SMTL ID : 8ewv.3 (5 other biounits)

DNA-encoded library (DEL)-enabled discovery of proximity inducing small molecules

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x X5K: N-{3-[1-(4-{[3-(cyclopropylamino)-3-oxopropyl](methyl)amino}-6-{methyl[(1,3,5-trimethyl-1H-pyrazol-4-yl)methyl]amino}-1,3,5-triazin-2-yl)piperidin-4-yl]propanoyl}-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide(Non-covalent)

X5K.1: 27 residues within 4Å: Chain C: R.18, W.37, F.40, Y.47, P.48, L.50, R.56, I.58, H.59, S.60, Y.61, H.64, W.66 Chain D: F.38, W.40, P.41, F.42, Q.44, P.45, V.46, K.50, L.51, Y.56, N.99, D.104, I.105, M.108 21 PLIP interactions: 10 interactions with chain D, 11 interactions with chain C Hydrophobic interactions: D:F.38, D:F.38, D:W.40, D:P.41, D:F.42, D:Q.44, D:V.46, C:R.18, C:I.58, C:I.58, C:Y.61, C:W.66 Hydrogen bonds: D:K.50, D:N.99, C:R.56, C:H.59, C:S.60, C:Y.61, C:H.64 pi-Cation interactions: D:K.50 pi-Stacking: C:Y.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mason, J.W. et al., DNA-encoded library-enabled discovery of proximity-inducing small molecules. Nat.Chem.Biol. (2024)

Release Date

2023-10-04

Peptides

Elongin-B: A
Elongin-C: B
von Hippel-Lindau disease tumor suppressor: C
Bromodomain-containing protein 4: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
J

C
K

D
L

Elongin-B

Elongin-C

von Hippel-Lindau disease tumor suppressor

Bromodomain-containing protein 4

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