5T3Q

Crystal structure of the c-Met kinase domain in complex with a pyrazolone inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5T3Q/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2016-08-26 Released: 2016-09-21 
• Deposition Author(s): Bellon, S.F., Whittington, D.A., Long, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.248 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 

Starting Model: experimental

Literature

Discovery of AMG337: Using structure guided scaffold hydridization to optimize physicochemical properties and target coverage of a MET kinase inhibitor

Boezio, A.A., Peterson, E.A., Harmange, J.-C.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 35.77 kDa 
• Atom Count: 2,472 
• Modelled Residue Count: 278 
• Deposited Residue Count: 309 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor receptor	A	309	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
75H	B [auth A]	N-{3-fluoro-4-[(7-methoxyquinolin-4-yl)oxy]phenyl}-1-(2-hydroxy-2-methylpropyl)-5-methyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazole-4-carboxamide C31 H29 F N4 O5 UYMSIPINLJNNOU-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
75H	BindingDB:  5T3Q	Ki: 2.7 (nM) from 1 assay(s)
		IC50: min: 2.7, max: 51 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.248 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.627	α = 90
b = 82.272	β = 90
c = 127.139	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-21 
Deposition Author(s): Bellon, S.F., Whittington, D.A., Long, A.M.

Revision History  

• Version 1.0: 2016-09-21
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2024-04-03
  Changes: Refinement description