data_PTJ
# 
_chem_comp.id                                    PTJ 
_chem_comp.name                                  "5'-O-[(S)-hydroxy{[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]oxy}phosphoryl]adenosine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C16 H25 N5 O13 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2013-06-26 
_chem_comp.pdbx_modified_date                    2014-03-28 
_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                        557.343 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     PTJ 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        3WDK 
_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 
PTJ O15   O15   O 0 1 N N N 5.238  23.796 64.290 -8.880 -1.860 0.019  O15   PTJ 1  
PTJ P1    P1    P 0 1 N N N 5.729  25.107 64.770 -7.805 -2.152 0.992  P1    PTJ 2  
PTJ O16   O16   O 0 1 N N N 5.226  25.488 66.109 -8.376 -1.986 2.488  O16   PTJ 3  
PTJ O17   O17   O 0 1 N N N 7.180  25.330 64.585 -7.284 -3.660 0.781  O17   PTJ 4  
PTJ O14   O14   O 0 1 N N N 5.028  26.161 63.774 -6.584 -1.126 0.767  O14   PTJ 5  
PTJ C16   C16   C 0 1 N N N 5.549  27.485 63.625 -5.932 -0.957 -0.493 C16   PTJ 6  
PTJ C13   C13   C 0 1 N N N 4.580  28.328 62.793 -4.824 0.088  -0.358 C13   PTJ 7  
PTJ C14   C14   C 0 1 N N N 5.147  29.743 62.655 -5.430 1.421  0.086  C14   PTJ 8  
PTJ C15   C15   C 0 1 N N N 4.422  27.706 61.404 -3.806 -0.380 0.684  C15   PTJ 9  
PTJ C12   C12   C 0 1 N N R 3.218  28.383 63.491 -4.126 0.270  -1.707 C12   PTJ 10 
PTJ O13   O13   O 0 1 N N N 3.368  28.999 64.773 -5.076 0.707  -2.680 O13   PTJ 11 
PTJ C11   C11   C 0 1 N N N 2.222  29.184 62.648 -3.033 1.299  -1.573 C11   PTJ 12 
PTJ O12   O12   O 0 1 N N N 1.383  28.612 61.954 -3.111 2.344  -2.174 O12   PTJ 13 
PTJ O11   O11   O 0 1 N N N 2.274  30.533 62.823 -1.974 1.055  -0.786 O11   PTJ 14 
PTJ P     P     P 0 1 N N N 1.326  31.523 61.976 -0.850 2.204  -0.697 P     PTJ 15 
PTJ O1P   O1P   O 0 1 N N N -0.092 31.182 62.228 -1.477 3.516  -0.004 O1P   PTJ 16 
PTJ O2P   O2P   O 0 1 N N N 1.820  31.547 60.581 -0.380 2.543  -2.059 O2P   PTJ 17 
PTJ "O5'" "O5'" O 0 1 N N N 1.651  32.944 62.657 0.391  1.675  0.183  "O5'" PTJ 18 
PTJ "C5'" "C5'" C 0 1 N N N 3.009  33.383 62.747 1.594  2.424  0.362  "C5'" PTJ 19 
PTJ "C4'" "C4'" C 0 1 N N R 3.045  34.896 62.964 2.560  1.634  1.248  "C4'" PTJ 20 
PTJ "O4'" "O4'" O 0 1 N N N 4.424  35.266 63.133 2.990  0.446  0.563  "O4'" PTJ 21 
PTJ "C3'" "C3'" C 0 1 N N S 2.539  35.614 61.721 3.816  2.478  1.535  "C3'" PTJ 22 
PTJ "O3'" "O3'" O 0 1 N N N 1.759  36.761 62.089 3.965  2.692  2.940  "O3'" PTJ 23 
PTJ "C2'" "C2'" C 0 1 N N R 3.823  36.036 61.032 4.984  1.618  0.992  "C2'" PTJ 24 
PTJ "O2'" "O2'" O 0 1 N N N 3.590  37.251 60.306 6.104  1.662  1.877  "O2'" PTJ 25 
PTJ "C1'" "C1'" C 0 1 N N R 4.671  36.365 62.245 4.356  0.201  0.962  "C1'" PTJ 26 
PTJ N9    N9    N 0 1 Y N N 6.115  36.451 61.928 5.037  -0.644 -0.022 N9    PTJ 27 
PTJ C8    C8    C 0 1 Y N N 6.750  35.685 61.045 4.652  -0.849 -1.313 C8    PTJ 28 
PTJ N7    N7    N 0 1 Y N N 8.057  35.829 61.241 5.486  -1.656 -1.903 N7    PTJ 29 
PTJ C5    C5    C 0 1 Y N N 8.232  36.695 62.237 6.456  -2.019 -1.029 C5    PTJ 30 
PTJ C4    C4    C 0 1 Y N N 7.030  37.067 62.672 6.183  -1.369 0.186  C4    PTJ 31 
PTJ N3    N3    N 0 1 Y N N 6.903  37.946 63.676 7.001  -1.557 1.217  N3    PTJ 32 
PTJ C2    C2    C 0 1 Y N N 8.047  38.487 64.273 8.055  -2.338 1.103  C2    PTJ 33 
PTJ N1    N1    N 0 1 Y N N 9.294  38.083 63.784 8.354  -2.967 -0.019 N1    PTJ 34 
PTJ C6    C6    C 0 1 Y N N 9.338  37.198 62.779 7.590  -2.846 -1.100 C6    PTJ 35 
PTJ N6    N6    N 0 1 N N N 10.488 36.862 62.201 7.912  -3.508 -2.272 N6    PTJ 36 
PTJ H1    H1    H 0 1 N N N 4.656  24.804 66.440 -9.115 -2.575 2.695  H1    PTJ 37 
PTJ H2    H2    H 0 1 N N N 7.568  24.567 64.174 -6.576 -3.921 1.387  H2    PTJ 38 
PTJ H3    H3    H 0 1 N N N 6.524  27.440 63.117 -5.500 -1.906 -0.809 H3    PTJ 39 
PTJ H4    H4    H 0 1 N N N 5.674  27.943 64.617 -6.658 -0.623 -1.236 H4    PTJ 40 
PTJ H5    H5    H 0 1 N N N 5.261  30.192 63.653 -6.155 1.755  -0.657 H5    PTJ 41 
PTJ H6    H6    H 0 1 N N N 6.128  29.698 62.159 -5.928 1.292  1.047  H6    PTJ 42 
PTJ H7    H7    H 0 1 N N N 4.460  30.356 62.054 -4.640 2.166  0.182  H7    PTJ 43 
PTJ H8    H8    H 0 1 N N N 4.015  26.689 61.501 -3.016 0.364  0.781  H8    PTJ 44 
PTJ H9    H9    H 0 1 N N N 3.735  28.320 60.803 -4.303 -0.509 1.646  H9    PTJ 45 
PTJ H10   H10   H 0 1 N N N 5.403  27.662 60.908 -3.373 -1.330 0.368  H10   PTJ 46 
PTJ H11   H11   H 0 1 N N N 2.838  27.357 63.606 -3.693 -0.680 -2.023 H11   PTJ 47 
PTJ H12   H12   H 0 1 N N N 3.986  28.500 65.294 -5.502 1.548  -2.464 H12   PTJ 48 
PTJ H13   H13   H 0 1 N N N -0.529 31.011 61.402 -1.806 3.367  0.893  H13   PTJ 49 
PTJ H14   H14   H 0 1 N N N 3.501  32.880 63.592 2.057  2.605  -0.608 H14   PTJ 50 
PTJ H15   H15   H 0 1 N N N 3.537  33.134 61.815 1.362  3.377  0.837  H15   PTJ 51 
PTJ H16   H16   H 0 1 N N N 2.440  35.171 63.840 2.069  1.366  2.183  H16   PTJ 52 
PTJ H17   H17   H 0 1 N N N 1.969  34.922 61.083 3.765  3.431  1.008  H17   PTJ 53 
PTJ H18   H18   H 0 1 N N N 0.960  36.477 62.518 4.741  3.218  3.178  H18   PTJ 54 
PTJ H19   H19   H 0 1 N N N 4.257  35.230 60.422 5.269  1.939  -0.010 H19   PTJ 55 
PTJ H20   H20   H 0 1 N N N 4.391  37.520 59.872 6.476  2.546  1.999  H20   PTJ 56 
PTJ H21   H21   H 0 1 N N N 4.326  37.310 62.690 4.391  -0.255 1.951  H21   PTJ 57 
PTJ H22   H22   H 0 1 N N N 6.285  35.056 60.300 3.783  -0.407 -1.778 H22   PTJ 58 
PTJ H23   H23   H 0 1 N N N 7.970  39.194 65.086 8.700  -2.468 1.960  H23   PTJ 59 
PTJ H24   H24   H 0 1 N N N 11.238 37.362 62.634 7.352  -3.404 -3.057 H24   PTJ 60 
PTJ H25   H25   H 0 1 N N N 10.639 35.879 62.305 8.698  -4.076 -2.308 H25   PTJ 61 
# 
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 
PTJ "O2'" "C2'" SING N N 1  
PTJ O2P   P     DOUB N N 2  
PTJ "C2'" "C3'" SING N N 3  
PTJ "C2'" "C1'" SING N N 4  
PTJ C8    N7    DOUB Y N 5  
PTJ C8    N9    SING Y N 6  
PTJ N7    C5    SING Y N 7  
PTJ C15   C13   SING N N 8  
PTJ "C3'" "O3'" SING N N 9  
PTJ "C3'" "C4'" SING N N 10 
PTJ N9    "C1'" SING N N 11 
PTJ N9    C4    SING Y N 12 
PTJ O12   C11   DOUB N N 13 
PTJ P     O1P   SING N N 14 
PTJ P     "O5'" SING N N 15 
PTJ P     O11   SING N N 16 
PTJ N6    C6    SING N N 17 
PTJ C5    C4    DOUB Y N 18 
PTJ C5    C6    SING Y N 19 
PTJ "C1'" "O4'" SING N N 20 
PTJ C11   O11   SING N N 21 
PTJ C11   C12   SING N N 22 
PTJ C14   C13   SING N N 23 
PTJ "O5'" "C5'" SING N N 24 
PTJ C4    N3    SING Y N 25 
PTJ "C5'" "C4'" SING N N 26 
PTJ C6    N1    DOUB Y N 27 
PTJ C13   C12   SING N N 28 
PTJ C13   C16   SING N N 29 
PTJ "C4'" "O4'" SING N N 30 
PTJ C12   O13   SING N N 31 
PTJ C16   O14   SING N N 32 
PTJ N3    C2    DOUB Y N 33 
PTJ O14   P1    SING N N 34 
PTJ N1    C2    SING Y N 35 
PTJ O15   P1    DOUB N N 36 
PTJ O17   P1    SING N N 37 
PTJ P1    O16   SING N N 38 
PTJ O16   H1    SING N N 39 
PTJ O17   H2    SING N N 40 
PTJ C16   H3    SING N N 41 
PTJ C16   H4    SING N N 42 
PTJ C14   H5    SING N N 43 
PTJ C14   H6    SING N N 44 
PTJ C14   H7    SING N N 45 
PTJ C15   H8    SING N N 46 
PTJ C15   H9    SING N N 47 
PTJ C15   H10   SING N N 48 
PTJ C12   H11   SING N N 49 
PTJ O13   H12   SING N N 50 
PTJ O1P   H13   SING N N 51 
PTJ "C5'" H14   SING N N 52 
PTJ "C5'" H15   SING N N 53 
PTJ "C4'" H16   SING N N 54 
PTJ "C3'" H17   SING N N 55 
PTJ "O3'" H18   SING N N 56 
PTJ "C2'" H19   SING N N 57 
PTJ "O2'" H20   SING N N 58 
PTJ "C1'" H21   SING N N 59 
PTJ C8    H22   SING N N 60 
PTJ C2    H23   SING N N 61 
PTJ N6    H24   SING N N 62 
PTJ N6    H25   SING N N 63 
# 
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 
PTJ SMILES           ACDLabs              12.01 "O=P(O)(O)OCC(C)(C)C(O)C(=O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O" 
PTJ InChI            InChI                1.03  
"InChI=1S/C16H25N5O13P2/c1-16(2,4-32-35(26,27)28)11(24)15(25)34-36(29,30)31-3-7-9(22)10(23)14(33-7)21-6-20-8-12(17)18-5-19-13(8)21/h5-7,9-11,14,22-24H,3-4H2,1-2H3,(H,29,30)(H2,17,18,19)(H2,26,27,28)/t7-,9-,10-,11+,14-/m1/s1" 
PTJ InChIKey         InChI                1.03  OMCOLJSEXCHENT-FSRKKXLISA-N 
PTJ SMILES_CANONICAL CACTVS               3.385 "CC(C)(CO[P](O)(O)=O)[C@@H](O)C(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23" 
PTJ SMILES           CACTVS               3.385 "CC(C)(CO[P](O)(O)=O)[CH](O)C(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23" 
PTJ SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC(C)(COP(=O)(O)O)[C@H](C(=O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)O" 
PTJ SMILES           "OpenEye OEToolkits" 1.7.6 "CC(C)(COP(=O)(O)O)C(C(=O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)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 
PTJ "SYSTEMATIC NAME" ACDLabs              12.01 "5'-O-[(S)-hydroxy{[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]oxy}phosphoryl]adenosine"                                                      
PTJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2R)-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
PTJ "Create component" 2013-06-26 PDBJ 
PTJ "Initial release"  2014-04-02 RCSB 
# 
