SMTL ID : 9dlw.1

Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-41114

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 01: N-{(1P)-5'-({(32E)-33-[(3P)-4-{[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]carbamoyl}-3-(4-chloro-2-fluorophenyl)-1H-pyrrol-2-yl]-31-oxo-3,6,9,12,15,18,21,24,27-nonaoxa-30-azatritriacont-32-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: 50 residues within 4Å: Chain A: T.45, C.47, T.87, H.88, L.89, T.103, W.104, H.128, Y.129, R.173, C.175, R.246, V.247, V.248, Y.257, G.258, A.259, L.261, L.269, M.270, E.272, R.273, 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, C.129, F.144, P.168, S.170, A.171, Y.186, K.254, Y.255, C.256, F.258, I.300, L.316 27 PLIP interactions: 14 interactions with chain A, 13 interactions with chain B Hydrophobic interactions: A:R.246, A:V.248, A:V.248, A:L.261, A:P.277, A:F.278, B:F.128, B:F.128, B:P.168, B:I.300 Hydrogen bonds: A:H.88, A:R.173, A:R.246, A:F.303, A:D.304, B:S.86, B:D.102, B:D.102, B:Y.126 pi-Stacking: A:W.104, A:F.278, B:F.128 Halogen bonds: A:R.173 Water bridges: B:G.84, B:S.86, B:Y.186 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 complexes provide insight into DCAF1 substrate specificity. To Be Published

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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