6GIN

Crystal structure of the ACVR1 (ALK2) kinase in complex with an Quinazolinone based ALK2 inhibitor with a 4-morpholinophenyl solvent accessible group.

• PDB DOI:  https://doi.org/10.2210/pdb6GIN/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2018-05-14 Released: 2018-05-23 
• Deposition Author(s): Williams, E., Hudson, L., Bezerra, G.A., Kopec, J., Mahajan, P., Kupinska, K., Hoelder, S., Burgess-Brown, N., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.228 
• R-Value Work: 0.175 

Literature

Novel Quinazolinone Inhibitors of ALK2 Flip between Alternate Binding Modes: Structure-Activity Relationship, Structural Characterization, Kinase Profiling, and Cellular Proof of Concept.

Hudson, L., Mui, J., Vazquez, S., Carvalho, D.M., Williams, E., Jones, C., Bullock, A.N., Hoelder, S.

(2018) J Med Chem 61: 7261-7272

• PubMed: 30085668 
• DOI: https://doi.org/10.1021/acs.jmedchem.8b00782
• Primary Citation of Related Structures:  
  6GI6, 6GIN, 6GIP


• PubMed Abstract: 
  

Structure-activity relationship and crystallographic data revealed that quinazolinone-containing fragments flip between two distinct modes of binding to activin receptor-like kinase-2 (ALK2). We explored both binding modes to discover potent inhibitors and characterized the chemical modifications that triggered the flip in binding mode. We report kinase selectivity and demonstrate that compounds of this series modulate ALK2 in cancer cells. These inhibitors are attractive starting points for the discovery of more advanced ALK2 inhibitors.

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Organizational Affiliation: 

Institute of Cancer Research , 15 Cotswold Road , Sutton , Surrey SM2 5NG , United Kingdom.

Biological Assembly 1  

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

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

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 70.77 kDa 
• Atom Count: 5,143 
• Modelled Residue Count: 592 
• Deposited Residue Count: 602 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Activin receptor type-1	A, B	301	Homo sapiens	Mutation(s): 1  Gene Names: ACVR1, ACVRLK2 EC: 2.7.11.30
UniProt & NIH Common Fund Data Resources
Find proteins for Q04771 (Homo sapiens) Explore Q04771  Go to UniProtKB:  Q04771
PHAROS:  Q04771

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IR2 (Subject of Investigation/LOI)	C [auth A], J [auth B]	3-(4-morpholin-4-ylphenyl)-6-quinolin-4-yl-quinazolin-4-one C27 H22 N4 O2 MTDJGYWCNQTZLJ-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], K [auth B], L [auth B], M [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	G [auth A], H [auth A], I [auth A], N [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
IR2	BindingDB:  6GIN	Kd: 330 (nM) from 1 assay(s)
		IC50: 32 (nM) from 1 assay(s)
	Binding MOAD:  6GIN	IC50: 32 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.228 
• R-Value Work: 0.175 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.08	α = 90
b = 86.39	β = 90
c = 139.29	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-23 
Deposition Author(s): Williams, E., Hudson, L., Bezerra, G.A., Kopec, J., Mahajan, P., Kupinska, K., Hoelder, S., Burgess-Brown, N., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A.N.

Revision History  

• Version 1.0: 2018-05-23
  Type: Initial release
  
• Version 1.1: 2018-08-22
  Changes: Data collection, Database references
• Version 1.2: 2018-09-05
  Changes: Data collection, Database references
• Version 1.3: 2019-04-03
  Changes: Data collection, Source and taxonomy