PROTACpedia
Development of Dual and Selective Degraders of Cyclin-Dependent Kinases 4 and 6. Angew Chem Int Ed Engl. 2019 May 6;58(19):6321-6326. PMID:30802347 DOI:10.1002/anie.201901336
Target: CDK6 Cyclin-dependent kinase 6 Q00534 Homo sapiens
E3 ligase: Cereblon
E3 binder: Thalidomide
SMILES: show
Ligand Name: Palbociclib
Ligand PDB Id: LQQ
PDB with Ligand: 5L2I
SMILES: show
Calculated Values
MW: 832.92
Hbond donors: 3
Hbond acceptors: 15
cLogP: 3.05
TPSA: 218.13

SMILES: show
Linker type: Alkane
Incubation time (hours): 4, 24, 72, 96
Cells: Jurkat; Molt4; Granta-519; Mino; Jeko; Rec1; Maver
IC50: = 25.7 nM
Tested a non-binding E3 control?: No
Tested competition with ligand?: No
Tested proteaseome inhibitor?: No
Proteomics data available?: Yes
Tested engagement in cells?: No
Off-targets reported?: Yes, can also degrade IKZF1/3
Comments: IC50: 25.7nM/7.57nM for CDK4/CDK6, respectively. BSJ-02-162 is capable of degrading both CDK4 and CDK6.
Contributed by: Yangwode Jing
Calculated Values
MW: 936.04
Hbond donors: 4
Hbond acceptors: 18
cLogP: 2.36
TPSA: 248.62

SMILES: show
Linker type: PEG
Incubation time (hours): 4
Cells: Jurkat
IC50: = 39 nM
Tested a non-binding E3 control?: No
Tested competition with ligand?: No
Tested proteaseome inhibitor?: No
Proteomics data available?: No
Tested engagement in cells?: No
Off-targets reported?: Yes, can also degrade IKZF1/3
Comments: IC50: 137nM/39nM for CDK4/CDK6, respectively; Show selective degradation of CDK6 (therefore active for CDK6 and inactive for CDK4).
Contributed by: Yangwode Jing
Calculated Values
MW: 859.99
Hbond donors: 4
Hbond acceptors: 15
cLogP: 3.87
TPSA: 220.93

SMILES: show
Linker type: Alkane
Incubation time (hours): 4
Cells: Jurkat
IC50: = 77 nM
Tested a non-binding E3 control?: No
Tested competition with ligand?: No
Tested proteaseome inhibitor?: No
Proteomics data available?: No
Tested engagement in cells?: No
Off-targets reported?: No
Comments: IC50: 77nM/27.6nM for CDK4/CDK6, respectively.
Contributed by: Yangwode Jing
Calculated Values
MW: 1,024.15
Hbond donors: 4
Hbond acceptors: 20
cLogP: 2.39
TPSA: 267.08

SMILES: show
Linker type: PEG
Incubation time (hours): 4
Cells: Jurkat
Tested a non-binding E3 control?: No
Tested competition with ligand?: No
Tested proteaseome inhibitor?: No
Proteomics data available?: No
Tested engagement in cells?: No
Off-targets reported?: No
Contributed by: Yangwode Jing
Calculated Values
MW: 818.89
Hbond donors: 3
Hbond acceptors: 15
cLogP: 2.66
TPSA: 218.13

SMILES: show
Linker type: Alkane
Incubation time (hours): 4
Cells: Jurkat
Tested a non-binding E3 control?: No
Tested competition with ligand?: No
Tested proteaseome inhibitor?: No
Proteomics data available?: No
Tested engagement in cells?: No
Off-targets reported?: No
Contributed by: Yangwode Jing
Calculated Values
MW: 937.02
Hbond donors: 3
Hbond acceptors: 18
cLogP: 2.32
TPSA: 245.82

SMILES: show
Linker type: PEG
Incubation time (hours): 4
Cells: Jurkat
IC50: = 37.7 nM
Tested a non-binding E3 control?: No
Tested competition with ligand?: No
Tested proteaseome inhibitor?: No
Proteomics data available?: Yes
Tested engagement in cells?: No
Off-targets reported?: No
Comments: IC50: 106nM/37.7nM for CDK4/CDK6, respectively. Show selectivity on CDK6 (therefore inactive for CDK4 and active for CDK6).
Contributed by: Yangwode Jing
Calculated Values
MW: 703.76
Hbond donors: 2
Hbond acceptors: 13
cLogP: 3.28
TPSA: 179.80

SMILES: show
Linker type: Other
Incubation time (hours): 4
Cells: Jurkat
IC50: = 130 nM
Tested a non-binding E3 control?: No
Tested competition with ligand?: No
Tested proteaseome inhibitor?: No
Proteomics data available?: No
Tested engagement in cells?: No
Off-targets reported?: No
Comments: IC50: 130nM/45.1nM for CDK4/CDK6 respectively.
Contributed by: Yangwode Jing
Calculated Values
MW: 889.03
Hbond donors: 3
Hbond acceptors: 15
cLogP: 4.62
TPSA: 218.13

SMILES: show
Linker type: Alkane
Incubation time (hours): 4
Cells: Jurkat
Tested a non-binding E3 control?: No
Tested competition with ligand?: No
Tested proteaseome inhibitor?: No
Proteomics data available?: No
Tested engagement in cells?: No
Off-targets reported?: No
Contributed by: Yangwode Jing
Calculated Values
MW: 804.87
Hbond donors: 3
Hbond acceptors: 15
cLogP: 2.27
TPSA: 218.13

SMILES: show
Linker type: Alkane
Incubation time (hours): 4
Cells: Jurkat
IC50: = 69.6 nM
Tested a non-binding E3 control?: No
Tested competition with ligand?: No
Tested proteaseome inhibitor?: No
Proteomics data available?: No
Tested engagement in cells?: No
Off-targets reported?: No
Comments: IC50: 69.6nM/34.6nM for CDK4/CDK6, respectively.
Contributed by: Yangwode Jing
Calculated Values
MW: 847.93
Hbond donors: 4
Hbond acceptors: 16
cLogP: 2.32
TPSA: 230.16

SMILES: show
Linker type: PEG
Incubation time (hours): 4
Cells: Jurkat
Tested a non-binding E3 control?: No
Tested competition with ligand?: No
Tested proteaseome inhibitor?: No
Proteomics data available?: No
Tested engagement in cells?: No
Off-targets reported?: No
Contributed by: Yangwode Jing
Calculated Values
MW: 891.99
Hbond donors: 4
Hbond acceptors: 17
cLogP: 2.34
TPSA: 239.39

SMILES: show
Linker type: PEG
Incubation time (hours): 4
Cells: Jurkat
Tested a non-binding E3 control?: No
Tested competition with ligand?: No
Tested proteaseome inhibitor?: No
Proteomics data available?: No
Tested engagement in cells?: No
Off-targets reported?: No
Contributed by: Yangwode Jing
E3 ligase: Cereblon
E3 binder: Thalidomide
SMILES: show
Ligand Name: Palbociclib
Ligand PDB Id: LQQ
PDB with Ligand: 5L2I
SMILES: show
Calculated Values
MW: 832.92
Hbond donors: 3
Hbond acceptors: 15
cLogP: 3.05
TPSA: 218.13

SMILES: show
Linker type: Alkane
Incubation time (hours): 4, 24, 72, 96
Cells: Jurkat; Molt4; Granta-519; Mino; Jeko; Rec1; Maver
IC50: = 26.9 nM
Tested a non-binding E3 control?: No
Tested competition with ligand?: No
Tested proteaseome inhibitor?: No
Proteomics data available?: Yes
Tested engagement in cells?: No
Off-targets reported?: No
Comments: IC50: 26.9nM/10.4nM for CDK4/CDK6, respectively. Can degrade both CDK4 and CDK6.
Contributed by: Yangwode Jing
E3 ligase: Cereblon
E3 binder: Thalidomide
SMILES: show
Ligand Name: Abemaciclib
Ligand PDB Id: 6ZV
PDB with Ligand: 5L2S
SMILES: show
Calculated Values
MW: 805.89
Hbond donors: 3
Hbond acceptors: 13
cLogP: 5.21
TPSA: 170.58

SMILES: show
Linker type: Alkane
Incubation time (hours): 4
Cells: Jurkat
IC50: = 8.26 nM
Tested a non-binding E3 control?: No
Tested competition with ligand?: No
Tested proteaseome inhibitor?: No
Proteomics data available?: No
Tested engagement in cells?: No
Off-targets reported?: Yes, can also degrade CDK9
Comments: IC50: 8.26nM/13.1nM for CDK4/CDK6, respectively.
Contributed by: Yangwode Jing
Calculated Values
MW: 862.94
Hbond donors: 4
Hbond acceptors: 14
cLogP: 4.33
TPSA: 199.68

SMILES: show
Linker type: Alkane
Incubation time (hours): 4
Cells: Jurkat
IC50: = 8.61 nM
Tested a non-binding E3 control?: No
Tested competition with ligand?: No
Tested proteaseome inhibitor?: No
Proteomics data available?: No
Tested engagement in cells?: No
Off-targets reported?: Yes, can also degrade CDK9
Comments: IC50: 8.61nM/12.5nM for CDK4/CDK6, respectively.
Contributed by: Yangwode Jing
E3 ligase: Cereblon
E3 binder: Thalidomide
SMILES: show
Ligand Name: Ribociclib
Ligand PDB Id: 6ZZ
PDB with Ligand: 5L2T
SMILES: show
Calculated Values
MW: 821.94
Hbond donors: 3
Hbond acceptors: 15
cLogP: 3.06
TPSA: 196.46

SMILES: show
Linker type: PEG
Incubation time (hours): 4
Cells: Jurkat
IC50: = 175 nM
Tested a non-binding E3 control?: No
Tested competition with ligand?: No
Tested proteaseome inhibitor?: No
Proteomics data available?: No
Tested engagement in cells?: No
Off-targets reported?: No
Comments: IC50: 175nM/142nM for CDK4/CDK6, respectively.
Contributed by: Yangwode Jing
Calculated Values
MW: 761.89
Hbond donors: 3
Hbond acceptors: 13
cLogP: 3.80
TPSA: 178.00

SMILES: show
Linker type: Alkane
Incubation time (hours): 4
Cells: Jurkat
IC50: = 79.7 nM
Tested a non-binding E3 control?: No
Tested competition with ligand?: No
Tested proteaseome inhibitor?: No
Proteomics data available?: No
Tested engagement in cells?: No
Off-targets reported?: No
Comments: IC50: 79.7nM/65.5nM for CDK4/CDK6, respectively.
Contributed by: Yangwode Jing