SMTL ID : 7ms5.2 (1 other biounit)

Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with 4-(4-(4-(3,4-difluoro-phenyl)-piperidin-1-ylsulfonyl)-phenyl)-4-oxo-butanoic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 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

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

EDO.2: 5 residues within 4Å: Chain A: L.17, D.18, N.19, P.20, D.45 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.17 Water bridges: A:L.17, A:A.21

1 x ZOG: 4-{4-[4-(3,4-difluorophenyl)piperidine-1-sulfonyl]phenyl}-4-oxobutanoic acid(Non-covalent)

ZOG.3: 9 residues within 4Å: Chain A: W.40, G.51, R.52, Y.54, A.64, V.65, Y.90, Y.92, M.97 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.40, A:W.40, A:Y.90, A:Y.90, A:Y.90, A:Y.92 Hydrogen bonds: A:R.52, A:R.52, A:Y.92, A:Y.92 Water bridges: A:G.60, A:V.65, A:M.97

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: E.94, D.95, D.96 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.94

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
B

Ubiquitin carboxyl-terminal hydrolase 5

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