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 #