SMTL ID : 8fy1.1

E3:PROTAC:target ternary complex structure (VCB/753b/BCL-2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.56 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x YF8: N-[8-(4-{[(1R,3R,4S)-4-(4-chlorophenyl)-1-methyl-3-{[4-(4-{[4-{[(2R)-4-(morpholin-4-yl)-1-(phenylsulfanyl)butan-2-yl]amino}-3-(trifluoromethanesulfonyl)benzene-1-sulfonyl]carbamoyl}phenyl)piperazin-1-yl]methyl}cyclohexyl]methyl}piperazin-1-yl)-8-oxooctanoyl]-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide(Non-covalent)

YF8.1: 45 residues within 4Å: Chain A: N.34, R.36, P.53, W.55, F.58, Y.65, P.66, L.68, R.74, I.76, H.77, S.78, Y.79, H.82, W.84 Chain D: A.102, D.105, F.106, R.109, Y.110, D.113, F.114, M.117, F.126, T.127, G.130, R.131, T.134, V.135, E.138, L.139, N.145, W.146, G.147, R.148, V.150, A.151, E.154, F.155, V.158, F.200, L.203, Y.204, P.206, S.207 34 PLIP interactions: 13 interactions with chain A, 21 interactions with chain D Hydrophobic interactions: A:R.36, A:Y.65, A:Y.65, A:I.76, A:I.76, A:Y.79, A:W.84, D:F.106, D:F.106, D:F.106, D:Y.110, D:D.113, D:M.117, D:F.126, D:T.134, D:V.135, D:E.138, D:R.148, D:V.150, D:V.150, D:F.155, D:Y.204 Hydrogen bonds: A:N.34, A:W.55, A:H.77, A:Y.79, A:Y.79, A:H.82, D:N.145, D:W.146, D:G.147, D:S.207 Salt bridges: D:D.113 Halogen bonds: D:F.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nayak, D. et al., Development and crystal structures of a potent second-generation dual degrader of BCL-2 and BCL-xL. Nat Commun (2024)

Release Date

2024-04-10

Peptides

von Hippel-Lindau disease tumor suppressor: A
Elongin-B: B
Elongin-C: C
Apoptosis regulator Bcl-2: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

von Hippel-Lindau disease tumor suppressor

Elongin-B

Elongin-C

Apoptosis regulator Bcl-2

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