data_CXY
# 
_chem_comp.id                                    CXY 
_chem_comp.name                                  "CYTIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C14 H23 N3 O15 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2005-01-04 
_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                        535.291 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     CXY 
_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        1WVG 
_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 
CXY O1B    O1B    O 0 1 N N N 63.438 19.257 53.266 3.064  -1.471 -1.372 O1B    CXY 1  
CXY PB     PB     P 0 1 N N S 63.359 20.723 52.889 2.907  -0.267 -0.526 PB     CXY 2  
CXY O2B    O2B    O 0 1 N N N 62.352 21.510 53.686 2.491  0.986  -1.448 O2B    CXY 3  
CXY "O1'"  "O1'"  O 0 1 N N N 63.027 20.856 51.284 4.299  0.053  0.217  "O1'"  CXY 4  
CXY O3A    O3A    O 0 1 N N N 64.844 21.069 53.140 1.760  -0.528 0.573  O3A    CXY 5  
CXY PA     PA     P 0 1 N N S 65.577 21.990 54.290 0.582  -1.339 -0.167 PA     CXY 6  
CXY O1A    O1A    O 0 1 N N N 64.972 23.337 54.357 0.981  -2.896 -0.263 O1A    CXY 7  
CXY O2A    O2A    O 0 1 N N N 67.018 21.981 53.921 0.389  -0.794 -1.529 O2A    CXY 8  
CXY O5D    O5*    O 0 1 N N N 65.229 21.178 55.615 -0.784 -1.186 0.671  O5D    CXY 9  
CXY C5D    C5*    C 0 1 N N N 65.948 19.963 55.867 -1.810 -1.823 -0.092 C5D    CXY 10 
CXY C4D    C4*    C 0 1 N N R 65.745 19.577 57.312 -3.142 -1.713 0.653  C4D    CXY 11 
CXY O4D    O4*    O 0 1 N N N 66.741 20.277 58.098 -3.569 -0.334 0.718  O4D    CXY 12 
CXY C3D    C3*    C 0 1 N N S 64.380 19.859 57.939 -4.260 -2.436 -0.130 C3D    CXY 13 
CXY O3D    O3*    O 0 1 N N N 63.923 18.879 58.939 -4.481 -3.743 0.404  O3D    CXY 14 
CXY C2D    C2*    C 0 1 N N R 64.704 21.227 58.566 -5.507 -1.545 0.085  C2D    CXY 15 
CXY O2D    O2*    O 0 1 N N N 63.768 21.482 59.617 -6.535 -2.276 0.755  O2D    CXY 16 
CXY C1D    C1*    C 0 1 N N R 66.081 20.952 59.126 -4.991 -0.388 0.969  C1D    CXY 17 
CXY N1     N1     N 0 1 N N N 66.845 22.164 59.437 -5.625 0.874  0.579  N1     CXY 18 
CXY C6     C6     C 0 1 N N N 67.159 23.068 58.435 -6.427 1.531  1.464  C6     CXY 19 
CXY C5     C5     C 0 1 N N N 67.857 24.154 58.656 -7.003 2.699  1.095  C5     CXY 20 
CXY C4     C4     C 0 1 N N N 68.320 24.482 59.960 -6.765 3.197  -0.203 C4     CXY 21 
CXY N3     N3     N 0 1 N N N 67.987 23.525 60.933 -5.978 2.523  -1.030 N3     CXY 22 
CXY C2     C2     C 0 1 N N N 67.254 22.366 60.741 -5.414 1.377  -0.650 C2     CXY 23 
CXY N4     N4     N 0 1 N N N 68.949 25.488 60.269 -7.342 4.379  -0.606 N4     CXY 24 
CXY O2     O2     O 0 1 N N N 66.977 21.579 61.653 -4.694 0.776  -1.429 O2     CXY 25 
CXY "C1'"  "C1'"  C 0 1 N N R 64.180 20.800 50.462 5.296  0.157  -0.802 "C1'"  CXY 26 
CXY "C2'"  "C2'"  C 0 1 N N R 63.954 21.801 49.356 6.648  -0.285 -0.238 "C2'"  CXY 27 
CXY "C3'"  "C3'"  C 0 1 N N S 62.715 21.346 48.609 7.004  0.600  0.961  "C3'"  CXY 28 
CXY "C4'"  "C4'"  C 0 1 N N R 62.924 19.942 48.042 6.928  2.068  0.525  "C4'"  CXY 29 
CXY "C5'"  "C5'"  C 0 1 N N N 63.290 18.983 49.167 5.555  2.333  -0.096 "C5'"  CXY 30 
CXY "O2'"  "O2'"  O 0 1 N N N 63.714 23.127 49.874 6.569  -1.648 0.182  "O2'"  CXY 31 
CXY "O3'"  "O3'"  O 0 1 N N N 62.487 22.220 47.488 8.328  0.300  1.406  "O3'"  CXY 32 
CXY "O4'"  "O4'"  O 0 1 N N N 61.748 19.508 47.362 7.111  2.915  1.661  "O4'"  CXY 33 
CXY "O5'"  "O5'"  O 0 1 N N N 64.416 19.471 49.903 5.379  1.510  -1.247 "O5'"  CXY 34 
CXY H2B    H2B    H 0 1 N N N 62.303 22.429 53.450 2.399  1.748  -0.860 H2B    CXY 35 
CXY H1A    H1A    H 0 1 N N N 65.395 23.869 55.021 1.098  -3.211 0.643  H1A    CXY 36 
CXY "H5'1" 1H5*   H 0 0 N N N 67.026 20.039 55.592 -1.559 -2.874 -0.233 "H5'1" CXY 37 
CXY "H5'2" 2H5*   H 0 0 N N N 65.667 19.146 55.162 -1.896 -1.336 -1.063 "H5'2" CXY 38 
CXY H4D    H4*    H 0 1 N N N 65.831 18.465 57.318 -3.051 -2.129 1.656  H4D    CXY 39 
CXY H3D    H3*    H 0 1 N N N 63.532 19.818 57.216 -4.009 -2.494 -1.189 H3D    CXY 40 
CXY H4     H4     H 0 1 N N N 63.075 19.054 59.329 -5.186 -4.144 -0.122 H4     CXY 41 
CXY H2D    H2*    H 0 1 N N N 64.659 22.105 57.880 -5.871 -1.162 -0.869 H2D    CXY 42 
CXY H7     H7     H 0 1 N N N 63.968 22.326 60.004 -6.771 -3.017 0.181  H7     CXY 43 
CXY H1D    H1*    H 0 1 N N N 65.992 20.390 60.085 -5.183 -0.600 2.021  H1D    CXY 44 
CXY H6     H6     H 0 1 N N N 66.832 22.913 57.393 -6.597 1.126  2.451  H6     CXY 45 
CXY H5     H5     H 0 1 N N N 68.050 24.777 57.766 -7.641 3.236  1.780  H5     CXY 46 
CXY HN41   1HN4   H 0 0 N N N 68.395 26.283 59.952 -7.174 4.721  -1.498 HN41   CXY 47 
CXY HN42   2HN4   H 0 0 N N N 69.281 25.723 61.204 -7.921 4.868  0.000  HN42   CXY 48 
CXY "H1'"  "H1'"  H 0 1 N N N 65.087 21.034 51.068 5.026  -0.485 -1.641 "H1'"  CXY 49 
CXY "H2'"  "H2'"  H 0 1 N N N 64.858 21.850 48.706 7.415  -0.183 -1.006 "H2'"  CXY 50 
CXY "H3'"  "H3'"  H 0 1 N N N 61.856 21.358 49.319 6.296  0.422  1.770  "H3'"  CXY 51 
CXY "H4'"  "H4'"  H 0 1 N N N 63.762 19.960 47.307 7.707  2.271  -0.210 "H4'"  CXY 52 
CXY H5D    "1H5'" H 0 1 N N N 63.461 17.948 48.788 5.485  3.382  -0.386 H5D    CXY 53 
CXY H5B    "2H5'" H 0 1 N N N 62.420 18.776 49.833 4.777  2.108  0.633  H5B    CXY 54 
CXY H3     H3     H 0 1 N N N 63.572 23.757 49.178 6.343  -2.169 -0.602 H3     CXY 55 
CXY H2     H2     H 0 1 N N N 61.711 21.935 47.020 8.512  0.888  2.152  H2     CXY 56 
CXY H1     H1     H 0 1 N N N 61.878 18.635 47.010 7.049  3.827  1.343  H1     CXY 57 
# 
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 
CXY O1B   PB     DOUB N N 1  
CXY PB    O2B    SING N N 2  
CXY PB    "O1'"  SING N N 3  
CXY PB    O3A    SING N N 4  
CXY O2B   H2B    SING N N 5  
CXY "O1'" "C1'"  SING N N 6  
CXY O3A   PA     SING N N 7  
CXY PA    O1A    SING N N 8  
CXY PA    O2A    DOUB N N 9  
CXY PA    O5D    SING N N 10 
CXY O1A   H1A    SING N N 11 
CXY O5D   C5D    SING N N 12 
CXY C5D   C4D    SING N N 13 
CXY C5D   "H5'1" SING N N 14 
CXY C5D   "H5'2" SING N N 15 
CXY C4D   O4D    SING N N 16 
CXY C4D   C3D    SING N N 17 
CXY C4D   H4D    SING N N 18 
CXY O4D   C1D    SING N N 19 
CXY C3D   O3D    SING N N 20 
CXY C3D   C2D    SING N N 21 
CXY C3D   H3D    SING N N 22 
CXY O3D   H4     SING N N 23 
CXY C2D   O2D    SING N N 24 
CXY C2D   C1D    SING N N 25 
CXY C2D   H2D    SING N N 26 
CXY O2D   H7     SING N N 27 
CXY C1D   N1     SING N N 28 
CXY C1D   H1D    SING N N 29 
CXY N1    C6     SING N N 30 
CXY N1    C2     SING N N 31 
CXY C6    C5     DOUB N N 32 
CXY C6    H6     SING N N 33 
CXY C5    C4     SING N N 34 
CXY C5    H5     SING N N 35 
CXY C4    N3     DOUB N N 36 
CXY C4    N4     SING N N 37 
CXY N3    C2     SING N N 38 
CXY C2    O2     DOUB N N 39 
CXY N4    HN41   SING N N 40 
CXY N4    HN42   SING N N 41 
CXY "C1'" "C2'"  SING N N 42 
CXY "C1'" "O5'"  SING N N 43 
CXY "C1'" "H1'"  SING N N 44 
CXY "C2'" "C3'"  SING N N 45 
CXY "C2'" "O2'"  SING N N 46 
CXY "C2'" "H2'"  SING N N 47 
CXY "C3'" "C4'"  SING N N 48 
CXY "C3'" "O3'"  SING N N 49 
CXY "C3'" "H3'"  SING N N 50 
CXY "C4'" "C5'"  SING N N 51 
CXY "C4'" "O4'"  SING N N 52 
CXY "C4'" "H4'"  SING N N 53 
CXY "C5'" "O5'"  SING N N 54 
CXY "C5'" H5D    SING N N 55 
CXY "C5'" H5B    SING N N 56 
CXY "O2'" H3     SING N N 57 
CXY "O3'" H2     SING N N 58 
CXY "O4'" H1     SING N N 59 
# 
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 
CXY SMILES           ACDLabs              10.04 O=P(OC1OCC(O)C(O)C1O)(O)OP(=O)(O)OCC3OC(N2C=CC(=NC2=O)N)C(O)C3O 
CXY InChI            InChI                1.02b 
InChI=1/C14H23N3O15P2/c15-7-1-2-17(14(23)16-7)12-10(21)9(20)6(30-12)4-29-33(24,25)32-34(26,27)31-13-11(22)8(19)5(18)3-28-13/h1-2,5-6,8-13,18-22H,3-4H2,(H,24,25)(H,26,27)(H2,15,16,23)/t5-,6-,8+,9-,10-,11-,12-,13-/m1/s1/f/h24,26H,15H2 
CXY InChIKey         InChI                1.02b NWSKPSPTJOAICE-AAIIRGSFDL 
CXY SMILES_CANONICAL CACTVS               3.341 NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)O[C@H]3OC[C@@H](O)[C@H](O)[C@H]3O)[C@@H](O)[C@H]2O 
CXY SMILES           CACTVS               3.341 NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]3OC[CH](O)[CH](O)[CH]3O)[CH](O)[CH]2O 
CXY 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(=NC3=O)N)O)O)O)O)O 
CXY SMILES           "OpenEye OEToolkits" 1.5.0 C1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=NC3=O)N)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 
CXY "SYSTEMATIC NAME" ACDLabs              10.04 "[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-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)" 
CXY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[(2R,3S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] [(2R,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl] hydrogen phosphate"                            
# 
