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), 0.291 (DCC) 
  • R-Value Work: 
    0.241 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 
    0.244 (Depositor) 

Starting Model: other
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wwPDB Validation 3D Report Full Report

Validation slider image for 8AN8

Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 68.35 kDa 
  • Atom Count: 4,176 
  • Modeled Residue Count: 507 
  • Deposited Residue Count: 592 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free:  0.298 (Depositor), 0.291 (DCC) 
  • R-Value Work:  0.241 (Depositor), 0.232 (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 


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