8K78 | pdb_00008k78

Crystal structure of cMET kinase domain bound by TPX-0022


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 
    0.290 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.244 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 8K78

Ligand Structure Quality Assessment 


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Literature

Structural insight into the macrocyclic inhibitor TPX-0022 of c-Met and c-Src.

Qu, L.Lin, H.Dai, S.Guo, M.Chen, X.Jiang, L.Zhang, H.Li, M.Liang, X.Chen, Z.Wei, H.Chen, Y.

(2023) Comput Struct Biotechnol J 21: 5712-5718

  • DOI: https://doi.org/10.1016/j.csbj.2023.11.028
  • Primary Citation Related Structures: 
    8K78, 8K79

  • PubMed Abstract: 

    c-Met has been an attractive target of prognostic and therapeutic studies in various cancers. TPX-0022 is a macrocyclic inhibitor of c-Met, c-Src and CSF1R kinases and is currently in phase I/II clinical trials in patients with advanced solid tumors harboring MET gene alterations. In this study, we determined the co-crystal structures of the c-Met/TPX-0022 and c-Src/TPX-0022 complexes to help elucidate the binding mechanism. TPX-0022 binds to the ATP pocket of c-Met and c-Src in a local minimum energy conformation and is stabilized by hydrophobic and hydrogen bond interactions. In addition, TPX-0022 exhibited potent activity against the resistance-relevant c-Met L1195F mutant and moderate activity against the c-Met G1163R, F1200I and Y1230H mutants but weak activity against the c-Met D1228N and Y1230C mutants. Overall, our study reveals the structural mechanism underlying the potency and selectivity of TPX-0022 and the ability to overcome acquire resistance mutations and provides insight into the development of selective c-Met macrocyclic inhibitors.


  • Organizational Affiliation
    • Department of Oncology, NHC Key Laboratory of Cancer Proteomics, State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.

Macromolecule Content 

  • Total Structure Weight: 35.25 kDa 
  • Atom Count: 2,397 
  • Modeled Residue Count: 298 
  • 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
IYC
(Subject of Investigation/LOI)

Query on IYC



Download:Ideal Coordinates CCD File
B [auth A]Elzovantinib
C20 H20 F N7 O2
UUDPUQDMSHQSKH-NSHDSACASA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
IYC BindingDB:  8K78 IC50: min: 0.14, max: 1.8 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free:  0.290 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.054α = 90
b = 66.625β = 107
c = 55.294γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
XDSdata scaling

Structure Validation

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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: 2024-07-31
    Type: Initial release