8AN8 | pdb_00008an8

Crystal structure of wild-type c-MET bound by compound 7.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 
    0.298 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.241 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.244 (Depositor) 

Starting Model: other
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 2.2 of the entry. See complete history


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

  • DOI: https://doi.org/10.1016/j.bmcl.2022.128948
  • Primary Citation of 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: gavin.collie@astrazeneca.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hepatocyte growth factor receptor
A, B
296Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08581
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MDI (Subject of Investigation/LOI)
Query on MDI

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B]
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
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
H [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
DI BindingDB:  8AN8 Kd: min: 650, max: 2.00e+4 (nM) from 4 assay(s)
IC50: min: 90, max: 3.00e+4 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free:  0.298 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.241 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.838α = 74.26
b = 52.181β = 77.64
c = 84.074γ = 70.55
Software Package:
Software NamePurpose
xia2data scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted MDIClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data

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

Funding OrganizationLocationGrant Number
Other privateUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-31
    Type: Initial release
  • Version 2.0: 2023-10-04
    Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-03-27
    Changes: Database references
  • Version 2.2: 2024-05-01
    Changes: Refinement description