data_VTM
# 
_chem_comp.id                                    VTM 
_chem_comp.name                                  "[3-[[6-[(3~{a}~{R},6~{a}~{S})-2,3,3~{a},4,6,6~{a}-hexahydro-1~{H}-pyrrolo[3,4-c]pyrrol-5-yl]-3-cyano-4-(trifluoromethyl)pyridin-2-yl]amino]-4-methylsulfanyl-phenyl]methoxy-methyl-phosphinic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C22 H25 F3 N5 O3 P S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-03-31 
_chem_comp.pdbx_modified_date                    2024-07-05 
_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                        527.500 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VTM 
_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        8OMJ 
_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 
VTM C6  C1  C 0 1 Y N N N N N -4.991  -2.182 19.974 3.534  -0.310 -0.955 C6  VTM 1  
VTM C7  C2  C 0 1 Y N N N N N -4.077  -1.537 19.129 2.947  0.925  -0.645 C7  VTM 2  
VTM C8  C3  C 0 1 Y N N N N N -6.145  -1.523 20.383 2.796  -1.458 -0.756 C8  VTM 3  
VTM C10 C4  C 0 1 Y N N N N N -4.410  -0.249 18.644 1.633  0.946  -0.144 C10 VTM 4  
VTM C20 C5  C 0 1 N N N N N N -7.780  1.851  19.789 -0.416 -2.246 0.818  C20 VTM 5  
VTM C21 C6  C 0 1 N N N N N N -8.663  -0.108 20.931 1.543  -3.527 0.701  C21 VTM 6  
VTM C22 C7  C 0 1 N N R N N N -9.461  1.123  21.350 0.484  -4.477 1.299  C22 VTM 7  
VTM C24 C8  C 0 1 N N N N N N -9.444  3.460  20.865 -1.106 -3.489 2.886  C24 VTM 8  
VTM C26 C9  C 0 1 N N N N N N -8.942  1.813  22.602 0.853  -4.771 2.768  C26 VTM 9  
VTM C28 C10 C 0 1 Y N N N N N -2.862  1.756  15.946 -0.809 3.260  1.283  C28 VTM 10 
VTM C11 C11 C 0 1 N N N N N N -2.850  -2.167 18.739 3.673  2.144  -0.835 C11 VTM 11 
VTM C12 C12 C 0 1 Y N N N N N -6.392  -0.244 19.877 1.501  -1.361 -0.250 C12 VTM 12 
VTM C23 C13 C 0 1 N N S N N N -9.227  2.110  20.207 -0.813 -3.628 1.377  C23 VTM 13 
VTM C27 C14 C 0 1 Y N N N N N -3.688  1.586  17.066 -0.318 2.195  0.526  C27 VTM 14 
VTM C29 C15 C 0 1 Y N N N N N -3.003  2.896  15.160 -2.150 3.292  1.638  C29 VTM 15 
VTM C3  C16 C 0 1 N N N N N N -5.730  7.875  17.201 -5.440 0.166  -3.602 C3  VTM 16 
VTM C30 C17 C 0 1 Y N N N N N -3.991  3.824  15.445 -2.995 2.272  1.243  C30 VTM 17 
VTM C31 C18 C 0 1 Y N N N N N -4.832  3.665  16.536 -2.508 1.218  0.492  C31 VTM 18 
VTM C32 C19 C 0 1 Y N N N N N -4.667  2.546  17.349 -1.174 1.176  0.134  C32 VTM 19 
VTM C34 C20 C 0 1 N N N N N N -2.426  -0.625 14.552 -0.824 5.660  2.722  C34 VTM 20 
VTM C35 C21 C 0 1 N N N N N N -5.846  4.719  16.872 -3.436 0.109  0.065  C35 VTM 21 
VTM C9  C22 C 0 1 N N N N N N -4.642  -3.512 20.593 4.938  -0.381 -1.500 C9  VTM 22 
VTM F13 F1  F 0 1 N N N N N N -5.565  -3.940 21.460 5.008  0.332  -2.702 F13 VTM 23 
VTM F14 F2  F 0 1 N N N N N N -4.495  -4.486 19.682 5.826  0.176  -0.575 F14 VTM 24 
VTM F15 F3  F 0 1 N N N N N N -3.505  -3.468 21.304 5.281  -1.717 -1.731 F15 VTM 25 
VTM N16 N1  N 0 1 Y N N N N N -5.554  0.341  19.008 0.964  -0.182 0.031  N16 VTM 26 
VTM N17 N2  N 0 1 N N N N N N -3.544  0.415  17.827 1.034  2.155  0.163  N17 VTM 27 
VTM N18 N3  N 0 1 N N N N N N -1.893  -2.722 18.462 4.249  3.112  -0.985 N18 VTM 28 
VTM N19 N4  N 0 1 N N N N N N -7.535  0.455  20.188 0.759  -2.513 -0.050 N19 VTM 29 
VTM N25 N5  N 0 1 N N N N N N -8.942  3.276  22.265 -0.428 -4.654 3.510  N25 VTM 30 
VTM O1  O1  O 0 1 N N N N N N -5.486  5.347  18.136 -4.013 0.433  -1.202 O1  VTM 31 
VTM O4  O2  O 0 1 N N N N N N -7.477  6.492  18.876 -4.458 -1.874 -2.124 O4  VTM 32 
VTM O5  O3  O 0 1 N N N N N N -5.185  7.195  19.718 -6.409 -0.644 -1.097 O5  VTM 33 
VTM P2  P1  P 0 1 N N N N N N -6.039  6.785  18.558 -5.056 -0.530 -1.962 P2  VTM 34 
VTM S33 S1  S 0 1 N N N N N N -1.607  0.551  15.624 0.272  4.554  1.791  S33 VTM 35 
VTM H1  H1  H 0 1 N N N N N N -6.833  -1.988 21.074 3.218  -2.424 -0.989 H1  VTM 36 
VTM H2  H2  H 0 1 N N N N N N -7.094  2.533  20.313 -1.233 -1.824 0.232  H2  VTM 37 
VTM H3  H3  H 0 1 N N N N N N -7.660  1.973  18.702 -0.143 -1.572 1.630  H3  VTM 38 
VTM H4  H4  H 0 1 N N N N N N -9.266  -0.768 20.290 2.118  -3.051 1.494  H4  VTM 39 
VTM H5  H5  H 0 1 N N N N N N -8.314  -0.669 21.811 2.204  -4.073 0.027  H5  VTM 40 
VTM H6  H6  H 0 1 N N N N N N -10.530 0.883  21.447 0.363  -5.387 0.711  H6  VTM 41 
VTM H7  H7  H 0 1 N N N N N N -8.872  4.243  20.346 -0.689 -2.558 3.269  H7  VTM 42 
VTM H8  H8  H 0 1 N N N N N N -10.511 3.726  20.866 -2.179 -3.530 3.072  H8  VTM 43 
VTM H9  H9  H 0 1 N N N N N N -9.604  1.613  23.457 1.257  -5.779 2.864  H9  VTM 44 
VTM H10 H10 H 0 1 N N N N N N -7.924  1.470  22.839 1.573  -4.038 3.133  H10 VTM 45 
VTM H11 H11 H 0 1 N N N N N N -9.927  1.942  19.375 -1.646 -4.072 0.832  H11 VTM 46 
VTM H12 H12 H 0 1 N N N N N N -2.339  3.058  14.324 -2.533 4.114  2.225  H12 VTM 47 
VTM H13 H13 H 0 1 N N N N N N -6.096  8.882  17.448 -4.524 0.244  -4.188 H13 VTM 48 
VTM H14 H14 H 0 1 N N N N N N -4.649  7.917  17.003 -6.146 -0.486 -4.117 H14 VTM 49 
VTM H15 H15 H 0 1 N N N N N N -6.252  7.504  16.307 -5.880 1.156  -3.483 H15 VTM 50 
VTM H16 H16 H 0 1 N N N N N N -4.108  4.687  14.806 -4.038 2.299  1.521  H16 VTM 51 
VTM H17 H17 H 0 1 N N N N N N -5.304  2.417  18.211 -0.797 0.351  -0.452 H17 VTM 52 
VTM H18 H18 H 0 1 N N N N N N -1.725  -1.430 14.286 -1.623 6.013  2.069  H18 VTM 53 
VTM H19 H19 H 0 1 N N N N N N -3.295  -1.053 15.074 -1.256 5.119  3.564  H19 VTM 54 
VTM H20 H20 H 0 1 N N N N N N -2.762  -0.115 13.637 -0.253 6.512  3.091  H20 VTM 55 
VTM H21 H21 H 0 1 N N N N N N -5.864  5.478  16.076 -2.875 -0.822 -0.019 H21 VTM 56 
VTM H22 H22 H 0 1 N N N N N N -6.840  4.257  16.961 -4.227 -0.008 0.805  H22 VTM 57 
VTM H23 H23 H 0 1 N N N N N N -2.641  -0.010 17.757 1.550  2.976  0.126  H23 VTM 58 
VTM H24 H24 H 0 1 N N N N N N -8.012  3.636  22.337 -0.264 -4.494 4.492  H24 VTM 59 
VTM H26 H26 H 0 1 N N N N N N -5.710  7.206  20.510 -7.084 -1.210 -1.496 H26 VTM 60 
# 
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 
VTM C34 S33 SING N N 1  
VTM C29 C30 DOUB Y N 2  
VTM C29 C28 SING Y N 3  
VTM C30 C31 SING Y N 4  
VTM S33 C28 SING N N 5  
VTM C28 C27 DOUB Y N 6  
VTM C31 C35 SING N N 7  
VTM C31 C32 DOUB Y N 8  
VTM C35 O1  SING N N 9  
VTM C27 C32 SING Y N 10 
VTM C27 N17 SING N N 11 
VTM C3  P2  SING N N 12 
VTM N17 C10 SING N N 13 
VTM O1  P2  SING N N 14 
VTM N18 C11 TRIP N N 15 
VTM P2  O4  DOUB N N 16 
VTM P2  O5  SING N N 17 
VTM C10 N16 DOUB Y N 18 
VTM C10 C7  SING Y N 19 
VTM C11 C7  SING N N 20 
VTM N16 C12 SING Y N 21 
VTM C7  C6  DOUB Y N 22 
VTM F14 C9  SING N N 23 
VTM C20 N19 SING N N 24 
VTM C20 C23 SING N N 25 
VTM C12 N19 SING N N 26 
VTM C12 C8  DOUB Y N 27 
VTM C6  C8  SING Y N 28 
VTM C6  C9  SING N N 29 
VTM N19 C21 SING N N 30 
VTM C23 C24 SING N N 31 
VTM C23 C22 SING N N 32 
VTM C9  F15 SING N N 33 
VTM C9  F13 SING N N 34 
VTM C24 N25 SING N N 35 
VTM C21 C22 SING N N 36 
VTM C22 C26 SING N N 37 
VTM N25 C26 SING N N 38 
VTM C8  H1  SING N N 39 
VTM C20 H2  SING N N 40 
VTM C20 H3  SING N N 41 
VTM C21 H4  SING N N 42 
VTM C21 H5  SING N N 43 
VTM C22 H6  SING N N 44 
VTM C24 H7  SING N N 45 
VTM C24 H8  SING N N 46 
VTM C26 H9  SING N N 47 
VTM C26 H10 SING N N 48 
VTM C23 H11 SING N N 49 
VTM C29 H12 SING N N 50 
VTM C3  H13 SING N N 51 
VTM C3  H14 SING N N 52 
VTM C3  H15 SING N N 53 
VTM C30 H16 SING N N 54 
VTM C32 H17 SING N N 55 
VTM C34 H18 SING N N 56 
VTM C34 H19 SING N N 57 
VTM C34 H20 SING N N 58 
VTM C35 H21 SING N N 59 
VTM C35 H22 SING N N 60 
VTM N17 H23 SING N N 61 
VTM N25 H24 SING N N 62 
VTM O5  H26 SING N N 63 
# 
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 
VTM InChI            InChI                1.06  "InChI=1S/C22H25F3N5O3PS/c1-34(31,32)33-12-13-3-4-19(35-2)18(5-13)28-21-16(7-26)17(22(23,24)25)6-20(29-21)30-10-14-8-27-9-15(14)11-30/h3-6,14-15,27H,8-12H2,1-2H3,(H,28,29)(H,31,32)/t14-,15+" 
VTM InChIKey         InChI                1.06  NSLCTDAHCNFOEO-GASCZTMLSA-N                                                                                                                                                                    
VTM SMILES_CANONICAL CACTVS               3.385 "CSc1ccc(CO[P](C)(O)=O)cc1Nc2nc(cc(c2C#N)C(F)(F)F)N3C[C@@H]4CNC[C@@H]4C3"                                                                                                                      
VTM SMILES           CACTVS               3.385 "CSc1ccc(CO[P](C)(O)=O)cc1Nc2nc(cc(c2C#N)C(F)(F)F)N3C[CH]4CNC[CH]4C3"                                                                                                                          
VTM SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CP(=O)(O)OCc1ccc(c(c1)Nc2c(c(cc(n2)N3C[C@H]4CNC[C@H]4C3)C(F)(F)F)C#N)SC"                                                                                                                      
VTM SMILES           "OpenEye OEToolkits" 2.0.7 "CP(=O)(O)OCc1ccc(c(c1)Nc2c(c(cc(n2)N3CC4CNCC4C3)C(F)(F)F)C#N)SC"                                                                                                                              
# 
_pdbx_chem_comp_identifier.comp_id           VTM 
_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        "[3-[[6-[(3~{a}~{R},6~{a}~{S})-2,3,3~{a},4,6,6~{a}-hexahydro-1~{H}-pyrrolo[3,4-c]pyrrol-5-yl]-3-cyano-4-(trifluoromethyl)pyridin-2-yl]amino]-4-methylsulfanyl-phenyl]methoxy-methyl-phosphinic 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 
VTM "Create component" 2023-03-31 PDBE 
VTM "Initial release"  2024-07-10 RCSB 
# 
