data_VDC
# 
_chem_comp.id                                    VDC 
_chem_comp.name                                  "N-{1-[(1R,2R)-2-fluorocyclopropyl]-2-oxo-1,2-dihydropyridin-3-yl}-2-[(1R,4r)-1-methyl-2-oxabicyclo[2.1.1]hexan-4-yl]-6-[(propan-2-yl)oxy]-2H-pyrazolo[3,4-b]pyridine-5-carboxamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C24 H26 F N5 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-09-11 
_chem_comp.pdbx_modified_date                    2024-06-21 
_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                        467.493 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VDC 
_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        8TVM 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
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 
VDC N1  N1  N 0 1 N N N N N N 35.370 -6.367  16.413 -1.952 1.337  -0.524 N1  VDC 1  
VDC N3  N2  N 0 1 Y N N N N N 30.875 -4.503  21.268 4.391  0.375  -0.081 N3  VDC 2  
VDC C4  C1  C 0 1 N N N N N N 37.044 -5.520  13.190 -5.264 2.640  -1.459 C4  VDC 3  
VDC C5  C2  C 0 1 N N N N N N 37.497 -6.732  12.833 -6.025 2.123  -0.468 C5  VDC 4  
VDC C6  C3  C 0 1 N N R N N N 37.807 -9.117  13.166 -6.319 0.810  1.570  C6  VDC 5  
VDC C7  C4  C 0 1 N N N N N N 38.396 -10.094 14.122 -6.481 -0.710 1.633  C7  VDC 6  
VDC C8  C5  C 0 1 N N S N N N 39.283 -9.297  13.237 -7.642 0.163  1.154  C8  VDC 7  
VDC C10 C6  C 0 1 Y N N N N N 33.925 -5.520  18.147 -0.076 -0.225 -0.412 C10 VDC 8  
VDC C13 C7  C 0 1 Y N N N N N 31.536 -3.709  20.398 3.370  1.236  -0.142 C13 VDC 9  
VDC C15 C8  C 0 1 N N N N N N 29.628 -4.730  23.635 6.884  -0.284 0.440  C15 VDC 10 
VDC C17 C9  C 0 1 N N N N N N 29.778 -2.572  22.518 6.494  1.444  -1.198 C17 VDC 11 
VDC C20 C10 C 0 1 Y N N N N N 32.113 -5.833  20.169 2.598  -0.918 -0.230 C20 VDC 12 
VDC C21 C11 C 0 1 Y N N N N N 33.626 -6.783  18.711 0.379  -1.564 -0.400 C21 VDC 13 
VDC C22 C12 C 0 1 N N N N N N 33.851 -9.178  18.646 -0.026 -3.902 -0.466 C22 VDC 14 
VDC C24 C13 C 0 1 N N N N N N 32.659 -9.562  17.804 0.050  -4.402 0.978  C24 VDC 15 
VDC C1  C14 C 0 1 N N N N N N 34.908 -5.267  17.048 -1.518 0.061  -0.512 C1  VDC 16 
VDC C11 C15 C 0 1 Y N N N N N 33.288 -4.396  18.647 0.834  0.820  -0.331 C11 VDC 17 
VDC C12 C16 C 0 1 Y N N N N N 32.359 -4.553  19.667 2.201  0.500  -0.237 C12 VDC 18 
VDC C14 C17 C 0 1 N N N N N N 29.882 -4.075  22.254 5.802  0.751  0.027  C14 VDC 19 
VDC C16 C18 C 0 1 N N N N N N 28.309 -3.942  23.435 7.690  1.012  0.698  C16 VDC 20 
VDC C18 C19 C 0 1 N N N N N N 27.061 -4.188  24.231 8.934  0.965  1.589  C18 VDC 21 
VDC C19 C20 C 0 1 N N N N N N 28.394 -4.422  21.969 6.333  1.472  1.305  C19 VDC 22 
VDC C2  C21 C 0 1 N N N N N N 36.090 -6.465  15.201 -3.326 1.609  -0.514 C2  VDC 23 
VDC C23 C22 C 0 1 N N N N N N 35.010 -10.122 18.451 -0.960 -4.808 -1.271 C23 VDC 24 
VDC C3  C23 C 0 1 N N N N N N 36.335 -5.361  14.375 -3.886 2.384  -1.493 C3  VDC 25 
VDC C9  C24 C 0 1 N N N N N N 36.563 -7.715  14.823 -4.149 1.094  0.512  C9  VDC 26 
VDC F1  F1  F 0 1 N N N N N N 40.026 -8.310  13.783 -7.948 0.140  -0.211 F1  VDC 27 
VDC N2  N3  N 0 1 N N N N N N 37.280 -7.830  13.620 -5.470 1.357  0.509  N2  VDC 28 
VDC N4  N4  N 0 1 Y N N N N N 31.202 -5.829  21.153 3.913  -0.939 -0.130 N4  VDC 29 
VDC N5  N5  N 0 1 Y N N N N N 32.752 -6.937  19.682 1.651  -1.870 -0.313 N5  VDC 30 
VDC O1  O1  O 0 1 N N N N N N 35.229 -4.121  16.750 -2.316 -0.854 -0.583 O1  VDC 31 
VDC O2  O2  O 0 1 N N N N N N 36.357 -8.719  15.528 -3.665 0.408  1.398  O2  VDC 32 
VDC O3  O3  O 0 1 N N N N N N 28.665 -2.558  23.405 7.839  1.605  -0.628 O3  VDC 33 
VDC O4  O4  O 0 1 N N N N N N 34.281 -7.862  18.209 -0.530 -2.565 -0.481 O4  VDC 34 
VDC H1  H1  H 0 1 N N N N N N 35.174 -7.237  16.866 -1.313 2.067  -0.535 H1  VDC 35 
VDC H3  H2  H 0 1 N N N N N N 37.231 -4.666  12.555 -5.719 3.246  -2.229 H3  VDC 36 
VDC H4  H3  H 0 1 N N N N N N 38.043 -6.843  11.908 -7.086 2.321  -0.452 H4  VDC 37 
VDC H5  H4  H 0 1 N N N N N N 37.318 -9.554  12.283 -6.300 1.354  2.515  H5  VDC 38 
VDC H6  H5  H 0 1 N N N N N N 38.370 -9.890  15.203 -5.955 -1.303 0.885  H6  VDC 39 
VDC H7  H6  H 0 1 N N N N N N 38.274 -11.174 13.950 -6.568 -1.166 2.619  H7  VDC 40 
VDC H8  H7  H 0 1 N N N N N N 39.720 -9.856  12.396 -8.493 0.282  1.824  H8  VDC 41 
VDC H10 H8  H 0 1 N N N N N N 31.443 -2.638  20.293 3.444  2.314  -0.119 H10 VDC 42 
VDC H12 H9  H 0 1 N N N N N N 29.546 -5.827  23.649 6.645  -0.855 1.337  H12 VDC 43 
VDC H11 H10 H 0 1 N N N N N N 30.276 -4.400  24.460 7.261  -0.897 -0.379 H11 VDC 44 
VDC H14 H11 H 0 1 N N N N N N 29.573 -2.008  21.596 6.487  0.799  -2.077 H14 VDC 45 
VDC H13 H12 H 0 1 N N N N N N 30.687 -2.177  22.996 6.043  2.412  -1.415 H13 VDC 46 
VDC H20 H13 H 0 1 N N N N N N 33.564 -9.157  19.708 0.970  -3.921 -0.910 H20 VDC 47 
VDC H25 H14 H 0 1 N N N N N N 32.302 -10.558 18.106 0.435  -5.422 0.990  H25 VDC 48 
VDC H24 H15 H 0 1 N N N N N N 31.855 -8.825  17.949 0.716  -3.756 1.551  H24 VDC 49 
VDC H26 H16 H 0 1 N N N N N N 32.951 -9.583  16.744 -0.945 -4.384 1.422  H26 VDC 50 
VDC H9  H17 H 0 1 N N N N N N 33.510 -3.416  18.251 0.502  1.847  -0.339 H9  VDC 51 
VDC H17 H18 H 0 1 N N N N N N 26.271 -3.500  23.897 9.662  0.278  1.159  H17 VDC 52 
VDC H16 H19 H 0 1 N N N N N N 26.730 -5.226  24.082 9.370  1.961  1.657  H16 VDC 53 
VDC H15 H20 H 0 1 N N N N N N 27.267 -4.018  25.298 8.654  0.622  2.585  H15 VDC 54 
VDC H18 H21 H 0 1 N N N N N N 28.164 -5.482  21.786 6.182  2.551  1.314  H18 VDC 55 
VDC H19 H22 H 0 1 N N N N N N 27.881 -3.801  21.220 6.068  0.985  2.244  H19 VDC 56 
VDC H21 H23 H 0 1 N N N N N N 34.719 -11.133 18.773 -1.955 -4.790 -0.827 H21 VDC 57 
VDC H22 H24 H 0 1 N N N N N N 35.291 -10.143 17.388 -1.014 -4.452 -2.299 H22 VDC 58 
VDC H23 H25 H 0 1 N N N N N N 35.867 -9.779  19.050 -0.575 -5.828 -1.259 H23 VDC 59 
VDC H2  H26 H 0 1 N N N N N N 35.972 -4.384  14.659 -3.273 2.793  -2.282 H2  VDC 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 
VDC O1  C1  DOUB N N 1  
VDC C1  N1  SING N N 2  
VDC N1  C2  SING N N 3  
VDC C2  C3  DOUB N N 4  
VDC C3  C4  SING N N 5  
VDC C4  C5  DOUB N N 6  
VDC C5  N2  SING N N 7  
VDC N2  C6  SING N N 8  
VDC C6  C7  SING N N 9  
VDC C7  C8  SING N N 10 
VDC C8  F1  SING N N 11 
VDC N2  C9  SING N N 12 
VDC C9  O2  DOUB N N 13 
VDC C1  C10 SING N N 14 
VDC C10 C11 DOUB Y N 15 
VDC C11 C12 SING Y N 16 
VDC C12 C13 DOUB Y N 17 
VDC C13 N3  SING Y N 18 
VDC N3  C14 SING N N 19 
VDC C14 C15 SING N N 20 
VDC C15 C16 SING N N 21 
VDC C16 O3  SING N N 22 
VDC O3  C17 SING N N 23 
VDC C16 C18 SING N N 24 
VDC C16 C19 SING N N 25 
VDC N3  N4  SING Y N 26 
VDC C12 C20 SING Y N 27 
VDC C20 N5  SING Y N 28 
VDC N5  C21 DOUB Y N 29 
VDC C21 O4  SING N N 30 
VDC O4  C22 SING N N 31 
VDC C22 C23 SING N N 32 
VDC C22 C24 SING N N 33 
VDC C2  C9  SING N N 34 
VDC C6  C8  SING N N 35 
VDC C10 C21 SING Y N 36 
VDC C14 C17 SING N N 37 
VDC C14 C19 SING N N 38 
VDC N4  C20 DOUB Y N 39 
VDC N1  H1  SING N N 40 
VDC C4  H3  SING N N 41 
VDC C5  H4  SING N N 42 
VDC C6  H5  SING N N 43 
VDC C7  H6  SING N N 44 
VDC C7  H7  SING N N 45 
VDC C8  H8  SING N N 46 
VDC C13 H10 SING N N 47 
VDC C15 H12 SING N N 48 
VDC C15 H11 SING N N 49 
VDC C17 H14 SING N N 50 
VDC C17 H13 SING N N 51 
VDC C22 H20 SING N N 52 
VDC C24 H25 SING N N 53 
VDC C24 H24 SING N N 54 
VDC C24 H26 SING N N 55 
VDC C11 H9  SING N N 56 
VDC C18 H17 SING N N 57 
VDC C18 H16 SING N N 58 
VDC C18 H15 SING N N 59 
VDC C19 H18 SING N N 60 
VDC C19 H19 SING N N 61 
VDC C23 H21 SING N N 62 
VDC C23 H22 SING N N 63 
VDC C23 H23 SING N N 64 
VDC C3  H2  SING N N 65 
# 
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 
VDC SMILES           ACDLabs              12.01 "FC1CC1N1C=CC=C(NC(=O)c2cc3cn(nc3nc2OC(C)C)C23CC(C)(C2)OC3)C1=O"                                                                                                                                         
VDC InChI            InChI                1.06  "InChI=1S/C24H26FN5O4/c1-13(2)34-21-15(20(31)26-17-5-4-6-29(22(17)32)18-8-16(18)25)7-14-9-30(28-19(14)27-21)24-10-23(3,11-24)33-12-24/h4-7,9,13,16,18H,8,10-12H2,1-3H3,(H,26,31)/t16-,18+,23-,24-/m0/s1" 
VDC InChIKey         InChI                1.06  YRZABOXBJPGNGN-PXAYELCQSA-N                                                                                                                                                                              
VDC SMILES_CANONICAL CACTVS               3.385 "CC(C)Oc1nc2nn(cc2cc1C(=O)NC3=CC=CN([C@@H]4C[C@@H]4F)C3=O)C56COC(C)(C5)C6"                                                                                                                               
VDC SMILES           CACTVS               3.385 "CC(C)Oc1nc2nn(cc2cc1C(=O)NC3=CC=CN([CH]4C[CH]4F)C3=O)C56COC(C)(C5)C6"                                                                                                                                   
VDC SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)Oc1c(cc2cn(nc2n1)C34CC(C3)(OC4)C)C(=O)NC5=CC=CN(C5=O)[C@@H]6C[C@@H]6F"                                                                                                                             
VDC SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)Oc1c(cc2cn(nc2n1)C34CC(C3)(OC4)C)C(=O)NC5=CC=CN(C5=O)C6CC6F"                                                                                                                                       
# 
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 
VDC "SYSTEMATIC NAME" ACDLabs              12.01 "N-{1-[(1R,2R)-2-fluorocyclopropyl]-2-oxo-1,2-dihydropyridin-3-yl}-2-[(1R,4r)-1-methyl-2-oxabicyclo[2.1.1]hexan-4-yl]-6-[(propan-2-yl)oxy]-2H-pyrazolo[3,4-b]pyridine-5-carboxamide" 
VDC "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "~{N}-[1-[(1~{R},2~{S})-2-fluoranylcyclopropyl]-2-oxidanylidene-pyridin-3-yl]-2-(1-methyl-2-oxabicyclo[2.1.1]hexan-4-yl)-6-propan-2-yloxy-pyrazolo[3,4-b]pyridine-5-carboxamide"     
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
VDC "Create component" 2023-09-11 RCSB 
VDC "Initial release"  2024-06-26 RCSB 
# 
