9H9O: NEDD4 HECT domain

Name: PDB 9H9O: Crystal structure of NEDD4 HECT domain in complex with norclomipramine
Published: 2025-06-04
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of NEDD4 HECT domain in complex with norclomipramine. Determined by X-ray diffraction at 2.12 Å resolution. Released 4 Jun 2025.

Method: X-ray diffraction
Resolution: 2.12 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,290
Mol. weight: 45.29 kDa
Ligands: A1ITH
Released: 4 Jun 2025

Explore 9H9O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9H9O contains 28 α-helices and 15 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 28 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	522-532	11
α-helix	534-536	3
β-strand	542-547	6	1
α-helix	549-551	3
α-helix	552-562	11
α-helix	566-570	5
β-strand	572-577	6	1
α-helix	585-600	16
α-helix	603-605	3
β-strand	608-610	3	2
β-strand	618-620	3	2
α-helix	624-627	4
α-helix	631-647	17
β-strand	656	1	2
α-helix	658-664	7
α-helix	667-669	3
α-helix	671-677	7
α-helix	679-690	12
α-helix	694-696	3
β-strand	699	1	3
β-strand	701-706	6	4
β-strand	709-714	6	4
α-helix	719-721	3
β-strand	723	1	3
α-helix	729-741	13
α-helix	743-745	3
α-helix	746-759	14
α-helix	762-765	4
α-helix	770-778	9
α-helix	785-790	6
β-strand	792-795	4	5
α-helix	803-813	11
α-helix	817-828	12
α-helix	832-834	3
α-helix	838-840	3
β-strand	842	1	6
β-strand	847	1	6
β-strand	850-854	5	5
α-helix	861-862	2
β-strand	863-865	3	5
α-helix	866-868	3
β-strand	870-873	4	5
α-helix	879-890	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 4 of E3 ubiquitin-protein ligase NEDD4	A	protein	375	Homo sapiens	P46934 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9H9O_1 Isoform 4 of E3 ubiquitin-protein ligase NEDD4 (chains A)
SRDYKRKYEFFRRKLKKQNDIPNKFEMKLRRATVLEDSYRRIMGVKRADFLKARLWIEFD
GEKGLDYGGVAREWFFLISKEMFNPYYGLFEYSATDNYTLQINPNSGLCNEDHLSYFKFI
GRVAGMAVYHGKLLDGFFIRPFYKMMLHKPITLHDMESVDSEYYNSLRWILENDPTELDL
RFIIDEELFGQTHQHELKNGGSEIVVTNKNKKEYIYLVIQWRFVNRIQKQMAAFKEGFFE
LIPQDLIKIFDENELELLMCGLGDVDVNDWREHTKYKNGYSANHQVIQWFWKAVLMMDSE
KRIRLLQFVTGTSRVPMNGFAELYGSNGPQSFTVEQWGTPEKLPRAHTCFNRLDLPPYES
FEELWDKLQMAIENT

Ligands and cofactors

ID	Name	Formula	Copies
A1ITH	Norclomipramine	C18 H21 Cl N2	1

Water and common crystallization additives (EDO) are not listed.

Primary citation

Structure-based design of potent and selective inhibitors of the HECT ligase NEDD4. Maspero, E., Cappa, A., Weber, J. et al. Commun Chem (2025) 8:164-164. DOI 10.1038/s42004-025-01557-4 · PubMed

Other PDB entries of the same protein (UniProt P46934 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4N7F 1.1 Å, Crystal structure of 3rd WW domain of human Nedd4-1
4N7H 1.7 Å, Crystal Structure of the Complex of 3rd WW domain of Human Nedd4 and 1st PPXY Motif of…
3B7Y 1.8 Å, Crystal structure of the C2 Domain of the E3 Ubiquitin-Protein Ligase NEDD4
9H9T 2.17 Å, Crystal structure of NEDD4 HECT domain in complex with covalent inhibitor
5C91 2.44 Å, NEDD4 HECT with covalently bound indole-based inhibitor
2XBF 2.5 Å, Nedd4 HECT structure
4BBN 2.51 Å, NEDD4 HECT-Ub:Ub complex
2XBB 2.68 Å, Nedd4 HECT:Ub complex
4BE8 3.0 Å, NEDD4 HECT A889F structure
5C7J 3.0 Å, Crystal structure of NEDD4 with a ub variant
2KPZ Human NEDD4 3RD WW Domain Complex with The Human T-cell Leukemia virus 1 GAG-Pro…
2KQ0 Human NEDD4 3rd WW Domain Complex with Ebola Zaire Virus Matrix Protein VP40 Derived…

Browse structure collections

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