2RFN | pdb_00002rfn

x-ray structure of c-Met with inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.294 (Depositor), 0.282 (DCC) 
  • R-Value Work: 
    0.238 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 
    0.241 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

c-Met inhibitors with novel binding mode show activity against several hereditary papillary renal cell carcinoma-related mutations.

Bellon, S.F.Kaplan-Lefko, P.Yang, Y.Zhang, Y.Moriguchi, J.Rex, K.Johnson, C.W.Rose, P.E.Long, A.M.O'Connor, A.B.Gu, Y.Coxon, A.Kim, T.S.Tasker, A.Burgess, T.L.Dussault, I.

(2008) J Biological Chem 283: 2675-2683

  • DOI: https://doi.org/10.1074/jbc.M705774200
  • Primary Citation Related Structures: 
    2RFN, 2RFS

  • PubMed Abstract: 

    c-Met is a receptor tyrosine kinase often deregulated in human cancers, thus making it an attractive drug target. One mechanism by which c-Met deregulation leads to cancer is through gain-of-function mutations. Therefore, small molecules capable of targeting these mutations could offer therapeutic benefits for affected patients. SU11274 was recently described and reported to inhibit the activity of the wild-type and some mutant forms of c-Met, whereas other mutants are resistant to inhibition. We identified a novel series of c-Met small molecule inhibitors that are active against multiple mutants previously identified in hereditary papillary renal cell carcinoma patients. AM7 is active against wild-type c-Met as well as several mutants, inhibits c-Met-mediated signaling in MKN-45 and U-87 MG cells, and inhibits tumor growth in these two models grown as xenografts. The crystal structures of AM7 and SU11274 bound to unphosphorylated c-Met have been determined. The AM7 structure reveals a novel binding mode compared with other published c-Met inhibitors and SU11274. The molecule binds the kinase linker and then extends into a new hydrophobic binding site. This binding site is created by a significant movement of the C-helix and so represents an inactive conformation of the c-Met kinase. Thus, our results demonstrate that it is possible to identify and design inhibitors that will likely be active against mutants found in different cancers.


  • Organizational Affiliation
    • Department of Molecular Structure, Amgen Inc., Thousand Oaks, CA 91320, USA.

Macromolecule Content 

  • Total Structure Weight: 71.92 kDa 
  • Atom Count: 4,490 
  • Modeled Residue Count: 537 
  • Deposited Residue Count: 620 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hepatocyte growth factor receptor
A, B
310Homo 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AM7

Query on AM7



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
2-benzyl-5-(3-fluoro-4-{[6-methoxy-7-(3-morpholin-4-ylpropoxy)quinolin-4-yl]oxy}phenyl)-3-methylpyrimidin-4(3H)-one
C35 H35 F N4 O5
PEGWVOKOYYAQEV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
AM7 BindingDB:  2RFN Ki: 8.9 (nM) from 1 assay(s)
IC50: min: 8.9, max: 17 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.294 (Depositor), 0.282 (DCC) 
  • R-Value Work:  0.238 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 0.241 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.509α = 90
b = 78.919β = 90
c = 129.128γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description