SMTL ID : 6dxh.1

Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with 4-(4-tert-butylphenyl)-4-oxobutanoate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

7 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.1: 2 residues within 4Å: Chain A: L.99, D.100 No protein-ligand interaction detected (PLIP) UNX.2: 2 residues within 4Å: Chain A: Y.54, F.55 No protein-ligand interaction detected (PLIP) UNX.3: 3 residues within 4Å: Chain A: Q.6, V.7, E.94 No protein-ligand interaction detected (PLIP) UNX.4: 2 residues within 4Å: Chain A: R.52, R.69 No protein-ligand interaction detected (PLIP) UNX.5: 4 residues within 4Å: Chain A: R.36, N.38, L.39, L.79 No protein-ligand interaction detected (PLIP) UNX.6: 5 residues within 4Å: Chain A: P.101, S.102, L.103, A.104, E.105 No protein-ligand interaction detected (PLIP) UNX.7: 3 residues within 4Å: Chain A: H.67, E.70, T.71 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 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 HH4: 4-(4-tert-butylphenyl)-4-oxobutanoic acid(Non-covalent)

HH4.9: 8 residues within 4Å: Chain A: W.40, G.51, R.52, A.64, V.65, Y.90, Y.92, M.97 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.40, A:W.40, A:Y.90, A:Y.90, A:Y.92 Hydrogen bonds: A:R.52, A:R.52, A:V.65, A:Y.92, A:Y.92 Salt bridges: A:R.52 pi-Stacking: A:Y.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mann, M.K. et al., Discovery of Small Molecule Antagonists of the USP5 Zinc Finger Ubiquitin-Binding Domain. J.Med.Chem. (2019)

Release Date

2018-07-18

Peptides

Ubiquitin carboxyl-terminal hydrolase 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ubiquitin carboxyl-terminal hydrolase 5

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