data_VNK
# 
_chem_comp.id                                    VNK 
_chem_comp.name                                  "N-hexanoyl-L-valyl-N~1~-[(3S,4S)-3-hydroxy-2,6-dimethylheptan-4-yl]-N~5~,N~5~-dimethyl-L-glutamamide" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C27 H52 N4 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "vinylketone carmaphycin analogue VNK1, double bound form" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2012-11-01 
_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                        512.726 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VNK 
_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        4HNP 
_chem_comp.pdbx_subcomponent_list                "6NA VAL QMM 05U" 
_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 
VNK C27 C27 C 0 1 N N N N N N 12.421 -136.590 22.479 -6.036  -0.503 -0.430 CA   6NA 1  
VNK C1  C1  C 0 1 N N N N N N 11.924 -137.453 21.334 -4.747  -1.039 0.137  C    6NA 2  
VNK O1  O1  O 0 1 N N N N N N 12.472 -138.514 21.060 -4.753  -1.652 1.183  O    6NA 3  
VNK C28 C28 C 0 1 N N N N N N 12.713 -137.415 23.730 -7.194  -0.868 0.502  CB   6NA 4  
VNK C29 C29 C 0 1 N N N N N N 13.530 -136.607 24.734 -8.503  -0.323 -0.074 CG   6NA 5  
VNK C30 C30 C 0 1 N N N N N N 13.491 -137.244 26.119 -9.660  -0.688 0.858  CD   6NA 6  
VNK C31 C31 C 0 1 N N N N N N 14.126 -136.337 27.150 -10.969 -0.144 0.282  C6   6NA 7  
VNK N1  N1  N 0 1 N N N N N N 10.874 -136.967 20.670 -3.587  -0.837 -0.519 N    VAL 8  
VNK C2  C2  C 0 1 N N S N N N 10.242 -137.611 19.531 -2.334  -1.358 0.032  CA   VAL 9  
VNK C5  C5  C 0 1 N N N N N N 11.068 -137.335 18.297 -1.179  -0.536 -0.481 C    VAL 10 
VNK O3  O3  O 0 1 N N N N N N 11.526 -136.214 18.123 -1.320  0.160  -1.464 O    VAL 11 
VNK C3  C3  C 0 1 N N N N N N 8.788  -137.120 19.478 -2.154  -2.815 -0.399 CB   VAL 12 
VNK C26 C26 C 0 1 N N N N N N 8.277  -136.737 18.094 -0.901  -3.392 0.264  CG1  VAL 13 
VNK C4  C4  C 0 1 N N N N N N 7.854  -138.141 20.114 -3.377  -3.628 0.028  CG2  VAL 14 
VNK C10 C10 C 0 1 N N N N N N 11.284 -138.195 14.966 2.434   -0.517 0.073  C    QMM 15 
VNK C9  C9  C 0 1 N N N N N N 15.482 -139.364 17.325 -0.121  3.728  -0.108 CD   QMM 16 
VNK C8  C8  C 0 1 N N N N N N 13.999 -139.172 17.523 -0.094  2.288  -0.552 CG   QMM 17 
VNK N2  N2  N 0 1 N N N N N N 11.290 -138.351 17.452 0.009   -0.574 0.154  N    QMM 18 
VNK O7  O7  O 0 1 N N N N N N 15.988 -140.454 17.552 0.755   4.157  0.612  OE1  QMM 19 
VNK N5  N5  N 0 1 N N N N N N 16.197 -138.309 16.925 -1.117  4.540  -0.516 NE2  QMM 20 
VNK C24 C24 C 0 1 N N N N N N 16.765 -138.206 15.586 -2.172  4.022  -1.390 CH1  QMM 21 
VNK C25 C25 C 0 1 N N N N N N 16.490 -137.184 17.805 -1.143  5.939  -0.084 CH2  QMM 22 
VNK C6  C6  C 0 1 N N S N N N 12.099 -138.204 16.239 1.163   0.133  -0.409 CA   QMM 23 
VNK C7  C7  C 0 1 N N N N N N 13.245 -139.213 16.203 1.135   1.595  0.041  CB   QMM 24 
VNK O2  O2  O 0 1 N N N N N N 10.119 -138.574 14.976 2.382   -1.476 0.813  O    QMM 25 
VNK N3  N3  N 0 1 N N N N N N 11.907 -137.744 13.868 3.629   -0.033 -0.319 N3   05U 26 
VNK C11 C11 C 0 1 N N S N N N 11.274 -137.601 12.566 4.861   -0.729 0.059  C11  05U 27 
VNK C12 C12 C 0 1 N N N N N N 11.220 -136.076 12.376 5.199   -1.780 -0.999 C12  05U 28 
VNK C13 C13 C 0 1 N N N N N N 9.875  -135.367 12.550 6.405   -2.601 -0.537 C13  05U 29 
VNK C15 C15 C 0 1 N N N N N N 9.080  -135.789 13.776 6.027   -3.404 0.709  C15  05U 30 
VNK C14 C14 C 0 1 N N N N N N 10.079 -133.858 12.596 6.827   -3.559 -1.653 C14  05U 31 
VNK C16 C16 C 0 1 N N S N N N 11.991 -138.271 11.373 6.007   0.280  0.159  C16  05U 32 
VNK O6  O6  O 0 1 N N N N N N 13.394 -137.964 11.473 6.190   0.920  -1.106 O6   05U 33 
VNK C17 C17 C 0 1 N N N N N N 11.822 -139.808 11.201 5.670   1.332  1.218  C17  05U 34 
VNK C23 C23 C 0 1 N N N N N N 10.527 -140.292 11.840 5.473   0.648  2.572  C23  05U 35 
VNK C18 C18 C 0 1 N N N N N N 12.935 -140.556 11.927 6.815   2.341  1.318  C18  05U 36 
VNK H22 H22 H 0 1 N N N N N N 13.344 -136.081 22.166 -5.970  0.581  -0.521 HAC1 6NA 37 
VNK H23 H23 H 0 1 N N N N N N 11.652 -135.841 22.719 -6.210  -0.940 -1.413 HAC2 6NA 38 
VNK H24 H24 H 0 1 N N N N N N 11.762 -137.713 24.196 -7.260  -1.952 0.592  HBC1 6NA 39 
VNK H25 H25 H 0 1 N N N N N N 13.279 -138.314 23.445 -7.020  -0.431 1.485  HBC2 6NA 40 
VNK H26 H26 H 0 1 N N N N N N 14.574 -136.559 24.391 -8.437  0.761  -0.164 HGC1 6NA 41 
VNK H27 H27 H 0 1 N N N N N N 13.117 -135.589 24.796 -8.677  -0.760 -1.057 HGC2 6NA 42 
VNK H28 H28 H 0 1 N N N N N N 12.444 -137.431 26.400 -9.726  -1.772 0.949  HDC1 6NA 43 
VNK H29 H29 H 0 1 N N N N N N 14.039 -138.197 26.092 -9.486  -0.251 1.842  HDC2 6NA 44 
VNK H30 H30 H 0 1 N N N N N N 14.085 -136.819 28.138 -10.903 0.941  0.192  H6C1 6NA 45 
VNK H31 H31 H 0 1 N N N N N N 15.175 -136.150 26.877 -11.143 -0.581 -0.701 H6C2 6NA 46 
VNK H32 H32 H 0 1 N N N N N N 13.580 -135.383 27.185 -11.794 -0.403 0.946  H6C3 6NA 47 
VNK H21 H21 H 0 1 N N N N N N 10.494 -136.095 20.979 -3.582  -0.346 -1.356 H    VAL 48 
VNK H13 H13 H 0 1 N N N N N N 10.226 -138.698 19.698 -2.364  -1.302 1.120  HA   VAL 49 
VNK H14 H14 H 0 1 N N N N N N 8.738  -136.213 20.098 -2.046  -2.862 -1.482 HB   VAL 50 
VNK H15 H15 H 0 1 N N N N N N 7.232  -136.401 18.168 -0.964  -3.251 1.343  HG11 VAL 51 
VNK H16 H16 H 0 1 N N N N N N 8.895  -135.923 17.687 -0.829  -4.456 0.040  HG12 VAL 52 
VNK H17 H17 H 0 1 N N N N N N 8.335  -137.610 17.427 -0.019  -2.879 -0.119 HG13 VAL 53 
VNK H18 H18 H 0 1 N N N N N N 8.230  -138.411 21.112 -4.270  -3.217 -0.444 HG21 VAL 54 
VNK H19 H19 H 0 1 N N N N N N 6.847  -137.709 20.207 -3.249  -4.666 -0.279 HG22 VAL 55 
VNK H20 H20 H 0 1 N N N N N N 7.810  -139.041 19.483 -3.485  -3.580 1.112  HG23 VAL 56 
VNK H7  H7  H 0 1 N N N N N N 13.827 -138.197 18.002 -0.997  1.784  -0.207 HG1  QMM 57 
VNK H8  H8  H 0 1 N N N N N N 13.620 -139.973 18.175 -0.045  2.244  -1.640 HG2  QMM 58 
VNK H12 H12 H 0 1 N N N N N N 10.888 -139.244 17.657 0.101   -1.069 0.983  H    QMM 59 
VNK H4  H4  H 0 1 N N N N N N 17.308 -137.254 15.490 -2.987  3.629  -0.783 HH1  QMM 60 
VNK H5  H5  H 0 1 N N N N N N 17.458 -139.043 15.417 -2.546  4.827  -2.023 HH1A QMM 61 
VNK H6  H6  H 0 1 N N N N N N 15.957 -138.243 14.841 -1.768  3.226  -2.015 HH1B QMM 62 
VNK H1  H1  H 0 1 N N N N N N 16.022 -137.353 18.786 -0.597  6.551  -0.802 HH2  QMM 63 
VNK H2  H2  H 0 1 N N N N N N 17.579 -137.090 17.930 -2.177  6.282  -0.027 HH2A QMM 64 
VNK H3  H3  H 0 1 N N N N N N 16.091 -136.259 17.363 -0.677  6.026  0.897  HH2B QMM 65 
VNK H11 H11 H 0 1 N N N N N N 12.574 -137.214 16.300 1.121   0.087  -1.497 HA   QMM 66 
VNK H9  H9  H 0 1 N N N N N N 12.839 -140.223 16.044 2.038   2.098  -0.303 HB2  QMM 67 
VNK H10 H10 H 0 1 N N N N N N 13.931 -138.960 15.381 1.087   1.639  1.130  HB3  QMM 68 
VNK H33 H33 H 0 1 N N N N N N 12.871 -137.489 13.949 3.673   0.777  -0.852 H33  05U 69 
VNK H34 H34 H 0 1 N N N N N N 10.244 -137.984 12.612 4.722   -1.216 1.024  H34  05U 70 
VNK H35 H35 H 0 1 N N N N N N 11.570 -135.863 11.355 4.343   -2.440 -1.142 H35  05U 71 
VNK H36 H36 H 0 1 N N N N N N 11.917 -135.633 13.102 5.436   -1.285 -1.941 H36  05U 72 
VNK H37 H37 H 0 1 N N N N N N 9.265  -135.593 11.663 7.231   -1.931 -0.301 H37  05U 73 
VNK H38 H38 H 0 1 N N N N N N 8.135  -135.227 13.812 5.255   -4.130 0.453  H38  05U 74 
VNK H39 H39 H 0 1 N N N N N N 8.864  -136.866 13.720 6.907   -3.926 1.085  H39  05U 75 
VNK H40 H40 H 0 1 N N N N N N 9.666  -135.580 14.683 5.649   -2.728 1.477  H40  05U 76 
VNK H41 H41 H 0 1 N N N N N N 9.106  -133.360 12.721 7.096   -2.987 -2.540 H41  05U 77 
VNK H42 H42 H 0 1 N N N N N N 10.734 -133.602 13.442 7.686   -4.144 -1.323 H42  05U 78 
VNK H43 H43 H 0 1 N N N N N N 10.545 -133.522 11.658 6.001   -4.229 -1.889 H43  05U 79 
VNK H44 H44 H 0 1 N N N N N N 11.600 -137.802 10.458 6.924   -0.237 0.441  H44  05U 80 
VNK H45 H45 H 0 1 N N N N N N 13.507 -137.027 11.578 5.412   1.401  -1.419 H45  05U 81 
VNK H46 H46 H 0 1 N N N N N N 11.833 -140.063 10.131 4.753   1.850  0.936  H46  05U 82 
VNK H47 H47 H 0 1 N N N N N N 10.434 -141.380 11.703 4.657   -0.071 2.501  H47  05U 83 
VNK H48 H48 H 0 1 N N N N N N 10.538 -140.057 12.915 6.390   0.130  2.854  H48  05U 84 
VNK H49 H49 H 0 1 N N N N N N 9.673  -139.789 11.364 5.233   1.397  3.326  H49  05U 85 
VNK H50 H50 H 0 1 N N N N N N 12.797 -141.639 11.793 6.955   2.829  0.353  H50  05U 86 
VNK H51 H51 H 0 1 N N N N N N 13.909 -140.256 11.513 6.575   3.091  2.072  H51  05U 87 
VNK H52 H52 H 0 1 N N N N N N 12.902 -140.312 12.999 7.732   1.824  1.599  H52  05U 88 
# 
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 
VNK C17 C16 SING N N 1  
VNK C17 C23 SING N N 2  
VNK C17 C18 SING N N 3  
VNK C16 O6  SING N N 4  
VNK C16 C11 SING N N 5  
VNK C12 C13 SING N N 6  
VNK C12 C11 SING N N 7  
VNK C13 C14 SING N N 8  
VNK C13 C15 SING N N 9  
VNK C11 N3  SING N N 10 
VNK N3  C10 SING N N 11 
VNK C10 O2  DOUB N N 12 
VNK C10 C6  SING N N 13 
VNK C24 N5  SING N N 14 
VNK C7  C6  SING N N 15 
VNK C7  C8  SING N N 16 
VNK C6  N2  SING N N 17 
VNK N5  C9  SING N N 18 
VNK N5  C25 SING N N 19 
VNK C9  C8  SING N N 20 
VNK C9  O7  DOUB N N 21 
VNK N2  C5  SING N N 22 
VNK C26 C3  SING N N 23 
VNK O3  C5  DOUB N N 24 
VNK C5  C2  SING N N 25 
VNK C3  C2  SING N N 26 
VNK C3  C4  SING N N 27 
VNK C2  N1  SING N N 28 
VNK N1  C1  SING N N 29 
VNK O1  C1  DOUB N N 30 
VNK C1  C27 SING N N 31 
VNK C27 C28 SING N N 32 
VNK C28 C29 SING N N 33 
VNK C29 C30 SING N N 34 
VNK C30 C31 SING N N 35 
VNK C25 H1  SING N N 36 
VNK C25 H2  SING N N 37 
VNK C25 H3  SING N N 38 
VNK C24 H4  SING N N 39 
VNK C24 H5  SING N N 40 
VNK C24 H6  SING N N 41 
VNK C8  H7  SING N N 42 
VNK C8  H8  SING N N 43 
VNK C7  H9  SING N N 44 
VNK C7  H10 SING N N 45 
VNK C6  H11 SING N N 46 
VNK N2  H12 SING N N 47 
VNK C2  H13 SING N N 48 
VNK C3  H14 SING N N 49 
VNK C26 H15 SING N N 50 
VNK C26 H16 SING N N 51 
VNK C26 H17 SING N N 52 
VNK C4  H18 SING N N 53 
VNK C4  H19 SING N N 54 
VNK C4  H20 SING N N 55 
VNK N1  H21 SING N N 56 
VNK C27 H22 SING N N 57 
VNK C27 H23 SING N N 58 
VNK C28 H24 SING N N 59 
VNK C28 H25 SING N N 60 
VNK C29 H26 SING N N 61 
VNK C29 H27 SING N N 62 
VNK C30 H28 SING N N 63 
VNK C30 H29 SING N N 64 
VNK C31 H30 SING N N 65 
VNK C31 H31 SING N N 66 
VNK C31 H32 SING N N 67 
VNK N3  H33 SING N N 68 
VNK C11 H34 SING N N 69 
VNK C12 H35 SING N N 70 
VNK C12 H36 SING N N 71 
VNK C13 H37 SING N N 72 
VNK C15 H38 SING N N 73 
VNK C15 H39 SING N N 74 
VNK C15 H40 SING N N 75 
VNK C14 H41 SING N N 76 
VNK C14 H42 SING N N 77 
VNK C14 H43 SING N N 78 
VNK C16 H44 SING N N 79 
VNK O6  H45 SING N N 80 
VNK C17 H46 SING N N 81 
VNK C23 H47 SING N N 82 
VNK C23 H48 SING N N 83 
VNK C23 H49 SING N N 84 
VNK C18 H50 SING N N 85 
VNK C18 H51 SING N N 86 
VNK C18 H52 SING N N 87 
# 
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 
VNK SMILES           ACDLabs              12.01 "O=C(NC(CC(C)C)C(O)C(C)C)C(NC(=O)C(NC(=O)CCCCC)C(C)C)CCC(=O)N(C)C"                                                                                                                                          
VNK InChI            InChI                1.03  "InChI=1S/C27H52N4O5/c1-10-11-12-13-22(32)30-24(18(4)5)27(36)28-20(14-15-23(33)31(8)9)26(35)29-21(16-17(2)3)25(34)19(6)7/h17-21,24-25,34H,10-16H2,1-9H3,(H,28,36)(H,29,35)(H,30,32)/t20-,21-,24-,25-/m0/s1" 
VNK InChIKey         InChI                1.03  NHNWMUWCUHYJIR-NBMBROAQSA-N                                                                                                                                                                                 
VNK SMILES_CANONICAL CACTVS               3.370 "CCCCCC(=O)N[C@@H](C(C)C)C(=O)N[C@@H](CCC(=O)N(C)C)C(=O)N[C@@H](CC(C)C)[C@@H](O)C(C)C"                                                                                                                      
VNK SMILES           CACTVS               3.370 "CCCCCC(=O)N[CH](C(C)C)C(=O)N[CH](CCC(=O)N(C)C)C(=O)N[CH](CC(C)C)[CH](O)C(C)C"                                                                                                                              
VNK SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CCCCCC(=O)N[C@@H](C(C)C)C(=O)N[C@@H](CCC(=O)N(C)C)C(=O)N[C@@H](CC(C)C)[C@H](C(C)C)O"                                                                                                                       
VNK SMILES           "OpenEye OEToolkits" 1.7.6 "CCCCCC(=O)NC(C(C)C)C(=O)NC(CCC(=O)N(C)C)C(=O)NC(CC(C)C)C(C(C)C)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 
VNK "SYSTEMATIC NAME" ACDLabs              12.01 "N-hexanoyl-L-valyl-N~1~-[(3S,4S)-3-hydroxy-2,6-dimethylheptan-4-yl]-N~5~,N~5~-dimethyl-L-glutamamide"                                   
VNK "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2S)-N-[(3S,4S)-2,6-dimethyl-3-oxidanyl-heptan-4-yl]-2-[[(2S)-2-(hexanoylamino)-3-methyl-butanoyl]amino]-N',N'-dimethyl-pentanediamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
VNK "Create component" 2012-11-01 RCSB 
VNK "Initial release"  2014-01-29 RCSB 
VNK "Modify synonyms"  2020-06-05 PDBE 
VNK "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      VNK 
_pdbx_chem_comp_synonyms.name         "vinylketone carmaphycin analogue VNK1, double bound form" 
_pdbx_chem_comp_synonyms.provenance   ? 
_pdbx_chem_comp_synonyms.type         ? 
# 
loop_
_pdbx_chem_comp_pcm.pcm_id 
_pdbx_chem_comp_pcm.comp_id 
_pdbx_chem_comp_pcm.modified_residue_id 
_pdbx_chem_comp_pcm.type 
_pdbx_chem_comp_pcm.category 
_pdbx_chem_comp_pcm.position 
_pdbx_chem_comp_pcm.polypeptide_position 
_pdbx_chem_comp_pcm.comp_id_linking_atom 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession 
1 VNK THR None "Covalent chemical modification" "Amino-acid backbone"   N-terminal     C17 N   ? ? 
2 VNK THR None "Covalent chemical modification" "Amino-acid side chain" "Any position" C16 OG1 ? ? 
# 
