SMTL ID : 6nft.1 (1 other biounit)

Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with (4-oxoquinazolin-3(4H)-yl)acetic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 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 KKG: (4-oxoquinazolin-3(4H)-yl)acetic acid(Non-covalent)

KKG.2: 9 residues within 4Å: Chain A: W.40, G.51, R.52, Y.54, A.64, V.65, Y.90, Y.92, M.97 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.90 Hydrogen bonds: A:R.52, A:R.52, A:Y.92 Water bridges: A:Y.54, A:V.65 pi-Stacking: A:Y.90

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

EDO.3: 4 residues within 4Å: Chain A: Q.6, V.7, E.94, V.98 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.94

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

UNX.4: 3 residues within 4Å: Chain A: N.42, A.64, H.67 No protein-ligand interaction detected (PLIP) UNX.5: 6 residues within 4Å: Chain A: E.37, N.38, L.39, L.79 Ligands: UNX.7, UNX.10 No protein-ligand interaction detected (PLIP) UNX.6: 2 residues within 4Å: Chain A: Q.6, V.7 No protein-ligand interaction detected (PLIP) UNX.7: 5 residues within 4Å: Chain A: E.37, N.38, K.78 Ligands: UNX.5, UNX.10 No protein-ligand interaction detected (PLIP) UNX.8: 4 residues within 4Å: Chain A: P.24, P.25, W.28, I.112 No protein-ligand interaction detected (PLIP) UNX.9: 1 residues within 4Å: Chain A: D.113 No protein-ligand interaction detected (PLIP) UNX.10: 5 residues within 4Å: Chain A: R.36, E.37, L.79 Ligands: UNX.5, UNX.7 No protein-ligand interaction detected (PLIP) UNX.11: 2 residues within 4Å: Chain A: G.80 Ligands: UNX.12 No protein-ligand interaction detected (PLIP) UNX.12: 2 residues within 4Å: Chain A: G.80 Ligands: UNX.11 No protein-ligand interaction detected (PLIP) UNX.13: 2 residues within 4Å: Chain A: G.2, V.4 No protein-ligand interaction detected (PLIP) UNX.14: 2 residues within 4Å: Chain A: G.86, A.87 No protein-ligand interaction detected (PLIP)

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

2019-01-02

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