data_PBT
# 
_chem_comp.id                                    PBT 
_chem_comp.name                                  "[3-HYDROXY-5-(5-METHYL-2,4-DIOXOTETRAHYDRO-1(2H)-PYRIMIDINYL)TETRAHYDRO-2-FURANYL]METHYL DIHYDROGEN PHOSPHATE" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H17 N2 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2001-10-04 
_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                        324.224 
_chem_comp.one_letter_code                       N 
_chem_comp.three_letter_code                     PBT 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        ? 
_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 
PBT P      P    P 0 1 N N N -1.362 -7.164 2.554  -3.968 -1.665 3.118  P      PBT 1  
PBT O1P    O1P  O 0 1 N N N -2.019 -7.318 3.870  -3.912 -2.311 1.636  O1P    PBT 2  
PBT O2P    O2P  O 0 1 N Y N ?      ?      ?      -4.901 -0.360 2.920  O2P    PBT 3  
PBT O3P    O3P  O 0 1 N Y N -0.680 -8.347 1.989  -4.406 -2.599 4.208  O3P    PBT 4  
PBT "O5'"  O5*  O 0 1 N N N -2.410 -6.632 1.455  -2.493 -1.028 3.315  "O5'"  PBT 5  
PBT "C5'"  C5*  C 0 1 N N N -3.831 -6.845 1.376  -2.005 -0.136 2.327  "C5'"  PBT 6  
PBT "C4'"  C4*  C 0 1 N N R -4.442 -6.310 0.081  -0.611 0.328  2.728  "C4'"  PBT 7  
PBT "O4'"  O4*  O 0 1 N N N -4.652 -4.857 0.165  0.247  -0.829 2.764  "O4'"  PBT 8  
PBT "C3'"  C3*  C 0 1 N N S -3.508 -6.528 -1.128 0.008  1.286  1.720  "C3'"  PBT 9  
PBT "O3'"  O3*  O 0 1 N N N -4.223 -6.976 -2.305 0.965  2.121  2.368  "O3'"  PBT 10 
PBT "C2'"  C2*  C 0 1 N N N -2.938 -5.074 -1.375 0.710  0.360  0.754  "C2'"  PBT 11 
PBT "C1'"  C1*  C 0 1 N N R -4.285 -4.325 -1.088 1.157  -0.778 1.657  "C1'"  PBT 12 
PBT N1     N1   N 0 1 N N N -4.399 -2.803 -1.131 1.164  -2.047 0.989  N1     PBT 13 
PBT C2     C2   C 0 1 N N N -5.677 -2.367 -1.652 2.326  -2.535 0.382  C2     PBT 14 
PBT O2     O2   O 0 1 N N N -6.663 -3.106 -1.767 3.415  -1.956 0.400  O2     PBT 15 
PBT N3     N3   N 0 1 N N N -5.792 -1.021 -2.078 2.173  -3.767 -0.267 N3     PBT 16 
PBT C4     C4   C 0 1 N N N -4.823 0.006  -1.996 1.083  -4.633 -0.213 C4     PBT 17 
PBT O4     O4   O 0 1 N N N -5.092 1.165  -2.325 1.030  -5.682 -0.852 O4     PBT 18 
PBT C5     C5   C 0 1 N N R -3.635 -0.302 -1.106 0.011  -4.203 0.774  C5     PBT 19 
PBT C5M    C5M  C 0 1 N N N -2.346 0.476  -1.445 -1.324 -4.878 0.481  C5M    PBT 20 
PBT C6     C6   C 0 1 N N N -3.309 -1.865 -0.929 -0.124 -2.687 0.747  C6     PBT 21 
PBT H1P    H1P  H 0 1 N N N -1.359 -7.351 4.552  -4.684 -2.823 1.313  H1P    PBT 22 
PBT H2P    H2P  H 0 1 N N N 0.422  0.099  -0.845 -5.874 -0.475 2.871  H2P    PBT 23 
PBT "H5'1" 1H5* H 0 0 N N N -4.295 -6.301 2.212  -1.971 -0.654 1.366  "H5'1" PBT 24 
PBT "H5'2" 2H5* H 0 0 N N N -4.022 -7.927 1.428  -2.683 0.718  2.254  "H5'2" PBT 25 
PBT "H4'"  H4*  H 0 1 N N N -5.388 -6.855 -0.052 -0.644 0.753  3.736  "H4'"  PBT 26 
PBT "H3'"  H3*  H 0 1 N N N -2.749 -7.301 -0.937 -0.722 1.941  1.236  "H3'"  PBT 27 
PBT HA     HA   H 0 1 N N N -5.145 -7.074 -2.098 1.332  2.718  1.693  HA     PBT 28 
PBT "H2'1" 1H2* H 0 0 N N N -2.458 -4.884 -2.346 -0.003 -0.001 0.003  "H2'1" PBT 29 
PBT "H2'2" 2H2* H 0 0 N N N -2.111 -4.792 -0.706 1.556  0.818  0.232  "H2'2" PBT 30 
PBT "H1'"  H1*  H 0 1 N N N -4.949 -4.505 -1.946 2.163  -0.604 2.054  "H1'"  PBT 31 
PBT H3     H3   H 0 1 N N N -6.667 -0.765 -2.488 2.965  -4.080 -0.822 H3     PBT 32 
PBT H5     H5   H 0 1 N N N -3.990 0.069  -0.133 0.354  -4.523 1.766  H5     PBT 33 
PBT H5M1   1H5M H 0 0 N N N -1.941 0.115  -2.402 -1.965 -4.861 1.367  H5M1   PBT 34 
PBT H5M2   2H5M H 0 0 N N N -1.603 0.319  -0.649 -1.845 -4.365 -0.332 H5M2   PBT 35 
PBT H5M3   3H5M H 0 0 N N N -2.575 1.549  -1.526 -1.170 -5.921 0.188  H5M3   PBT 36 
PBT H6C1   1H6C H 0 0 N N N -2.582 -2.097 -1.721 -0.484 -2.336 -0.228 H6C1   PBT 37 
PBT H6C2   2H6C H 0 0 N N N -2.956 -2.003 0.104  -0.829 -2.358 1.519  H6C2   PBT 38 
# 
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 
PBT P     O1P    SING N N 1  
PBT P     O2P    SING N N 2  
PBT P     O3P    DOUB N N 3  
PBT P     "O5'"  SING N N 4  
PBT O1P   H1P    SING N N 5  
PBT O2P   H2P    SING N N 6  
PBT "O5'" "C5'"  SING N N 7  
PBT "C5'" "C4'"  SING N N 8  
PBT "C5'" "H5'1" SING N N 9  
PBT "C5'" "H5'2" SING N N 10 
PBT "C4'" "O4'"  SING N N 11 
PBT "C4'" "C3'"  SING N N 12 
PBT "C4'" "H4'"  SING N N 13 
PBT "O4'" "C1'"  SING N N 14 
PBT "C3'" "O3'"  SING N N 15 
PBT "C3'" "C2'"  SING N N 16 
PBT "C3'" "H3'"  SING N N 17 
PBT "O3'" HA     SING N N 18 
PBT "C2'" "C1'"  SING N N 19 
PBT "C2'" "H2'1" SING N N 20 
PBT "C2'" "H2'2" SING N N 21 
PBT "C1'" N1     SING N N 22 
PBT "C1'" "H1'"  SING N N 23 
PBT N1    C2     SING N N 24 
PBT N1    C6     SING N N 25 
PBT C2    O2     DOUB N N 26 
PBT C2    N3     SING N N 27 
PBT N3    C4     SING N N 28 
PBT N3    H3     SING N N 29 
PBT C4    O4     DOUB N N 30 
PBT C4    C5     SING N N 31 
PBT C5    C5M    SING N N 32 
PBT C5    C6     SING N N 33 
PBT C5    H5     SING N N 34 
PBT C5M   H5M1   SING N N 35 
PBT C5M   H5M2   SING N N 36 
PBT C5M   H5M3   SING N N 37 
PBT C6    H6C1   SING N N 38 
PBT C6    H6C2   SING N N 39 
# 
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 
PBT SMILES           ACDLabs              10.04 "O=C1N(CC(C(=O)N1)C)C2OC(C(O)C2)COP(=O)(O)O"                                                                                                      
PBT SMILES_CANONICAL CACTVS               3.341 "C[C@@H]1CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                    
PBT SMILES           CACTVS               3.341 "C[CH]1CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                          
PBT SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@@H]1CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O"                                                                                      
PBT SMILES           "OpenEye OEToolkits" 1.5.0 "CC1CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O"                                                                                                        
PBT InChI            InChI                1.03  "InChI=1S/C10H17N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h5-8,13H,2-4H2,1H3,(H,11,14,15)(H2,16,17,18)/t5-,6+,7-,8-/m1/s1" 
PBT InChIKey         InChI                1.03  PGRQANKWVMVANW-ULAWRXDQSA-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 
PBT "SYSTEMATIC NAME" ACDLabs              10.04 
;5'-thymidylic acid
;
PBT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-[(5R)-5-methyl-2,4-dioxo-1,3-diazinan-1-yl]oxolan-2-yl]methyl dihydrogen 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 
PBT "Create component"  2001-10-04 EBI  
PBT "Modify descriptor" 2011-06-04 RCSB 
# 
