SMTL ID : 8oo5.1

Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 13

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

2 x VUF: 1-[4-[4-(2-azanylethylamino)-2-[1-(4-chlorophenyl)cyclohexyl]quinazolin-7-yl]piperazin-1-yl]ethanone(Non-covalent)

VUF.1: 20 residues within 4Å: Chain A: T.22, C.23, A.62, T.64, H.65, T.80, H.105, Y.106, R.150, C.152, I.187, R.223, L.238, K.252, P.254, F.255, F.280, D.281 Ligands: EDO.3, EDO.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:T.64, A:H.65, A:T.80, A:Y.106, A:R.150, A:L.238, A:P.254, A:F.255, A:F.280 Hydrogen bonds: A:F.280, A:D.281 Water bridges: A:L.66 VUF.2: 12 residues within 4Å: Chain A: R.29, F.32, L.42, L.44, E.53, A.54, S.55, Y.56, M.91, S.93, V.94, F.95 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.44, A:A.54 Hydrogen bonds: A:R.29 Halogen bonds: A:L.42

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

EDO.3: 7 residues within 4Å: Chain A: R.150, N.186, I.187, S.188, G.189, V.190 Ligands: VUF.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.150, A:S.188, A:G.189 EDO.4: 6 residues within 4Å: Chain A: R.223, V.225, A.236, D.281, L.282 Ligands: VUF.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.223, A:R.223, A:A.236, A:D.281 EDO.5: 8 residues within 4Å: Chain A: Q.239, K.252, S.253, N.278, N.296, G.298, S.299, M.300 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.253, A:N.278, A:N.296, A:M.300 Water bridges: A:N.278 EDO.6: 1 residues within 4Å: Chain A: T.39 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.39, A:T.39, A:T.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schroder, M. et al., Reinstating targeted protein degradation with DCAF1 PROTACs in CRBN PROTAC resistant settings. Biorxiv (2023)

Release Date

2023-05-24

Peptides

DDB1- and CUL4-associated factor 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
P

DDB1- and CUL4-associated factor 1

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