data_ZKD
# 
_chem_comp.id                                    ZKD 
_chem_comp.name                                  URIDINE-DIPHOSPHATE-1-DEOXY-1-THIO-N-ACETYLGLUCOSAMINE 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C17 H27 N3 O16 P2 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2010-06-07 
_chem_comp.pdbx_modified_date                    2011-06-04 
_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                        623.419 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     ZKD 
_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        2XGO 
_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 
ZKD N1     N1     N 0 1 N N N 29.895 7.661  2.333  6.448  -1.004 -0.148 N1     ZKD 1  
ZKD C2     C2     C 0 1 N N N 30.263 7.945  3.681  7.119  -2.076 0.310  C2     ZKD 2  
ZKD O2     O2     O 0 1 N N N 30.207 9.104  4.104  7.244  -2.239 1.508  O2     ZKD 3  
ZKD N3     N3     N 0 1 N N N 30.716 6.897  4.531  7.654  -2.972 -0.541 N3     ZKD 4  
ZKD C4     C4     C 0 1 N N N 30.787 5.571  4.049  7.523  -2.807 -1.872 C4     ZKD 5  
ZKD O4     O4     O 0 1 N N N 31.161 4.662  4.795  8.007  -3.617 -2.643 O4     ZKD 6  
ZKD C5     C5     C 0 1 N N N 30.405 5.304  2.726  6.819  -1.683 -2.367 C5     ZKD 7  
ZKD C6     C6     C 0 1 N N N 29.956 6.325  1.866  6.293  -0.800 -1.492 C6     ZKD 8  
ZKD PA     PA     P 0 1 N N N 27.752 8.170  -4.222 0.564  1.922  -0.568 PA     ZKD 9  
ZKD PB     PB     P 0 1 N N N 25.130 7.189  -4.459 -2.262 1.038  -0.431 PB     ZKD 10 
ZKD "C1'"  "C1'"  C 0 1 N N R 24.101 6.078  -1.408 -4.939 -0.428 0.010  "C1'"  ZKD 11 
ZKD O1A    O1A    O 0 1 N N N 28.104 6.715  -4.213 0.863  1.862  -2.149 O1A    ZKD 12 
ZKD C1B    C1B    C 0 1 N N R 29.410 8.782  1.466  5.871  -0.049 0.802  C1B    ZKD 13 
ZKD O1B    O1B    O 0 1 N N N 25.567 6.013  -5.269 -2.560 1.159  -1.875 O1B    ZKD 14 
ZKD "N2'"  "N2'"  N 0 1 N N N 21.753 6.072  -2.450 -5.570 -1.380 2.174  "N2'"  ZKD 15 
ZKD "O2'"  "O2'"  O 0 1 N N N 31.018 10.491 0.744  7.718  1.450  1.409  "O2'"  ZKD 16 
ZKD "C2'"  "C2'"  C 0 1 N N S 22.836 6.732  -1.937 -5.771 -1.494 0.728  "C2'"  ZKD 17 
ZKD O2A    O2A    O 0 1 N N N 28.627 9.166  -4.913 0.221  3.309  -0.184 O2A    ZKD 18 
ZKD C2B    C2B    C 0 1 N N R 30.179 9.448  0.311  6.522  1.348  0.635  C2B    ZKD 19 
ZKD O2B    O2B    O 0 1 N N N 23.814 7.820  -4.720 -2.834 2.328  0.345  O2B    ZKD 20 
ZKD "C3'"  "C3'"  C 0 1 N N R 22.888 8.256  -1.740 -7.252 -1.283 0.398  "C3'"  ZKD 21 
ZKD "O3'"  "O3'"  O 0 1 N N N 21.794 8.902  -2.373 -7.675 -0.012 0.895  "O3'"  ZKD 22 
ZKD O3A    O3A    O 0 1 N N N 26.231 8.321  -4.755 -0.668 0.947  -0.218 O3A    ZKD 23 
ZKD C3B    C3B    C 0 1 N N S 28.987 10.119 -0.340 5.422  2.286  1.189  C3B    ZKD 24 
ZKD O3B    O3B    O 0 1 N N N 28.407 11.103 0.537  5.700  2.633  2.547  O3B    ZKD 25 
ZKD "C4'"  "C4'"  C 0 1 N N S 22.874 8.442  -0.215 -7.437 -1.327 -1.122 "C4'"  ZKD 26 
ZKD "O4'"  "O4'"  O 0 1 N N N 22.729 9.801  0.184  -7.075 -2.621 -1.609 "O4'"  ZKD 27 
ZKD C4B    C4B    C 0 1 N N R 28.012 8.960  -0.418 4.131  1.449  1.099  C4B    ZKD 28 
ZKD O4B    O4B    O 0 1 N N N 28.242 8.216  0.803  4.478  0.186  0.505  O4B    ZKD 29 
ZKD "C5'"  "C5'"  C 0 1 N N R 24.135 7.799  0.413  -6.541 -0.267 -1.768 "C5'"  ZKD 30 
ZKD "O5'"  "O5'"  O 0 1 N N N 24.303 6.378  0.010  -5.182 -0.504 -1.396 "O5'"  ZKD 31 
ZKD C5B    C5B    C 0 1 N N N 28.418 8.239  -1.684 3.103  2.172  0.227  C5B    ZKD 32 
ZKD O5B    O5B    O 0 1 N N N 27.562 8.670  -2.722 1.871  1.448  0.244  O5B    ZKD 33 
ZKD "C6'"  "C6'"  C 0 1 N N N 24.088 7.872  1.964  -6.967 1.122  -1.288 "C6'"  ZKD 34 
ZKD "O6'"  "O6'"  O 0 1 N N N 24.170 9.243  2.419  -6.236 2.118  -2.006 "O6'"  ZKD 35 
ZKD "C7'"  "C7'"  C 0 1 N N N 21.515 4.755  -2.661 -4.520 -1.991 2.759  "C7'"  ZKD 36 
ZKD "O7'"  "O7'"  O 0 1 N N N 20.475 4.351  -3.170 -3.742 -2.635 2.088  "O7'"  ZKD 37 
ZKD "C8'"  "C8'"  C 0 1 N N N 22.569 3.715  -2.271 -4.313 -1.873 4.247  "C8'"  ZKD 38 
ZKD "S1'"  "S1'"  S 0 1 N N N 25.542 6.816  -2.252 -3.178 -0.713 0.337  "S1'"  ZKD 39 
ZKD H5     H5     H 0 1 N N N 30.456 4.290  2.358  6.705  -1.533 -3.431 H5     ZKD 40 
ZKD H6     H6     H 0 1 N N N 29.659 6.090  0.854  5.752  0.064  -1.851 H6     ZKD 41 
ZKD "H1'"  "H1'"  H 0 1 N N N 24.002 4.995  -1.573 -5.222 0.560  0.375  "H1'"  ZKD 42 
ZKD HO1A   HO1A   H 0 0 N N N 28.179 6.401  -5.107 1.096  0.980  -2.472 HO1A   ZKD 43 
ZKD H1B    H1B    H 0 1 N N N 29.384 9.604  2.197  5.990  -0.408 1.825  H1B    ZKD 44 
ZKD "HO2'" "HO2'" H 0 0 N N N 31.207 10.383 1.669  8.162  2.306  1.337  "HO2'" ZKD 45 
ZKD H2B    H2B    H 0 1 N N N 30.812 8.758  -0.266 6.721  1.560  -0.416 H2B    ZKD 46 
ZKD HO2B   HO2B   H 0 0 N N N 23.358 7.955  -3.897 -2.674 2.316  1.299  HO2B   ZKD 47 
ZKD "H3'"  "H3'"  H 0 1 N N N 23.779 8.710  -2.198 -7.845 -2.072 0.861  "H3'"  ZKD 48 
ZKD "HO3'" "HO3'" H 0 0 N N N 21.101 9.046  -1.739 -8.605 0.188  0.721  "HO3'" ZKD 49 
ZKD H3B    H3B    H 0 1 N N N 29.235 10.621 -1.287 5.342  3.183  0.576  H3B    ZKD 50 
ZKD HO3B   HO3B   H 0 0 N N N 28.279 10.724 1.399  6.532  3.111  2.669  HO3B   ZKD 51 
ZKD "H4'"  "H4'"  H 0 1 N N N 21.981 7.924  0.165  -8.479 -1.124 -1.368 "H4'"  ZKD 52 
ZKD "HO4'" "HO4'" H 0 0 N N N 22.697 9.851  1.132  -7.168 -2.720 -2.567 "HO4'" ZKD 53 
ZKD H4B    H4B    H 0 1 N N N 26.937 9.187  -0.476 3.725  1.287  2.098  H4B    ZKD 54 
ZKD "H5'"  "H5'"  H 0 1 N N N 24.992 8.377  0.036  -6.637 -0.322 -2.852 "H5'"  ZKD 55 
ZKD H5B    H5B    H 0 1 N N N 29.462 8.477  -1.934 2.939  3.177  0.615  H5B    ZKD 56 
ZKD H5BA   H5BA   H 0 0 N N N 28.336 7.151  -1.548 3.474  2.234  -0.796 H5BA   ZKD 57 
ZKD "H6'"  "H6'"  H 0 1 N N N 23.142 7.434  2.315  -8.034 1.256  -1.466 "H6'"  ZKD 58 
ZKD "H6'A" "H6'A" H 0 0 N N N 24.945 7.315  2.369  -6.761 1.217  -0.222 "H6'A" ZKD 59 
ZKD "HO6'" "HO6'" H 0 0 N N N 24.188 9.261  3.369  -6.455 3.026  -1.753 "HO6'" ZKD 60 
ZKD "H8'"  "H8'"  H 0 1 N N N 23.182 3.466  -3.150 -5.106 -1.262 4.677  "H8'"  ZKD 61 
ZKD "H8'A" "H8'A" H 0 0 N N N 23.213 4.125  -1.480 -4.337 -2.866 4.697  "H8'A" ZKD 62 
ZKD "H8'B" "H8'B" H 0 0 N N N 22.069 2.807  -1.903 -3.348 -1.408 4.444  "H8'B" ZKD 63 
ZKD HN3    HN3    H 0 1 N N N 30.985 7.100  5.473  8.135  -3.740 -0.194 HN3    ZKD 64 
ZKD "HN2'" "HN2'" H 0 0 N N N 20.999 6.671  -2.718 -6.192 -0.865 2.711  "HN2'" ZKD 65 
ZKD "H2'"  "H2'"  H 0 1 N N N 22.281 6.152  -2.689 -5.460 -2.484 0.394  "H2'"  ZKD 66 
# 
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 
ZKD C1B   N1     SING N N 1  
ZKD C6    N1     SING N N 2  
ZKD N1    C2     SING N N 3  
ZKD C2    O2     DOUB N N 4  
ZKD C2    N3     SING N N 5  
ZKD C4    N3     SING N N 6  
ZKD C5    C4     SING N N 7  
ZKD C4    O4     DOUB N N 8  
ZKD C6    C5     DOUB N N 9  
ZKD C5    H5     SING N N 10 
ZKD C6    H6     SING N N 11 
ZKD O2A   PA     DOUB N N 12 
ZKD O3A   PA     SING N N 13 
ZKD PA    O1A    SING N N 14 
ZKD PA    O5B    SING N N 15 
ZKD O1B   PB     DOUB N N 16 
ZKD O3A   PB     SING N N 17 
ZKD O2B   PB     SING N N 18 
ZKD PB    "S1'"  SING N N 19 
ZKD "S1'" "C1'"  SING N N 20 
ZKD "C2'" "C1'"  SING N N 21 
ZKD "C1'" "O5'"  SING N N 22 
ZKD "C1'" "H1'"  SING N N 23 
ZKD O1A   HO1A   SING N N 24 
ZKD C2B   C1B    SING N N 25 
ZKD O4B   C1B    SING N N 26 
ZKD C1B   H1B    SING N N 27 
ZKD "C7'" "N2'"  SING N N 28 
ZKD "N2'" "C2'"  SING N N 29 
ZKD C2B   "O2'"  SING N N 30 
ZKD "O2'" "HO2'" SING N N 31 
ZKD "C2'" "C3'"  SING N N 32 
ZKD C3B   C2B    SING N N 33 
ZKD C2B   H2B    SING N N 34 
ZKD O2B   HO2B   SING N N 35 
ZKD "O3'" "C3'"  SING N N 36 
ZKD "C3'" "C4'"  SING N N 37 
ZKD "C3'" "H3'"  SING N N 38 
ZKD "O3'" "HO3'" SING N N 39 
ZKD C4B   C3B    SING N N 40 
ZKD C3B   O3B    SING N N 41 
ZKD C3B   H3B    SING N N 42 
ZKD O3B   HO3B   SING N N 43 
ZKD "C4'" "O4'"  SING N N 44 
ZKD "C4'" "C5'"  SING N N 45 
ZKD "C4'" "H4'"  SING N N 46 
ZKD "O4'" "HO4'" SING N N 47 
ZKD C5B   C4B    SING N N 48 
ZKD C4B   O4B    SING N N 49 
ZKD C4B   H4B    SING N N 50 
ZKD "O5'" "C5'"  SING N N 51 
ZKD "C5'" "C6'"  SING N N 52 
ZKD "C5'" "H5'"  SING N N 53 
ZKD O5B   C5B    SING N N 54 
ZKD C5B   H5B    SING N N 55 
ZKD C5B   H5BA   SING N N 56 
ZKD "C6'" "O6'"  SING N N 57 
ZKD "C6'" "H6'"  SING N N 58 
ZKD "C6'" "H6'A" SING N N 59 
ZKD "O6'" "HO6'" SING N N 60 
ZKD "O7'" "C7'"  DOUB N N 61 
ZKD "C7'" "C8'"  SING N N 62 
ZKD "C8'" "H8'"  SING N N 63 
ZKD "C8'" "H8'A" SING N N 64 
ZKD "C8'" "H8'B" SING N N 65 
ZKD N3    HN3    SING N N 66 
ZKD "N2'" "HN2'" SING N N 67 
ZKD "C2'" "H2'"  SING N N 68 
# 
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 
ZKD SMILES           ACDLabs              10.04 "O=P(SC1OC(C(O)C(O)C1NC(=O)C)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O" 
ZKD SMILES_CANONICAL CACTVS               3.352 "CC(=O)N[C@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]1S[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O" 
ZKD SMILES           CACTVS               3.352 "CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1S[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O" 
ZKD SMILES_CANONICAL "OpenEye OEToolkits" 1.6.1 "CC(=O)NC1[C@H]([C@@H]([C@H](O[C@@H]1S[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)CO)O)O" 
ZKD SMILES           "OpenEye OEToolkits" 1.6.1 "CC(=O)NC1C(C(C(OC1SP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)CO)O)O" 
ZKD InChI            InChI                1.03  
;InChI=1S/C17H27N3O16P2S/c1-6(22)18-10-13(26)11(24)7(4-21)35-16(10)39-38(31,32)36-37(29,30)33-5-8-12(25)14(27)15(34-8)20-3-2-9(23)19-17(20)28/h2-3,7-8,10-16,21,24-27H,4-5H2,1H3,(H,18,22)(H,29,30)(H,31,32)(H,19,23,28)/t7-,8-,10+,11-,12-,13-,14-,15-,16-/m1/s1
;
ZKD InChIKey         InChI                1.03  NBABRWVWQSKDQY-ZYQOOJPVSA-N 
# 
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 
ZKD "SYSTEMATIC NAME" ACDLabs              10.04 
"S-[(2R,3S,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl] O-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl} dihydrogen thiodiphosphate (non-preferred name)" 
ZKD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[(2R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]sulfanyl-[[(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 
ZKD "Create component"  2010-06-07 EBI  
ZKD "Modify descriptor" 2011-06-04 RCSB 
# 
