SMTL ID : 7jtp.1

Crystal structure of Protac MS67 in complex with the WD repeat-containing protein 5 and pVHL:ElonginC:ElonginB

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain C: Y.47 Chain D: N.104, Y.105, F.123 Ligands: X6M.2 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Y.47, D:N.104 Water bridges: C:Y.47

1 x X6M: N-(6-fluoro-3'-{[6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carbonyl]amino}-4'-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-carbonyl)glycyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide(Non-covalent)

X6M.2: 34 residues within 4Å: Chain C: R.18, F.25, W.37, F.40, Y.47, P.48, R.56, I.58, H.59, S.60, Y.61, H.64, W.66 Chain D: S.23, S.24, A.39, G.63, I.64, S.65, D.66, D.81, Y.105, F.107, C.108, F.123, D.146, P.147, S.149, Y.165, C.235, F.237, I.279, L.295 Ligands: GOL.1 31 PLIP interactions: 16 interactions with chain D, 15 interactions with chain C Hydrophobic interactions: D:A.39, D:D.66, D:Y.105, D:F.107, D:F.107, D:F.123, D:F.123, D:P.147, D:P.147, D:Y.165, D:I.279, C:W.37, C:Y.47, C:I.58, C:I.58, C:W.66 Hydrogen bonds: D:S.65, D:D.81, C:H.59, C:S.60, C:Y.61, C:Y.61, C:Y.61, C:H.64 Water bridges: D:G.63, C:R.18, C:R.18, C:Y.61 Salt bridges: D:D.66 pi-Stacking: D:F.107, C:Y.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, X. et al., A selective WDR5 degrader inhibits acute myeloid leukemia in patient-derived mouse models. Sci Transl Med (2021)

Release Date

2021-10-06

Peptides

Elongin-B: A
Elongin-C: B
von Hippel-Lindau disease tumor suppressor: C
WD repeat-containing protein 5: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

B
K

C
L

D
A

Elongin-B

Elongin-C

von Hippel-Lindau disease tumor suppressor

WD repeat-containing protein 5

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