data_3VF
# 
_chem_comp.id                                    3VF 
_chem_comp.name                                  "N-[(2-cyanopyrimidin-4-yl)methyl]-3-[2-(3,5-dichlorophenyl)-2-methylpropanoyl]-4-methoxybenzamide" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C24 H20 Cl2 N4 O3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2014-11-13 
_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                        483.347 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     3VF 
_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        4WX4 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  EBI 
_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 
3VF C1  C1  C  0 1 Y N N N N N -6.550  -2.773 18.734 4.912  0.711  -0.998 C1  3VF 1  
3VF C2  C2  C  0 1 Y N N N N N -7.374  -3.132 19.809 5.681  0.185  -2.028 C2  3VF 2  
3VF C3  C3  C  0 1 Y N N N N N -7.376  -2.329 20.970 7.009  -0.123 -1.772 C3  3VF 3  
3VF C11 C4  C  0 1 Y N N N N N -11.343 -4.883 13.372 -1.178 -3.222 0.283  C11 3VF 4  
3VF C12 C5  C  0 1 Y N N N N N -10.088 -5.198 12.841 -1.771 -2.057 -0.236 C12 3VF 5  
3VF C13 C6  C  0 1 Y N N N N N -8.937  -5.045 13.580 -0.965 -0.989 -0.634 C13 3VF 6  
3VF C14 C7  C  0 1 Y N N N N N -9.009  -4.506 14.883 0.418  -1.085 -0.513 C14 3VF 7  
3VF C15 C8  C  0 1 Y N N N N N -10.240 -4.129 15.354 0.997  -2.250 0.006  C15 3VF 8  
3VF C16 C9  C  0 1 Y N N N N N -11.423 -4.333 14.622 0.204  -3.304 0.398  C16 3VF 9  
3VF C17 C10 C  0 1 N N N N N N -10.024 -5.720 11.404 -3.231 -1.966 -0.360 C17 3VF 10 
3VF C18 C11 C  0 1 N N N N N N -9.456  -7.147 11.104 -3.856 -0.777 -1.044 C18 3VF 11 
3VF C20 C12 C  0 1 Y N N N N N -7.936  -6.977 10.843 -3.516 0.477  -0.281 C20 3VF 12 
3VF C22 C13 C  0 1 N N N N N N -7.743  -4.374 15.631 1.276  0.041  -0.932 C22 3VF 13 
3VF C23 C14 C  0 1 Y N N N N N -6.982  -7.531 11.674 -3.842 1.714  -0.804 C23 3VF 14 
3VF C24 C15 C  0 1 Y N N N N N -5.648  -7.363 11.370 -3.530 2.866  -0.104 C24 3VF 15 
3VF C25 C16 C  0 1 Y N N N N N -5.207  -6.620 10.286 -2.892 2.780  1.120  C25 3VF 16 
3VF C26 C17 C  0 1 Y N N N N N -6.184  -6.079 9.467  -2.566 1.541  1.644  C26 3VF 17 
3VF C27 C18 C  0 1 Y N N N N N -7.545  -6.236 9.732  -2.883 0.390  0.945  C27 3VF 18 
3VF C30 C19 C  0 1 N N N N N N -13.698 -5.006 13.184 -1.284 -5.409 1.200  C30 3VF 19 
3VF N4  N1  N  0 1 Y N N N N N -6.576  -1.246 21.050 7.500  0.091  -0.564 N4  3VF 20 
3VF C5  C20 C  0 1 Y N N N N N -5.768  -0.980 19.920 6.738  0.595  0.397  C5  3VF 21 
3VF N6  N2  N  0 1 Y N N N N N -5.784  -1.700 18.818 5.465  0.900  0.186  N6  3VF 22 
3VF C7  C21 C  0 1 N N N N N N -6.434  -3.572 17.481 3.466  1.066  -1.231 C7  3VF 23 
3VF N8  N3  N  0 1 N N N N N N -7.741  -3.690 16.789 2.615  -0.051 -0.815 N8  3VF 24 
3VF C9  C22 C  0 1 N N N N N N -4.968  0.208  20.097 7.304  0.814  1.694  C9  3VF 25 
3VF N10 N4  N  0 1 N N N N N N -4.782  0.955  21.038 7.752  0.988  2.724  N10 3VF 26 
3VF O19 O1  O  0 1 N N N N N N -10.349 -4.980 10.491 -3.934 -2.847 0.087  O19 3VF 27 
3VF O21 O2  O  0 1 N N N N N N -12.410 -5.099 12.553 -1.954 -4.260 0.676  O21 3VF 28 
3VF CL1 CL1 CL 0 0 N N N N N N -4.438  -8.086 12.401 -3.939 4.420  -0.762 CL1 3VF 29 
3VF CL2 CL2 CL 0 0 N N N N N N -5.687  -5.155 8.078  -1.771 1.432  3.183  CL2 3VF 30 
3VF C31 C23 C  0 1 N N N N N N -9.742  -8.085 12.274 -3.317 -0.667 -2.471 C31 3VF 31 
3VF C32 C24 C  0 1 N N N N N N -10.165 -7.685 9.816  -5.376 -0.953 -1.085 C32 3VF 32 
3VF O33 O3  O  0 1 N N N N N N -6.690  -4.845 15.178 0.774  1.053  -1.383 O33 3VF 33 
3VF H1  H1  H  0 1 N N N N N N -7.999  -4.011 19.750 5.254  0.020  -3.006 H1  3VF 34 
3VF H2  H2  H  0 1 N N N N N N -8.021  -2.583 21.798 7.635  -0.533 -2.551 H2  3VF 35 
3VF H3  H3  H  0 1 N N N N N N -7.983  -5.336 13.165 -1.413 -0.091 -1.034 H3  3VF 36 
3VF H4  H4  H  0 1 N N N N N N -10.303 -3.658 16.324 2.071  -2.321 0.099  H4  3VF 37 
3VF H5  H5  H  0 1 N N N N N N -12.380 -4.060 15.040 0.658  -4.199 0.798  H5  3VF 38 
3VF H6  H6  H  0 1 N N N N N N -7.277  -8.089 12.551 -4.341 1.782  -1.760 H6  3VF 39 
3VF H7  H7  H  0 1 N N N N N N -4.155  -6.471 10.090 -2.648 3.679  1.667  H7  3VF 40 
3VF H8  H8  H  0 1 N N N N N N -8.284  -5.789 9.084  -2.629 -0.577 1.354  H8  3VF 41 
3VF H9  H9  H  0 1 N N N N N N -14.486 -5.196 12.440 -0.613 -5.814 0.443  H9  3VF 42 
3VF H10 H10 H  0 1 N N N N N N -13.766 -5.752 13.989 -0.708 -5.123 2.080  H10 3VF 43 
3VF H11 H11 H  0 1 N N N N N N -13.828 -3.998 13.606 -2.020 -6.164 1.476  H11 3VF 44 
3VF H12 H12 H  0 1 N N N N N N -6.070  -4.579 17.732 3.212  1.952  -0.650 H12 3VF 45 
3VF H13 H13 H  0 1 N N N N N N -5.716  -3.080 16.808 3.308  1.269  -2.290 H13 3VF 46 
3VF H14 H14 H  0 1 N N N N N N -8.575  -3.283 17.163 3.016  -0.858 -0.455 H14 3VF 47 
3VF H17 H17 H  0 1 N N N N N N -9.244  -7.706 13.179 -3.667 -1.516 -3.058 H17 3VF 48 
3VF H18 H18 H  0 1 N N N N N N -10.827 -8.135 12.447 -3.672 0.259  -2.924 H18 3VF 49 
3VF H19 H19 H  0 1 N N N N N N -9.362  -9.090 12.039 -2.227 -0.666 -2.449 H19 3VF 50 
3VF H20 H20 H  0 1 N N N N N N -11.241 -7.802 10.011 -5.769 -0.950 -0.068 H20 3VF 51 
3VF H21 H21 H  0 1 N N N N N N -10.017 -6.972 8.991  -5.821 -0.133 -1.649 H21 3VF 52 
3VF H22 H22 H  0 1 N N N N N N -9.734  -8.659 9.540  -5.619 -1.900 -1.566 H22 3VF 53 
# 
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 
3VF CL2 C26 SING N N 1  
3VF C26 C27 DOUB Y N 2  
3VF C26 C25 SING Y N 3  
3VF C27 C20 SING Y N 4  
3VF C32 C18 SING N N 5  
3VF C25 C24 DOUB Y N 6  
3VF O19 C17 DOUB N N 7  
3VF C20 C18 SING N N 8  
3VF C20 C23 DOUB Y N 9  
3VF C18 C17 SING N N 10 
3VF C18 C31 SING N N 11 
3VF C24 C23 SING Y N 12 
3VF C24 CL1 SING N N 13 
3VF C17 C12 SING N N 14 
3VF O21 C30 SING N N 15 
3VF O21 C11 SING N N 16 
3VF C12 C11 DOUB Y N 17 
3VF C12 C13 SING Y N 18 
3VF C11 C16 SING Y N 19 
3VF C13 C14 DOUB Y N 20 
3VF C16 C15 DOUB Y N 21 
3VF C14 C15 SING Y N 22 
3VF C14 C22 SING N N 23 
3VF O33 C22 DOUB N N 24 
3VF C22 N8  SING N N 25 
3VF N8  C7  SING N N 26 
3VF C7  C1  SING N N 27 
3VF C1  N6  DOUB Y N 28 
3VF C1  C2  SING Y N 29 
3VF N6  C5  SING Y N 30 
3VF C2  C3  DOUB Y N 31 
3VF C5  C9  SING N N 32 
3VF C5  N4  DOUB Y N 33 
3VF C9  N10 TRIP N N 34 
3VF C3  N4  SING Y N 35 
3VF C2  H1  SING N N 36 
3VF C3  H2  SING N N 37 
3VF C13 H3  SING N N 38 
3VF C15 H4  SING N N 39 
3VF C16 H5  SING N N 40 
3VF C23 H6  SING N N 41 
3VF C25 H7  SING N N 42 
3VF C27 H8  SING N N 43 
3VF C30 H9  SING N N 44 
3VF C30 H10 SING N N 45 
3VF C30 H11 SING N N 46 
3VF C7  H12 SING N N 47 
3VF C7  H13 SING N N 48 
3VF N8  H14 SING N N 49 
3VF C31 H17 SING N N 50 
3VF C31 H18 SING N N 51 
3VF C31 H19 SING N N 52 
3VF C32 H20 SING N N 53 
3VF C32 H21 SING N N 54 
3VF C32 H22 SING N N 55 
# 
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 
3VF SMILES           ACDLabs              12.01 "N#Cc1nc(ccn1)CNC(=O)c3ccc(OC)c(C(=O)C(c2cc(Cl)cc(Cl)c2)(C)C)c3"                                                                                         
3VF InChI            InChI                1.03  "InChI=1S/C24H20Cl2N4O3/c1-24(2,15-9-16(25)11-17(26)10-15)22(31)19-8-14(4-5-20(19)33-3)23(32)29-13-18-6-7-28-21(12-27)30-18/h4-11H,13H2,1-3H3,(H,29,32)" 
3VF InChIKey         InChI                1.03  WCQQOAFZCDVMEP-UHFFFAOYSA-N                                                                                                                              
3VF SMILES_CANONICAL CACTVS               3.385 "COc1ccc(cc1C(=O)C(C)(C)c2cc(Cl)cc(Cl)c2)C(=O)NCc3ccnc(n3)C#N"                                                                                           
3VF SMILES           CACTVS               3.385 "COc1ccc(cc1C(=O)C(C)(C)c2cc(Cl)cc(Cl)c2)C(=O)NCc3ccnc(n3)C#N"                                                                                           
3VF SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "CC(C)(c1cc(cc(c1)Cl)Cl)C(=O)c2cc(ccc2OC)C(=O)NCc3ccnc(n3)C#N"                                                                                           
3VF SMILES           "OpenEye OEToolkits" 1.9.2 "CC(C)(c1cc(cc(c1)Cl)Cl)C(=O)c2cc(ccc2OC)C(=O)NCc3ccnc(n3)C#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 
3VF "SYSTEMATIC NAME" ACDLabs              12.01 "N-[(2-cyanopyrimidin-4-yl)methyl]-3-[2-(3,5-dichlorophenyl)-2-methylpropanoyl]-4-methoxybenzamide"         
3VF "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "3-[2-[3,5-bis(chloranyl)phenyl]-2-methyl-propanoyl]-N-[(2-cyanopyrimidin-4-yl)methyl]-4-methoxy-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 
3VF "Create component" 2014-11-13 EBI  
3VF "Initial release"  2015-01-14 RCSB 
3VF "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            3VF 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_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               C9 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
