data_UD4 # _chem_comp.id UD4 _chem_comp.name "UDP-2-acetamido-4-amino-2,4,6-trideoxy-alpha-D-glucopyranose" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H28 N4 O15 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "(2R,3R,4S,5S,6R)-3-(acetylamino)-5-amino-4-hydroxy-6-methyltetrahydro-2H-pyran-2-yl" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2008-05-21 _chem_comp.pdbx_modified_date 2021-03-13 _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 590.370 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UD4 _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 3BSS _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 UD4 N3 N3 N 0 1 N N N 3.991 -39.279 -11.483 -6.747 -2.999 -0.873 N3 UD4 1 UD4 C2 C2 C 0 1 N N N 4.357 -38.129 -12.070 -6.271 -1.808 -1.279 C2 UD4 2 UD4 N1 N1 N 0 1 N N N 3.592 -37.631 -13.145 -5.643 -0.985 -0.420 N1 UD4 3 UD4 C4 C4 C 0 1 N N N 2.914 -39.964 -11.916 -6.606 -3.385 0.412 C4 UD4 4 UD4 C5 C5 C 0 1 N N N 2.139 -39.500 -12.976 -5.946 -2.529 1.326 C5 UD4 5 UD4 C6 C6 C 0 1 N N N 2.508 -38.303 -13.590 -5.473 -1.342 0.890 C6 UD4 6 UD4 "O7'" "O7'" O 0 1 N N N -3.400 -31.496 -20.671 7.161 1.208 -1.675 "O7'" UD4 7 UD4 "C7'" "C7'" C 0 1 N N N -2.254 -31.292 -20.283 6.166 1.044 -2.350 "C7'" UD4 8 UD4 "C8'" "C8'" C 0 1 N N N -1.042 -31.645 -21.120 5.894 1.950 -3.524 "C8'" UD4 9 UD4 "N2'" "N2'" N 0 1 N N N -2.006 -30.730 -19.096 5.305 0.052 -2.051 "N2'" UD4 10 UD4 "C2'" "C2'" C 0 1 N N R -3.047 -30.367 -18.143 5.569 -0.828 -0.910 "C2'" UD4 11 UD4 "C3'" "C3'" C 0 1 N N S -3.181 -28.839 -18.026 4.869 -2.173 -1.128 "C3'" UD4 12 UD4 "O3'" "O3'" O 0 1 N N N -3.634 -28.286 -19.274 5.417 -2.816 -2.280 "O3'" UD4 13 UD4 "C4'" "C4'" C 0 1 N N S -4.127 -28.423 -16.877 5.087 -3.056 0.105 "C4'" UD4 14 UD4 N4A N4A N 0 1 N N N -4.114 -26.963 -16.726 4.358 -4.320 -0.062 N4A UD4 15 UD4 "C5'" "C5'" C 0 1 N N R -3.726 -29.125 -15.571 4.568 -2.325 1.345 "C5'" UD4 16 UD4 "C6'" "C6'" C 0 1 N N N -4.719 -28.910 -14.423 4.837 -3.174 2.589 "C6'" UD4 17 UD4 "O5'" "O5'" O 0 1 N N N -3.617 -30.546 -15.773 5.238 -1.069 1.472 "O5'" UD4 18 UD4 "C1'" "C1'" C 0 1 N N R -2.713 -30.984 -16.788 5.031 -0.183 0.370 "C1'" UD4 19 UD4 "O1'" "O1'" O 0 1 N N N -1.403 -30.569 -16.414 3.633 0.075 0.222 "O1'" UD4 20 UD4 PB PB P 0 1 N N R -0.374 -31.617 -15.770 2.883 1.293 0.961 PB UD4 21 UD4 O2B O2B O 0 1 N N N 0.922 -30.891 -15.584 3.125 1.209 2.419 O2B UD4 22 UD4 O1B O1B O 0 1 N N N -1.062 -32.244 -14.577 3.451 2.692 0.402 O1B UD4 23 UD4 O3A O3A O 0 1 N N N -0.402 -32.752 -16.919 1.301 1.203 0.674 O3A UD4 24 UD4 PA PA P 0 1 N N R 0.777 -33.431 -17.798 0.004 1.890 1.334 PA UD4 25 UD4 O2A O2A O 0 1 N N N 0.203 -34.754 -18.202 -0.307 1.198 2.753 O2A UD4 26 UD4 O1A O1A O 0 1 N N N 1.265 -32.397 -18.789 0.259 3.334 1.535 O1A UD4 27 UD4 O5B O5B O 0 1 N N N 1.933 -33.684 -16.709 -1.261 1.700 0.356 O5B UD4 28 UD4 C5B C5B C 0 1 N N N 1.738 -34.497 -15.540 -2.538 2.288 0.611 C5B UD4 29 UD4 C4B C4B C 0 1 N N R 3.094 -34.571 -14.865 -3.507 1.909 -0.511 C4B UD4 30 UD4 O4B O4B O 0 1 N N N 2.966 -35.421 -13.724 -3.764 0.495 -0.477 O4B UD4 31 UD4 C2B C2B C 0 1 N N S 4.126 -35.205 -15.819 -4.856 2.625 -0.302 C2B UD4 32 UD4 O3B O3B O 0 1 N N N 5.347 -34.452 -15.810 -5.153 3.467 -1.418 O3B UD4 33 UD4 C3B C3B C 0 1 N N R 4.318 -36.600 -15.253 -5.885 1.473 -0.203 C3B UD4 34 UD4 "O2'" "O2'" O 0 1 N N N 5.617 -37.151 -15.502 -7.083 1.798 -0.911 "O2'" UD4 35 UD4 C1B C1B C 0 1 N N R 4.018 -36.387 -13.764 -5.134 0.306 -0.892 C1B UD4 36 UD4 O2 O2 O 0 1 N N N 5.361 -37.484 -11.674 -6.411 -1.470 -2.439 O2 UD4 37 UD4 O4 O4 O 0 1 N N N 2.596 -41.038 -11.347 -7.041 -4.461 0.781 O4 UD4 38 UD4 H5 H5 H 0 1 N N N 1.275 -40.053 -13.314 -5.824 -2.821 2.358 H5 UD4 39 UD4 H6 H6 H 0 1 N N N 1.930 -37.916 -14.416 -4.968 -0.676 1.573 H6 UD4 40 UD4 "H8'" "H8'" H 0 1 N N N -1.337 -31.731 -22.176 6.695 2.685 -3.608 "H8'" UD4 41 UD4 "H8'A" "H8'A" H 0 0 N N N -0.282 -30.857 -21.015 5.848 1.357 -4.437 "H8'A" UD4 42 UD4 "H8'B" "H8'B" H 0 0 N N N -0.627 -32.604 -20.777 4.944 2.463 -3.374 "H8'B" UD4 43 UD4 "HN2'" "HN2'" H 0 0 N N N -1.054 -30.549 -18.848 4.509 -0.079 -2.590 "HN2'" UD4 44 UD4 "H2'" "H2'" H 0 1 N N N -4.013 -30.755 -18.497 6.643 -0.988 -0.814 "H2'" UD4 45 UD4 "H3'" "H3'" H 0 1 N N N -2.185 -28.436 -17.789 3.801 -2.009 -1.274 "H3'" UD4 46 UD4 "HO3'" "HO3'" H 0 0 N N N -3.734 -27.345 -19.186 5.019 -3.675 -2.478 "HO3'" UD4 47 UD4 "H4'" "H4'" H 0 1 N N N -5.153 -28.735 -17.121 6.151 -3.262 0.221 "H4'" UD4 48 UD4 HN4A HN4A H 0 0 N N N -4.111 -26.728 -15.754 4.487 -4.920 0.740 HN4A UD4 49 UD4 HN4B HN4B H 0 0 N N N -3.295 -26.590 -17.161 3.378 -4.152 -0.234 HN4B UD4 50 UD4 "H5'" "H5'" H 0 1 N N N -2.762 -28.674 -15.291 3.496 -2.156 1.245 "H5'" UD4 51 UD4 "H6'" "H6'" H 0 1 N N N -4.173 -28.859 -13.470 5.909 -3.342 2.689 "H6'" UD4 52 UD4 "H6'A" "H6'A" H 0 0 N N N -5.266 -27.969 -14.583 4.467 -2.654 3.472 "H6'A" UD4 53 UD4 "H6'B" "H6'B" H 0 0 N N N -5.431 -29.748 -14.392 4.326 -4.133 2.491 "H6'B" UD4 54 UD4 "H1'" "H1'" H 0 1 N N N -2.787 -32.078 -16.881 5.556 0.754 0.553 "H1'" UD4 55 UD4 HO1B HO1B H 0 0 N N N -0.430 -32.375 -13.880 3.327 2.815 -0.549 HO1B UD4 56 UD4 HO2A HO2A H 0 0 N N N 0.081 -34.773 -19.144 -0.484 0.249 2.698 HO2A UD4 57 UD4 H5B H5B H 0 1 N N N 0.992 -34.045 -14.870 -2.922 1.923 1.563 H5B UD4 58 UD4 H5BA H5BA H 0 0 N N N 1.359 -35.496 -15.800 -2.436 3.373 0.652 H5BA UD4 59 UD4 H4B H4B H 0 1 N N N 3.426 -33.560 -14.585 -3.083 2.185 -1.476 H4B UD4 60 UD4 H2B H2B H 0 1 N N N 3.801 -35.223 -16.870 -4.840 3.206 0.620 H2B UD4 61 UD4 HO3B HO3B H 0 0 N N N 5.624 -34.286 -16.703 -5.991 3.943 -1.339 HO3B UD4 62 UD4 H3B H3B H 0 1 N N N 3.667 -37.350 -15.725 -6.103 1.235 0.838 H3B UD4 63 UD4 "HO2'" "HO2'" H 0 0 N N N 5.736 -37.273 -16.437 -7.542 2.579 -0.572 "HO2'" UD4 64 UD4 H1B H1B H 0 1 N N N 4.907 -36.047 -13.213 -5.223 0.379 -1.976 H1B UD4 65 UD4 HN3 HN3 H 0 1 N N N 4.524 -39.632 -10.714 -7.198 -3.580 -1.505 HN3 UD4 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 UD4 C2 N3 SING N N 1 UD4 C4 N3 SING N N 2 UD4 N1 C2 SING N N 3 UD4 C2 O2 DOUB N N 4 UD4 C1B N1 SING N N 5 UD4 C6 N1 SING N N 6 UD4 C5 C4 SING N N 7 UD4 C4 O4 DOUB N N 8 UD4 C6 C5 DOUB N N 9 UD4 C5 H5 SING N N 10 UD4 C6 H6 SING N N 11 UD4 "O7'" "C7'" DOUB N N 12 UD4 "C8'" "C7'" SING N N 13 UD4 "C7'" "N2'" SING N N 14 UD4 "C8'" "H8'" SING N N 15 UD4 "C8'" "H8'A" SING N N 16 UD4 "C8'" "H8'B" SING N N 17 UD4 "N2'" "C2'" SING N N 18 UD4 "N2'" "HN2'" SING N N 19 UD4 "C2'" "C3'" SING N N 20 UD4 "C2'" "C1'" SING N N 21 UD4 "C2'" "H2'" SING N N 22 UD4 "O3'" "C3'" SING N N 23 UD4 "C3'" "C4'" SING N N 24 UD4 "C3'" "H3'" SING N N 25 UD4 "O3'" "HO3'" SING N N 26 UD4 "C4'" N4A SING N N 27 UD4 "C4'" "C5'" SING N N 28 UD4 "C4'" "H4'" SING N N 29 UD4 N4A HN4A SING N N 30 UD4 N4A HN4B SING N N 31 UD4 "O5'" "C5'" SING N N 32 UD4 "C5'" "C6'" SING N N 33 UD4 "C5'" "H5'" SING N N 34 UD4 "C6'" "H6'" SING N N 35 UD4 "C6'" "H6'A" SING N N 36 UD4 "C6'" "H6'B" SING N N 37 UD4 "C1'" "O5'" SING N N 38 UD4 "C1'" "O1'" SING N N 39 UD4 "C1'" "H1'" SING N N 40 UD4 "O1'" PB SING N N 41 UD4 O3A PB SING N N 42 UD4 PB O2B DOUB N N 43 UD4 PB O1B SING N N 44 UD4 O1B HO1B SING N N 45 UD4 PA O3A SING N N 46 UD4 O1A PA DOUB N N 47 UD4 O2A PA SING N N 48 UD4 PA O5B SING N N 49 UD4 O2A HO2A SING N N 50 UD4 O5B C5B SING N N 51 UD4 C5B C4B SING N N 52 UD4 C5B H5B SING N N 53 UD4 C5B H5BA SING N N 54 UD4 C2B C4B SING N N 55 UD4 C4B O4B SING N N 56 UD4 C4B H4B SING N N 57 UD4 C1B O4B SING N N 58 UD4 C2B O3B SING N N 59 UD4 C2B C3B SING N N 60 UD4 C2B H2B SING N N 61 UD4 O3B HO3B SING N N 62 UD4 "O2'" C3B SING N N 63 UD4 C3B C1B SING N N 64 UD4 C3B H3B SING N N 65 UD4 "O2'" "HO2'" SING N N 66 UD4 C1B H1B SING N N 67 UD4 N3 HN3 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 UD4 SMILES ACDLabs 10.04 "O=P(OC1OC(C(N)C(O)C1NC(=O)C)C)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O" UD4 SMILES_CANONICAL CACTVS 3.341 "C[C@H]1O[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](NC(C)=O)[C@@H](O)[C@@H]1N" UD4 SMILES CACTVS 3.341 "C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](NC(C)=O)[CH](O)[CH]1N" UD4 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[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)NC(=O)C)O)N" UD4 SMILES "OpenEye OEToolkits" 1.5.0 "CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C)O)N" UD4 InChI InChI 1.03 "InChI=1S/C17H28N4O15P2/c1-6-10(18)13(25)11(19-7(2)22)16(33-6)35-38(30,31)36-37(28,29)32-5-8-12(24)14(26)15(34-8)21-4-3-9(23)20-17(21)27/h3-4,6,8,10-16,24-26H,5,18H2,1-2H3,(H,19,22)(H,28,29)(H,30,31)(H,20,23,27)/t6-,8-,10-,11-,12-,13+,14-,15-,16-/m1/s1" UD4 InChIKey InChI 1.03 FUUMLYWEEZBCQR-UINYWEPJSA-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 UD4 "SYSTEMATIC NAME" ACDLabs 10.04 "(2R,3R,4S,5S,6R)-3-(acetylamino)-5-amino-4-hydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)" UD4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4S,5S,6R)-3-acetamido-5-amino-4-hydroxy-6-methyl-oxan-2-yl] [[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] hydrogen phosphate" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site UD4 "Create component" 2008-05-21 RCSB UD4 "Modify descriptor" 2011-06-04 RCSB UD4 "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id UD4 _pdbx_chem_comp_synonyms.name "(2R,3R,4S,5S,6R)-3-(acetylamino)-5-amino-4-hydroxy-6-methyltetrahydro-2H-pyran-2-yl" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##