data_UD6 # _chem_comp.id UD6 _chem_comp.name ;[[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4R,5R,6R)-6-(hydroxymethyl)-4,5-bis(oxidanyl)-3-(2-oxidanylidenepropyl)oxan-2-yl] hydrogen phosphate ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H28 N2 O17 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms UDP-2-ketoGlc _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2011-05-11 _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 606.366 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UD6 _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 3RUH _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 UD6 N1 N1 N 0 1 N N N -24.903 -15.693 43.212 -5.880 -1.015 -0.587 N1 UD6 1 UD6 C2 C2 C 0 1 N N N -25.765 -15.437 42.132 -5.726 -1.229 0.732 C2 UD6 2 UD6 O2 O2 O 0 1 N N N -25.890 -14.296 41.679 -5.145 -0.402 1.410 O2 UD6 3 UD6 N3 N3 N 0 1 N N N -26.493 -16.502 41.578 -6.206 -2.344 1.313 N3 UD6 4 UD6 C4 C4 C 0 1 N N N -26.356 -17.798 42.089 -6.853 -3.269 0.576 C4 UD6 5 UD6 O4 O4 O 0 1 N N N -26.996 -18.717 41.591 -7.288 -4.278 1.101 O4 UD6 6 UD6 C5 C5 C 0 1 N N N -25.502 -18.053 43.156 -7.021 -3.057 -0.813 C5 UD6 7 UD6 C6 C6 C 0 1 N N N -24.772 -17.010 43.713 -6.530 -1.930 -1.370 C6 UD6 8 UD6 PA PA P 0 1 N N N -20.729 -17.521 46.043 -0.189 1.964 0.861 PA UD6 9 UD6 PB PB P 0 1 N N N -19.999 -16.123 48.513 2.366 0.493 1.162 PB UD6 10 UD6 "C1'" "C1'" C 0 1 N N R -18.685 -16.582 50.664 4.755 -0.422 0.391 "C1'" UD6 11 UD6 "O1'" "O1'" O 0 1 N N N -18.676 -16.535 49.256 3.430 -0.004 0.060 "O1'" UD6 12 UD6 O1A O1A O 0 1 N N N -21.801 -18.536 46.092 0.260 3.504 0.722 O1A UD6 13 UD6 C1B C1B C 0 1 N N R -24.125 -14.577 43.808 -5.352 0.211 -1.190 C1B UD6 14 UD6 O1B O1B O 0 1 N N N -19.713 -14.836 47.836 2.953 1.600 1.950 O1B UD6 15 UD6 "C2'" "C2'" C 0 1 N N R -17.274 -16.235 51.153 5.694 -0.117 -0.780 "C2'" UD6 16 UD6 "O2'" "O2'" O 0 1 N N N -25.404 -13.658 45.624 -7.279 1.721 -1.372 "O2'" UD6 17 UD6 O2A O2A O 0 1 N N N -19.634 -17.674 45.061 -0.559 1.683 2.266 O2A UD6 18 UD6 C2B C2B C 0 1 N N R -24.276 -14.477 45.324 -6.088 1.456 -0.630 C2B UD6 19 UD6 O2B O2B O 0 1 N N N -21.152 -16.225 49.439 2.000 -0.729 2.144 O2B UD6 20 UD6 "C3'" "C3'" C 0 1 N N R -16.316 -17.283 50.607 5.246 -0.919 -2.006 "C3'" UD6 21 UD6 "O3'" "O3'" O 0 1 N N N -15.035 -17.098 51.197 6.159 -0.697 -3.082 "O3'" UD6 22 UD6 O3A O3A O 0 1 N N N -20.066 -17.419 47.518 1.030 1.008 0.425 O3A UD6 23 UD6 C3B C3B C 0 1 N N S -22.982 -13.774 45.723 -5.041 2.576 -0.846 C3B UD6 24 UD6 O3B O3B O 0 1 N N N -23.176 -12.352 45.720 -5.326 3.302 -2.043 O3B UD6 25 UD6 "C4'" "C4'" C 0 1 N N R -16.838 -18.705 50.902 5.227 -2.408 -1.649 "C4'" UD6 26 UD6 "O4'" "O4'" O 0 1 N N N -16.754 -18.968 52.310 6.550 -2.838 -1.322 "O4'" UD6 27 UD6 C4B C4B C 0 1 N N R -21.999 -14.142 44.597 -3.703 1.822 -0.974 C4B UD6 28 UD6 O4B O4B O 0 1 N N N -22.740 -14.888 43.617 -3.980 0.424 -0.793 O4B UD6 29 UD6 "C5'" "C5'" C 0 1 N N R -18.279 -18.927 50.372 4.306 -2.625 -0.445 "C5'" UD6 30 UD6 "O5'" "O5'" O 0 1 N N N -19.119 -17.925 50.989 4.761 -1.827 0.650 "O5'" UD6 31 UD6 C5B C5B C 0 1 N N N -20.906 -15.100 45.030 -2.730 2.304 0.105 C5B UD6 32 UD6 O5B O5B O 0 1 N N N -21.452 -16.104 45.861 -1.456 1.686 -0.093 O5B UD6 33 UD6 "C6'" "C6'" C 0 1 N N N -18.950 -20.304 50.600 4.328 -4.101 -0.045 "C6'" UD6 34 UD6 "O6'" "O6'" O 0 1 N N N -18.149 -21.145 51.439 3.382 -4.325 1.003 "O6'" UD6 35 UD6 "C7'" "C7'" C 0 1 N N N -17.465 -13.655 51.090 6.194 2.160 0.066 "C7'" UD6 36 UD6 "O7'" "O7'" O 0 1 N N N -18.442 -13.687 51.840 6.586 1.580 1.051 "O7'" UD6 37 UD6 "C8'" "C8'" C 0 1 N N N -16.942 -12.315 50.578 6.255 3.664 0.004 "C8'" UD6 38 UD6 "C9'" "C9'" C 0 1 N N N -16.832 -14.832 50.684 5.644 1.379 -1.099 "C9'" UD6 39 UD6 H5 H5 H 0 1 N N N -25.407 -19.054 43.549 -7.536 -3.788 -1.420 H5 UD6 40 UD6 H6 H6 H 0 1 N N N -24.099 -17.206 44.535 -6.653 -1.749 -2.428 H6 UD6 41 UD6 "H1'" "H1'" H 0 1 N N N -19.359 -15.864 51.154 5.095 0.113 1.278 "H1'" UD6 42 UD6 HO1A HO1A H 0 0 N N N -21.635 -19.204 45.438 0.516 3.759 -0.175 HO1A UD6 43 UD6 H1B H1B H 0 1 N N N -24.479 -13.648 43.337 -5.438 0.171 -2.276 H1B UD6 44 UD6 "H2'" "H2'" H 0 1 N N N -17.269 -16.228 52.253 6.713 -0.398 -0.513 "H2'" UD6 45 UD6 "HO2'" "HO2'" H 0 0 N N N -25.505 -13.590 46.566 -7.774 2.490 -1.060 "HO2'" UD6 46 UD6 H2B H2B H 0 1 N N N -24.430 -15.436 45.840 -6.311 1.331 0.430 H2B UD6 47 UD6 HO2B HO2B H 0 0 N N N -21.597 -15.387 49.485 1.611 -1.492 1.695 HO2B UD6 48 UD6 "H3'" "H3'" H 0 1 N N N -16.240 -17.167 49.516 4.246 -0.602 -2.303 "H3'" UD6 49 UD6 "HO3'" "HO3'" H 0 0 N N N -14.433 -17.750 50.859 5.936 -1.175 -3.892 "HO3'" UD6 50 UD6 H3B H3B H 0 1 N N N -22.635 -14.067 46.725 -5.020 3.248 0.012 H3B UD6 51 UD6 HO3B HO3B H 0 0 N N N -22.367 -11.921 45.969 -6.183 3.748 -2.038 HO3B UD6 52 UD6 "H4'" "H4'" H 0 1 N N N -16.199 -19.420 50.363 4.857 -2.981 -2.499 "H4'" UD6 53 UD6 "HO4'" "HO4'" H 0 0 N N N -17.076 -19.844 52.489 6.612 -3.773 -1.085 "HO4'" UD6 54 UD6 H4B H4B H 0 1 N N N -21.551 -13.199 44.250 -3.275 1.993 -1.962 H4B UD6 55 UD6 "H5'" "H5'" H 0 1 N N N -18.177 -18.864 49.279 3.289 -2.335 -0.708 "H5'" UD6 56 UD6 H5B H5B H 0 1 N N N -20.457 -15.567 44.141 -2.622 3.386 0.040 H5B UD6 57 UD6 H5BA H5BA H 0 0 N N N -20.135 -14.546 45.585 -3.115 2.034 1.088 H5BA UD6 58 UD6 "H6'" "H6'" H 0 1 N N N -19.926 -20.147 51.083 4.068 -4.715 -0.907 "H6'" UD6 59 UD6 "H6'A" "H6'A" H 0 0 N N N -19.084 -20.799 49.627 5.326 -4.368 0.304 "H6'A" UD6 60 UD6 "HO6'" "HO6'" H 0 0 N N N -18.585 -21.980 51.560 3.342 -5.242 1.307 "HO6'" UD6 61 UD6 "H8'" "H8'" H 0 1 N N N -17.560 -11.500 50.983 6.679 4.050 0.931 "H8'" UD6 62 UD6 "H8'A" "H8'A" H 0 0 N N N -15.900 -12.180 50.903 6.881 3.967 -0.836 "H8'A" UD6 63 UD6 "H8'B" "H8'B" H 0 0 N N N -16.989 -12.299 49.479 5.250 4.063 -0.130 "H8'B" UD6 64 UD6 "H9'" "H9'" H 0 1 N N N -15.791 -14.730 51.025 6.243 1.581 -1.987 "H9'" UD6 65 UD6 "H9'A" "H9'A" H 0 0 N N N -16.934 -14.850 49.589 4.611 1.677 -1.281 "H9'A" UD6 66 UD6 HN3 HN3 H 0 1 N N N -27.114 -16.333 40.813 -6.087 -2.482 2.266 HN3 UD6 67 # # 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 UD6 C2 N1 SING N N 1 UD6 N1 C6 SING N N 2 UD6 N1 C1B SING N N 3 UD6 N3 C2 SING N N 4 UD6 O2 C2 DOUB N N 5 UD6 N3 C4 SING N N 6 UD6 O4 C4 DOUB N N 7 UD6 C4 C5 SING N N 8 UD6 C5 C6 DOUB N N 9 UD6 C5 H5 SING N N 10 UD6 C6 H6 SING N N 11 UD6 O2A PA DOUB N N 12 UD6 O5B PA SING N N 13 UD6 PA O1A SING N N 14 UD6 PA O3A SING N N 15 UD6 O3A PB SING N N 16 UD6 O1B PB DOUB N N 17 UD6 PB "O1'" SING N N 18 UD6 PB O2B SING N N 19 UD6 "O1'" "C1'" SING N N 20 UD6 "C1'" "O5'" SING N N 21 UD6 "C1'" "C2'" SING N N 22 UD6 "C1'" "H1'" SING N N 23 UD6 O1A HO1A SING N N 24 UD6 O4B C1B SING N N 25 UD6 C1B C2B SING N N 26 UD6 C1B H1B SING N N 27 UD6 "C3'" "C2'" SING N N 28 UD6 "C9'" "C2'" SING N N 29 UD6 "C2'" "H2'" SING N N 30 UD6 C2B "O2'" SING N N 31 UD6 "O2'" "HO2'" SING N N 32 UD6 C2B C3B SING N N 33 UD6 C2B H2B SING N N 34 UD6 O2B HO2B SING N N 35 UD6 "C3'" "C4'" SING N N 36 UD6 "C3'" "O3'" SING N N 37 UD6 "C3'" "H3'" SING N N 38 UD6 "O3'" "HO3'" SING N N 39 UD6 C4B C3B SING N N 40 UD6 O3B C3B SING N N 41 UD6 C3B H3B SING N N 42 UD6 O3B HO3B SING N N 43 UD6 "C5'" "C4'" SING N N 44 UD6 "C4'" "O4'" SING N N 45 UD6 "C4'" "H4'" SING N N 46 UD6 "O4'" "HO4'" SING N N 47 UD6 O4B C4B SING N N 48 UD6 C4B C5B SING N N 49 UD6 C4B H4B SING N N 50 UD6 "C5'" "C6'" SING N N 51 UD6 "C5'" "O5'" SING N N 52 UD6 "C5'" "H5'" SING N N 53 UD6 C5B O5B SING N N 54 UD6 C5B H5B SING N N 55 UD6 C5B H5BA SING N N 56 UD6 "C6'" "O6'" SING N N 57 UD6 "C6'" "H6'" SING N N 58 UD6 "C6'" "H6'A" SING N N 59 UD6 "O6'" "HO6'" SING N N 60 UD6 "C8'" "C7'" SING N N 61 UD6 "C9'" "C7'" SING N N 62 UD6 "C7'" "O7'" DOUB N N 63 UD6 "C8'" "H8'" SING N N 64 UD6 "C8'" "H8'A" SING N N 65 UD6 "C8'" "H8'B" SING N N 66 UD6 "C9'" "H9'" SING N N 67 UD6 "C9'" "H9'A" SING N N 68 UD6 N3 HN3 SING N N 69 # # 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 UD6 SMILES ACDLabs 12.01 "O=C1C=CN(C(=O)N1)C2OC(C(O)C2O)COP(=O)(OP(=O)(OC3OC(C(O)C(O)C3CC(=O)C)CO)O)O" UD6 SMILES_CANONICAL CACTVS 3.370 "CC(=O)C[C@@H]1[C@@H](O)[C@@H](O)[C@@H](CO)O[C@@H]1O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O" UD6 SMILES CACTVS 3.370 "CC(=O)C[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O" UD6 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "CC(=O)C[C@@H]1[C@H]([C@H]([C@H](O[C@@H]1OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)CO)O)O" UD6 SMILES "OpenEye OEToolkits" 1.7.2 "CC(=O)CC1C(C(C(OC1OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)CO)O)O" UD6 InChI InChI 1.03 "InChI=1S/C18H28N2O17P2/c1-7(22)4-8-12(24)13(25)9(5-21)35-17(8)36-39(31,32)37-38(29,30)33-6-10-14(26)15(27)16(34-10)20-3-2-11(23)19-18(20)28/h2-3,8-10,12-17,21,24-27H,4-6H2,1H3,(H,29,30)(H,31,32)(H,19,23,28)/t8-,9-,10-,12-,13+,14-,15-,16-,17-/m1/s1" UD6 InChIKey InChI 1.03 ODPRJDNNGDXFOQ-YIUJVFLPSA-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 UD6 "SYSTEMATIC NAME" ACDLabs 12.01 "(2R,3R,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-(2-oxopropyl)tetrahydro-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)" UD6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "[[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4R,5R,6R)-6-(hydroxymethyl)-4,5-bis(oxidanyl)-3-(2-oxidanylidenepropyl)oxan-2-yl] 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 UD6 "Create component" 2011-05-11 RCSB UD6 "Modify descriptor" 2011-06-04 RCSB UD6 "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id UD6 _pdbx_chem_comp_synonyms.name UDP-2-ketoGlc _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##