data_VN6
# 
_chem_comp.id                                    VN6 
_chem_comp.name                                  "5-[[3-(aminomethyl)azetidin-1-yl]methyl]-N-[4-[4-(4-cyano-6-methyl-pyrimidin-2-yl)piperazin-1-yl]sulfonylphenyl]-2-[methyl(methylsulfonyl)amino]benzamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C30 H37 N9 O5 S2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-09-14 
_chem_comp.pdbx_modified_date                    2024-04-12 
_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                        667.802 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VN6 
_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        8QK5 
_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 
VN6 C5  C1  C 0 1 Y N N N N N 5.753  7.685  5.623  9.533  -2.421 -0.226 C5  VN6 1  
VN6 C6  C2  C 0 1 Y N N N N N 4.864  6.747  5.145  10.301 -1.704 0.678  C6  VN6 2  
VN6 N7  N1  N 0 1 N N N N N N 4.004  10.720 4.792  6.383  -0.790 0.077  N7  VN6 3  
VN6 C8  C3  C 0 1 N N N N N N 5.107  11.651 4.987  5.966  0.339  0.919  C8  VN6 4  
VN6 C26 C4  C 0 1 Y N N N N N -2.175 12.287 11.944 -5.140 -0.786 -0.600 C26 VN6 5  
VN6 C27 C5  C 0 1 Y N N N N N -3.214 11.905 12.798 -6.432 -1.238 -0.442 C27 VN6 6  
VN6 C28 C6  C 0 1 Y N N N N N -3.721 12.801 13.734 -7.350 -0.495 0.284  C28 VN6 7  
VN6 C29 C7  C 0 1 Y N N N N N -3.213 14.091 13.823 -6.981 0.705  0.857  C29 VN6 8  
VN6 C30 C8  C 0 1 Y N N N N N -2.200 14.507 12.966 -5.683 1.176  0.710  C30 VN6 9  
VN6 C32 C9  C 0 1 N N N N N N -1.849 16.344 14.506 -4.874 2.425  2.684  C32 VN6 10 
VN6 C37 C10 C 0 1 N N N N N N 7.048  7.255  6.320  10.139 -3.559 -1.007 C37 VN6 11 
VN6 C38 C11 C 0 1 N N N N N N 2.744  6.239  4.054  10.450 0.113  2.324  C38 VN6 12 
VN6 C40 C12 C 0 1 N N N N N N -3.785 10.521 12.799 -6.850 -2.546 -1.062 C40 VN6 13 
VN6 C42 C13 C 0 1 N N N N N N -4.899 8.744  11.747 -7.222 -4.894 -0.582 C42 VN6 14 
VN6 C1  C14 C 0 1 Y N N N N N 3.689  7.174  4.537  9.698  -0.657 1.380  C1  VN6 15 
VN6 N2  N2  N 0 1 Y N N N N N 3.441  8.467  4.406  8.413  -0.387 1.157  N2  VN6 16 
VN6 C3  C15 C 0 1 Y N N N N N 4.352  9.381  4.809  7.717  -1.097 0.285  C3  VN6 17 
VN6 N4  N3  N 0 1 Y N N N N N 5.470  8.995  5.470  8.261  -2.099 -0.392 N4  VN6 18 
VN6 C9  C16 C 0 1 N N N N N N 4.482  12.931 5.542  4.450  0.530  0.797  C9  VN6 19 
VN6 C10 C17 C 0 1 N N N N N N 3.158  11.113 3.715  6.119  -0.522 -1.343 C10 VN6 20 
VN6 C11 C18 C 0 1 N N N N N N 2.447  12.410 4.171  4.610  -0.366 -1.558 C11 VN6 21 
VN6 N12 N4  N 0 1 N N N N N N 3.491  13.454 4.548  4.109  0.658  -0.628 N12 VN6 22 
VN6 S13 S1  S 0 1 N N N N N N 2.788  14.870 5.071  3.185  1.920  -1.172 S13 VN6 23 
VN6 C14 C19 C 0 1 Y N N N N N 1.800  14.576 6.484  1.501  1.406  -1.090 C14 VN6 24 
VN6 O15 O1  O 0 1 N N N N N N 3.839  15.800 5.363  3.332  2.964  -0.219 O15 VN6 25 
VN6 O16 O2  O 0 1 N N N N N N 1.966  15.354 4.010  3.490  2.076  -2.551 O16 VN6 26 
VN6 C17 C20 C 0 1 Y N N N N N 0.483  14.287 6.305  0.919  0.775  -2.174 C17 VN6 27 
VN6 C18 C21 C 0 1 Y N N N N N -0.331 14.047 7.384  -0.400 0.371  -2.113 C18 VN6 28 
VN6 C19 C22 C 0 1 Y N N N N N 0.165  14.078 8.682  -1.143 0.600  -0.962 C19 VN6 29 
VN6 C20 C23 C 0 1 Y N N N N N 2.346  14.603 7.798  0.766  1.631  0.060  C20 VN6 30 
VN6 C21 C24 C 0 1 Y N N N N N 1.504  14.331 8.903  -0.555 1.235  0.125  C21 VN6 31 
VN6 N22 N5  N 0 1 N N N N N N -0.722 13.743 9.719  -2.479 0.193  -0.897 N22 VN6 32 
VN6 C23 C25 C 0 1 N N N N N N -0.533 14.025 11.046 -3.370 0.916  -0.190 C23 VN6 33 
VN6 O24 O3  O 0 1 N N N N N N 0.488  14.601 11.441 -3.035 1.972  0.311  O24 VN6 34 
VN6 C25 C26 C 0 1 Y N N N N N -1.635 13.584 12.036 -4.751 0.427  -0.025 C25 VN6 35 
VN6 N31 N6  N 0 1 N N N N N N -1.643 15.837 13.113 -5.309 2.384  1.285  N31 VN6 36 
VN6 S33 S2  S 0 1 N N N N N N -2.295 16.881 12.037 -5.356 3.777  0.391  S33 VN6 37 
VN6 C34 C27 C 0 1 N N N N N N -4.021 17.149 12.439 -7.028 4.429  0.655  C34 VN6 38 
VN6 O35 O4  O 0 1 N N N N N N -1.565 18.095 12.112 -4.390 4.619  1.004  O35 VN6 39 
VN6 O36 O5  O 0 1 N N N N N N -2.189 16.347 10.712 -5.198 3.337  -0.951 O36 VN6 40 
VN6 N39 N7  N 0 1 N N N N N N 1.966  5.524  3.664  11.046 0.724  3.074  N39 VN6 41 
VN6 N41 N8  N 0 1 N N N N N N -4.281 10.086 11.520 -6.611 -3.638 -0.109 N41 VN6 42 
VN6 C43 C28 C 0 1 N N N N N N -5.618 10.675 11.254 -5.293 -4.259 -0.336 C43 VN6 43 
VN6 C44 C29 C 0 1 N N N N N N -6.167 9.270  11.090 -5.958 -5.625 -0.107 C44 VN6 44 
VN6 C45 C30 C 0 1 N N N N N N -6.137 8.881  9.610  -6.002 -6.062 1.359  C45 VN6 45 
VN6 N46 N9  N 0 1 N N N N N N -7.288 8.017  9.278  -6.546 -7.424 1.448  N46 VN6 46 
VN6 H1  H1  H 0 1 N N N N N N 5.077  5.693  5.242  11.341 -1.949 0.836  H1  VN6 47 
VN6 H2  H2  H 0 1 N N N N N N 5.834  11.239 5.702  6.223  0.133  1.958  H2  VN6 48 
VN6 H3  H3  H 0 1 N N N N N N 5.610  11.854 4.030  6.474  1.245  0.590  H3  VN6 49 
VN6 H4  H4  H 0 1 N N N N N N -1.788 11.589 11.216 -4.428 -1.371 -1.163 H4  VN6 50 
VN6 H5  H5  H 0 1 N N N N N N -4.516 12.491 14.397 -8.361 -0.858 0.401  H5  VN6 51 
VN6 H6  H6  H 0 1 N N N N N N -3.607 14.774 14.561 -7.703 1.278  1.421  H6  VN6 52 
VN6 H7  H7  H 0 1 N N N N N N -1.408 15.636 15.223 -3.796 2.277  2.733  H7  VN6 53 
VN6 H8  H8  H 0 1 N N N N N N -1.364 17.326 14.614 -5.128 3.394  3.115  H8  VN6 54 
VN6 H9  H9  H 0 1 N N N N N N -2.926 16.443 14.704 -5.376 1.636  3.244  H9  VN6 55 
VN6 H10 H10 H 0 1 N N N N N N 7.615  8.147  6.624  10.017 -4.487 -0.449 H10 VN6 56 
VN6 H11 H11 H 0 1 N N N N N N 6.804  6.655  7.209  9.637  -3.646 -1.970 H11 VN6 57 
VN6 H12 H12 H 0 1 N N N N N N 7.655  6.654  5.627  11.200 -3.366 -1.165 H12 VN6 58 
VN6 H13 H13 H 0 1 N N N N N N -4.616 10.491 13.519 -7.910 -2.507 -1.313 H13 VN6 59 
VN6 H14 H14 H 0 1 N N N N N N -2.997 9.823  13.119 -6.269 -2.720 -1.968 H14 VN6 60 
VN6 H15 H15 H 0 1 N N N N N N -5.015 8.468  12.806 -8.120 -5.175 -0.030 H15 VN6 61 
VN6 H16 H16 H 0 1 N N N N N N -4.412 7.920  11.204 -7.364 -4.929 -1.662 H16 VN6 62 
VN6 H17 H17 H 0 1 N N N N N N 5.267  13.682 5.712  3.937  -0.333 1.220  H17 VN6 63 
VN6 H18 H18 H 0 1 N N N N N N 3.973  12.712 6.492  4.151  1.433  1.330  H18 VN6 64 
VN6 H19 H19 H 0 1 N N N N N N 2.418  10.327 3.506  6.626  0.396  -1.640 H19 VN6 65 
VN6 H20 H20 H 0 1 N N N N N N 3.756  11.304 2.811  6.488  -1.353 -1.944 H20 VN6 66 
VN6 H21 H21 H 0 1 N N N N N N 1.823  12.794 3.351  4.417  -0.054 -2.585 H21 VN6 67 
VN6 H22 H22 H 0 1 N N N N N N 1.813  12.194 5.043  4.112  -1.315 -1.360 H22 VN6 68 
VN6 H23 H23 H 0 1 N N N N N N 0.074  14.246 5.306  1.497  0.597  -3.069 H23 VN6 69 
VN6 H24 H24 H 0 1 N N N N N N -1.376 13.830 7.221  -0.854 -0.122 -2.960 H24 VN6 70 
VN6 H25 H25 H 0 1 N N N N N N 3.391  14.829 7.950  1.225  2.121  0.906  H25 VN6 71 
VN6 H26 H26 H 0 1 N N N N N N 1.904  14.322 9.906  -1.130 1.415  1.021  H26 VN6 72 
VN6 H27 H27 H 0 1 N N N N N N -1.560 13.259 9.468  -2.765 -0.609 -1.361 H27 VN6 73 
VN6 H28 H28 H 0 1 N N N N N N -4.102 17.559 13.457 -7.148 5.357  0.096  H28 VN6 74 
VN6 H29 H29 H 0 1 N N N N N N -4.458 17.859 11.722 -7.761 3.699  0.310  H29 VN6 75 
VN6 H30 H30 H 0 1 N N N N N N -4.563 16.193 12.385 -7.179 4.622  1.717  H30 VN6 76 
VN6 H32 H32 H 0 1 N N N N N N -5.670 11.292 10.345 -4.919 -4.125 -1.351 H32 VN6 77 
VN6 H33 H33 H 0 1 N N N N N N -6.045 11.233 12.100 -4.555 -4.001 0.423  H33 VN6 78 
VN6 H34 H34 H 0 1 N N N N N N -7.106 9.056  11.621 -5.614 -6.408 -0.782 H34 VN6 79 
VN6 H35 H35 H 0 1 N N N N N N -5.204 8.338  9.397  -4.994 -6.046 1.773  H35 VN6 80 
VN6 H36 H36 H 0 1 N N N N N N -6.179 9.792  8.995  -6.637 -5.379 1.923  H36 VN6 81 
VN6 H37 H37 H 0 1 N N N N N N -7.253 7.772  8.309  -6.585 -7.735 2.407  H37 VN6 82 
VN6 H38 H38 H 0 1 N N N N N N -7.252 7.186  9.833  -7.455 -7.479 1.013  H38 VN6 83 
# 
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 
VN6 N39 C38 TRIP N N 1  
VN6 C10 C11 SING N N 2  
VN6 C10 N7  SING N N 3  
VN6 O16 S13 DOUB N N 4  
VN6 C38 C1  SING N N 5  
VN6 C11 N12 SING N N 6  
VN6 N2  C1  DOUB Y N 7  
VN6 N2  C3  SING Y N 8  
VN6 C1  C6  SING Y N 9  
VN6 N12 S13 SING N N 10 
VN6 N12 C9  SING N N 11 
VN6 N7  C3  SING N N 12 
VN6 N7  C8  SING N N 13 
VN6 C3  N4  DOUB Y N 14 
VN6 C8  C9  SING N N 15 
VN6 S13 O15 DOUB N N 16 
VN6 S13 C14 SING N N 17 
VN6 C6  C5  DOUB Y N 18 
VN6 N4  C5  SING Y N 19 
VN6 C5  C37 SING N N 20 
VN6 C17 C14 DOUB Y N 21 
VN6 C17 C18 SING Y N 22 
VN6 C14 C20 SING Y N 23 
VN6 C18 C19 DOUB Y N 24 
VN6 C20 C21 DOUB Y N 25 
VN6 C19 C21 SING Y N 26 
VN6 C19 N22 SING N N 27 
VN6 N46 C45 SING N N 28 
VN6 C45 C44 SING N N 29 
VN6 N22 C23 SING N N 30 
VN6 O36 S33 DOUB N N 31 
VN6 C23 O24 DOUB N N 32 
VN6 C23 C25 SING N N 33 
VN6 C44 C43 SING N N 34 
VN6 C44 C42 SING N N 35 
VN6 C43 N41 SING N N 36 
VN6 N41 C42 SING N N 37 
VN6 N41 C40 SING N N 38 
VN6 C26 C25 DOUB Y N 39 
VN6 C26 C27 SING Y N 40 
VN6 C25 C30 SING Y N 41 
VN6 S33 O35 DOUB N N 42 
VN6 S33 C34 SING N N 43 
VN6 S33 N31 SING N N 44 
VN6 C27 C40 SING N N 45 
VN6 C27 C28 DOUB Y N 46 
VN6 C30 N31 SING N N 47 
VN6 C30 C29 DOUB Y N 48 
VN6 N31 C32 SING N N 49 
VN6 C28 C29 SING Y N 50 
VN6 C6  H1  SING N N 51 
VN6 C8  H2  SING N N 52 
VN6 C8  H3  SING N N 53 
VN6 C26 H4  SING N N 54 
VN6 C28 H5  SING N N 55 
VN6 C29 H6  SING N N 56 
VN6 C32 H7  SING N N 57 
VN6 C32 H8  SING N N 58 
VN6 C32 H9  SING N N 59 
VN6 C37 H10 SING N N 60 
VN6 C37 H11 SING N N 61 
VN6 C37 H12 SING N N 62 
VN6 C40 H13 SING N N 63 
VN6 C40 H14 SING N N 64 
VN6 C42 H15 SING N N 65 
VN6 C42 H16 SING N N 66 
VN6 C9  H17 SING N N 67 
VN6 C9  H18 SING N N 68 
VN6 C10 H19 SING N N 69 
VN6 C10 H20 SING N N 70 
VN6 C11 H21 SING N N 71 
VN6 C11 H22 SING N N 72 
VN6 C17 H23 SING N N 73 
VN6 C18 H24 SING N N 74 
VN6 C20 H25 SING N N 75 
VN6 C21 H26 SING N N 76 
VN6 N22 H27 SING N N 77 
VN6 C34 H28 SING N N 78 
VN6 C34 H29 SING N N 79 
VN6 C34 H30 SING N N 80 
VN6 C43 H32 SING N N 81 
VN6 C43 H33 SING N N 82 
VN6 C44 H34 SING N N 83 
VN6 C45 H35 SING N N 84 
VN6 C45 H36 SING N N 85 
VN6 N46 H37 SING N N 86 
VN6 N46 H38 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 
VN6 InChI            InChI                1.06  "InChI=1S/C30H37N9O5S2/c1-21-14-25(17-32)35-30(33-21)38-10-12-39(13-11-38)46(43,44)26-7-5-24(6-8-26)34-29(40)27-15-22(18-37-19-23(16-31)20-37)4-9-28(27)36(2)45(3,41)42/h4-9,14-15,23H,10-13,16,18-20,31H2,1-3H3,(H,34,40)" 
VN6 InChIKey         InChI                1.06  YZXAAZBUIFNWLC-UHFFFAOYSA-N                                                                                                                                                                                                 
VN6 SMILES_CANONICAL CACTVS               3.385 "CN(c1ccc(CN2CC(CN)C2)cc1C(=O)Nc3ccc(cc3)[S](=O)(=O)N4CCN(CC4)c5nc(C)cc(n5)C#N)[S](C)(=O)=O"                                                                                                                                
VN6 SMILES           CACTVS               3.385 "CN(c1ccc(CN2CC(CN)C2)cc1C(=O)Nc3ccc(cc3)[S](=O)(=O)N4CCN(CC4)c5nc(C)cc(n5)C#N)[S](C)(=O)=O"                                                                                                                                
VN6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1cc(nc(n1)N2CCN(CC2)S(=O)(=O)c3ccc(cc3)NC(=O)c4cc(ccc4N(C)S(=O)(=O)C)CN5CC(C5)CN)C#N"                                                                                                                                    
VN6 SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1cc(nc(n1)N2CCN(CC2)S(=O)(=O)c3ccc(cc3)NC(=O)c4cc(ccc4N(C)S(=O)(=O)C)CN5CC(C5)CN)C#N"                                                                                                                                    
# 
_pdbx_chem_comp_identifier.comp_id           VN6 
_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        "5-[[3-(aminomethyl)azetidin-1-yl]methyl]-~{N}-[4-[4-(4-cyano-6-methyl-pyrimidin-2-yl)piperazin-1-yl]sulfonylphenyl]-2-[methyl(methylsulfonyl)amino]benzamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
VN6 "Create component" 2023-09-14 PDBE 
VN6 "Initial release"  2024-04-17 RCSB 
# 
