ISDA

Deposition Date 2014-08-27

Release Date 2014-09-10

Last Version Date 2024-10-09

Entry Detail

PDB ID:

4W9J

Keywords:

TRANSCRIPTION

Title:

pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-4-methylpentanamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 13)

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli BL21(DE3)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.20 Å

R-Value Free:

0.26

R-Value Work:

0.21

R-Value Observed:

0.21

Space Group:

P 41 2 2

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription elongation factor B polypeptide 2
Gene (Uniprot):ELOB
Chain IDs:A, D, G, J
Chain Length:104
Number of Molecules:4
Biological Source:Homo sapiens

UniProt ID:Q15370 Pfam ID:PF00240

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription elongation factor B polypeptide 1
Gene (Uniprot):ELOC
Chain IDs:B, E, H, K
Chain Length:97
Number of Molecules:4
Biological Source:Homo sapiens

UniProt ID:Q15369 Pfam ID:PF03931

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Von Hippel-Lindau disease tumor suppressor
Gene (Uniprot):VHL
Chain IDs:C, F, I, L
Chain Length:162
Number of Molecules:4
Biological Source:Homo sapiens

UniProt ID:P40337 Pfam ID:PF01847, PF17211 EC:2.3.2.B13

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
CAS	A	CYS	modified residue

Ligand Molecules

3JH

Primary Citation

Structure-Guided Design and Optimization of Small Molecules Targeting the Protein-Protein Interaction between the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase and the Hypoxia Inducible Factor (HIF) Alpha Subunit with in Vitro Nanomolar Affinities.

Galdeano, C, Gadd, M.S, Soares, P, Scaffidi, S, Van Molle, I, Birced, I, Hewitt, S, Dias, D.M, Ciulli, A.Show

J.Med.Chem. 57 8657 8663 (2014)

PMID: 25166285 DOI: 10.1021/jm5011258

Abstact

E3 ubiquitin ligases are attractive targets in the ubiquitin-proteasome system, however, the development of small-molecule ligands has been rewarded with limited success. The von Hippel-Lindau protein (pVHL) is the substrate recognition subunit of the VHL E3 ligase that targets HIF-1α for degradation. We recently reported inhibitors of the pVHL:HIF-1α interaction, however they exhibited moderate potency. Herein, we report the design and optimization, guided by X-ray crystal structures, of a ligand series with nanomolar binding affinities.

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Primary Citation of related structures