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                    2008-10-14 
_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 InChI            InChI                1.02b 
InChI=1/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/f/h15,24,26H 
UDX InChIKey         InChI                1.02b DQQDLYVHOTZLOR-ZFROKUESDS 
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 
# 
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"                                         
# 
