7Y4U | pdb_00007y4u

Crystal structure of cMET kinase domain bound by compound 9Y


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 
    0.278 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.238 (Depositor) 
  • R-Value Observed: 
    0.240 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7Y4U

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of D6808, a Highly Selective and Potent Macrocyclic c-Met Inhibitor for Gastric Cancer Harboring MET Gene Alteration Treatment.

Wang, C.Li, J.Qu, L.Tang, X.Song, X.Yang, F.Chen, X.Lin, Q.Lin, W.Zhou, Y.Tu, Z.Chen, Y.Zhang, Z.Lu, X.

(2022) J Med Chem 65: 15140-15164

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00981
  • Primary Citation Related Structures: 
    7Y4T, 7Y4U, 8GVJ

  • PubMed Abstract: 

    MET alterations have been validated as a driven factor in NSCLC and gastric cancers. The c-Met inhibitors, capmatinib, tepotinib, and savolitinib, are only approved for the treatment of NSCLC harboring exon 14 skipping mutant MET. We used a molecular hybridization in conjunction with macrocyclization strategy for structural optimization to obtain a series of 2-(2-(quinolin-6-yl)ethyl)pyridazin-3(2 H )-one derivatives as new c-Met inhibitors. One of the macrocyclic compounds, D6808, potently inhibited c-Met kinase and MET -amplified Hs746T gastric cancer cells with IC 50 values of 2.9 and 0.7 nM, respectively. It also strongly suppressed Ba/F3-Tpr-Met cells harboring resistance-relevant mutations (F1200L/M1250T/H1094Y/F1200I/L1195V) with IC 50 values of 4.2, 3.2, 1.0, 39.0, and 33.4 nM, respectively. Furthermore, D6808 exhibited extraordinary target specificity in a Kinome profiling against 373 wild-type kinases and served as a promising macrocycle-based compound for further anticancer drug development.


  • Organizational Affiliation
    • International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China.

Macromolecule Content 

  • Total Structure Weight: 35.37 kDa 
  • Atom Count: 2,302 
  • Modeled Residue Count: 281 
  • Deposited Residue Count: 309 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hepatocyte growth factor receptor309Homo 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
I94
(Subject of Investigation/LOI)

Query on I94



Download:Ideal Coordinates CCD File
B [auth A]~{N}-methyl-4-[1-[2-[3-(1-methylpyrazol-4-yl)quinolin-6-yl]ethyl]-6-oxidanylidene-pyridazin-3-yl]-2-(trifluoromethyl)benzamide
C28 H23 F3 N6 O2
QUMBDXILECDMAC-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
I94 BindingDB:  7Y4U IC50: 4.8 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free:  0.278 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.238 (Depositor) 
  • R-Value Observed: 0.240 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.625α = 90
b = 65.625β = 90
c = 187.911γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description