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
#