Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 62738.12 
• Atom Count: 4306 
• Residue Count: 522 
• Unique protein chains: 1

3FPD

G9a-like protein lysine methyltransferase inhibition by BIX-01294

• DOI: 10.2210/pdb3FPD/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2009-01-05 Released: 2009-02-17 
• Deposition Author(s): Chang, Y., Zhang, X., Horton, J.R., Cheng, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.262 
• R-Value Work: 0.221 

Literature

Structural basis for G9a-like protein lysine methyltransferase inhibition by BIX-01294.

Chang, Y., Zhang, X., Horton, J.R., Upadhyay, A.K., Spannhoff, A., Liu, J., Snyder, J.P., Bedford, M.T., Cheng, X.

(2009) Nat.Struct.Mol.Biol. 16: 312-317

• PubMed: 19219047 
• DOI: 10.1038/nsmb.1560


• PubMed Abstract: 
  

Histone lysine methylation is an important epigenetic mark that regulates gene expression and chromatin organization. G9a and G9a-like protein (GLP) are euchromatin-associated methyltransferases that repress transcription by methylating histone H3 Lys9. BIX-01294 was originally identified as a G9a inhibitor during a chemical library screen of small molecules and has previously been used in the generation of induced pluripotent stem cells. Here we present the crystal structure of the catalytic SET domain of GLP in complex with BIX-01294 and S-adenosyl-L-homocysteine. The inhibitor is bound in the substrate peptide groove at the location where the histone H3 residues N-terminal to the target lysine lie in the previously solved structure of the complex with histone peptide. The inhibitor resembles the bound conformation of histone H3 Lys4 to Arg8, and is positioned in place by residues specific for G9a and GLP through specific interactions.

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Organizational Affiliation: 

Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Histone-lysine N-methyltransferase, H3 lysine-9 specific 5	A, B	261	Homo sapiens	Mutation(s): 0  Gene Names: EHMT1 (EUHMTASE1, GLP, KIAA1876, KMT1D) EC: 2.1.1.-, 2.1.1.43
Find proteins for Q9H9B1 (Homo sapiens) Go to Gene View: EHMT1 Go to UniProtKB:  Q9H9B1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
SAH	A, B	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
Q4A	A, B	N-(1-benzylpiperidin-4-yl)-6,7-dimethoxy-2-(4-methyl-1,4-diazepan-1-yl)quinazolin-4-amine C28 H38 N6 O2 OSXFATOLZGZLSK-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
Q4A	IC50: 0.7 - 700 nM (100) BINDINGDB
SAH	IC50: 230 nM (100) BINDINGDB
Q4A	IC50: 700 nM BINDINGMOAD
Q4A	IC50: 700 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.262 
• R-Value Work: 0.221 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 75.300	α = 90.00
b = 95.200	β = 90.00
c = 101.700	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-01-05 
• Released Date: 2009-02-17 
• Deposition Author(s): Chang, Y., Zhang, X., Horton, J.R., Cheng, X.

Revision History 

• Version 1.0: 2009-02-17
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance