SMTL ID : 6p9g.1

Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with 2-(4-oxoquinazolin-3(4H)-yl)propanoic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 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 O4Y: (2R)-2-(4-oxoquinazolin-3(4H)-yl)propanoic acid(Non-covalent)

O4Y.2: 10 residues within 4Å: Chain A: W.40, G.51, R.52, A.64, V.65, Y.90, Y.92, D.95 Ligands: UNX.7, UNX.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.40, A:Y.90, A:Y.90 Hydrogen bonds: A:R.52, A:V.65, A:Y.92, A:Y.92 pi-Stacking: A:Y.90

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

UNX.3: 2 residues within 4Å: Chain A: S.102, E.105 No protein-ligand interaction detected (PLIP) UNX.4: 4 residues within 4Å: Chain A: R.5, Q.6, M.97, V.98 No protein-ligand interaction detected (PLIP) UNX.5: 3 residues within 4Å: Chain A: N.38, L.39, L.79 No protein-ligand interaction detected (PLIP) UNX.6: 2 residues within 4Å: Chain A: Y.54, F.55 No protein-ligand interaction detected (PLIP) UNX.7: 8 residues within 4Å: Chain A: C.50, G.51, R.52, N.62, H.63, A.64, V.65 Ligands: O4Y.2 No protein-ligand interaction detected (PLIP) UNX.8: 3 residues within 4Å: Chain A: W.40, M.97 Ligands: O4Y.2 No protein-ligand interaction detected (PLIP) UNX.9: 2 residues within 4Å: Chain A: H.10, S.13 No protein-ligand interaction detected (PLIP) UNX.10: 5 residues within 4Å: Chain A: K.9, H.10, A.11, F.12, S.13 No protein-ligand interaction detected (PLIP) UNX.11: 2 residues within 4Å: Chain A: L.99, D.100 No protein-ligand interaction detected (PLIP) UNX.12: 3 residues within 4Å: Chain A: D.18, N.19, P.20 No protein-ligand interaction detected (PLIP) UNX.13: 2 residues within 4Å: Chain A: Q.16, H.109 No protein-ligand interaction detected (PLIP) UNX.14: 3 residues within 4Å: Chain A: K.9, E.94 Ligands: UNX.15 No protein-ligand interaction detected (PLIP) UNX.15: 2 residues within 4Å: Chain A: K.9 Ligands: UNX.14 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

2019-09-18

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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