SMTL ID : 8oga.1

Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: H.105, Y.106, K.149, R.150, N.151, C.152 Ligands: VLW.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.105, A:N.151 EDO.2: 10 residues within 4Å: Chain A: R.150, N.151, C.152, N.186, I.187, S.188, G.189, V.190, R.223 Ligands: VLW.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.150, A:S.188 Water bridges: A:R.223 EDO.3: 8 residues within 4Å: Chain A: R.223, V.224, V.225, G.235, A.236, F.255, D.281, L.282 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.223, A:R.223, A:A.236

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 7 residues within 4Å: Chain A: N.57, C.58, H.59, N.60, S.82, Q.83, P.84 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.60 Water bridges: A:H.59 DMS.5: 1 residues within 4Å: Chain A: M.97 1 PLIP interactions: 1 interactions with chain A Water bridges: A:M.97

1 x VLW: 5-[1-(4-methoxyphenyl)cyclopropyl]-8-(4-methylpiperazin-1-yl)-2,3-dihydroimidazo[2,1-a]isoquinoline(Non-covalent)

VLW.6: 20 residues within 4Å: Chain A: T.22, C.23, A.62, T.64, H.65, T.80, Y.106, R.150, C.152, I.187, R.223, L.238, K.252, P.254, F.255, F.280, D.281, M.305 Ligands: EDO.1, EDO.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.64, A:Y.106, A:R.223, A:L.238, A:P.254, A:F.280

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vulpetti, A. et al., Discovery of New Binders for DCAF1, an Emerging Ligase Target in the Targeted Protein Degradation Field. Acs Med.Chem.Lett. (2023)

Release Date

2023-06-14

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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