9CBF

Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with m-Aminomethyl Phenylthioketone

• PDB DOI: https://doi.org/10.2210/pdb9CBF/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Danio rerio
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-06-19 Released: 2024-09-11 
• Deposition Author(s): Goulart Stollmaier, J., Christianson, D.W.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.258 
• R-Value Work: 0.235 
• R-Value Observed: 0.236 

Starting Model: experimental

Literature

Design, Synthesis and Structural Evaluation of Acetylated Phenylthioketone Inhibitors of HDAC10

Goulart Stollmaier, J., Watson, P.R., Christianson, D.W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 75.76 kDa 
• Atom Count: 4,460 
• Modelled Residue Count: 609 
• Deposited Residue Count: 676 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyamine deacetylase HDAC10	A	676	Danio rerio	Mutation(s): 0  Gene Names: hdac10 EC: 3.5.1.48 (PDB Primary Data), 3.5.1.62 (PDB Primary Data)
UniProt
Find proteins for F1QCV2 (Danio rerio) Explore F1QCV2  Go to UniProtKB:  F1QCV2

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AVR (Subject of Investigation/LOI)	E [auth A]	1-[3-(aminomethyl)phenyl]-2-sulfanylethan-1-one C9 H11 N O S YLFKZKMYAGKUCQ-UHFFFAOYSA-N
PO4	F [auth A], G [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	J [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	B [auth A], C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	H [auth A], I [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.258 
• R-Value Work: 0.235 
• R-Value Observed: 0.236 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.411	α = 90
b = 80.411	β = 90
c = 236.953	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-11 
Deposition Author(s): Goulart Stollmaier, J., Christianson, D.W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM49758

Revision History  

• Version 1.0: 2024-09-11
  Type: Initial release