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 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 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 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" APK InChI InChI 1.03 "InChI=1S/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" APK InChIKey InChI 1.03 JVYVZNSNEJRNON-UOYPZJKHSA-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" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site APK "Create component" 2006-02-21 RCSB APK "Modify descriptor" 2011-06-04 RCSB #