SMTL ID : 7ms6.1

Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with (2-fluoro-4-((4-phenylpiperidin-1-yl)sulfonyl)benzoyl)glycine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x ZPV: N-[2-fluoro-4-(4-phenylpiperidine-1-sulfonyl)benzoyl]glycine(Non-covalent)

ZPV.1: 13 residues within 4Å: Chain A: W.40, G.51, R.52, Y.54, F.55, D.56, S.58, A.64, V.65, Y.90, Y.92, M.97 Ligands: EDO.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.54, A:Y.54, A:F.55, A:Y.90, A:Y.90 Hydrogen bonds: A:R.52, A:R.52, A:V.65, A:Y.92, A:Y.92 Water bridges: A:Y.54, A:Y.54, A:G.60 Salt bridges: A:R.52 pi-Stacking: A:Y.54

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 1 residues within 4Å: Chain A: H.67 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.67

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

EDO.3: 3 residues within 4Å: Chain A: Y.54, F.55 Ligands: ZPV.1 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: C.30, C.33, C.50, H.63 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.30, A:C.33, A:C.50, A:H.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mann, M.K. et al., Structure-Activity Relationship of USP5 Inhibitors. J.Med.Chem. (2021)

Release Date

2021-06-09

Peptides

Ubiquitin carboxyl-terminal hydrolase 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ubiquitin carboxyl-terminal hydrolase 5

Related Entries With Identical Sequence