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1 A R R RA-selective pocket Cl Adenine pocket and hinge-binding moiety Cl ulfonamide series PLX7 PLX Br BR BR TV PLX RI TQ D RI9 C B PLX7 M ulfonamide concentration Monomer Dimer RA-elective Pocket Unoccupied RA-elective Pocket ccupied.5 M M elix C In PDB CC Chain A vs Chain B elix C ut PDB G7 Chain A - PLX vs Chain B AP RA-elective Pocket ccupied AP elix C In upplementary igure ature tructural & Molecular Biology doi:./nsmb.9 elix C ut BR Monomer Dimer M PLX Monomer Dimer edimentation coefficient (s)
2 upplementary igure ulfonamide inhibitors occupy the RA-selective pocket and retain dimer-breaker ability at nonsaturating concentrations in vitro. (a) tructure.sdf files of sulfonamide compounds were obtained from the PDB and displayed using ChemBioDraw.. (b) Comparison of the two protomers in crystal structures of BRA bound to PLX7 (PDB ID CC 5 ) or PLX (PDB ID G7 ). Protomers in a helix αc-out, off-like state conformation (blue) have the RA-selective pocket occupied. or the protomer displaying a helix αc-in, on state conformation (orange), the RA-selective pocket is not occupied due to an alternate binding mode of the inhibitor arising from the indicated rotation of the terminal sulfonamide motif. (c) edimentation velocity AUC analysis of a solution of the BRA kinase domain (5 µm of protein) in a titration series with saturating ( µm) and non-saturating (.5 µm and µm) of the sulfonamide inhibitors PLX7, PLX or BR. ature tructural & Molecular Biology doi:./nsmb.9
3 A C-pine R-pine C-pine BRA dimer on state Linear R-spine C-pine R-pine C-pine R-pine BRA forced dimer Minor Kinked R-spine BRA monomer off state Major Kinked R-spine (. Å) (. Å) R-pine C-pine R-pine B CDK on state Linear R-spine CDK off state Broken R-spine (5. Å) B C W7 elix C 77 W5 R5 M57 5 K57 5 K57 V5 T59 Y5 A599 D55 BRA forced dimer - PLX7 (PDB CC Chain A) upplementary igure ature tructural & Molecular Biology doi:./nsmb.9 E5 L55 R59 V5 BRA monomer - PLX7 Q5 L/5
4 upplementary igure The monomer off-state structure of BRA closely resembles the forced dimer sulfonamide co-structures. (a) ydrophobic spines representation of BRA in the dimer on state, monomer off state and forced dimer intermediate-state (Top). ydrophobic spines representation of CDK in on and off states (Bottom). (b) Binding mode of PLX7 in the BRA monomer structure (PDB ID W5; this study) and forced dimer structure (PDB ID CC 5 ). (c) Dimer interface residues of the on state dimers (orange) and off-like state forced dimers (green). ature tructural & Molecular Biology doi:./nsmb.9
5 7. Å ide to ide Dimer (Reference Conformation) Protomer Protomer ymmetry Related Protomer Protomer Protomer 9 ymmetry Related Protomer ymmetry Related Protomer. Å 7.9 Å 5.7 Å. Å Protomer ymmetry Related Protomer ymmetry Related Protomer. Å. Å Protomer.7 Å ymmetry Related Protomer upplementary igure ature tructural & Molecular Biology doi:./nsmb.9
6 upplementary igure Crystal contacts in the BRA monomeric structure in complex with PLX7. Protomer and and their symmetry related mates are shown in light and dark blue, respectively. The side-toside dimer configuration of on state structure is shown in orange and yellow for reference. ature tructural & Molecular Biology doi:./nsmb.9
7 upplementary Table. elix αc position and presence of helix A- in BRA kinase domain dimer structures. PDB ID αc Position A- elix Present B in no DQ in no PB in no PPJ in no PPK in no PR in no PRI in no QC in no PD in no E in no 5 in no UW in no UWJ in no IDP in no II5 in no Q9 in no DB in no G9C in no JVG in no KP in no KQ in no C in no CC out no G7 out no K out no EG out no KC out yes TV out yes TV out yes EX out yes EE out yes MBJ out yes PP7 out yes ature tructural and Molecular Biology: doi:./nsmb.9
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