8VLB

Crystal structure of EloBC-VHL-CDO1 complex bound to compound 4 molecular glue

• PDB DOI: https://doi.org/10.2210/pdb8VLB/pdb

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


• Deposited: 2024-01-11 Released: 2024-03-13 
• Deposition Author(s): Shu, W., Ma, X., Tutter, A., Buckley, D., Golosov, A., Michaud, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.258 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 

Literature

A small molecule VHL molecular glue degrader for cysteine dioxygenase 1

Tutter, A., Buckley, D., Golosov, A., Ma, X., Shu, W., Michaud, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 66.49 kDa 
• Atom Count: 4,356 
• Modelled Residue Count: 533 
• Deposited Residue Count: 577 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
von Hippel-Lindau disease tumor suppressor	A	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-B	B	118	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-C	C	96	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine dioxygenase type 1	D	201	Homo sapiens	Mutation(s): 0  Gene Names: CDO1 EC: 1.13.11.20
UniProt & NIH Common Fund Data Resources
Find proteins for Q16878 (Homo sapiens) Explore Q16878  Go to UniProtKB:  Q16878
PHAROS:  Q16878 GTEx:  ENSG00000129596

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3JF (Subject of Investigation/LOI)	E [auth A]	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
CIT	F [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
FE2	G [auth D]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.258 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.44	α = 90
b = 178.116	β = 90
c = 104.166	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-13 
Deposition Author(s): Shu, W., Ma, X., Tutter, A., Buckley, D., Golosov, A., Michaud, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-03-13
  Type: Initial release