data_TDX
# 
_chem_comp.id                                    TDX 
_chem_comp.name                                  "THYMIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C15 H24 N2 O15 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2001-11-23 
_chem_comp.pdbx_modified_date                    2011-06-04 
_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                        534.303 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     TDX 
_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        1KEP 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
# 
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 
TDX O4     O4     O 0 1 N N N -20.770 -11.286 72.139 3.417  -1.244 -7.574 O4     TDX 1  
TDX C4     C4     C 0 1 N N N -20.925 -10.052 72.244 2.512  -0.683 -6.982 C4     TDX 2  
TDX N3     N3     N 0 1 N N N -21.942 -9.520  72.946 1.638  -1.396 -6.244 N3     TDX 3  
TDX C2     C2     C 0 1 N N N -22.093 -8.214  73.042 0.638  -0.775 -5.591 C2     TDX 4  
TDX O2     O2     O 0 1 N N N -23.080 -7.789  73.721 -0.145 -1.431 -4.932 O2     TDX 5  
TDX C5     C5     C 0 1 N N N -20.005 -9.162  71.558 2.374  0.723  -7.057 C5     TDX 6  
TDX C5M    C5M    C 0 1 N N N -18.858 -9.722  70.738 3.340  1.543  -7.872 C5M    TDX 7  
TDX C6     C6     C 0 1 N N N -20.225 -7.828  71.652 1.362  1.320  -6.392 C6     TDX 8  
TDX N1     N1     N 0 1 N N N -21.234 -7.378  72.420 0.493  0.560  -5.657 N1     TDX 9  
TDX C1B    C1*    C 0 1 N N R -21.459 -5.943  72.500 -0.605 1.207  -4.935 C1B    TDX 10 
TDX C2B    C2*    C 0 1 N N N -20.243 -5.063  72.794 -1.955 0.657  -5.434 C2B    TDX 11 
TDX C3B    C3*    C 0 1 N N S -20.580 -3.791  72.001 -2.619 0.073  -4.164 C3B    TDX 12 
TDX O3B    O3*    O 0 1 N N N -21.390 -2.833  72.760 -4.015 0.379  -4.131 O3B    TDX 13 
TDX O4B    O4*    O 0 1 N N N -21.989 -5.542  71.219 -0.511 0.910  -3.532 O4B    TDX 14 
TDX C4B    C4*    C 0 1 N N R -21.433 -4.293  70.814 -1.864 0.815  -3.032 C4B    TDX 15 
TDX C5B    C5*    C 0 1 N N N -20.577 -4.457  69.570 -1.907 0.005  -1.734 C5B    TDX 16 
TDX O5B    O5*    O 0 1 N N N -19.416 -5.204  69.920 -1.204 0.710  -0.709 O5B    TDX 17 
TDX PA     PA     P 0 1 N N S -18.205 -5.389  68.872 -1.290 -0.193 0.619  PA     TDX 18 
TDX O1A    O1A    O 0 1 N N N -18.671 -6.235  67.713 -0.662 -1.509 0.362  O1A    TDX 19 
TDX O2A    O2A    O 0 1 N N N -17.031 -5.897  69.662 -2.833 -0.405 1.026  O2A    TDX 20 
TDX O3A    O3A    O 0 1 N N N -17.969 -3.955  68.184 -0.514 0.544  1.821  O3A    TDX 21 
TDX PB     PB     P 0 1 N N R -17.446 -2.563  68.844 -0.639 -0.410 3.112  PB     TDX 22 
TDX O1B    O1B    O 0 1 N N N -16.700 -2.712  70.140 -0.022 -1.722 2.816  O1B    TDX 23 
TDX O2B    O2B    O 0 1 N N N -18.600 -1.652  68.885 -2.193 -0.618 3.477  O2B    TDX 24 
TDX "O1'"  "O1'"  O 0 1 N N N -16.425 -2.104  67.685 0.118  0.270  4.358  "O1'"  TDX 25 
TDX "C1'"  "C1'"  C 0 1 N N R -16.783 -2.340  66.319 -0.027 -0.620 5.466  "C1'"  TDX 26 
TDX "O5'"  "O5'"  O 0 1 N N N -17.192 -1.108  65.753 1.061  -1.541 5.481  "O5'"  TDX 27 
TDX "C5'"  "C5'"  C 0 1 N N N -16.178 -0.077  65.824 2.268  -0.783 5.427  "C5'"  TDX 28 
TDX "C2'"  "C2'"  C 0 1 N N R -15.583 -2.864  65.548 -0.040 0.184  6.768  "C2'"  TDX 29 
TDX "O2'"  "O2'"  O 0 1 N N N -15.087 -4.055  66.149 -1.149 1.086  6.761  "O2'"  TDX 30 
TDX "C3'"  "C3'"  C 0 1 N N S -14.453 -1.824  65.540 1.264  0.978  6.879  "C3'"  TDX 31 
TDX "O3'"  "O3'"  O 0 1 N N N -13.326 -2.256  64.740 1.333  1.617  8.155  "O3'"  TDX 32 
TDX "C4'"  "C4'"  C 0 1 N N R -14.979 -0.500  64.998 2.441  0.008  6.725  "C4'"  TDX 33 
TDX "O4'"  "O4'"  O 0 1 N N N -13.982 0.520   65.058 3.666  0.742  6.678  "O4'"  TDX 34 
TDX H3     H3     H 0 1 N N N -22.616 -10.123 73.418 1.728  -2.360 -6.185 H3     TDX 35 
TDX H5M1   1H5M   H 0 0 N N N -19.278 -10.434 69.990 4.080  0.885  -8.329 H5M1   TDX 36 
TDX H5M2   2H5M   H 0 0 N N N -18.152 -9.039  70.211 2.797  2.076  -8.652 H5M2   TDX 37 
TDX H5M3   3H5M   H 0 0 N N N -18.263 -10.404 71.390 3.844  2.261  -7.225 H5M3   TDX 38 
TDX H6     H6     H 0 1 N N N -19.587 -7.113  71.107 1.238  2.392  -6.440 H6     TDX 39 
TDX H1B    H1*    H 0 1 N N N -22.136 -5.788  73.372 -0.564 2.286  -5.089 H1B    TDX 40 
TDX "H2'1" 1H2*   H 0 0 N N N -19.256 -5.523  72.556 -2.565 1.460  -5.848 "H2'1" TDX 41 
TDX "H2'2" 2H2*   H 0 0 N N N -20.023 -4.903  73.875 -1.798 -0.124 -6.176 "H2'2" TDX 42 
TDX H3B    H3*    H 0 1 N N N -19.640 -3.261  71.719 -2.457 -1.002 -4.100 H3B    TDX 43 
TDX "HO3'" *HO3   H 0 0 N N N -21.598 -2.046  72.270 -4.410 -0.035 -4.911 "HO3'" TDX 44 
TDX H4B    H4*    H 0 1 N N N -22.236 -3.564  70.556 -2.284 1.809  -2.877 H4B    TDX 45 
TDX "H5'1" 1H5*   H 0 0 N N N -20.331 -3.483  69.087 -2.944 -0.139 -1.431 "H5'1" TDX 46 
TDX "H5'2" 2H5*   H 0 0 N N N -21.138 -4.910  68.720 -1.437 -0.964 -1.896 "H5'2" TDX 47 
TDX H2A    H2A    H 0 1 N N N -16.317 -6.006  69.044 -3.203 0.473  1.185  H2A    TDX 48 
TDX H2B    H2B    H 0 1 N N N -18.295 -0.839  69.270 -2.557 0.258  3.662  H2B    TDX 49 
TDX "H1'"  "H1'"  H 0 1 N N N -17.603 -3.094  66.268 -0.964 -1.168 5.370  "H1'"  TDX 50 
TDX H5B    "1H5'" H 0 1 N N N -15.901 0.173   66.875 3.114  -1.459 5.299  H5B    TDX 51 
TDX H5D    "2H5'" H 0 1 N N N -16.569 0.923   65.522 2.226  -0.093 4.585  H5D    TDX 52 
TDX "H2'"  "H2'"  H 0 1 N N N -15.915 -3.073  64.504 -0.128 -0.494 7.616  "H2'"  TDX 53 
TDX "HO2'" "'HO2" H 0 0 N N N -14.337 -4.383  65.667 -1.948 0.546  6.690  "HO2'" TDX 54 
TDX "H3'"  "H3'"  H 0 1 N N N -14.101 -1.700  66.591 1.304  1.729  6.091  "H3'"  TDX 55 
TDX HO3A   "'HO3" H 0 0 N N N -12.627 -1.613  64.735 2.175  2.092  8.184  HO3A   TDX 56 
TDX "H4'"  "H4'"  H 0 1 N N N -15.265 -0.642  63.930 2.461  -0.678 7.572  "H4'"  TDX 57 
TDX "HO4'" "'HO4" H 0 0 N N N -13.231 0.255   64.540 4.376  0.095  6.574  "HO4'" TDX 58 
# 
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 
TDX O4    C4     DOUB N N 1  
TDX C4    N3     SING N N 2  
TDX C4    C5     SING N N 3  
TDX N3    C2     SING N N 4  
TDX N3    H3     SING N N 5  
TDX C2    O2     DOUB N N 6  
TDX C2    N1     SING N N 7  
TDX C5    C5M    SING N N 8  
TDX C5    C6     DOUB N N 9  
TDX C5M   H5M1   SING N N 10 
TDX C5M   H5M2   SING N N 11 
TDX C5M   H5M3   SING N N 12 
TDX C6    N1     SING N N 13 
TDX C6    H6     SING N N 14 
TDX N1    C1B    SING N N 15 
TDX C1B   C2B    SING N N 16 
TDX C1B   O4B    SING N N 17 
TDX C1B   H1B    SING N N 18 
TDX C2B   C3B    SING N N 19 
TDX C2B   "H2'1" SING N N 20 
TDX C2B   "H2'2" SING N N 21 
TDX C3B   O3B    SING N N 22 
TDX C3B   C4B    SING N N 23 
TDX C3B   H3B    SING N N 24 
TDX O3B   "HO3'" SING N N 25 
TDX O4B   C4B    SING N N 26 
TDX C4B   C5B    SING N N 27 
TDX C4B   H4B    SING N N 28 
TDX C5B   O5B    SING N N 29 
TDX C5B   "H5'1" SING N N 30 
TDX C5B   "H5'2" SING N N 31 
TDX O5B   PA     SING N N 32 
TDX PA    O1A    DOUB N N 33 
TDX PA    O2A    SING N N 34 
TDX PA    O3A    SING N N 35 
TDX O2A   H2A    SING N N 36 
TDX O3A   PB     SING N N 37 
TDX PB    O1B    DOUB N N 38 
TDX PB    O2B    SING N N 39 
TDX PB    "O1'"  SING N N 40 
TDX O2B   H2B    SING N N 41 
TDX "O1'" "C1'"  SING N N 42 
TDX "C1'" "O5'"  SING N N 43 
TDX "C1'" "C2'"  SING N N 44 
TDX "C1'" "H1'"  SING N N 45 
TDX "O5'" "C5'"  SING N N 46 
TDX "C5'" "C4'"  SING N N 47 
TDX "C5'" H5B    SING N N 48 
TDX "C5'" H5D    SING N N 49 
TDX "C2'" "O2'"  SING N N 50 
TDX "C2'" "C3'"  SING N N 51 
TDX "C2'" "H2'"  SING N N 52 
TDX "O2'" "HO2'" SING N N 53 
TDX "C3'" "O3'"  SING N N 54 
TDX "C3'" "C4'"  SING N N 55 
TDX "C3'" "H3'"  SING N N 56 
TDX "O3'" HO3A   SING N N 57 
TDX "C4'" "O4'"  SING N N 58 
TDX "C4'" "H4'"  SING N N 59 
TDX "O4'" "HO4'" SING N N 60 
# 
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 
TDX SMILES           ACDLabs              10.04 "O=P(OC1OCC(O)C(O)C1O)(O)OP(=O)(O)OCC3OC(N2C=C(C(=O)NC2=O)C)CC3O" 
TDX SMILES_CANONICAL CACTVS               3.341 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[C@H]3OC[C@@H](O)[C@H](O)[C@H]3O)O2)C(=O)NC1=O" 
TDX SMILES           CACTVS               3.341 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]3OC[CH](O)[CH](O)[CH]3O)O2)C(=O)NC1=O" 
TDX SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@@H](CO3)O)O)O)O" 
TDX SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(CO3)O)O)O)O" 
TDX InChI            InChI                1.03  
"InChI=1S/C15H24N2O15P2/c1-6-3-17(15(23)16-13(6)22)10-2-7(18)9(30-10)5-29-33(24,25)32-34(26,27)31-14-12(21)11(20)8(19)4-28-14/h3,7-12,14,18-21H,2,4-5H2,1H3,(H,24,25)(H,26,27)(H,16,22,23)/t7-,8+,9+,10+,11-,12+,14+/m0/s1" 
TDX InChIKey         InChI                1.03  AJUADKZRQSBUAK-KDGZBOQCSA-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 
TDX "SYSTEMATIC NAME" ACDLabs              10.04 "[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl (2R,3R,4S,5R)-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)" 
TDX "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl [hydroxy-[(2R,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy-phosphoryl] 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 
TDX "Create component"  2001-11-23 PDBJ 
TDX "Modify descriptor" 2011-06-04 RCSB 
# 
