data_VDT
# 
_chem_comp.id                                    VDT 
_chem_comp.name                                  "5-(2-cyclopropylethynyl)-6-(2-methoxyphenyl)pyrimidine-2,4-diamine" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C16 H16 N4 O" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-03-01 
_chem_comp.pdbx_modified_date                    2024-03-01 
_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                        280.324 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VDT 
_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        8COQ 
_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 
VDT C10 C1  C 0 1 Y N N N N N -6.968 -12.264 -12.567 1.919  3.018  -0.133 C10 VDT 1  
VDT C13 C2  C 0 1 Y N N N N N -4.983 -10.715 -11.297 -0.067 1.631  1.226  C13 VDT 2  
VDT C15 C3  C 0 1 N N N N N N -8.729 -8.337  -8.920  -5.130 0.293  -0.905 C15 VDT 3  
VDT C01 C4  C 0 1 Y N N N N N -3.850 -8.084  -15.119 1.770  -2.615 0.398  C01 VDT 4  
VDT C02 C5  C 0 1 Y N N N N N -5.072 -9.104  -13.306 0.762  -0.537 0.320  C02 VDT 5  
VDT C03 C6  C 0 1 Y N N N N N -5.531 -7.879  -12.901 -0.462 -1.157 0.012  C03 VDT 6  
VDT C04 C7  C 0 1 Y N N N N N -5.070 -6.820  -13.670 -0.487 -2.561 -0.090 C04 VDT 7  
VDT C05 C8  C 0 1 N N N N N N -6.447 -7.644  -11.697 -1.649 -0.383 -0.194 C05 VDT 8  
VDT C06 C9  C 0 1 N N N N N N -7.150 -7.430  -10.768 -2.622 0.252  -0.362 C06 VDT 9  
VDT C07 C10 C 0 1 N N N N N N -8.075 -7.133  -9.587  -3.842 1.049  -0.573 C07 VDT 10 
VDT C08 C11 C 0 1 Y N N N N N -5.503 -10.354 -12.545 0.851  0.935  0.440  C08 VDT 11 
VDT C09 C12 C 0 1 Y N N N N N -6.483 -11.099 -13.171 1.847  1.638  -0.248 C09 VDT 12 
VDT C11 C13 C 0 1 Y N N N N N -6.447 -12.628 -11.337 1.010  3.695  0.657  C11 VDT 13 
VDT C12 C14 C 0 1 Y N N N N N -5.470 -11.877 -10.702 0.020  3.004  1.334  C12 VDT 14 
VDT C14 C15 C 0 1 N N N N N N -7.848 -11.347 -15.146 3.727  1.756  -1.696 C14 VDT 15 
VDT C16 C16 C 0 1 N N N N N N -7.523 -7.631  -8.253  -4.952 0.932  0.474  C16 VDT 16 
VDT N01 N1  N 0 1 Y N N N N N -4.273 -6.894  -14.719 0.637  -3.240 0.109  N01 VDT 17 
VDT N02 N2  N 0 1 Y N N N N N -4.298 -9.117  -14.385 1.841  -1.298 0.503  N02 VDT 18 
VDT N03 N3  N 0 1 N N N N N N -5.535 -5.525  -13.233 -1.664 -3.223 -0.391 N03 VDT 19 
VDT N04 N4  N 0 1 N N N N N N -2.974 -8.283  -16.276 2.914  -3.365 0.601  N04 VDT 20 
VDT O01 O1  O 0 1 N N N N N N -6.903 -10.584 -14.422 2.740  0.972  -1.024 O01 VDT 21 
VDT H1  H1  H 0 1 N N N N N N -7.728 -12.863 -13.047 2.688  3.563  -0.659 H1  VDT 22 
VDT H2  H2  H 0 1 N N N N N N -4.229 -10.113 -10.811 -0.841 1.095  1.755  H2  VDT 23 
VDT H3  H3  H 0 1 N N N N N N -9.733 -8.246  -8.480  -5.830 0.768  -1.593 H3  VDT 24 
VDT H4  H4  H 0 1 N N N N N N -8.609 -9.340  -9.354  -5.075 -0.794 -0.966 H4  VDT 25 
VDT H5  H5  H 0 1 N N N N N N -8.628 -6.182  -9.593  -3.694 2.021  -1.043 H5  VDT 26 
VDT H6  H6  H 0 1 N N N N N N -6.813 -13.524 -10.858 1.072  4.769  0.747  H6  VDT 27 
VDT H7  H7  H 0 1 N N N N N N -5.085 -12.193 -9.744  -0.692 3.542  1.942  H7  VDT 28 
VDT H8  H8  H 0 1 N N N N N N -8.085 -10.837 -16.091 3.237  2.468  -2.359 H8  VDT 29 
VDT H9  H9  H 0 1 N N N N N N -7.429 -12.341 -15.361 4.325  2.296  -0.961 H9  VDT 30 
VDT H10 H10 H 0 1 N N N N N N -8.765 -11.457 -14.549 4.375  1.102  -2.280 H10 VDT 31 
VDT H11 H11 H 0 1 N N N N N N -6.544 -8.131  -8.213  -5.533 1.827  0.693  H11 VDT 32 
VDT H12 H12 H 0 1 N N N N N N -7.668 -7.036  -7.339  -4.778 0.266  1.319  H12 VDT 33 
VDT H13 H13 H 0 1 N N N N N N -5.160 -4.816  -13.831 -2.480 -2.720 -0.535 H13 VDT 34 
VDT H14 H14 H 0 1 N N N N N N -6.534 -5.499  -13.272 -1.672 -4.191 -0.459 H14 VDT 35 
VDT H15 H15 H 0 1 N N N N N N -2.763 -7.398  -16.691 2.879  -4.332 0.532  H15 VDT 36 
VDT H16 H16 H 0 1 N N N N N N -2.126 -8.724  -15.980 3.752  -2.925 0.814  H16 VDT 37 
# 
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 
VDT N04 C01 SING N N 1  
VDT C14 O01 SING N N 2  
VDT C01 N01 DOUB Y N 3  
VDT C01 N02 SING Y N 4  
VDT N01 C04 SING Y N 5  
VDT O01 C09 SING N N 6  
VDT N02 C02 DOUB Y N 7  
VDT C04 N03 SING N N 8  
VDT C04 C03 DOUB Y N 9  
VDT C02 C03 SING Y N 10 
VDT C02 C08 SING N N 11 
VDT C09 C10 DOUB Y N 12 
VDT C09 C08 SING Y N 13 
VDT C03 C05 SING N N 14 
VDT C10 C11 SING Y N 15 
VDT C08 C13 DOUB Y N 16 
VDT C05 C06 TRIP N N 17 
VDT C11 C12 DOUB Y N 18 
VDT C13 C12 SING Y N 19 
VDT C06 C07 SING N N 20 
VDT C07 C15 SING N N 21 
VDT C07 C16 SING N N 22 
VDT C15 C16 SING N N 23 
VDT C10 H1  SING N N 24 
VDT C13 H2  SING N N 25 
VDT C15 H3  SING N N 26 
VDT C15 H4  SING N N 27 
VDT C07 H5  SING N N 28 
VDT C11 H6  SING N N 29 
VDT C12 H7  SING N N 30 
VDT C14 H8  SING N N 31 
VDT C14 H9  SING N N 32 
VDT C14 H10 SING N N 33 
VDT C16 H11 SING N N 34 
VDT C16 H12 SING N N 35 
VDT N03 H13 SING N N 36 
VDT N03 H14 SING N N 37 
VDT N04 H15 SING N N 38 
VDT N04 H16 SING N N 39 
# 
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 
VDT InChI            InChI                1.06  "InChI=1S/C16H16N4O/c1-21-13-5-3-2-4-11(13)14-12(9-8-10-6-7-10)15(17)20-16(18)19-14/h2-5,10H,6-7H2,1H3,(H4,17,18,19,20)" 
VDT InChIKey         InChI                1.06  ZJTKSYLILOEUOG-UHFFFAOYSA-N                                                                                              
VDT SMILES_CANONICAL CACTVS               3.385 "COc1ccccc1c2nc(N)nc(N)c2C#CC3CC3"                                                                                       
VDT SMILES           CACTVS               3.385 "COc1ccccc1c2nc(N)nc(N)c2C#CC3CC3"                                                                                       
VDT SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "COc1ccccc1c2c(c(nc(n2)N)N)C#CC3CC3"                                                                                     
VDT SMILES           "OpenEye OEToolkits" 2.0.7 "COc1ccccc1c2c(c(nc(n2)N)N)C#CC3CC3"                                                                                     
# 
_pdbx_chem_comp_identifier.comp_id           VDT 
_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-(2-cyclopropylethynyl)-6-(2-methoxyphenyl)pyrimidine-2,4-diamine" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
VDT "Create component" 2023-03-01 PDBE 
VDT "Initial release"  2024-03-06 RCSB 
# 
