SMTL ID : 8ood.1

Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 15

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 7 residues within 4Å: Chain A: T.80, G.81, Q.82, N.98, H.100, N.101 Ligands: ACT.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.80, A:H.100, H2O.2

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 5 residues within 4Å: Chain A: N.98, C.99, H.100, N.101, S.123 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.101, A:S.123 Water bridges: A:H.100 ACT.3: 4 residues within 4Å: Chain A: T.80, N.101, S.102 Ligands: MG.1 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.80

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

EDO.4: 9 residues within 4Å: Chain A: R.191, C.193, N.227, I.228, S.229, G.230, V.231, R.264 Ligands: VY3.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.227, A:S.229, A:G.230 Water bridges: A:N.242 EDO.5: 7 residues within 4Å: Chain A: H.106, L.107, E.108, Y.147, V.148, E.149, R.264 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.106 Water bridges: A:E.108, A:Y.147, A:Y.147, A:R.264 EDO.6: 5 residues within 4Å: Chain A: V.51, R.318, Q.338, V.349, R.351 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.351, A:R.351 Water bridges: A:R.318 EDO.7: 7 residues within 4Å: Chain A: F.224, N.225, M.226, N.242, T.243, D.261, Q.262 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.261 Water bridges: A:N.225, A:N.242, A:Q.262 EDO.8: 5 residues within 4Å: Chain A: G.297, S.298, S.299, D.315, N.319 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.298, A:D.315, A:N.319 Water bridges: A:S.299, A:S.299

2 x VY3: ~{N}-[2-[2-[2-[2-[2-[2-[3-[4-[4-(2-azanylethylamino)-2-[1-(4-chlorophenyl)cyclopentyl]quinazolin-7-yl]piperazin-1-yl]-3-oxidanylidene-propoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethyl]ethanamide(Non-covalent)

VY3.9: 21 residues within 4Å: Chain A: T.63, C.64, A.103, T.105, H.106, T.121, W.122, H.146, Y.147, R.191, C.193, I.228, R.264, L.279, M.292, K.293, P.295, F.296, F.321, D.322 Ligands: EDO.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:T.105, A:Y.147, A:L.279, A:P.295, A:F.296, A:F.321 Hydrogen bonds: A:H.106, A:F.321, A:D.322 Water bridges: A:A.103, A:L.107, A:T.121, A:T.121 VY3.10: 13 residues within 4Å: Chain A: R.70, F.73, L.83, K.84, L.85, E.94, A.95, S.96, Y.97, M.132, S.134, V.135, F.136 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.85, A:A.95 Water bridges: A:S.96 Halogen bonds: A:L.83

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
A

DDB1- and CUL4-associated factor 1

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