9BC9

Structure of KLHDC2 bound to SJ10278

• PDB DOI: https://doi.org/10.2210/pdb9BC9/pdb

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


• Deposited: 2024-04-08 Released: 2024-11-06 
• Deposition Author(s): Scott, D.C., Dharuman, S., Griffith, E., Chai, S.C., Ronnebaum, J., King, M.T., Tangallapally, R., Lee, C., Gee, C.T., Lee, H.W., Ochoada, J., Miller, D.J., Jayasinghe, T., Paulo, J.A., Elledge, S.J., Harper, J.W., Chen, T., Lee, R.E., Schulman, B.A.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.261 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 

Starting Model: experimental

Literature

Principles of isoform-specific targeted protein degradation engaging the C-degron E3 KLHDC2

Scott, D.C., Dharuman, S., Griffith, E., Chai, S.C., Ronnebaum, J., King, M.T., Tangallapally, R., Lee, C., Gee, C.T., Lee, H.W., Ochoada, J., Miller, D.J., Jayasinghe, T., Paulo, J.A., Elledge, S.J., Harper, J.W., Chen, T., Lee, R.E., Schulman, B.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 80.32 kDa 
• Atom Count: 5,386 
• Modelled Residue Count: 643 
• Deposited Residue Count: 696 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch domain-containing protein 2	A, B	348	Homo sapiens	Mutation(s): 0  Gene Names: KLHDC2, HCA33
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2U9 (Homo sapiens) Explore Q9Y2U9  Go to UniProtKB:  Q9Y2U9
PHAROS:  Q9Y2U9 GTEx:  ENSG00000165516

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1APK (Subject of Investigation/LOI)	C [auth A], E [auth B]	N-({2-[2-chloro-4-(methoxymethoxy)phenyl]-1,3-thiazol-4-yl}acetyl)glycine C15 H15 Cl N2 O5 S MOVMDJVZNRFJJJ-UHFFFAOYSA-N
NCO	D [auth A]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.261 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.528	α = 90
b = 87.877	β = 104.31
c = 89.896	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-06 
Deposition Author(s): Scott, D.C., Dharuman, S., Griffith, E., Chai, S.C., Ronnebaum, J., King, M.T., Tangallapally, R., Lee, C., Gee, C.T., Lee, H.W., Ochoada, J., Miller, D.J., Jayasinghe, T., Paulo, J.A., Elledge, S.J., Harper, J.W., Chen, T., Lee, R.E., Schulman, B.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01CA247365-04
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01-AI157312

Revision History  

• Version 1.0: 2024-11-06
  Type: Initial release