SMTL ID : 9qje.1 (1 other biounit)

USP7 Covalently Bound to N-(6-Fluoro-3-nitropyridin-2-yl)-5-(1-methyl-1H-pyrazol-4-yl)isoquinolin-3-amine (GCL36, 7a) with Partial Occupancy

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

monomer

Ligands

1 x 01: ~{N}-(3-nitropyridin-2-yl)isoquinolin-3-amine

01.1: 10 residues within 4Å: Chain A: C.19, Y.20, L.84, F.87, M.88, N.256, H.257, G.258, Y.261 Ligands: EDO.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.20, A:L.84, A:L.84 Hydrogen bonds: A:N.256, A:G.258

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

EDO.2: 7 residues within 4Å: Chain A: Y.20, D.91, V.92, Q.93, F.205, Y.261 Ligands: 01.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.92, A:Q.93, A:Y.261 Water bridges: A:Q.93 EDO.4: 7 residues within 4Å: Chain A: G.2, S.3, K.4, V.10, D.67, P.69, D.279 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.3, A:K.4, A:D.67

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 7 residues within 4Å: Chain A: N.155, I.156, F.157, E.222, F.223, P.224, L.227 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.156, A:E.222

1 x BR: BROMIDE ION(Non-covalent)

BR.5: 4 residues within 4Å: Chain A: Q.15, G.71, T.72, K.73 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ernst, L.N. et al., Design, Synthesis, and Molecular Evaluation of S N Ar-Reactive N-(6-Fluoro-3-Nitropyridin-2-yl)Isoquinolin-3-Amines as Covalent USP7 Inhibitors Reveals an Unconventional Binding Mode. Arch Pharm (2025)

Release Date

2025-09-10

Peptides

Ubiquitin carboxyl-terminal hydrolase 7: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ubiquitin carboxyl-terminal hydrolase 7

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