SMTL ID : 9b9h.1

Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-40333

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 01: N-{(1P)-5'-({(17E)-18-[(3P)-4-{[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]carbamoyl}-3-(4-chloro-2-fluorophenyl)-1H-pyrrol-2-yl]-16-oxo-3,6,9,12-tetraoxa-15-azaoctadec-17-en-1-yl}carbamoyl)-2'-fluoro-4-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide

01.1: 37 residues within 4Å: Chain A: T.87, H.88, T.103, W.104, Y.129, R.173, C.175, R.246, V.247, V.248, Y.257, G.258, A.259, L.261, M.274, P.277, F.278, I.302, F.303, D.304, L.305 Chain B: S.44, S.45, A.60, G.84, I.85, S.86, D.87, D.102, Y.126, F.128, P.168, S.170, Y.186, C.256, I.300, L.316 26 PLIP interactions: 13 interactions with chain A, 13 interactions with chain B Hydrophobic interactions: A:Y.129, A:R.246, A:V.248, A:L.261, A:P.277, A:F.278, B:A.60, B:F.128, B:F.128, B:P.168, B:Y.186, B:Y.186, B:I.300 Hydrogen bonds: A:R.246, A:F.303, A:D.304, A:D.304, B:S.86, B:Y.126 Water bridges: A:C.47, B:G.84, B:Y.186 pi-Stacking: A:F.278, B:F.128 Halogen bonds: A:R.173 Salt bridges: B:D.87

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

DDB1- and CUL4-associated factor 1

WD repeat-containing protein 5

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