data_NKK
# 
_chem_comp.id                                    NKK 
_chem_comp.name                                  "N~2~-(naphthalen-2-ylcarbonyl)-L-lysyl-N-[(1S)-4-carbamimidamido-1-formylbutyl]-L-lysinamide" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C29 H44 N8 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2008-08-22 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        568.711 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     NKK 
_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        3E90 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              Y 
# 
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.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
NKK CAW  CAW  C 0 1 N N N N N N 16.991 58.735 -0.573 5.971   0.696  -2.966 CAW  NKK 1  
NKK CBJ  CBJ  C 0 1 Y N N N N N 15.166 51.425 0.154  -6.311  -0.060 0.083  CBJ  NKK 2  
NKK CBI  CBI  C 0 1 Y N N N N N 15.469 50.503 -0.841 -7.333  -0.582 0.890  CBI  NKK 3  
NKK CBL  CBL  C 0 1 Y N N N N N 15.081 50.740 -2.155 -8.684  -0.460 0.522  CBL  NKK 4  
NKK CBM  CBM  C 0 1 Y N N N N N 15.392 49.819 -3.149 -9.651  -0.978 1.328  CBM  NKK 5  
NKK CBO  CBO  C 0 1 Y N N N N N 16.088 48.657 -2.834 -9.322  -1.630 2.515  CBO  NKK 6  
NKK CBN  CBN  C 0 1 Y N N N N N 16.479 48.420 -1.521 -8.024  -1.767 2.903  CBN  NKK 7  
NKK CBH  CBH  C 0 1 Y N N N N N 16.171 49.344 -0.528 -6.998  -1.246 2.098  CBH  NKK 8  
NKK CBG  CBG  C 0 1 Y N N N N N 16.572 49.113 0.783  -5.647  -1.372 2.473  CBG  NKK 9  
NKK CBF  CBF  C 0 1 Y N N N N N 16.272 50.037 1.777  -4.672  -0.860 1.679  CBF  NKK 10 
NKK CBK  CBK  C 0 1 Y N N N N N 15.566 51.194 1.466  -4.991  -0.201 0.478  CBK  NKK 11 
NKK CAA  CAA  C 0 1 N N N N N N 15.206 52.184 2.574  -3.910  0.342  -0.370 CAA  NKK 12 
NKK OAB  OAB  O 0 1 N N N N N N 14.257 52.958 2.454  -4.180  0.909  -1.410 OAB  NKK 13 
NKK N    N    N 0 1 N N N N N N 15.957 52.094 3.669  -2.624  0.208  0.010  N    NKK 14 
NKK CA   CA   C 0 1 N N S N N N 15.763 52.968 4.834  -1.551  0.746  -0.831 CA   NKK 15 
NKK CB   CB   C 0 1 N N N N N N 16.495 52.353 6.028  -1.340  2.225  -0.503 CB   NKK 16 
NKK CG   CG   C 0 1 N N N N N N 15.857 50.995 6.325  -2.592  3.016  -0.889 CG   NKK 17 
NKK CD   CD   C 0 1 N N N N N N 16.626 50.195 7.378  -2.381  4.496  -0.562 CD   NKK 18 
NKK CE   CE   C 0 1 N N N N N N 16.666 50.910 8.729  -3.633  5.287  -0.947 CE   NKK 19 
NKK NZ   NZ   N 0 1 N N N N N N 17.389 50.058 9.684  -3.431  6.707  -0.633 NZ   NKK 20 
NKK C    C    C 0 1 N N N N N N 16.288 54.367 4.501  -0.277  -0.014 -0.566 C    NKK 21 
NKK O    O    O 0 1 N N N N N N 15.946 55.356 5.147  -0.265  -0.916 0.244  O    NKK 22 
NKK NAL  NAL  N 0 1 N N N N N N 17.121 54.416 3.467  0.850   0.309  -1.231 NAL  NKK 23 
NKK CAM  CAM  C 0 1 N N S N N N 17.688 55.680 2.975  2.089   -0.429 -0.974 CAM  NKK 24 
NKK CAP  CAP  C 0 1 N N N N N N 19.218 55.661 3.016  2.118   -1.693 -1.836 CAP  NKK 25 
NKK CAQ  CAQ  C 0 1 N N N N N N 19.777 55.692 4.441  0.990   -2.632 -1.403 CAQ  NKK 26 
NKK CAR  CAR  C 0 1 N N N N N N 21.306 55.744 4.418  1.018   -3.895 -2.264 CAR  NKK 27 
NKK CAS  CAS  C 0 1 N N N N N N 21.895 55.789 5.829  -0.109  -4.834 -1.831 CAS  NKK 28 
NKK NAT  NAT  N 0 1 N N N N N N 21.403 56.986 6.524  -0.082  -6.048 -2.658 NAT  NKK 29 
NKK CAN  CAN  C 0 1 N N N N N N 17.237 55.854 1.525  3.272   0.440  -1.317 CAN  NKK 30 
NKK OAO  OAO  O 0 1 N N N N N N 17.228 54.903 0.746  3.097   1.564  -1.735 OAO  NKK 31 
NKK NAU  NAU  N 0 1 N N N N N N 16.838 57.082 1.205  4.524   -0.034 -1.160 NAU  NKK 32 
NKK CAV  CAV  C 0 1 N N S N N N 16.385 57.395 -0.155 5.674   0.811  -1.493 CAV  NKK 33 
NKK OAX  OAX  O 0 1 N N N N N N 16.594 59.004 -1.919 5.289   -0.013 -3.666 OAX  NKK 34 
NKK CAY  CAY  C 0 1 N N N N N N 14.855 57.442 -0.172 6.893   0.353  -0.690 CAY  NKK 35 
NKK CAZ  CAZ  C 0 1 N N N N N N 14.326 56.139 0.432  6.638   0.586  0.801  CAZ  NKK 36 
NKK CBA  CBA  C 0 1 N N N N N N 12.801 56.022 0.456  7.857   0.128  1.604  CBA  NKK 37 
NKK NBB  NBB  N 0 1 N N N N N N 12.485 54.683 0.975  7.614   0.351  3.031  NBB  NKK 38 
NKK CBC  CBC  C 0 1 N N N N N N 11.230 54.251 1.037  8.575   0.013  3.954  CBC  NKK 39 
NKK NBE  NBE  N 0 1 N N N N N N 10.983 53.023 1.486  8.358   0.212  5.223  NBE  NKK 40 
NKK NBD  NBD  N 0 1 N N N N N N 10.238 55.037 0.631  9.766   -0.533 3.537  NBD  NKK 41 
NKK H1AW H1AW H 0 0 N N N N N N 17.612 59.369 0.043  6.791   1.252  -3.397 H1AW NKK 42 
NKK HBJ  HBJ  H 0 1 N N N N N N 14.619 52.323 -0.092 -6.551  0.444  -0.842 HBJ  NKK 43 
NKK HBL  HBL  H 0 1 N N N N N N 14.538 51.640 -2.404 -8.954  0.043  -0.395 HBL  NKK 44 
NKK HBM  HBM  H 0 1 N N N N N N 15.092 50.007 -4.169 -10.689 -0.882 1.043  HBM  NKK 45 
NKK HBO  HBO  H 0 1 N N N N N N 16.324 47.941 -3.607 -10.109 -2.032 3.136  HBO  NKK 46 
NKK HBN  HBN  H 0 1 N N N N N N 17.021 47.520 -1.272 -7.785  -2.275 3.825  HBN  NKK 47 
NKK HBG  HBG  H 0 1 N N N N N N 17.118 48.214 1.029  -5.387  -1.876 3.391  HBG  NKK 48 
NKK HBF  HBF  H 0 1 N N N N N N 16.588 49.856 2.794  -3.638  -0.961 1.974  HBF  NKK 49 
NKK HN   HN   H 0 1 N N N N N N 16.681 51.405 3.700  -2.408  -0.245 0.840  HN   NKK 50 
NKK HA   HA   H 0 1 N N N N N N 14.697 53.061 5.091  -1.826  0.641  -1.880 HA   NKK 51 
NKK H1B  H1B  H 0 1 N N N N N N 17.561 52.223 5.789  -1.154  2.338  0.564  H1B  NKK 52 
NKK H2B  H2B  H 0 1 N N N N N N 16.415 53.012 6.905  -0.485  2.603  -1.064 H2B  NKK 53 
NKK H1G  H1G  H 0 1 N N N N N N 14.836 51.166 6.697  -2.779  2.903  -1.957 H1G  NKK 54 
NKK H2G  H2G  H 0 1 N N N N N N 15.866 50.412 5.392  -3.447  2.638  -0.328 H2G  NKK 55 
NKK H1D  H1D  H 0 1 N N N N N N 16.130 49.222 7.511  -2.194  4.609  0.506  H1D  NKK 56 
NKK H2D  H2D  H 0 1 N N N N N N 17.661 50.076 7.026  -1.526  4.873  -1.122 H2D  NKK 57 
NKK H1E  H1E  H 0 1 N N N N N N 17.183 51.875 8.625  -3.820  5.174  -2.015 H1E  NKK 58 
NKK H2E  H2E  H 0 1 N N N N N N 15.643 51.095 9.088  -4.488  4.909  -0.386 H2E  NKK 59 
NKK H1NZ H1NZ H 0 0 N N N N N N 17.553 49.161 9.273  -4.244  7.252  -0.878 H1NZ NKK 60 
NKK H2NZ H2NZ H 0 0 N N N N N N 18.264 50.484 9.915  -3.192  6.832  0.340  H2NZ NKK 61 
NKK HNAL HNAL H 0 0 N N N N N N 17.371 53.564 3.008  0.841   1.030  -1.880 HNAL NKK 62 
NKK HAM  HAM  H 0 1 N N N N N N 17.341 56.505 3.614  2.135   -0.706 0.079  HAM  NKK 63 
NKK H1AP H1AP H 0 0 N N N N N N 19.566 54.739 2.528  1.982   -1.422 -2.883 H1AP NKK 64 
NKK H2AP H2AP H 0 0 N N N N N N 19.575 56.565 2.500  3.077   -2.196 -1.712 H2AP NKK 65 
NKK H1AQ H1AQ H 0 0 N N N N N N 19.394 56.584 4.959  1.125   -2.903 -0.356 H1AQ NKK 66 
NKK H2AQ H2AQ H 0 0 N N N N N N 19.460 54.779 4.967  0.031   -2.129 -1.527 H2AQ NKK 67 
NKK H1AR H1AR H 0 0 N N N N N N 21.682 54.845 3.908  0.883   -3.624 -3.312 H1AR NKK 68 
NKK H2AR H2AR H 0 0 N N N N N N 21.610 56.660 3.890  1.978   -4.398 -2.140 H2AR NKK 69 
NKK H1AS H1AS H 0 0 N N N N N N 21.589 54.890 6.384  0.026   -5.105 -0.784 H1AS NKK 70 
NKK H2AS H2AS H 0 0 N N N N N N 22.993 55.824 5.768  -1.068  -4.331 -1.955 H2AS NKK 71 
NKK H1AT H1AT H 0 0 N N N N N N 21.291 56.785 7.497  0.820   -6.497 -2.611 H1AT NKK 72 
NKK H2AT H2AT H 0 0 N N N N N N 22.061 57.731 6.411  -0.818  -6.684 -2.391 H2AT NKK 73 
NKK HNAU HNAU H 0 0 N N N N N N 16.847 57.801 1.900  4.664   -0.934 -0.826 HNAU NKK 74 
NKK HAV  HAV  H 0 1 N N N N N N 16.712 56.624 -0.869 5.446   1.848  -1.248 HAV  NKK 75 
NKK H1AY H1AY H 0 0 N N N N N N 14.501 58.299 0.420  7.067   -0.709 -0.867 H1AY NKK 76 
NKK H2AY H2AY H 0 0 N N N N N N 14.492 57.555 -1.204 7.768   0.922  -1.002 H2AY NKK 77 
NKK H1AZ H1AZ H 0 0 N N N N N N 14.718 55.306 -0.170 6.464   1.647  0.978  H1AZ NKK 78 
NKK H2AZ H2AZ H 0 0 N N N N N N 14.660 56.119 1.480  5.763   0.016  1.113  H2AZ NKK 79 
NKK H1BA H1BA H 0 0 N N N N N N 12.368 56.797 1.106  8.031   -0.933 1.426  H1BA NKK 80 
NKK H2BA H2BA H 0 0 N N N N N N 12.380 56.163 -0.550 8.733   0.697  1.291  H2BA NKK 81 
NKK HNBB HNBB H 0 0 N N N N N N 13.226 54.088 1.286  6.773   0.736  3.325  HNBB NKK 82 
NKK H1BE H1BE H 0 0 N N N N N N 10.002 52.832 1.469  9.037   -0.026 5.874  H1BE NKK 83 
NKK H1BD H1BD H 0 0 N N N N N N 10.593 55.915 0.309  9.927   -0.681 2.592  H1BD NKK 84 
NKK H2BD H2BD H 0 0 N N N N N N 9.270  54.785 0.646  10.445  -0.771 4.188  H2BD NKK 85 
# 
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 
NKK CBM CBO  DOUB Y N 1  
NKK CBM CBL  SING Y N 2  
NKK CBO CBN  SING Y N 3  
NKK CBL CBI  DOUB Y N 4  
NKK OAX CAW  DOUB N N 5  
NKK CBN CBH  DOUB Y N 6  
NKK CBI CBH  SING Y N 7  
NKK CBI CBJ  SING Y N 8  
NKK CAW CAV  SING N N 9  
NKK CBH CBG  SING Y N 10 
NKK CAY CAV  SING N N 11 
NKK CAY CAZ  SING N N 12 
NKK CAV NAU  SING N N 13 
NKK CBJ CBK  DOUB Y N 14 
NKK CAZ CBA  SING N N 15 
NKK CBA NBB  SING N N 16 
NKK NBD CBC  SING N N 17 
NKK OAO CAN  DOUB N N 18 
NKK CBG CBF  DOUB Y N 19 
NKK NBB CBC  SING N N 20 
NKK CBC NBE  DOUB N N 21 
NKK NAU CAN  SING N N 22 
NKK CBK CBF  SING Y N 23 
NKK CBK CAA  SING N N 24 
NKK CAN CAM  SING N N 25 
NKK OAB CAA  DOUB N N 26 
NKK CAA N    SING N N 27 
NKK CAM CAP  SING N N 28 
NKK CAM NAL  SING N N 29 
NKK CAP CAQ  SING N N 30 
NKK NAL C    SING N N 31 
NKK N   CA   SING N N 32 
NKK CAR CAQ  SING N N 33 
NKK CAR CAS  SING N N 34 
NKK C   CA   SING N N 35 
NKK C   O    DOUB N N 36 
NKK CA  CB   SING N N 37 
NKK CAS NAT  SING N N 38 
NKK CB  CG   SING N N 39 
NKK CG  CD   SING N N 40 
NKK CD  CE   SING N N 41 
NKK CE  NZ   SING N N 42 
NKK CAW H1AW SING N N 43 
NKK CBJ HBJ  SING N N 44 
NKK CBL HBL  SING N N 45 
NKK CBM HBM  SING N N 46 
NKK CBO HBO  SING N N 47 
NKK CBN HBN  SING N N 48 
NKK CBG HBG  SING N N 49 
NKK CBF HBF  SING N N 50 
NKK N   HN   SING N N 51 
NKK CA  HA   SING N N 52 
NKK CB  H1B  SING N N 53 
NKK CB  H2B  SING N N 54 
NKK CG  H1G  SING N N 55 
NKK CG  H2G  SING N N 56 
NKK CD  H1D  SING N N 57 
NKK CD  H2D  SING N N 58 
NKK CE  H1E  SING N N 59 
NKK CE  H2E  SING N N 60 
NKK NZ  H1NZ SING N N 61 
NKK NZ  H2NZ SING N N 62 
NKK NAL HNAL SING N N 63 
NKK CAM HAM  SING N N 64 
NKK CAP H1AP SING N N 65 
NKK CAP H2AP SING N N 66 
NKK CAQ H1AQ SING N N 67 
NKK CAQ H2AQ SING N N 68 
NKK CAR H1AR SING N N 69 
NKK CAR H2AR SING N N 70 
NKK CAS H1AS SING N N 71 
NKK CAS H2AS SING N N 72 
NKK NAT H1AT SING N N 73 
NKK NAT H2AT SING N N 74 
NKK NAU HNAU SING N N 75 
NKK CAV HAV  SING N N 76 
NKK CAY H1AY SING N N 77 
NKK CAY H2AY SING N N 78 
NKK CAZ H1AZ SING N N 79 
NKK CAZ H2AZ SING N N 80 
NKK CBA H1BA SING N N 81 
NKK CBA H2BA SING N N 82 
NKK NBB HNBB SING N N 83 
NKK NBE H1BE SING N N 84 
NKK NBD H1BD SING N N 85 
NKK NBD H2BD SING N N 86 
# 
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 
NKK SMILES           ACDLabs              10.04 "O=CC(NC(=O)C(NC(=O)C(NC(=O)c2ccc1c(cccc1)c2)CCCCN)CCCCN)CCCNC(=[N@H])N"                                                                                                                                                                                       
NKK SMILES_CANONICAL CACTVS               3.341 "NCCCC[C@H](NC(=O)[C@H](CCCCN)NC(=O)c1ccc2ccccc2c1)C(=O)N[C@@H](CCCNC(N)=N)C=O"                                                                                                                                                                                
NKK SMILES           CACTVS               3.341 "NCCCC[CH](NC(=O)[CH](CCCCN)NC(=O)c1ccc2ccccc2c1)C(=O)N[CH](CCCNC(N)=N)C=O"                                                                                                                                                                                    
NKK SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "[H]/N=C(\N)/NCCC[C@@H](C=O)NC(=O)[C@H](CCCCN)NC(=O)[C@H](CCCCN)NC(=O)c1ccc2ccccc2c1"                                                                                                                                                                          
NKK SMILES           "OpenEye OEToolkits" 1.5.0 "[H]N=C(N)NCCCC(C=O)NC(=O)C(CCCCN)NC(=O)C(CCCCN)NC(=O)c1ccc2ccccc2c1"                                                                                                                                                                                          
NKK InChI            InChI                1.03  "InChI=1S/C29H44N8O4/c30-15-5-3-11-24(27(40)35-23(19-38)10-7-17-34-29(32)33)37-28(41)25(12-4-6-16-31)36-26(39)22-14-13-20-8-1-2-9-21(20)18-22/h1-2,8-9,13-14,18-19,23-25H,3-7,10-12,15-17,30-31H2,(H,35,40)(H,36,39)(H,37,41)(H4,32,33,34)/t23-,24-,25-/m0/s1" 
NKK InChIKey         InChI                1.03  VYVVOKKLVHYYQD-SDHOMARFSA-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 
NKK "SYSTEMATIC NAME" ACDLabs              10.04 "N~2~-(naphthalen-2-ylcarbonyl)-L-lysyl-N-[(1S)-4-carbamimidamido-1-formylbutyl]-L-lysinamide"                                                            
NKK "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "N-[(2S)-6-amino-1-[[(2S)-6-amino-1-[[(2S)-5-carbamimidamido-1-oxo-pentan-2-yl]amino]-1-oxo-hexan-2-yl]amino]-1-oxo-hexan-2-yl]naphthalene-2-carboxamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
NKK "Create component"     2008-08-22 RCSB 
NKK "Modify aromatic_flag" 2011-06-04 RCSB 
NKK "Modify descriptor"    2011-06-04 RCSB 
NKK "Modify PCM"           2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            NKK 
_pdbx_chem_comp_pcm.modified_residue_id                SER 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               CAW 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   OG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
