data_VLK
# 
_chem_comp.id                                    VLK 
_chem_comp.name                                  "(2R)-2-[[methanoyl(oxidanyl)amino]methyl]-N-[(2S)-3-methyl-1-oxidanylidene-1-[2-(sulfanylmethyl)pyrrolidin-1-yl]butan-2-yl]heptanamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C19 H35 N3 O4 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-03-15 
_chem_comp.pdbx_modified_date                    2023-12-22 
_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                        401.564 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VLK 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        8OFE 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
# 
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 
VLK C1  C1  C 0 1 N N N N N N -5.928  21.982 7.542 6.288  -4.354 -0.963 C1  VLK 1  
VLK C2  C2  C 0 1 N N N N N N -4.657  21.403 8.126 5.073  -3.501 -1.334 C2  VLK 2  
VLK C6  C3  C 0 1 N N R N N N -5.008  16.936 5.830 2.361  0.498  -0.065 C6  VLK 3  
VLK C5  C4  C 0 1 N N N N N N -4.060  18.117 6.051 3.640  -0.288 0.231  C5  VLK 4  
VLK C4  C5  C 0 1 N N N N N N -4.756  19.332 6.638 3.749  -1.468 -0.737 C4  VLK 5  
VLK C3  C6  C 0 1 N N N N N N -3.898  20.466 7.194 4.964  -2.321 -0.366 C3  VLK 6  
VLK C11 C7  C 0 1 N N N N N N -9.243  18.957 5.169 -2.429 -0.231 -0.410 C11 VLK 7  
VLK C10 C8  C 0 1 N N S N N N -8.493  17.800 4.519 -1.248 -0.691 0.405  C10 VLK 8  
VLK C8  C9  C 0 1 N N N N N N -2.293  15.372 6.547 3.291  3.394  -0.758 C8  VLK 9  
VLK C18 C10 C 0 1 N N N N N N -8.647  15.570 3.403 -0.373 -1.025 2.721  C18 VLK 10 
VLK C17 C11 C 0 1 N N N N N N -9.391  16.572 4.276 -1.572 -0.558 1.894  C17 VLK 11 
VLK C19 C12 C 0 1 N N N N N N -9.845  15.917 5.567 -1.878 0.905  2.221  C19 VLK 12 
VLK C7  C13 C 0 1 N N N N N N -4.328  15.695 5.274 2.335  1.769  0.786  C7  VLK 13 
VLK C9  C14 C 0 1 N N N N N N -6.115  17.325 4.858 1.161  -0.353 0.266  C9  VLK 14 
VLK N1  N1  N 0 1 N N N N N N -3.541  15.145 6.361 3.419  2.660  0.366  N1  VLK 15 
VLK N2  N2  N 0 1 N N N N N N -7.341  17.485 5.359 -0.082 0.136  0.084  N2  VLK 16 
VLK N3  N3  N 0 1 N N N N N N -10.105 19.629 4.378 -3.619 -0.849 -0.279 N3  VLK 17 
VLK O1  O1  O 0 1 N N N N N N -4.135  14.406 7.383 4.601  2.751  1.140  O1  VLK 18 
VLK O2  O2  O 0 1 N N N N N N -1.782  15.089 7.588 4.188  4.131  -1.106 O2  VLK 19 
VLK O3  O3  O 0 1 N N N N N N -5.870  17.479 3.675 1.314  -1.476 0.696  O3  VLK 20 
VLK O4  O4  O 0 1 N N N N N N -9.058  19.270 6.345 -2.309 0.696  -1.182 O4  VLK 21 
VLK H1  H1  H 0 1 N N N N N N -6.405  22.642 8.282 6.365  -5.195 -1.653 H1  VLK 22 
VLK H2  H2  H 0 1 N N N N N N -5.686  22.560 6.638 7.191  -3.747 -1.026 H2  VLK 23 
VLK H3  H3  H 0 1 N N N N N N -6.617  21.165 7.282 6.172  -4.728 0.054  H3  VLK 24 
VLK H5  H4  H 0 1 N N N N N N -4.922  20.842 9.035 5.189  -3.127 -2.351 H5  VLK 25 
VLK H4  H5  H 0 1 N N N N N N -3.990  22.237 8.391 4.170  -4.108 -1.270 H4  VLK 26 
VLK H12 H6  H 0 1 N N N N N N -5.469  16.677 6.795 2.336  0.766  -1.121 H12 VLK 27 
VLK H10 H7  H 0 1 N N N N N N -3.262  17.803 6.740 4.504  0.364  0.108  H10 VLK 28 
VLK H11 H8  H 0 1 N N N N N N -3.619  18.399 5.084 3.609  -0.660 1.255  H11 VLK 29 
VLK H8  H9  H 0 1 N N N N N N -5.386  19.760 5.844 2.846  -2.075 -0.673 H8  VLK 30 
VLK H9  H10 H 0 1 N N N N N N -5.394  18.975 7.460 3.865  -1.094 -1.754 H9  VLK 31 
VLK H6  H11 H 0 1 N N N N N N -3.058  20.026 7.752 4.848  -2.695 0.651  H6  VLK 32 
VLK H7  H12 H 0 1 N N N N N N -3.509  21.054 6.350 5.867  -1.714 -0.429 H7  VLK 33 
VLK H18 H13 H 0 1 N N N N N N -8.129  18.144 3.540 -1.030 -1.733 0.172  H18 VLK 34 
VLK H16 H14 H 0 1 N N N N N N -1.703  15.820 5.761 2.389  3.324  -1.348 H16 VLK 35 
VLK H31 H15 H 0 1 N N N N N N -9.285  14.691 3.227 -0.604 -0.930 3.782  H31 VLK 36 
VLK H30 H16 H 0 1 N N N N N N -8.395  16.039 2.440 -0.155 -2.067 2.488  H30 VLK 37 
VLK H32 H17 H 0 1 N N N N N N -7.723  15.256 3.911 0.495  -0.410 2.482  H32 VLK 38 
VLK H29 H18 H 0 1 N N N N N N -10.284 16.908 3.728 -2.440 -1.173 2.133  H29 VLK 39 
VLK H35 H19 H 0 1 N N N N N N -10.380 16.654 6.184 -1.011 1.520  1.982  H35 VLK 40 
VLK H33 H20 H 0 1 N N N N N N -10.516 15.077 5.335 -2.733 1.238  1.632  H33 VLK 41 
VLK H34 H21 H 0 1 N N N N N N -8.968  15.545 6.117 -2.110 1.000  3.282  H34 VLK 42 
VLK H14 H22 H 0 1 N N N N N N -5.080  14.965 4.940 1.378  2.274  0.656  H14 VLK 43 
VLK H13 H23 H 0 1 N N N N N N -3.677  15.963 4.429 2.467  1.506  1.836  H13 VLK 44 
VLK H17 H24 H 0 1 N N N N N N -7.476  17.386 6.345 -0.204 1.035  -0.260 H17 VLK 45 
VLK H15 H27 H 0 1 N N N N N N -3.501  14.254 8.074 5.259  3.364  0.783  H15 VLK 46 
VLK C14 C15 C 0 1 N N N N N N ?       ?      ?     -4.878 -0.428 -0.911 C14 VLK 47 
VLK C12 C16 C 0 1 N N N N N N ?       ?      ?     -5.961 -1.448 -0.501 C12 VLK 48 
VLK C15 C17 C 0 1 N N N N N N ?       ?      ?     -5.131 -2.702 -0.122 C15 VLK 49 
VLK C16 C18 C 0 1 N N N N N N ?       ?      ?     -3.874 -2.065 0.516  C16 VLK 50 
VLK C13 C19 C 0 1 N N N N N N ?       ?      ?     -5.265 0.969  -0.420 C13 VLK 51 
VLK H19 H26 H 0 1 N N N N N N ?       ?      ?     -4.765 -0.423 -1.996 H19 VLK 52 
VLK H20 H38 H 0 1 N N N N N N ?       ?      ?     -6.527 -1.085 0.357  H20 VLK 53 
VLK H21 H28 H 0 1 N N N N N N ?       ?      ?     -6.625 -1.663 -1.339 H21 VLK 54 
VLK H22 H29 H 0 1 N N N N N N ?       ?      ?     -5.665 -3.321 0.599  H22 VLK 55 
VLK H23 H30 H 0 1 N N N N N N ?       ?      ?     -4.866 -3.278 -1.008 H23 VLK 56 
VLK H24 H31 H 0 1 N N N N N N ?       ?      ?     -3.027 -2.748 0.451  H24 VLK 57 
VLK H25 H25 H 0 1 N N N N N N ?       ?      ?     -4.069 -1.798 1.554  H25 VLK 58 
VLK H27 H34 H 0 1 N N N N N N ?       ?      ?     -6.267 1.213  -0.773 H27 VLK 59 
VLK H28 H37 H 0 1 N N N N N N ?       ?      ?     -5.249 0.987  0.670  H28 VLK 60 
VLK S1  S1  S 0 1 N N N N N N ?       ?      ?     -4.084 2.185  -1.063 S1  VLK 61 
VLK H26 H35 H 0 1 N N N N N N ?       ?      ?     -4.540 3.346  -0.559 H26 VLK 62 
# 
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 
VLK C18 C17 SING N N 1  
VLK O3  C9  DOUB N N 2  
VLK C17 C10 SING N N 3  
VLK C17 C19 SING N N 4  
VLK N3  C11 SING N N 5  
VLK C10 C11 SING N N 6  
VLK C10 N2  SING N N 7  
VLK C9  N2  SING N N 8  
VLK C9  C6  SING N N 9  
VLK C11 O4  DOUB N N 10 
VLK C7  C6  SING N N 11 
VLK C7  N1  SING N N 12 
VLK C6  C5  SING N N 13 
VLK C5  C4  SING N N 14 
VLK N1  C8  SING N N 15 
VLK N1  O1  SING N N 16 
VLK C8  O2  DOUB N N 17 
VLK C4  C3  SING N N 18 
VLK C3  C2  SING N N 19 
VLK C1  C2  SING N N 20 
VLK C1  H1  SING N N 21 
VLK C1  H2  SING N N 22 
VLK C1  H3  SING N N 23 
VLK C2  H5  SING N N 24 
VLK C2  H4  SING N N 25 
VLK C6  H12 SING N N 26 
VLK C5  H10 SING N N 27 
VLK C5  H11 SING N N 28 
VLK C4  H8  SING N N 29 
VLK C4  H9  SING N N 30 
VLK C3  H6  SING N N 31 
VLK C3  H7  SING N N 32 
VLK C10 H18 SING N N 33 
VLK C8  H16 SING N N 34 
VLK C18 H31 SING N N 35 
VLK C18 H30 SING N N 36 
VLK C18 H32 SING N N 37 
VLK C17 H29 SING N N 38 
VLK C19 H35 SING N N 39 
VLK C19 H33 SING N N 40 
VLK C19 H34 SING N N 41 
VLK C7  H14 SING N N 42 
VLK C7  H13 SING N N 43 
VLK N2  H17 SING N N 44 
VLK O1  H15 SING N N 45 
VLK N3  C14 SING N N 46 
VLK C14 C12 SING N N 47 
VLK C12 C15 SING N N 48 
VLK C15 C16 SING N N 49 
VLK C16 N3  SING N N 50 
VLK C14 C13 SING N N 51 
VLK C14 H19 SING N N 52 
VLK C12 H20 SING N N 53 
VLK C12 H21 SING N N 54 
VLK C15 H22 SING N N 55 
VLK C15 H23 SING N N 56 
VLK C16 H24 SING N N 57 
VLK C16 H25 SING N N 58 
VLK C13 H27 SING N N 59 
VLK C13 H28 SING N N 60 
VLK C13 S1  SING N N 61 
VLK S1  H26 SING N N 62 
# 
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 
VLK InChI            InChI                1.06  "InChI=1S/C19H35N3O4S/c1-4-5-6-8-15(11-21(26)13-23)18(24)20-17(14(2)3)19(25)22-10-7-9-16(22)12-27/h13-17,26-27H,4-12H2,1-3H3,(H,20,24)/t15-,16?,17+/m1/s1" 
VLK InChIKey         InChI                1.06  KKQZXQHPCTWHGR-SKQWJGTPSA-N                                                                                                                                
VLK SMILES_CANONICAL CACTVS               3.385 "CCCCC[C@H](CN(O)C=O)C(=O)N[C@@H](C(C)C)C(=O)N1CCCC1CS"                                                                                                    
VLK SMILES           CACTVS               3.385 "CCCCC[CH](CN(O)C=O)C(=O)N[CH](C(C)C)C(=O)N1CCCC1CS"                                                                                                       
VLK SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCCCC[C@H](CN(C=O)O)C(=O)N[C@@H](C(C)C)C(=O)N1CCCC1CS"                                                                                                    
VLK SMILES           "OpenEye OEToolkits" 2.0.7 "CCCCCC(CN(C=O)O)C(=O)NC(C(C)C)C(=O)N1CCCC1CS"                                                                                                             
# 
_pdbx_chem_comp_identifier.comp_id           VLK 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "(2~{R})-2-[[methanoyl(oxidanyl)amino]methyl]-~{N}-[(2~{S})-3-methyl-1-oxidanylidene-1-[2-(sulfanylmethyl)pyrrolidin-1-yl]butan-2-yl]heptanamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
VLK "Create component"  2023-03-15 PDBE 
VLK "Modify descriptor" 2023-03-23 PDBE 
VLK "Initial release"   2023-12-27 RCSB 
# 
