8ANS | pdb_00008ans

Crystal structure of D1228V c-MET bound by compound 1.

• PDB DOI: https://doi.org/10.2210/pdb8ANS/pdb

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


• Deposited: 2022-08-05 Released: 2022-08-31 
• Deposition Author(s): Collie, G.W.
• Funding Organization(s): Other private

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.277 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

Discovery of a selective c-MET inhibitor with a novel binding mode.

Collie, G.W., Barlind, L., Bazzaz, S., Borjesson, U., Dale, I.L., Disch, J.S., Habeshian, S., Jetson, R., Khurana, P., Madin, A., Michaelides, I.N., Peng, L., Snijder, A., Stubbs, C.J.

(2022) Bioorg Med Chem Lett 75: 128948-128948

• PubMed: 35987508 
• DOI: https://doi.org/10.1016/j.bmcl.2022.128948
• Primary Citation Related Structures: 
  8AN8, 8ANS


• PubMed Abstract: 
  

  The c-MET receptor tyrosine kinase has received considerable attention as a cancer drug target yet there remains a need for inhibitors which are selective for c-MET and able to target emerging drug-resistant mutants. We report here the discovery, by screening a DNA-encoded chemical library, of a highly selective c-MET inhibitor which was shown by X-ray crystallography to bind to the kinase in an unprecedented manner. These results represent a novel mode of inhibiting c-MET with a small molecule and may provide a route to targeting drug-resistant forms of the kinase whilst avoiding potential toxicity issues associated with broad kinome inhibition.

---

Organizational Affiliation: 
• Discovery Sciences, R&D, AstraZeneca, Cambridge, U.K. Electronic address: [e-mail].
Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden.
X-Chem, Inc., Waltham, MA 02453, United States.
Discovery Sciences, R&D, AstraZeneca, Cambridge, U.K.
Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, PR China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.01 kDa 
• Atom Count: 2,227 
• Modeled Residue Count: 277 
• Deposited Residue Count: 296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor receptor	A	296	Homo sapiens	Mutation(s): 1  Gene Names: MET EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P08581 (Homo sapiens) Explore P08581  Go to UniProtKB:  P08581
PHAROS:  P08581 GTEx:  ENSG00000105976

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MDI (Subject of Investigation/LOI)	C [auth A]	3-[bis(fluoranyl)methyl]-~{N}-methyl-~{N}-[(1~{R})-8-methyl-5-(3-methyl-1~{H}-indazol-6-yl)-1,2,3,4-tetrahydronaphthalen-1-yl]pyridine-2-carboxamide C27 H26 F2 N4 O ZGVMLURVURNUQI-HSZRJFAPSA-N
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.277 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.89	α = 90
b = 52.83	β = 90
c = 96.18	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
xia2	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-08-31 
Deposition Author(s): Collie, G.W.

---

Funding Organization	Location	Grant Number
Other private	United Kingdom	--

Revision History  

• Version 1.0: 2022-08-31
  Type: Initial release
  
• Version 1.1: 2022-09-07
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description