SMTL ID : 9b9w.1

Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-40792

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 01: (4P)-N-[(1R)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(25E)-1-{(1P)-6-fluoro-3'-[4-fluoro-2-(trifluoromethyl)benzamido]-4'-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-1,24-dioxo-5,8,11,14,17,20-hexaoxa-2,23-diazahexacos-25-en-26-yl]-1H-pyrrole-3-carboxamide

01.1: 40 residues within 4Å: Chain A: S.44, S.45, A.60, G.84, I.85, S.86, D.87, D.102, F.128, C.129, P.168, S.170, Y.186, K.254, Y.255, C.256, I.300, L.316 Chain B: C.61, A.85, T.87, H.88, W.104, Y.129, R.173, C.175, R.246, V.247, V.248, G.258, A.259, L.261, K.275, P.277, F.278, I.302, F.303, D.304, L.305, M.328 22 PLIP interactions: 9 interactions with chain A, 13 interactions with chain B Hydrophobic interactions: A:F.128, A:P.168, A:I.300, B:R.246, B:R.246, B:V.248, B:L.261, B:P.277 Hydrogen bonds: A:S.86, A:Y.186, A:K.254, B:L.89, B:R.173, B:R.246, B:F.303, B:D.304 Water bridges: A:Y.186 Salt bridges: A:D.87 pi-Stacking: A:F.128, B:W.104, B:F.278 Halogen bonds: B:R.173

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mabanglo, M.F. et al., Crystal structures of DCAF1-PROTAC-WDR5 ternary complexes provide insight into DCAF1 substrate specificity. Nat Commun (2024)

Release Date

2024-11-06

Peptides

WD repeat-containing protein 5: A
DDB1- and CUL4-associated factor 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

WD repeat-containing protein 5

DDB1- and CUL4-associated factor 1

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