data_UDX # _chem_comp.id UDX _chem_comp.name "URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C14 H22 N2 O16 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms UDP-ALPHA-D-XYLOPYRANOSE _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-12-13 _chem_comp.pdbx_modified_date 2021-03-01 _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 536.276 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UDX _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1DLI _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 UDX "C1'" "C1'" C 0 1 N N R -16.704 14.729 55.547 -0.186 -0.590 5.370 "C1'" UDX 1 UDX "C2'" "C2'" C 0 1 N N R -17.756 14.850 54.469 -0.246 0.226 6.663 "C2'" UDX 2 UDX "O2'" "O2'" O 0 1 N N N -17.668 16.155 53.934 -1.366 1.113 6.616 "O2'" UDX 3 UDX "C3'" "C3'" C 0 1 N N S -19.160 14.623 55.062 1.047 1.037 6.804 "C3'" UDX 4 UDX "O3'" "O3'" O 0 1 N N N -20.147 14.667 54.040 1.068 1.689 8.075 "O3'" UDX 5 UDX "C4'" "C4'" C 0 1 N N R -19.182 13.257 55.697 2.239 0.081 6.688 "C4'" UDX 6 UDX "O4'" "O4'" O 0 1 N N N -20.488 12.974 56.189 3.454 0.832 6.665 "O4'" UDX 7 UDX "C5'" "C5'" C 0 1 N N N -18.150 13.244 56.818 2.111 -0.725 5.394 "C5'" UDX 8 UDX "O5'" "O5'" O 0 1 N N N -16.842 13.506 56.269 0.912 -1.497 5.423 "O5'" UDX 9 UDX PB PB P 0 1 N N S -15.543 16.266 57.292 -0.739 -0.407 2.999 PB UDX 10 UDX O1B O1B O 0 1 N N N -14.624 15.114 57.402 -2.174 -0.611 3.299 O1B UDX 11 UDX O2B O2B O 0 1 N N N -16.106 16.883 58.529 -0.044 -1.830 2.707 O2B UDX 12 UDX O3B O3B O 0 1 N N N -16.769 15.850 56.371 -0.021 0.292 4.259 O3B UDX 13 UDX O3A O3A O 0 1 N N N -14.807 17.451 56.530 -0.591 0.537 1.704 O3A UDX 14 UDX PA PA P 0 1 N N R -14.523 17.870 55.021 -1.327 -0.219 0.488 PA UDX 15 UDX O1A O1A O 0 1 N N N -14.778 19.330 54.983 -2.752 -0.426 0.827 O1A UDX 16 UDX O2A O2A O 0 1 N N N -15.264 16.969 54.124 -0.622 -1.645 0.239 O2A UDX 17 UDX O5D O5* O 0 1 N N N -12.954 17.628 54.826 -1.217 0.674 -0.845 O5D UDX 18 UDX C5D C5* C 0 1 N N N -12.403 16.317 54.909 -1.885 -0.046 -1.882 C5D UDX 19 UDX C4D C4* C 0 1 N N R -10.889 16.375 54.817 -1.816 0.752 -3.185 C4D UDX 20 UDX O4D O4* O 0 1 N N N -10.505 16.734 53.457 -0.446 0.925 -3.581 O4D UDX 21 UDX C3D C3* C 0 1 N N S -10.336 17.459 55.732 -2.528 -0.020 -4.312 C3D UDX 22 UDX O3D O3* O 0 1 N N N -9.053 17.031 56.212 -3.617 0.739 -4.839 O3D UDX 23 UDX C2D C2* C 0 1 N N R -10.174 18.654 54.803 -1.428 -0.213 -5.389 C2D UDX 24 UDX O2D O2* O 0 1 N N N -9.117 19.488 55.229 -1.959 -0.012 -6.700 O2D UDX 25 UDX C1D C1* C 0 1 N N R -9.773 17.985 53.505 -0.418 0.904 -5.024 C1D UDX 26 UDX N1 N1 N 0 1 N N N -10.084 18.893 52.413 0.923 0.569 -5.509 N1 UDX 27 UDX C6 C6 C 0 1 N N N -11.380 19.132 52.068 1.584 1.443 -6.329 C6 UDX 28 UDX C2 C2 C 0 1 N N N -9.048 19.467 51.754 1.495 -0.590 -5.140 C2 UDX 29 UDX O2 O2 O 0 1 N N N -7.880 19.268 52.071 0.889 -1.352 -4.411 O2 UDX 30 UDX N3 N3 N 0 1 N N N -9.418 20.295 50.715 2.724 -0.924 -5.575 N3 UDX 31 UDX C4 C4 C 0 1 N N N -10.709 20.581 50.316 3.409 -0.091 -6.384 C4 UDX 32 UDX O4 O4 O 0 1 N N N -10.931 21.356 49.395 4.523 -0.390 -6.774 O4 UDX 33 UDX C5 C5 C 0 1 N N N -11.711 19.933 51.076 2.820 1.135 -6.776 C5 UDX 34 UDX "H1'" "H1'" H 0 1 N N N -15.690 14.695 55.083 -1.114 -1.151 5.253 "H1'" UDX 35 UDX "H2'1" "1H2'" H 0 0 N N N -17.587 14.083 53.676 -0.348 -0.445 7.515 "H2'1" UDX 36 UDX "HO'2" "2HO'" H 0 0 N N N -18.329 16.231 53.256 -2.155 0.562 6.522 "HO'2" UDX 37 UDX "H3'1" "1H3'" H 0 0 N N N -19.381 15.420 55.809 1.100 1.782 6.010 "H3'1" UDX 38 UDX "HO'3" "3HO'" H 0 0 N N N -21.012 14.527 54.405 1.897 2.185 8.121 "HO'3" UDX 39 UDX "H4'1" "1H4'" H 0 0 N N N -18.927 12.467 54.952 2.246 -0.597 7.542 "H4'1" UDX 40 UDX "HO'4" "4HO'" H 0 0 N N N -20.501 12.112 56.589 4.177 0.194 6.589 "HO'4" UDX 41 UDX "H5'1" "1H5'" H 0 0 N N N -18.411 13.950 57.640 2.082 -0.043 4.544 "H5'1" UDX 42 UDX "H5'2" "2H5'" H 0 0 N N N -18.178 12.297 57.406 2.968 -1.390 5.295 "H5'2" UDX 43 UDX HOB2 2HOB H 0 0 N N N -16.696 17.623 58.458 0.886 -1.652 2.516 HOB2 UDX 44 UDX HOA2 2HOA H 0 0 N N N -15.094 17.219 53.223 0.302 -1.465 0.021 HOA2 UDX 45 UDX H5A1 1H5* H 0 0 N N N -12.743 15.780 55.824 -1.400 -1.012 -2.023 H5A1 UDX 46 UDX H5A2 2H5* H 0 0 N N N -12.840 15.633 54.144 -2.928 -0.199 -1.604 H5A2 UDX 47 UDX H4A1 1H4* H 0 0 N N N -10.486 15.377 55.111 -2.288 1.725 -3.048 H4A1 UDX 48 UDX H3A1 1H3* H 0 0 N N N -10.977 17.685 56.615 -2.879 -0.986 -3.948 H3A1 UDX 49 UDX HOA3 3HO* H 0 0 N N N -8.707 17.707 56.782 -3.981 0.231 -5.577 HOA3 UDX 50 UDX H2A1 1H2* H 0 0 N N N -11.085 19.293 54.747 -0.967 -1.197 -5.304 H2A1 UDX 51 UDX HOC2 2HO* H 0 0 N N N -9.015 20.233 54.649 -2.577 -0.737 -6.865 HOC2 UDX 52 UDX "H1'1" 1H1* H 0 0 N N N -8.684 17.759 53.424 -0.743 1.862 -5.429 "H1'1" UDX 53 UDX H61 1H6 H 0 1 N N N -12.204 18.651 52.620 1.119 2.374 -6.618 H61 UDX 54 UDX HN3 HN3 H 0 1 N N N -8.663 20.738 50.190 3.120 -1.767 -5.302 HN3 UDX 55 UDX H51 1H5 H 0 1 N N N -12.790 20.056 50.888 3.353 1.815 -7.424 H51 UDX 56 # # 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 UDX "C1'" "C2'" SING N N 1 UDX "C1'" "O5'" SING N N 2 UDX "C1'" O3B SING N N 3 UDX "C1'" "H1'" SING N N 4 UDX "C2'" "O2'" SING N N 5 UDX "C2'" "C3'" SING N N 6 UDX "C2'" "H2'1" SING N N 7 UDX "O2'" "HO'2" SING N N 8 UDX "C3'" "O3'" SING N N 9 UDX "C3'" "C4'" SING N N 10 UDX "C3'" "H3'1" SING N N 11 UDX "O3'" "HO'3" SING N N 12 UDX "C4'" "O4'" SING N N 13 UDX "C4'" "C5'" SING N N 14 UDX "C4'" "H4'1" SING N N 15 UDX "O4'" "HO'4" SING N N 16 UDX "C5'" "O5'" SING N N 17 UDX "C5'" "H5'1" SING N N 18 UDX "C5'" "H5'2" SING N N 19 UDX PB O1B DOUB N N 20 UDX PB O2B SING N N 21 UDX PB O3B SING N N 22 UDX PB O3A SING N N 23 UDX O2B HOB2 SING N N 24 UDX O3A PA SING N N 25 UDX PA O1A DOUB N N 26 UDX PA O2A SING N N 27 UDX PA O5D SING N N 28 UDX O2A HOA2 SING N N 29 UDX O5D C5D SING N N 30 UDX C5D C4D SING N N 31 UDX C5D H5A1 SING N N 32 UDX C5D H5A2 SING N N 33 UDX C4D O4D SING N N 34 UDX C4D C3D SING N N 35 UDX C4D H4A1 SING N N 36 UDX O4D C1D SING N N 37 UDX C3D O3D SING N N 38 UDX C3D C2D SING N N 39 UDX C3D H3A1 SING N N 40 UDX O3D HOA3 SING N N 41 UDX C2D O2D SING N N 42 UDX C2D C1D SING N N 43 UDX C2D H2A1 SING N N 44 UDX O2D HOC2 SING N N 45 UDX C1D N1 SING N N 46 UDX C1D "H1'1" SING N N 47 UDX N1 C6 SING N N 48 UDX N1 C2 SING N N 49 UDX C6 C5 DOUB N N 50 UDX C6 H61 SING N N 51 UDX C2 O2 DOUB N N 52 UDX C2 N3 SING N N 53 UDX N3 C4 SING N N 54 UDX N3 HN3 SING N N 55 UDX C4 O4 DOUB N N 56 UDX C4 C5 SING N N 57 UDX C5 H51 SING N N 58 # # 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 UDX SMILES ACDLabs 10.04 "O=P(OC1OCC(O)C(O)C1O)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O" UDX SMILES_CANONICAL CACTVS 3.341 "O[C@@H]1CO[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](O)[C@H]1O" UDX SMILES CACTVS 3.341 "O[CH]1CO[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](O)[CH]1O" UDX SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[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)O)O)O" UDX SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)O)O)O" UDX InChI InChI 1.03 "InChI=1S/C14H22N2O16P2/c17-5-3-28-13(11(22)8(5)19)31-34(26,27)32-33(24,25)29-4-6-9(20)10(21)12(30-6)16-2-1-7(18)15-14(16)23/h1-2,5-6,8-13,17,19-22H,3-4H2,(H,24,25)(H,26,27)(H,15,18,23)/t5-,6-,8+,9-,10-,11-,12-,13-/m1/s1" UDX InChIKey InChI 1.03 DQQDLYVHOTZLOR-OCIMBMBZSA-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 UDX "SYSTEMATIC NAME" ACDLabs 10.04 "[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4S,5R)-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)" UDX "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] [(2R,3R,4S,5R)-3,4,5-trihydroxyoxan-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 UDX "Create component" 1999-12-13 RCSB UDX "Modify descriptor" 2011-06-04 RCSB UDX "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id UDX _pdbx_chem_comp_synonyms.name UDP-ALPHA-D-XYLOPYRANOSE _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##