDN 38 
UDN O2B   O16 O 0 1 N N N 65.945 -8.362  21.227 2.829  1.702  -2.539 O2B   UDN 39 
UDN H1    H1  H 0 1 N N N 68.921 -7.621  22.915 5.145  0.418  -1.542 H1    UDN 40 
UDN H2    H2  H 0 1 N N N 68.840 -5.752  24.467 6.656  -1.114 -0.335 H2    UDN 41 
UDN H3    H3  H 0 1 N N N 67.454 -4.319  22.190 4.147  -1.931 1.205  H3    UDN 42 
UDN H4    H4  H 0 1 N N N 69.219 -2.788  22.046 5.288  -0.938 3.153  H4    UDN 43 
UDN H5    H5  H 0 1 N N N 69.525 -4.678  20.691 3.793  0.510  1.828  H5    UDN 44 
UDN H6    H6  H 0 1 N N N 71.759 -4.579  20.269 5.095  1.463  3.754  H6    UDN 45 
UDN H7    H7  H 0 1 N N N 71.511 -3.107  21.269 6.347  1.989  2.603  H7    UDN 46 
UDN H8    H8  H 0 1 N N N 64.766 -7.183  26.530 4.997  -5.148 -2.012 H8    UDN 47 
UDN H9    H9  H 0 1 N N N 64.250 -6.445  24.975 4.884  -3.892 -3.267 H9    UDN 48 
UDN H10   H10 H 0 1 N N N 64.959 -8.096  24.995 6.414  -4.767 -3.019 H10   UDN 49 
UDN H11   H11 H 0 1 N N N 66.244 -6.565  23.167 4.297  -2.195 -1.677 H11   UDN 50 
UDN H12   H12 H 0 1 N N N 68.403 -6.087  20.628 3.077  -0.968 -1.199 H12   UDN 51 
UDN H13   H13 H 0 1 N N N 67.035 -6.060  21.792 3.048  -0.441 0.501  H13   UDN 52 
UDN H14   H14 H 0 1 N N N 66.680 -3.797  24.325 5.762  -3.279 2.337  H14   UDN 53 
UDN H15   H15 H 0 1 N N N 69.900 -2.859  24.281 7.311  0.261  2.733  H15   UDN 54 
UDN H16   H16 H 0 1 N N N 73.274 -4.414  22.015 4.738  3.706  3.015  H16   UDN 55 
UDN H17   H17 H 0 1 N N N 67.069 -12.382 10.370 -6.174 -3.550 2.137  H17   UDN 56 
UDN H18   H18 H 0 1 N N N 63.719 -11.379 12.637 -7.792 -3.570 -1.706 H18   UDN 57 
UDN H19   H19 H 0 1 N N N 65.103 -9.693  13.823 -6.949 -1.300 -2.013 H19   UDN 58 
UDN H20   H20 H 0 1 N N N 68.586 -9.389  13.025 -5.781 0.492  -1.267 H20   UDN 59 
UDN H21   H21 H 0 1 N N N 66.579 -7.491  13.081 -6.379 0.619  1.740  H21   UDN 60 
UDN H22   H22 H 0 1 N N N 67.980 -6.172  11.969 -7.934 2.220  0.891  H22   UDN 61 
UDN H23   H23 H 0 1 N N N 67.099 -6.515  14.479 -5.206 2.724  1.831  H23   UDN 62 
UDN H24   H24 H 0 1 N N N 66.721 -8.049  15.171 -3.410 1.247  1.654  H24   UDN 63 
UDN H25   H25 H 0 1 N N N 69.083 -5.755  15.194 -6.199 3.636  -0.177 H25   UDN 64 
UDN H26   H26 H 0 1 N N N 66.921 -8.473  17.192 -3.299 2.345  -1.193 H26   UDN 65 
UDN H27   H27 H 0 1 N N N 68.704 -8.256  17.222 -2.743 3.232  0.246  H27   UDN 66 
UDN H28   H28 H 0 1 N N N 67.108 -4.338  19.164 -0.945 1.262  -3.016 H28   UDN 67 
UDN H29   H29 H 0 1 N N N 65.964 -9.257  21.546 2.557  1.013  -3.161 H29   UDN 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 
UDN O4    C4    DOUB N N 1  
UDN N3    C4    SING N N 2  
UDN N3    C2    SING N N 3  
UDN C4    C5    SING N N 4  
UDN O2    C2    DOUB N N 5  
UDN C2    N1    SING N N 6  
UDN "O2'" C2D   SING N N 7  
UDN C5    C6    DOUB N N 8  
UDN N1    C6    SING N N 9  
UDN N1    C1D   SING N N 10 
UDN C2D   C1D   SING N N 11 
UDN C2D   C3D   SING N N 12 
UDN C1D   O4D   SING N N 13 
UDN C3D   O3D   SING N N 14 
UDN C3D   C4D   SING N N 15 
UDN O4D   C4D   SING N N 16 
UDN C4D   C5D   SING N N 17 
UDN C5D   O5D   SING N N 18 
UDN O5D   PA    SING N N 19 
UDN O2A   PA    DOUB N N 20 
UDN PA    O1A   SING N N 21 
UDN PA    O3A   SING N N 22 
UDN O3A   PB    SING N N 23 
UDN PB    O1B   DOUB N N 24 
UDN PB    O2B   SING N N 25 
UDN PB    CB    SING N N 26 
UDN "C6'" "C5'" SING N N 27 
UDN "C6'" "O6'" SING N N 28 
UDN CB    "C1'" SING N N 29 
UDN "C5'" "O5'" SING N N 30 
UDN "C5'" "C4'" SING N N 31 
UDN "O5'" "C1'" SING N N 32 
UDN "C1'" "C2'" SING N N 33 
UDN "C4'" "C3'" SING N N 34 
UDN "C4'" "O4'" SING N N 35 
UDN "C3'" "C2'" SING N N 36 
UDN "C3'" "O3'" SING N N 37 
UDN "C2'" "N2'" SING N N 38 
UDN "N2'" "C7'" SING N N 39 
UDN "C7'" "C8'" SING N N 40 
UDN "C7'" "O7'" DOUB N N 41 
UDN "C1'" H1    SING N N 42 
UDN "C2'" H2    SING N N 43 
UDN "C3'" H3    SING N N 44 
UDN "C4'" H4    SING N N 45 
UDN "C5'" H5    SING N N 46 
UDN "C6'" H6    SING N N 47 
UDN "C6'" H7    SING N N 48 
UDN "C8'" H8    SING N N 49 
UDN "C8'" H9    SING N N 50 
UDN "C8'" H10   SING N N 51 
UDN "N2'" H11   SING N N 52 
UDN CB    H12   SING N N 53 
UDN CB    H13   SING N N 54 
UDN "O3'" H14   SING N N 55 
UDN "O4'" H15   SING N N 56 
UDN "O6'" H16   SING N N 57 
UDN N3    H17   SING N N 58 
UDN C5    H18   SING N N 59 
UDN C6    H19   SING N N 60 
UDN C1D   H20   SING N N 61 
UDN C2D   H21   SING N N 62 
UDN "O2'" H22   SING N N 63 
UDN C3D   H23   SING N N 64 
UDN C4D   H24   SING N N 65 
UDN O3D   H25   SING N N 66 
UDN C5D   H26   SING N N 67 
UDN C5D   H27   SING N N 68 
UDN O1A   H28   SING N N 69 
UDN O2B   H29   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 
UDN 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
;
UDN InChIKey         InChI                1.03  KUFKOJZYUNOEES-HCUIDVLSSA-N 
UDN SMILES_CANONICAL CACTVS               3.385 "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" 
UDN SMILES           CACTVS               3.385 "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" 
UDN SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CC(=O)N[C@H]1[C@H](O[C@@H]([C@@H]([C@@H]1O)O)CO)CP(=O)(O)OP(=O)(O)OCC2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O" 
UDN SMILES           "OpenEye OEToolkits" 2.0.6 "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" 
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
UDN "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 
"[(2~{S},3~{R},4~{R},5~{R},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]methyl-[[(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-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 
UDN "Create component" 2017-10-15 EBI  
UDN "Initial release"  2018-02-07 RCSB 
# 
