SMTL ID : 9b9t.1

Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-40407

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 01: N-{(1P)-5'-[(17-{(4P)-4-[(2P)-4-{[(1R)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]carbamoyl}-3-(4-chloro-2-fluorophenyl)-1H-pyrrol-2-yl]-1H-pyrazol-1-yl}-16-oxo-3,6,9,12-tetraoxa-15-azaheptadecan-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: 42 residues within 4Å: Chain A: A.42, 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, C.256, I.300, L.316 Chain B: T.87, H.88, W.104, Y.129, R.173, C.175, R.246, V.247, V.248, Y.257, G.258, A.259, L.261, M.270, E.271, E.272, R.273, K.275, P.277, F.278, I.302, F.303, D.304, L.305 25 PLIP interactions: 17 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:R.246, B:V.248, B:L.261, B:F.278, A:F.128, A:P.168, A:I.300 Hydrogen bonds: B:T.87, B:H.88, B:R.173, B:R.246, B:K.275, B:D.304, A:S.86, A:S.86 Water bridges: B:R.173, B:E.271, B:E.271, A:S.86 pi-Stacking: B:H.88, B:W.104, B:F.278, A:F.128 Halogen bonds: B:R.173 Salt bridges: A:D.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mabanglo, M.F. et al., Crystal structures of DCAF1-PROTAC-WDR5 complexes provide insight into DCAF1 substrate specificity. To Be Published

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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