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 #