data_APK
# 
_chem_comp.id                                    APK 
_chem_comp.name                                  "5'-O-[(S)-{[(5S)-5-AMINO-6-OXOHEXYL]AMINO}(HYDROXY)PHOSPHORYL]ADENOSINE" 
_chem_comp.type                                  "L-PEPTIDE LINKING" 
_chem_comp.pdbx_type                             ATOMP 
_chem_comp.formula                               "C16 H26 N7 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               LYS 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2006-02-21 
_chem_comp.pdbx_modified_date                    2009-01-07 
_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                        459.394 
_chem_comp.one_letter_code                       K 
_chem_comp.three_letter_code                     APK 
_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        1VS0 
_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 
APK O      O    O 0 1 N N N -4.424  57.892 135.133 8.492  3.718  -0.344 O      APK 1  
APK C      C    C 0 1 N N N -5.229  57.857 134.215 7.312  3.473  -0.417 C      APK 2  
APK CA     CA   C 0 1 N N S -6.405  56.946 134.309 6.849  2.162  -1.000 CA     APK 3  
APK N      N    N 0 1 N N N -5.854  55.712 134.871 8.016  1.366  -1.402 N      APK 4  
APK CB     CB   C 0 1 N N N -7.422  57.563 135.288 6.043  1.394  0.049  CB     APK 5  
APK CG     CG   C 0 1 N N N -8.089  58.751 134.674 5.469  0.123  -0.580 CG     APK 6  
APK CD     CD   C 0 1 N N N -9.054  59.430 135.676 4.663  -0.646 0.470  CD     APK 7  
APK CE     CE   C 0 1 N N N -9.674  60.664 135.041 4.089  -1.917 -0.159 CE     APK 8  
APK NZ     NZ   N 0 1 N N N -8.612  61.643 134.748 3.315  -2.655 0.848  NZ     APK 9  
APK P      P    P 0 1 N N S -9.154  62.849 133.765 1.880  -3.127 0.106  P      APK 10 
APK O1P    O1P  O 0 1 N N N -8.107  63.892 133.551 1.050  -3.880 1.072  O1P    APK 11 
APK O2P    O2P  O 0 1 N N N -10.474 63.267 134.256 2.214  -4.065 -1.160 O2P    APK 12 
APK "O5'"  O5*  O 0 1 N N N -9.443  61.996 132.449 1.078  -1.822 -0.389 "O5'"  APK 13 
APK "C5'"  C5*  C 0 1 N N N -8.428  61.761 131.545 0.608  -1.157 0.785  "C5'"  APK 14 
APK "C4'"  C4*  C 0 1 N N R -8.942  61.528 130.138 -0.168 0.099  0.383  "C4'"  APK 15 
APK "O4'"  O4*  O 0 1 N N N -7.951  60.682 129.550 -1.374 -0.271 -0.306 "O4'"  APK 16 
APK "C3'"  C3*  C 0 1 N N S -10.194 60.691 130.190 -0.579 0.887  1.642  "C3'"  APK 17 
APK "O3'"  O3*  O 0 1 N N N -11.234 61.531 129.836 -0.016 2.201  1.624  "O3'"  APK 18 
APK "C2'"  C2*  C 0 1 N N R -10.094 59.845 128.976 -2.126 0.958  1.553  "C2'"  APK 19 
APK "O2'"  O2*  O 0 1 N N N -10.422 60.694 127.896 -2.599 2.249  1.942  "O2'"  APK 20 
APK "C1'"  C1*  C 0 1 N N R -8.624  59.575 128.886 -2.377 0.708  0.045  "C1'"  APK 21 
APK N9     N9   N 0 1 Y N N -8.202  58.332 129.511 -3.722 0.170  -0.176 N9     APK 22 
APK C8     C8   C 0 1 Y N N -7.153  58.220 130.327 -4.069 -1.148 -0.204 C8     APK 23 
APK N7     N7   N 0 1 Y N N -6.992  56.963 130.660 -5.346 -1.266 -0.422 N7     APK 24 
APK C5     C5   C 0 1 Y N N -7.953  56.249 130.061 -5.898 -0.036 -0.548 C5     APK 25 
APK C4     C4   C 0 1 Y N N -8.726  57.117 129.313 -4.864 0.901  -0.386 C4     APK 26 
APK N3     N3   N 0 1 Y N N -9.757  56.653 128.576 -5.146 2.197  -0.472 N3     APK 27 
APK C2     C2   C 0 1 Y N N -10.037 55.369 128.612 -6.379 2.601  -0.696 C2     APK 28 
APK N1     N1   N 0 1 Y N N -9.315  54.514 129.323 -7.384 1.759  -0.850 N1     APK 29 
APK C6     C6   C 0 1 Y N N -8.271  54.901 130.055 -7.197 0.445  -0.785 C6     APK 30 
APK N6     N6   N 0 1 N N N -7.540  54.013 130.757 -8.257 -0.430 -0.947 N6     APK 31 
APK HC     H    H 0 1 N N N -5.090  58.480 133.344 6.588  4.193  -0.065 HC     APK 32 
APK HA     HA   H 0 1 N N N -6.913  56.777 133.348 6.222  2.354  -1.871 HA     APK 33 
APK H      1HN  H 0 1 N N N -4.972  55.906 135.301 8.564  1.214  -0.569 H      APK 34 
APK H2     2HN  H 0 1 N Y N -5.728  55.040 134.141 7.666  0.463  -1.687 H2     APK 35 
APK HB2    1HB  H 0 1 N N N -6.891  57.884 136.196 6.694  1.125  0.882  HB2    APK 36 
APK HB3    2HB  H 0 1 N N N -8.185  56.810 135.536 5.228  2.020  0.412  HB3    APK 37 
APK HG2    1HG  H 0 1 N N N -8.670  58.414 133.803 4.818  0.391  -1.412 HG2    APK 38 
APK HG3    2HG  H 0 1 N N N -7.319  59.477 134.373 6.284  -0.504 -0.943 HG3    APK 39 
APK HD2    1HD  H 0 1 N N N -8.493  59.727 136.575 5.314  -0.915 1.302  HD2    APK 40 
APK HD3    2HD  H 0 1 N N N -9.850  58.723 135.951 3.848  -0.020 0.833  HD3    APK 41 
APK HE2    1HE  H 0 1 N N N -10.405 61.108 135.733 3.438  -1.649 -0.992 HE2    APK 42 
APK HE3    2HE  H 0 1 N N N -10.183 60.382 134.107 4.904  -2.543 -0.522 HE3    APK 43 
APK HZ     HNZ  H 0 1 N N N -8.299  62.045 135.608 3.830  -3.500 1.047  HZ     APK 44 
APK HO2P   HO2P H 0 0 N N N -10.447 63.357 135.201 2.755  -3.537 -1.763 HO2P   APK 45 
APK "H5'1" 1H5* H 0 0 N N N -7.900  60.850 131.864 -0.048 -1.825 1.344  "H5'1" APK 46 
APK "H5'2" 2H5* H 0 0 N N N -7.764  62.638 131.532 1.457  -0.875 1.408  "H5'2" APK 47 
APK "H4'"  H4*  H 0 1 N N N -9.134  62.475 129.612 0.449  0.726  -0.262 "H4'"  APK 48 
APK "H3'"  H3*  H 0 1 N N N -10.321 60.176 131.154 -0.272 0.354  2.542  "H3'"  APK 49 
APK "HO3'" HO3* H 0 0 N N N -11.761 61.724 130.603 -0.357 2.662  2.402  "HO3'" APK 50 
APK "H2'"  H2*  H 0 1 N N N -10.718 58.939 128.982 -2.587 0.178  2.159  "H2'"  APK 51 
APK "HO2'" HO2* H 0 0 N N N -10.496 61.589 128.207 -2.414 2.342  2.887  "HO2'" APK 52 
APK "H1'"  H1*  H 0 1 N N N -8.366  59.478 127.821 -2.233 1.625  -0.526 "H1'"  APK 53 
APK H8     H8   H 0 1 N N N -6.533  59.038 130.661 -3.385 -1.972 -0.065 H8     APK 54 
APK HC2    H2   H 0 1 N N N -10.880 55.000 128.046 -6.575 3.662  -0.756 HC2    APK 55 
APK HN61   1HN6 H 0 0 N N N -7.709  53.028 130.795 -8.108 -1.387 -0.898 HN61   APK 56 
APK HN62   2HN6 H 0 0 N N N -6.803  54.491 131.234 -9.150 -0.085 -1.110 HN62   APK 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 
APK O     C      DOUB N N 1  
APK C     CA     SING N N 2  
APK C     HC     SING N N 3  
APK CA    N      SING N N 4  
APK CA    CB     SING N N 5  
APK CA    HA     SING N N 6  
APK N     H      SING N N 7  
APK N     H2     SING N N 8  
APK CB    CG     SING N N 9  
APK CB    HB2    SING N N 10 
APK CB    HB3    SING N N 11 
APK CG    CD     SING N N 12 
APK CG    HG2    SING N N 13 
APK CG    HG3    SING N N 14 
APK CD    CE     SING N N 15 
APK CD    HD2    SING N N 16 
APK CD    HD3    SING N N 17 
APK CE    NZ     SING N N 18 
APK CE    HE2    SING N N 19 
APK CE    HE3    SING N N 20 
APK NZ    P      SING N N 21 
APK NZ    HZ     SING N N 22 
APK P     O1P    DOUB N N 23 
APK P     O2P    SING N N 24 
APK P     "O5'"  SING N N 25 
APK O2P   HO2P   SING N N 26 
APK "O5'" "C5'"  SING N N 27 
APK "C5'" "C4'"  SING N N 28 
APK "C5'" "H5'1" SING N N 29 
APK "C5'" "H5'2" SING N N 30 
APK "C4'" "O4'"  SING N N 31 
APK "C4'" "C3'"  SING N N 32 
APK "C4'" "H4'"  SING N N 33 
APK "O4'" "C1'"  SING N N 34 
APK "C3'" "O3'"  SING N N 35 
APK "C3'" "C2'"  SING N N 36 
APK "C3'" "H3'"  SING N N 37 
APK "O3'" "HO3'" SING N N 38 
APK "C2'" "O2'"  SING N N 39 
APK "C2'" "C1'"  SING N N 40 
APK "C2'" "H2'"  SING N N 41 
APK "O2'" "HO2'" SING N N 42 
APK "C1'" N9     SING N N 43 
APK "C1'" "H1'"  SING N N 44 
APK N9    C8     SING Y N 45 
APK N9    C4     SING Y N 46 
APK C8    N7     DOUB Y N 47 
APK C8    H8     SING N N 48 
APK N7    C5     SING Y N 49 
APK C5    C4     DOUB Y N 50 
APK C5    C6     SING Y N 51 
APK C4    N3     SING Y N 52 
APK N3    C2     DOUB Y N 53 
APK C2    N1     SING Y N 54 
APK C2    HC2    SING N N 55 
APK N1    C6     DOUB Y N 56 
APK C6    N6     SING N N 57 
APK N6    HN61   SING N N 58 
APK N6    HN62   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 
APK SMILES           ACDLabs              10.04 "O=CC(N)CCCCNP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O" 
APK InChI            InChI                1.02b 
"InChI=1/C16H26N7O7P/c17-9(5-24)3-1-2-4-22-31(27,28)29-6-10-12(25)13(26)16(30-10)23-8-21-11-14(18)19-7-20-15(11)23/h5,7-10,12-13,16,25-26H,1-4,6,17H2,(H2,18,19,20)(H2,22,27,28)/t9-,10+,12+,13+,16+/m0/s1/f/h22,27H,18H2" 
APK InChIKey         InChI                1.02b JVYVZNSNEJRNON-BTNQIDLWDZ 
APK SMILES_CANONICAL CACTVS               3.341 "N[C@@H](CCCCN[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C=O" 
APK SMILES           CACTVS               3.341 "N[CH](CCCCN[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C=O" 
APK SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(NCCCC[C@@H](C=O)N)O)O)O)N" 
APK SMILES           "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(NCCCCC(C=O)N)O)O)O)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 
APK "SYSTEMATIC NAME" ACDLabs              10.04 "5'-O-[(S)-{[(5S)-5-amino-6-oxohexyl]amino}(hydroxy)phosphoryl]adenosine"                                                  
APK "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "N-[(5S)-5-amino-6-oxo-hexyl]-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy]phosphonamidic acid" 
# 
