9QE5 | pdb_00009qe5

VCB in complex with VHL-binding compound 82

• PDB DOI: https://doi.org/10.2210/pdb9QE5/pdb

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


• Deposited: 2025-03-07 Released: 2025-04-23 
• Deposition Author(s): Braun, M.B., Dierlamm, N., Hartmann, M.D.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.273 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Starting Model: experimental

Literature

Breaking Barriers in PROTAC Design: Improving Solubility of USP7-Targeting Degraders

Wittenburg, S., Zuleeg, M.R., Peter, K., Lemnitzer, P., Voget, R., Bricelj, A., Gobec, M., Dierlamm, N., Braun, M.B., Geiger, T.M., Heim, C., Stakemeier, A., Wagner, K.G., Nowak, R.P., Hartmann, M.D., Sosic, I., Guetschow, M., Kroenke, J., Steinebach, C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 198.14 kDa 
• Atom Count: 10,783 
• Modeled Residue Count: 1,343 
• Deposited Residue Count: 1,716 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-B	A, D, G, J	129	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-C	B, E, H, K	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
von Hippel-Lindau disease tumor suppressor	C, F, I, L	203	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1I58 (Subject of Investigation/LOI)	M [auth C], N [auth F], O [auth I], P [auth L]	(2~{S},4~{R})-1-[(2~{S})-1-(1-fluoranylcyclopropyl)carbonylpiperidin-2-yl]carbonyl-~{N}-[(1~{S})-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide C27 H33 F N4 O4 S PMUQVDYDZIRJQF-AEMJNJESSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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: 2.50 Å
• R-Value Free:  0.273 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.215	α = 90
b = 94.215	β = 90
c = 366.025	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-23 
Deposition Author(s): Braun, M.B., Dierlamm, N., Hartmann, M.D.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-04-23
  Type: Initial release