PROTACpedia
PHOTACs enable optical control of protein degradation. Sci Adv. 2020 Feb 21;6(8):eaay5064. PMID:32128406 DOI:10.1126/sciadv.aay5064
Target: FKBP1A Peptidyl-prolyl cis-trans isomerase FKBP1A P62942 Homo sapiens
E3 ligase: Cereblon
E3 binder: Pomalidomide
SMILES: show
Nc1cccc2c1C(=O)N(C1CCC(=O)NC1=O)C2=O

 Ligand Name: SLF
SMILES: show
CCC(C)(C)C(=O)C(=O)N1CCCC[C@H]1C(=O)OC(CCc1ccc(OC)c(OC)c1)c1cccc(N)c1

Calculated Values
MW: 1,092.17
Hbond donors: 3
Hbond acceptors: 16
cLogP: 8.16
TPSA: 267.07

SMILES: show
O=C([C@H]1N(C(C(C(C)(C)CC)=O)=O)CCCC1)O[C@@H](C2=CC=CC(OCC(NC3=CC=C(/N=N/C4=CC=C(NC(COC5=CC=CC(C(N6C(CC7)C(NC7=O)=O)=O)=C5C6=O)=O)C=C4)C=C3)=O)=C2)CCC8=CC=C(OC)C(OC)=C8

Linker type: Other
Incubation time (hours): 4
Cells: RS4;11
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: Light-activated PROTAC. The cis form is active.
Contributed by: Yangwode Jing
E3 ligase: Cereblon
E3 binder: Lenalidomide
SMILES: show
Nc1cccc2c1CN(C1CCC(=O)NC1=O)C2=O

 Ligand Name: SLF
SMILES: show
CCC(C)(C)C(=O)C(=O)N1CCCC[C@H]1C(=O)OC(CCc1ccc(OC)c(OC)c1)c1cccc(N)c1

Calculated Values
MW: 1,030.14
Hbond donors: 3
Hbond acceptors: 15
cLogP: 6.17
TPSA: 250.00

SMILES: show
O=C([C@H]1N(C(C(C(C)(C)CC)=O)=O)CCCC1)O[C@@H](C2=CC=CC(OCC(NCCNC(COC3=CC=C(/N=N\C4=CC=CC5=C4CN(C(CC6)C(NC6=O)=O)C5=O)C=C3)=O)=O)=C2)CCC7=CC=C(OC)C(OC)=C7

Linker type: Other
Incubation time (hours): 4
Cells: RS4;11
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: Light-activated PROTAC. The cis form is active.
Contributed by: Yangwode Jing
Calculated Values
MW: 1,104.22
Hbond donors: 3
Hbond acceptors: 17
cLogP: 6.58
TPSA: 268.46

SMILES: show
O=C(NCCCNC(COC1=C(OC)C=C(/N=N/C2=CC=CC3=C2CN(C(CC4)C(NC4=O)=O)C3=O)C=C1OC)=O)COc5cc([C@@H](CCc6cc(OC)c(OC)cc6)OC([C@@H]7CCCCN7C(C(C(C)(C)CC)=O)=O)=O)ccc5

Linker type: Other
Incubation time (hours): 4
Cells: RS4;11
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: Light-activated PROTAC. The cis form is active.
Contributed by: Yangwode Jing
Calculated Values
MW: 1,132.28
Hbond donors: 3
Hbond acceptors: 17
cLogP: 7.36
TPSA: 268.46

SMILES: show
O=C(NCCCCCNC(COC1=C(OC)C=C(/N=N/C2=CC=CC3=C2CN(C(CC4)C(NC4=O)=O)C3=O)C=C1OC)=O)COc5cc([C@@H](CCc6cc(OC)c(OC)cc6)OC([C@@H]7CCCCN7C(C(C(C)(C)CC)=O)=O)=O)ccc5

Linker type: Other
Incubation time (hours): 4
Cells: RS4;11
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: Light-activated PROTAC. The cis form is active.
Contributed by: Yangwode Jing
Calculated Values
MW: 1,146.30
Hbond donors: 3
Hbond acceptors: 17
cLogP: 7.75
TPSA: 268.46

SMILES: show
O=C(NCCCCCCNC(COC1=C(OC)C=C(/N=N/C2=CC=CC3=C2CN(C(CC4)C(NC4=O)=O)C3=O)C=C1OC)=O)COc5cc([C@@H](CCc6cc(OC)c(OC)cc6)OC([C@@H]7CCCCN7C(C(C(C)(C)CC)=O)=O)=O)ccc5

Linker type: Other
Incubation time (hours): 4
Cells: RS4;11
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: Light-activated PROTAC. The cis form is active.
Contributed by: Yangwode Jing
Calculated Values
MW: 1,118.25
Hbond donors: 3
Hbond acceptors: 17
cLogP: 6.97
TPSA: 268.46

SMILES: show
O=C(NCCCCNC(COC1=C(OC)C=C(/N=N/C2=CC=CC3=C2CN(C(CC4)C(NC4=O)=O)C3=O)C=C1OC)=O)COc5cc([C@@H](CCc6cc(OC)c(OC)cc6)OC([C@@H]7CCCCN7C(C(C(C)(C)CC)=O)=O)=O)ccc5

Linker type: Other
Incubation time (hours): 4
Cells: RS4;11
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: Light-activated PROTAC. The cis form is active.
Contributed by: Yangwode Jing
Target: BRD4 Bromodomain-containing protein 4 O60885 Homo sapiens
E3 ligase: Cereblon
E3 binder: Pomalidomide
SMILES: show
Nc1cccc2c1C(=O)N(C1CCC(=O)NC1=O)C2=O

 Ligand Name: JQ1
Ligand PDB Id: JQ1
PDB with Ligand: 3MXF
SMILES: show
Cc1sc2c(c1C)C(c1ccc(Cl)cc1)=N[C@@H](CC(=O)OC(C)(C)C)c1nnc(C)n1-2

Calculated Values
MW: 923.41
Hbond donors: 3
Hbond acceptors: 14
cLogP: 7.34
TPSA: 218.77

SMILES: show
O=C(NCC1=CC=C(/N=N/C2=CC=C(NC(COC3=CC=CC(C(N4C(CC5)C(NC5=O)=O)=O)=C3C4=O)=O)C=C2)C=C1)C[C@H]6C7=NN=C(C)N7C8=C(C(C)=C(C)S8)C(C9=CC=C(Cl)C=C9)=N6

Linker type: Other
Incubation time (hours): 4
Cells: RS4;11
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: Light-activated PROTAC. The cis form is active.
Contributed by: Yangwode Jing
Calculated Values
MW: 909.38
Hbond donors: 3
Hbond acceptors: 14
cLogP: 7.66
TPSA: 218.77

SMILES: show
O=C(NC1=CC=C(/N=N/C2=CC=C(NC(COC3=CC=CC(C(N4C(CC5)C(NC5=O)=O)=O)=C3C4=O)=O)C=C2)C=C1)C[C@H]6C7=NN=C(C)N7C8=C(C(C)=C(C)S8)C(C9=CC=C(Cl)C=C9)=N6

Linker type: Other
Incubation time (hours): 4
Cells: RS4;11
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: Light-activated PROTAC. The cis form is active.
Contributed by: Yangwode Jing
Calculated Values
MW: 935.42
Hbond donors: 3
Hbond acceptors: 14
cLogP: 7.76
TPSA: 218.77

SMILES: show
O=C(NC1=CC=C2/N=N\C3=CC=C(NC(COC4=CC=CC(C(N5C(CC6)C(NC6=O)=O)=O)=C4C5=O)=O)C=C3CCC2=C1)C[C@H]7C8=NN=C(C)N8C9=C(C(C)=C(C)S9)C(C%10=CC=C(Cl)C=C%10)=N7

Linker type: Other
Incubation time (hours): 4
Cells: RS4;11
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: Light-activated PROTAC. The cis form is active.
Contributed by: Yangwode Jing
Calculated Values
MW: 937.44
Hbond donors: 3
Hbond acceptors: 14
cLogP: 7.38
TPSA: 218.77

SMILES: show
O=C(NCCC1=CC=C(/N=N/C2=CC=C(NC(COC3=CC=CC(C(N4C(CC5)C(NC5=O)=O)=O)=C3C4=O)=O)C=C2)C=C1)C[C@H]6C7=NN=C(C)N7C8=C(C(C)=C(C)S8)C(C9=CC=C(Cl)C=C9)=N6

Linker type: Other
Incubation time (hours): 4
Cells: RS4;11
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: Light-activated PROTAC. The cis form is active.
Contributed by: Yangwode Jing
Calculated Values
MW: 921.39
Hbond donors: 3
Hbond acceptors: 16
cLogP: 5.33
TPSA: 237.23

SMILES: show
O=C(NCCNC(COC1=C(OC)C=C(/N=N/C2=CC3=C(C(N(C(CC4)C(NC4=O)=O)C3=O)=O)C=C2)C=C1OC)=O)C[C@H]5C6=NN=C(C)N6C7=C(C(C)=C(C)S7)C(C8=CC=C(Cl)C=C8)=N5

Linker type: Other
Incubation time (hours): 4
Cells: RS4;11
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: Light-activated PROTAC. The cis form is active.
Contributed by: Yangwode Jing
E3 ligase: Cereblon
E3 binder: Lenalidomide
SMILES: show
Nc1cccc2c1CN(C1CCC(=O)NC1=O)C2=O

 Ligand Name: JQ1
Ligand PDB Id: JQ1
PDB with Ligand: 3MXF
SMILES: show
Cc1sc2c(c1C)C(c1ccc(Cl)cc1)=N[C@@H](CC(=O)OC(C)(C)C)c1nnc(C)n1-2

Calculated Values
MW: 935.46
Hbond donors: 3
Hbond acceptors: 15
cLogP: 6.47
TPSA: 220.16

SMILES: show
O=C(NCCCCNC(COC1=C(OC)C=C(/N=N/C2=CC=CC3=C2CN(C(CC4)C(NC4=O)=O)C3=O)C=C1OC)=O)C[C@H]5C6=NN=C(C)N6C7=C(C(C)=C(C)S7)C(C8=CC=C(Cl)C=C8)=N5

Linker type: Other
Incubation time (hours): 4
Cells: RS4;11
EC50 (cells): = 88.5 nM
Tested a non-binding E3 control?: Yes
Tested competition with ligand?: No
Tested proteaseome inhibitor?: No
Proteomics data available?: No
Tested engagement in cells?: No
Off-targets reported?: No
Comments: Light-activated PROTAC. The cis form is active. Tested Cullin-RING inhibitors (MLN4924), which proved that PROTAC is UPS-dependent.
Contributed by: Yangwode Jing
Calculated Values
MW: 949.49
Hbond donors: 3
Hbond acceptors: 15
cLogP: 6.86
TPSA: 220.16

SMILES: show
O=C(NCCCCCNC(COC1=C(OC)C=C(/N=N/C2=CC=CC3=C2CN(C(CC4)C(NC4=O)=O)C3=O)C=C1OC)=O)C[C@H]5C6=NN=C(C)N6C7=C(C(C)=C(C)S7)C(C8=CC=C(Cl)C=C8)=N5

Linker type: Other
Incubation time (hours): 4
Cells: RS4;11
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: Light-activated PROTAC. The cis form is active.
Contributed by: Yangwode Jing
Calculated Values
MW: 921.44
Hbond donors: 3
Hbond acceptors: 15
cLogP: 6.08
TPSA: 220.16

SMILES: show
O=C(NCCCNC(COC1=C(OC)C=C(/N=N/C2=CC=CC3=C2CN(C(CC4)C(NC4=O)=O)C3=O)C=C1OC)=O)C[C@H]5C6=NN=C(C)N6C7=C(C(C)=C(C)S7)C(C8=CC=C(Cl)C=C8)=N5

Linker type: Other
Incubation time (hours): 4
Cells: RS4;11
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: Light-activated PROTAC. The cis form is active.
Contributed by: Yangwode Jing
Calculated Values
MW: 963.52
Hbond donors: 3
Hbond acceptors: 15
cLogP: 7.26
TPSA: 220.16

SMILES: show
O=C(NCCCCCCNC(COC1=C(OC)C=C(/N=N/C2=CC=CC3=C2CN(C(CC4)C(NC4=O)=O)C3=O)C=C1OC)=O)C[C@H]5C6=NN=C(C)N6C7=C(C(C)=C(C)S7)C(C8=CC=C(Cl)C=C8)=N5

Linker type: Other
Incubation time (hours): 4
Cells: RS4;11
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: Light-activated PROTAC. The cis form is active.
Contributed by: Yangwode Jing
Calculated Values
MW: 875.41
Hbond donors: 3
Hbond acceptors: 13
cLogP: 6.46
TPSA: 201.70

SMILES: show
O=C(NCCCCNC(COC1=CC=C(/N=N/C2=CC=CC3=C2CN(C(CC4)C(NC4=O)=O)C3=O)C=C1)=O)C[C@H]5C6=NN=C(C)N6C7=C(C(C)=C(C)S7)C(C8=CC=C(Cl)C=C8)=N5

Linker type: Other
Incubation time (hours): 4
Cells: RS4;11
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: Light-activated PROTAC. The cis form is active.
Contributed by: Yangwode Jing
Calculated Values
MW: 903.47
Hbond donors: 3
Hbond acceptors: 13
cLogP: 7.24
TPSA: 201.70

SMILES: show
O=C(NCCCCCCNC(COC1=CC=C(/N=N/C2=CC=CC3=C2CN(C(CC4)C(NC4=O)=O)C3=O)C=C1)=O)C[C@H]5C6=NN=C(C)N6C7=C(C(C)=C(C)S7)C(C8=CC=C(Cl)C=C8)=N5

Linker type: Other
Incubation time (hours): 4
Cells: RS4;11
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: Light-activated PROTAC. The cis form is active.
Contributed by: Yangwode Jing
Calculated Values
MW: 847.36
Hbond donors: 3
Hbond acceptors: 13
cLogP: 5.68
TPSA: 201.70

SMILES: show
O=C(NCCNC(COC1=CC=C(/N=N/C2=CC=CC3=C2CN(C(CC4)C(NC4=O)=O)C3=O)C=C1)=O)C[C@@H]5C6=NN=C(C)N6C7=C(C(C)=C(C)S7)C(C8=CC=C(Cl)C=C8)=N5

Linker type: Other
Incubation time (hours): 4
Cells: RS4;11
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: Light-activated PROTAC. The cis form is active.
Contributed by: Yangwode Jing
Calculated Values
MW: 907.41
Hbond donors: 3
Hbond acceptors: 15
cLogP: 5.69
TPSA: 220.16

SMILES: show
O=C(NCCNC(COC1=C(OC)C=C(/N=N/C2=CC=CC3=C2CN([C@@H](CC4)C(NC4=O)=O)C3=O)C=C1OC)=O)C[C@H]5C6=NN=C(C)N6C7=C(C(C)=C(C)S7)C(C8=CC=C(Cl)C=C8)=N5

Linker type: Other
Incubation time (hours): 4
Cells: RS4;11
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: Light-activated PROTAC. The cis form is active.
Contributed by: Yangwode Jing