SMTL ID : 9h9o.1

Crystal structure of NEDD4 HECT domain in complex with norclomipramine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

monomer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: Q.101, I.102, R.222, F.223, I.227 Ligands: EDO.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.102 Water bridges: A:W.221, A:I.227 EDO.2: 4 residues within 4Å: Chain A: R.40, R.41, G.44, V.45 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.41, A:R.41 EDO.3: 7 residues within 4Å: Chain A: Q.101, I.102, I.139, F.142, M.145, F.223 Ligands: EDO.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.102, A:F.223 EDO.4: 4 residues within 4Å: Chain A: T.192, H.193, Q.194, H.195 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.194, A:H.195

1 x 01: Norclomipramine

01.5: 9 residues within 4Å: Chain A: L.35, E.36, Y.39, Y.87, L.89, N.110, Y.116, F.119, I.120 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.35, A:Y.39, A:Y.39, A:Y.87, A:Y.116, A:Y.116, A:Y.116, A:F.119 Water bridges: A:N.110 pi-Stacking: A:Y.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maspero, E. et al., Structure-based design of potent and selective inhibitors of the HECT ligase NEDD4. Commun Chem (2025)

Release Date

2025-06-04

Peptides

Isoform 4 of E3 ubiquitin-protein ligase NEDD4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Isoform 4 of E3 ubiquitin-protein ligase NEDD4

Related Entries With Identical Sequence