PFI-6 A novel chemical probe for MLLT1/3

The probe and control are available from Sigma.



PFI-6PFI-6N (Negative control)

Increasing numbers of papers describing YEATS biology are emerging, and there is a growing need for high quality chemical probes that can be used to study YEATS domains. A collaboration between Pfizer and the SGC has resulted in the discovery of PFI-6, a potent inhibitor of MLLT1/3. PFI-6 has a unique chemotype relative to the current MLLT1/3 chemical probe NVS-MLLT-1.  PFI-6N has also been developed as a structurally similar negative control compound.


Physical and chemical properties for PFI-6
Molecular weight391.43
Molecular formulaC22H21N3O4
IUPAC name(R0-N-(2,3-dihydro-1H-inden-1-yl)-5-(4-(dimethylcarbamoyl)-3-hydroxyphenyl)isoxazole-3-carboxamide
No. of chiral centres0
No. of rotatable bonds6
No. of hydrogen bond acceptors7
No. of hydrogen bond donors2
Storagestore as a dry poweder or as DMSO stock solutions (10mM) at -20 °C
DissolutionSoluble in DMSO up to 10mM

Physical and chemical properties for PFI-6N
Molecular weight357.41
Molecular formulaC19H23N3O4
IUPAC nameN-cyclopentyl-5-(4-(dimethylcarbamoyl)-3-hydroxyphenyl)-N-methylisoxazole-3-carboxamide
No. of chiral centres0
No. of rotatable bonds6
No. of hydrogen bond acceptors7
No. of hydrogen bond donors1
StorageStore as a dry powder or as DMSO stock solutions (10mM) at -20 °C
DissolutionSoluble in DMSO up to 10mM


PFI-6: O=C(N(C)C)C1=C(O)C=C(C2=CC(C(N[C@@H]3CCC4=C3C=CC=C4)=O)=NO2)C=C1
PFI-6N: O=C(N(C)C)C1=C(O)C=C(C2=CC(C(N(C)C3CCCC3)=O)=NO2)C=C1


PFI-6: 1S/C22H21N3O4/c1-25(2)22(28)16-9-7-14(11-19(16)26)20-12-18(24-29-20)21(27)23-17-10-8-13-5-3-4-6-15(13)17/h3-7,9,11-12,17,26H,8,10H2,1-2H3,(H,23,27)/t17-/m1/s1
PFI-6-N: 1S/C19H23N3O4/c1-21(2)18(24)14-9-8-12(10-16(14)23)17-11-15(20-26-17)19(25)22(3)13-6-4-5-7-13/h8-11,13,23H,4-7H2,1-3H3



selectivity profile

PFI-6 shows potent activity on MLLT1/3 (Table 1). PFI-6 is universally inactive in the SGC Bromodomain panel, and showed no activity in an Invitrogen panel of 40 kinases (screening conducted at 10µM). Additionally, PFI-6 showed no activity in a panel of 25 PDEs, ion channels and GPCRs >50µM. The negative control, PFI-6N, was not reactive against MLLT1 >30µM, MLLT3 >30µM, YEATS2 >30µM and YEATS4 >30µM.


HTRF IC50 (µM)0.140.16>40>40
BLI Kd (µM)0.110.11n.d.n.d.
ITCKD (µM)0.0820.076n.d.n.d.
Tm Shift (°C)3.615.130.00-0.02

Table 1: Potency Against Target Family 

Figure 1: PFI-6 specfically inhibits MLLT1 and MLLT3.

in vitro potency
cell based assay data

In the NanoBRET cellular target engagement assay, PFI-6 displayed potent inhibition, with an average IC50 value of 0.76 μM (±0.1) (Figure 1). In comparison, PFI-6N had no inhibitory properties (up to 30 μM) (Figure 1). Further in cell validation using a Fluorescence Recovery After Photobleaching (FRAP) assay was used to confirm target inhibition by PFI-6  (Figure 2) . 

Figure 1: A NanoBRET assay was used to determine MLLT3 target engagement in cells.

Figure 2: Confirmation of MLLT1 target engagement in cells by Fluorescence Recovery After Photobleaching analysis.


pk properties
co-crystal structures

The figure below shows PFI-6 is soaked into the YEATS domain. PDB codes will be added when they become available. 



synthetic schemes
materials and methods