SMTL ID : 7jto.1

Crystal structure of Protac MS33 in complex with the WD repeat-containing protein 5 and pVHL:ElonginC:ElonginB

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

4 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.1: 4 residues within 4Å: Chain A: Y.49, E.287, I.289, K.305 No protein-ligand interaction detected (PLIP) SCN.2: 2 residues within 4Å: Chain A: K.246, Q.263 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.263 SCN.4: 3 residues within 4Å: Chain A: L.138, K.139, T.140 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.128 SCN.7: 2 residues within 4Å: Chain B: R.9, T.12 No protein-ligand interaction detected (PLIP)

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 1 residues within 4Å: Chain A: K.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.6 EDO.5: 5 residues within 4Å: Chain A: N.8, A.10, K.12, K.305, D.307 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.8 EDO.9: 4 residues within 4Å: Chain C: M.30, L.31, T.42, E.44 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.44 Water bridges: C:S.32, C:T.42 EDO.10: 5 residues within 4Å: Chain C: M.90, N.93 Chain D: I.129, V.130, L.133 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:V.130, C:N.93 EDO.11: 3 residues within 4Å: Chain D: I.58, H.59 Ligands: VKA.6 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.59, D:H.59, D:H.59

1 x VKA: 3-methyl-N-(11-{[2-(4-{[4'-(4-methylpiperazin-1-yl)-3'-{[6-oxo-4-(trifluoromethyl)-5,6-dihydropyridine-3-carbonyl]amino}[1,1'-biphenyl]-3-yl]methyl}piperazin-1-yl)ethyl]amino}-11-oxoundecanoyl)-L-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide(Non-covalent)

VKA.6: 35 residues within 4Å: Chain A: A.21, S.23, S.24, A.39, G.63, I.64, S.65, D.66, D.81, F.107, P.147, S.149, Y.165, P.190, E.232, K.233, C.235, I.279, L.295 Chain D: R.18, F.25, P.35, W.37, F.40, Y.47, P.48, L.50, R.56, I.58, H.59, S.60, Y.61, H.64, W.66 Ligands: EDO.11 29 PLIP interactions: 13 interactions with chain D, 16 interactions with chain A Hydrophobic interactions: D:W.37, D:F.40, D:I.58, D:I.58, D:Y.61, D:W.66, A:F.107, A:F.107, A:F.107, A:P.147, A:P.147, A:Y.165, A:Y.165, A:P.190 Hydrogen bonds: D:W.37, D:R.56, D:H.59, D:Y.61, D:H.64, A:S.65, A:K.233, A:K.233 Water bridges: D:Y.61, A:S.65, A:Y.165, A:Y.165 pi-Stacking: D:Y.47, A:F.107 Salt bridges: A:D.66

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 3 residues within 4Å: Chain C: A.29, M.30, S.32 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.32

1 x NA: SODIUM ION(Non-functional Binders)

NA.12: 4 residues within 4Å: Chain D: R.31, T.73, D.75, Q.113 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.31, D:T.73 Water bridges: D:R.110

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
J

C
K

D
L

WD repeat-containing protein 5

Elongin-B

Elongin-C

von Hippel-Lindau disease tumor suppressor

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