SMTL ID : 8ogc.1

Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

monomer

Ligands

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

DMS.1: 11 residues within 4Å: Chain A: R.264, V.265, V.266, Y.275, G.276, A.277, F.296, I.320, D.322, L.323 Ligands: VMZ.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.264, A:L.323 pi-Cation interactions: A:F.296

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: S.50, V.51, F.89, S.90 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.50, A:F.89, H2O.3, H2O.4

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

ACT.3: 1 residues within 4Å: Chain A: M.138 2 PLIP interactions: 2 interactions with chain A Water bridges: A:M.138, A:M.138 ACT.4: 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

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

EDO.5: 10 residues within 4Å: Chain A: R.191, N.192, C.193, N.227, I.228, S.229, G.230, V.231, R.264 Ligands: VMZ.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.229, A:G.230

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

VMZ.6: 22 residues within 4Å: Chain A: T.63, C.64, C.79, A.103, T.105, H.106, T.121, 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: DMS.1, EDO.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:T.105, A:Y.147, A:R.191, 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:C.65, A:A.103, A:R.264 VMZ.7: 14 residues within 4Å: Chain A: R.70, F.73, M.75, L.83, K.84, L.85, E.94, A.95, S.96, Y.97, M.132, S.134, V.135, F.136 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.73, A:L.85, A:A.95, A:M.132, A:F.136 Halogen bonds: A:L.83

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
A

DDB1- and CUL4-associated factor 1

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