3K5K

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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

  • DOI: 10.1021/jm901543m
  • Primary Citation of 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 ...

    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.


    Organizational Affiliation

    Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase, H3 lysine-9 specific 3A, B283Homo sapiensMutation(s): 0 
Gene Names: EHMT2BAT8C6orf30G9AKMT1CNG36
EC: 2.1.1.43 (PDB Primary Data), 2.1.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96KQ7 (Homo sapiens)
Explore Q96KQ7 
Go to UniProtKB:  Q96KQ7
PHAROS:  Q96KQ7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DXQ (Subject of Investigation/LOI)
Query on DXQ

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
G [auth A], P [auth B]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A], J [auth A], R [auth B], S [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
UNX
Query on UNX

Download Ideal Coordinates CCD File 
K [auth A], T [auth B]UNKNOWN ATOM OR ION
X
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding 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)
Binding MOAD:  3K5K Kd: 23 (nM) from 1 assay(s)
PDBBind:  3K5K Kd: 23 (nM) from 1 assay(s)
SAH BindingDB:  3K5K Ki: 570 (nM) from 1 assay(s)
IC50: min: 2000, max: 4100 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.674α = 90
b = 78.074β = 91.81
c = 72.507γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
PHASERphasing
REFMACrefinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Revision History  (Full details and data files)

  • 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