3K5K | pdb_00003k5k

Discovery of a 2,4-Diamino-7-aminoalkoxy-quinazoline as a Potent Inhibitor of Histone Lysine Methyltransferase, G9a

• PDB DOI: https://doi.org/10.2210/pdb3K5K/pdb

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


• Deposited: 2009-10-07 Released: 2009-11-10 
• Deposition Author(s): Dong, A., Wasney, G.A., Liu, F., Chen, X., Allali-Hassani, A., Senisterra, G., Chau, I., Bountra, C., Weigelt, J., Edwards, A.M., Arrowsmith, C.H., Frye, S.V., Bochkarev, A., Brown, P.J., Jin, J., Vedadi, M., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.264 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Discovery of a 2,4-diamino-7-aminoalkoxyquinazoline as a potent and selective inhibitor of histone lysine methyltransferase G9a.

Liu, F., Chen, X., Allali-Hassani, A., Quinn, A.M., Wasney, G.A., Dong, A., Barsyte, D., Kozieradzki, I., Senisterra, G., Chau, I., Siarheyeva, A., Kireev, D.B., Jadhav, A., Herold, J.M., Frye, S.V., Arrowsmith, C.H., Brown, P.J., Simeonov, A., Vedadi, M., Jin, J.

(2009) J Med Chem 52: 7950-7953

• PubMed: 19891491 
• DOI: https://doi.org/10.1021/jm901543m
• Primary Citation Related Structures: 
  3K5K


• PubMed Abstract: 
  

  SAR exploration of the 2,4-diamino-6,7-dimethoxyquinazoline template led to the discovery of 8 (UNC0224) as a potent and selective G9a inhibitor. A high resolution X-ray crystal structure of the G9a-8 complex, the first cocrystal structure of G9a with a small molecule inhibitor, was obtained. The cocrystal structure validated our binding hypothesis and will enable structure-based design of novel inhibitors. 8 is a useful tool for investigating the biology of G9a and its roles in chromatin remodeling.

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Organizational Affiliation: 
• Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA.

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.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 67.62 kDa 
• Atom Count: 4,816 
• Modeled Residue Count: 541 
• Deposited Residue Count: 566 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase, H3 lysine-9 specific 3	A, B	283	Homo sapiens	Mutation(s): 0  Gene Names: EHMT2, BAT8, C6orf30, G9A, KMT1C, NG36 EC: 2.1.1.43 (PDB Primary Data), 2.1.1 (UniProt), 2.1.1.367 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96KQ7 (Homo sapiens) Explore Q96KQ7  Go to UniProtKB:  Q96KQ7
PHAROS:  Q96KQ7 GTEx:  ENSG00000204371

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DXQ	H [auth A], Q [auth B]	7-[3-(dimethylamino)propoxy]-6-methoxy-2-(4-methyl-1,4-diazepan-1-yl)-N-(1-methylpiperidin-4-yl)quinazolin-4-amine C26 H43 N7 O2 XIVUGRBSBIXXJE-UHFFFAOYSA-N
SAH	G [auth A], P [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
ZN	C [auth A], D [auth A], E [auth A], F [auth A], L [auth B], M [auth B], N [auth B], O [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	I [auth A], J [auth A], R [auth B], S [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNX	K [auth A], T [auth B]	UNKNOWN ATOM OR ION X

Binding Affinity Annotations
ID	Source	Binding Affinity
DXQ	BindingDB:  3K5K	Ki: 2.6 (nM) from 1 assay(s)
		Kd: 23 (nM) from 1 assay(s)
		IC50: min: 15, max: 5.70e+4 (nM) from 6 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.264 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.674	α = 90
b = 78.074	β = 91.81
c = 72.507	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
PHASER	phasing
REFMAC	refinement
Coot	model building
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-10 
Deposition Author(s): Dong, A., Wasney, G.A., Liu, F., Chen, X., Allali-Hassani, A., Senisterra, G., Chau, I., Bountra, C., Weigelt, J., Edwards, A.M., Arrowsmith, C.H., Frye, S.V., Bochkarev, A., Brown, P.J., Jin, J., Vedadi, M., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-11-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Advisory, Refinement description
• Version 1.3: 2023-09-06
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Data collection, Structure summary