SMTL ID : 6xmx.1

Cryo-EM structure of BCL6 bound to BI-3802

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

8 x U52: 2-[6-[[5-chloranyl-2-[(3~{S},5~{R})-3,5-dimethylpiperidin-1-yl]pyrimidin-4-yl]amino]-1-methyl-2-oxidanylidene-quinolin-3-yl]oxy-~{N}-methyl-ethanamide(Non-covalent)

U52.1: 22 residues within 4Å: Chain A: M.91, A.92, C.93, S.94, G.95, Y.98, F.129, Q.153, M.154, E.155, H.156, V.157 Chain B: F.51, H.54, N.61, R.64, L.65 Chain E: E.81, P.120, E.121, C.124, I.125 9 PLIP interactions: 7 interactions with chain A, 1 interactions with chain E, 1 interactions with chain B Hydrophobic interactions: A:Y.98, E:E.121 Hydrogen bonds: A:M.91, A:E.155, A:E.155, A:H.156, A:V.157, B:H.54 pi-Stacking: A:Y.98 U52.2: 21 residues within 4Å: Chain A: F.51, H.54, N.61, R.64, L.65 Chain B: M.91, A.92, C.93, S.94, G.95, Y.98, F.129, Q.153, M.154, E.155, H.156, V.157 Chain D: P.120, E.121, C.124, I.125 9 PLIP interactions: 2 interactions with chain D, 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: D:E.121, D:I.125, B:Y.98 Hydrogen bonds: B:M.91, B:E.155, B:H.156, B:V.157, A:H.54 pi-Stacking: B:Y.98 U52.3: 22 residues within 4Å: Chain A: E.81, P.120, E.121, C.124, I.125 Chain C: M.91, A.92, C.93, S.94, G.95, Y.98, F.129, Q.153, M.154, E.155, H.156, V.157 Chain D: F.51, H.54, N.61, R.64, L.65 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:Y.98, A:E.121 Hydrogen bonds: C:M.91, C:E.155, C:E.155, C:H.156, C:V.157 pi-Stacking: C:Y.98 U52.4: 17 residues within 4Å: Chain C: F.51, H.54, N.61, R.64, L.65 Chain D: M.91, A.92, C.93, S.94, G.95, Y.98, F.129, Q.153, M.154, E.155, H.156, V.157 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.98 Hydrogen bonds: D:M.91, D:E.155, D:H.156, D:V.157, C:H.54 pi-Stacking: D:Y.98 U52.5: 22 residues within 4Å: Chain E: M.91, A.92, C.93, S.94, G.95, Y.98, F.129, Q.153, M.154, E.155, H.156, V.157 Chain F: F.51, H.54, N.61, R.64, L.65 Chain G: E.81, P.120, E.121, C.124, I.125 8 PLIP interactions: 1 interactions with chain G, 7 interactions with chain E Hydrophobic interactions: G:E.121, E:Y.98 Hydrogen bonds: E:M.91, E:E.155, E:E.155, E:H.156, E:V.157 pi-Stacking: E:Y.98 U52.6: 24 residues within 4Å: Chain B: E.81, P.120, E.121, C.124, I.125 Chain E: F.51, H.54, N.61, R.64, L.65, R.68, I.70 Chain F: M.91, A.92, C.93, S.94, G.95, Y.98, F.129, Q.153, M.154, E.155, H.156, V.157 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain F Hydrophobic interactions: B:E.121, F:Y.98 Hydrogen bonds: F:M.91, F:E.155, F:H.156, F:V.157 pi-Stacking: F:Y.98 U52.7: 17 residues within 4Å: Chain G: M.91, A.92, C.93, S.94, G.95, Y.98, F.129, Q.153, M.154, E.155, H.156, V.157 Chain H: F.51, H.54, N.61, R.64, L.65 8 PLIP interactions: 7 interactions with chain G, 1 interactions with chain H Hydrophobic interactions: G:Y.98 Hydrogen bonds: G:M.91, G:E.155, G:E.155, G:H.156, G:V.157, H:H.54 pi-Stacking: G:Y.98 U52.8: 22 residues within 4Å: Chain F: E.81, P.120, E.121, C.124, I.125 Chain G: F.51, H.54, N.61, R.64, L.65 Chain H: M.91, A.92, C.93, S.94, G.95, Y.98, F.129, Q.153, M.154, E.155, H.156, V.157 7 PLIP interactions: 6 interactions with chain H, 1 interactions with chain F Hydrophobic interactions: H:Y.98, F:E.121 Hydrogen bonds: H:M.91, H:E.155, H:H.156, H:V.157 pi-Stacking: H:Y.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Slabicki, M. et al., Small-molecule-induced polymerization triggers degradation of BCL6. Nature (2020)

Release Date

2020-11-25

Peptides

B-cell lymphoma 6 protein: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

B-cell lymphoma 6 protein