4W9H | pdb_00004w9h

pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-acetamido-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 7)

PDB DOI: https://doi.org/10.2210/pdb4W9H/pdb

Classification: LIGASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-08-27 Released: 2014-09-10
Deposition Author(s): Gadd, M.S., Soares, P., Galdeano, C., van Molle, I., Ciulli, A.
Funding Organization(s): European Research Council, Biotechnology and Biological Sciences Research Council, Marie Sklodowska-Curie Actions

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.253 (Depositor), 0.259 (DCC)
R-Value Work:
0.210 (Depositor), 0.217 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

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.

(2014) J Med Chem 57: 8657-8663

PubMed: 25166285 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/jm5011258
Primary Citation Related Structures:
4W9C, 4W9D, 4W9E, 4W9F, 4W9G, 4W9H, 4W9I, 4W9J, 4W9K, 4W9L

PubMed Abstract:
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.

Organizational Affiliation

Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Dow Street, Dundee, DD1 5EH, Scotland, U.K.

Macromolecule Content

Total Structure Weight: 169.05 kDa
Atom Count: 11,271
Modeled Residue Count: 1,332
Deposited Residue Count: 1,452
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor B polypeptide 2	A, D, G, J	104	Homo sapiens	Mutation(s): 0 Gene Names: TCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens) Explore Q15370 Go to UniProtKB: Q15370
PHAROS: Q15370 GTEx: ENSG00000103363
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15370
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor B polypeptide 1	B, E	97	Homo sapiens	Mutation(s): 0 Gene Names: TCEB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens) Explore Q15369 Go to UniProtKB: Q15369
PHAROS: Q15369 GTEx: ENSG00000154582
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15369
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Von Hippel-Lindau disease tumor suppressor	C, F, I, L	162	Homo sapiens	Mutation(s): 0 Gene Names: VHL
UniProt & NIH Common Fund Data Resources
Find proteins for P40337 (Homo sapiens) Explore P40337 Go to UniProtKB: P40337
PHAROS: P40337 GTEx: ENSG00000134086
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40337
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor B polypeptide 1	H, K	97	Homo sapiens	Mutation(s): 0 Gene Names: TCEB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens) Explore Q15369 Go to UniProtKB: Q15369
PHAROS: Q15369 GTEx: ENSG00000154582
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15369
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3JF Query on 3JF Download:Ideal Coordinates CCD File SDF format, chain P [auth L] SDF format, chain O [auth I] SDF format, chain N [auth F] SDF format, chain M [auth C] MOL2 format, chain P [auth L] MOL2 format, chain O [auth I] MOL2 format, chain N [auth F] MOL2 format, chain M [auth C] mmCIF format, chain P [auth L] mmCIF format, chain O [auth I] mmCIF format, chain N [auth F] mmCIF format, chain M [auth C]	M [auth C], N [auth F], O [auth I], P [auth L]	N-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide C₂₄ H₃₂ N₄ O₄ S GFVIEZBZIUKYOG-SVFBPWRDSA-N		Interactions Focus chain M [auth C] Focus chain N [auth F] Focus chain O [auth I] Focus chain P [auth L] Interactions & Density Focus chain M [auth C] Focus chain N [auth F] Focus chain O [auth I] Focus chain P [auth L]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAS Query on CAS	A, D, G, J	L-PEPTIDE LINKING	C₅ H₁₂ As N O₂ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.253 (Depositor), 0.259 (DCC)
R-Value Work: 0.210 (Depositor), 0.217 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.98	α = 90
b = 92.98	β = 90
c = 364.372	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
XSCALE	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2014-09-10

Deposition Author(s):

Funding Organization	Location	Grant Number
European Research Council		ERC-2012-StG-311460
Biotechnology and Biological Sciences Research Council	United Kingdom	BBSRC BB/G023123/1
Marie Sklodowska-Curie Actions		EC PIEF-GA-2012-328030

Revision History (Full details and data files)

Version 1.0: 2014-09-10
Type: Initial release
Version 1.1: 2014-11-05
Changes: Database references
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-10-23
Changes: Structure summary