7B3W | pdb_00007b3w

Crystal structure of c-MET bound by compound 4

• PDB DOI: https://doi.org/10.2210/pdb7B3W/pdb

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


• Deposited: 2020-12-01 Released: 2020-12-09 
• Deposition Author(s): Collie, G.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.261 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Starting Model: other

Literature

Structural Basis for Targeting the Folded P-Loop Conformation of c-MET.

Collie, G.W., Michaelides, I.N., Embrey, K., Stubbs, C.J., Borjesson, U., Dale, I.L., Snijder, A., Barlind, L., Song, K., Khurana, P., Phillips, C., Storer, R.I.

(2021) ACS Med Chem Lett 12: 162-167

• PubMed: 33488978 
• DOI: https://doi.org/10.1021/acsmedchemlett.0c00392
• Primary Citation Related Structures: 
  7B3Q, 7B3T, 7B3V, 7B3W, 7B3Z, 7B40, 7B41, 7B42, 7B43, 7B44


• PubMed Abstract: 
  

  We report here a fragment screen directed toward the c-MET kinase from which we discovered a series of inhibitors able to bind to a rare conformation of the protein in which the P-loop adopts a collapsed, or folded, arrangement. Preliminary SAR exploration led to an inhibitor ( 7 ) with nanomolar biochemical activity against c-MET and promising cell activity and kinase selectivity. These findings increase our structural understanding of the folded P-loop conformation of c-MET and provide a sound structural and chemical basis for further investigation of this underexplored yet potentially therapeutically exploitable conformational state.

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Organizational Affiliation: 
• Discovery Sciences, R&D, AstraZeneca, Cambridge, United Kingdom.
Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden.
Oncology, R&D, AstraZeneca, Boston, United States.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 34.1 kDa 
• Atom Count: 2,217 
• Modeled Residue Count: 259 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor receptor	A	299	Homo sapiens	Mutation(s): 0  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
SVH (Subject of Investigation/LOI)	C [auth A]	3-(6-fluoranyl-1~{H}-indazol-4-yl)-4,5-dihydro-1~{H}-pyrrolo[3,4-b]pyrrol-6-one C13 H9 F N4 O HAQWDJLVWPNOMF-UHFFFAOYSA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.261 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.82	α = 90
b = 66.82	β = 90
c = 188.63	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-12-09 
Deposition Author(s): Collie, G.W.

Revision History  

• Version 1.0: 2020-12-09
  Type: Initial release
  
• Version 1.1: 2020-12-23
  Changes: Database references
• Version 1.2: 2021-02-03
  Changes: Database references
• Version 1.3: 2024-05-01
  Changes: Data collection, Database references, Refinement description