8P0F

Crystal structure of the VCB complex with compound 1.

• PDB DOI: https://doi.org/10.2210/pdb8P0F/pdb

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


• Deposited: 2023-05-10 Released: 2023-05-31 
• Deposition Author(s): Bader, G., Boettcher, J., Wolkerstorfer, B.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.257 
• R-Value Work: 0.229 
• R-Value Observed: 0.230 

Starting Model: experimental

Literature

Drugit: Crowd-sourcing molecular design of non-peptidic VHL binders

Scott, T., Smethurst, C., Westermaier, Y., Mayer, M., Greb, P., Kousek, R., Biberger, T., Bader, G., Jandova, Z., Schmalhorst, P., Fuchs, J., Magarkar, A., Hoenke, C., Gerstberger, T., Combs, S., Pape, R., Phul, S., Kothiwale, S., Bergner, A., Moretti, R.

(2023) ChemRxiv 

• DOI: https://doi.org/10.26434/chemrxiv-2023-lczzd

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 83.73 kDa 
• Atom Count: 5,817 
• Modelled Residue Count: 675 
• Deposited Residue Count: 726 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
von Hippel-Lindau disease tumor suppressor	A, D	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-C	B, E	97	Homo sapiens	Mutation(s): 0  Gene Names: ELOC, TCEB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens) Explore Q15369  Go to UniProtKB:  Q15369
PHAROS:  Q15369 GTEx:  ENSG00000154582

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-B	C, F	104	Homo sapiens	Mutation(s): 0  Gene Names: ELOB, TCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens) Explore Q15370  Go to UniProtKB:  Q15370
PHAROS:  Q15370 GTEx:  ENSG00000103363

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WBN (Subject of Investigation/LOI)	G [auth A], I [auth D]	(3~{R},5~{R})-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-5-oxidanyl-2-oxidanylidene-1-pyridin-2-yl-piperidine-3-carboxamide C22 H22 N4 O3 S LCYOGYSKPSKGLU-QZTJIDSGSA-N
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.257 
• R-Value Work: 0.229 
• R-Value Observed: 0.230 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.387	α = 81.7
b = 47.72	β = 76.66
c = 98.756	γ = 82.8

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling
BUSTER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-31 
Deposition Author(s): Bader, G., Boettcher, J., Wolkerstorfer, B.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-05-31
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references